P1. “More evidence of the en bloc duplication of the proto-MHC ancestral region and plesiomorphic organisation of human chromosome 9q34 region”
Alexandre Vienne, Takashi Shiina, Laurent Abbi-Rached, Etienne Danchin, Verane Vitiello, André Gilles, Hidetoshi Inoko and Pierre Pontarotti
Addresses: EA Biodiversité 2202, Université Aix-Marseille I, 3 place Victor Hugo, 13331 Marseille Cedex 3, France.
Department of Molecular Life Science, Tokai University School of Medicine, Boscheidei, Isehara, Kanagawa, 259-1193, JAPAN.
Stanford University School of Medicine, Department of Structural Biology, Sherman Fairchild Research Building, 299 Campus Drive West, D-151, Stanford, California 94305-5136
Abstract:
The actual structure and organisation of the vertebrate MHC and of its three paralogous regions have always been of great interest. In a recent study, the cloning of nine human MHC anchors genes on a Branchiostoma floridae (amphioxus) cosmid library and the identification and analysis of 31 surrounding genes led to the most probable model of two rounds of en bloc duplication giving rise to these regions. These events were estimated to have occurred after the cephalochordata-craniata divergence (approximately 766 Mya ago) and before the Gnathostomata radiation (approximately 528 Mya ago). Furthermore, it was also shown that after this large-scale duplication, one of this region corresponding to the human 9q33-q34, retained an ancestral organisation. In the present study, the identification of four new cosmids in the amphioxus proto-MHC region by the chromosomal walking technique, their sequencing, the structural annotation of their genes content and the analysis of their phylogenetic relationships among species reinforce these results and give more evidence for the plesiomorphic state of the human chromosome 9q33-34 MHC paralogous region.
P2. “A strange Hox-like multihomeobox gene: an amphioxus oddity or a fingerprint of Hox / ParaHox evolution?”
Josep Gardenyes, Elisa Serra & Jordi Garcia-Fernàndez
Address: Departament de Genètica Facultat de Biologia Universitat de Barcelona Av. Diagonal, 645 1a Planta / Lab 1 08028 Barcelona Spain
P3. “Evolutional and functional inferences of the Adh gene family from a comparative expression analysis through animal evolution”
Laura Godoy, Cristian Cañestro, Ricard Albalat, Roser Gonzàlez-Duarte
08028 Barcelona. Spain
Abstract:
Gene and genome duplications in the vertebrate lineage explain the complexity of extant gene families. Among these, the medium-chain alcohol dehydrogenase (MDR-ADH), which expanded by tandem duplications after the cephalochordate-vertebrate split, is a good model with which to analyze the evolution of gene function. Although the ancestral member of this family, ADH3, has been strictly conserved throughout animal evolution, its physiological role is still controversial. Previous evidence indicates that it contributes to formaldehyde cytoprotection, retinoic acid metabolism and nitric oxide homeostasis. We have performed in situ hybridization during Drosophila, ascidian (C.intestinalis), amphioxus (B. floridae) and zebrafish (D. rerio) development. We have shown that Adh3 expression was restricted to the fat body in Drosophila embryos, to the anterior endoderm in C.intestinalis tailbud and to the mid- hindgut of larvae in the amphioxus, whereas in the zebrafish larvae the signal appeared widespread. This comprehensive expression analysis, including the reported mouse pattern, revealed that ancestral Adh3 was tissue-specific while a widespread expression was later attained in vertebrates. These variations occurred concomitantly with the expansion of the ADH family and the acquisition of new functions but were unlinked to the genomic changes that led to the transition from fractional to global methylation in vertebrates. Our data challenge the housekeeping role of ADH3 and question its involvement in the prevertebrate retinoic acid pathway.
Diana Dalfó, Jon Permanyer, Roser Gonzàlez-Duarte and Ricard Albalat
Address: Departament de Genètica. Facultat de Biologia. Universitat de Barcelona 08028 Barcelona. Spain
Abstract:
Chordates diverged into three subphyla: urochordates, cephalochordates and vertebrates. The first two, being a plausible approximation to the ancestral chordate and lacking the complexity of the current vertebrates, provide a good starting point for gene family studies. Using ascidians (C. intestinalis) and amphioxus (B. floridae and B. lanceolatum) we have approached the evolution of the retinoic acid (RA) metabolism in chordates.
RA is involved in patterning the body plan through the regulation of developmental genes, which control the anterior-posterior (AP) axis formation. This regulation does not uniquely affect vertebrates but is considered a chordate innovation, as amphioxus (subphylum cephalochordata) and ascidians (subphylum urochordata) show a vertebrate-like response to RA. However, in the absence of a clear candidate for retinol oxidation and considering that some favoured enzymes are absent in cephalochordates and urochordates, retinol oxidation in these lineages could be questioned.
Our data show that the morphological effects of retinol treatment in B. floridae and C. intestinalis larvae are comparable to those reported for RA, which suggests an in vivo transformation of retinol to RA in these animals. Regarding the candidates to carry out this transformation, we recently identified a pro-orthologous gene in amphioxus of the vertebrate retinol dehydrogenase Now, we report the characterization of a C. intestinalis gene, phylogenetically related to the vertebrate retinol dehydrogenases and hydroxysteroid dehydrogenases type 2. Phylogenetic studies of these enzymes and their evolutionary implications will be discussed.
P5. “Hypothetical GABAA receptor-associated protein gene expresses in Amphioxus embryonic development”
Y. Lin, K. Liang, Y. Zhang and H. Zhang*
Address: Institute of Developmental Biology, Life Science College, Shandong University, Jinan 250100, China
*Corresponding author, e-mail:zhw@sdu.edu.cn
Abstract:
Amphioxus, widely regarded as the closest living relative of the vertebrates, is an important animal for phylogenetic analysis. A hypothetical GABAA receptor-associated protein (GABARAP) gene is identified in amphioxus by screening a Qingdao amphioxus (Branchiostoma belcheri tsingtauense) 18-hour-neurula cDNA library. It is highly homologous to GABAA receptor-associated protein which is known from human and mouse as a multiple gene family. The GABARAP gene expression pattern in embryonic amphioxus is detected by whole mount in situ hybridization combined with histology study. The transcripts of GABARAP gene are detectable from fertilized eggs to early cleavage stages. Expression is conspicuous in cytoplasm of the blastomeres in animal pole region. But there is no transcript in the blastula and early gastrula. At the following stages, the transcripts appear again and localize in many regions: it shows in regions near the blastopore at first, especially in the future dorsal region at 9h past fertilization (hpf); then expresses strongly in neural plate (10.5 hpf), neural tube and neurenteric canal (12 hpf). It also expresses in archenteron and weakly in entoderm at 12 hpf. The expression pattern in the later stages can be described as following: expresses clearly segmented in mesodermal somites and other tissues like head, gut and tail. The characteristic of the GABARAP gene expression in embryonic development suggests that it might function in cleavage and pattern of neural tissues in this animal.
Supported by CNSF (No. 30070094, No. 30270693) and CSNSF (No. L2000D03).
P6. “Amphimdp, A Gene Expresses in the Developing Muscle of Qingdao Amphioxus”
K. Liang, Y. Lin, Y. Zhang, P. Zhang* and H. Zhang+
Addresses: Institute of Developmental Biology, Life Science College, Shandong University, Jinan 250100, China
Institute of Oceanology Chinese Academy of Sciences, China. +Corresponding author, e-mail:zhw@sdu.edu.cn
Abstract:
A full open reading frame sequence of amphimdp is obtained by sequencing and systemic analyzing the Qingdao amphioxus (Branchiostoma belcheri tsingtauense) neurula cDNA library. Homology analysis of the nucleotide sequence and deduced amino acid sequence reveal that the gene is homologous to the mdp77 in chicken. Southern blotting analysis shows that there might be only one copy of amphimdp in amphioxus. Whole mount in situ hybridization followed by sectioning indicates that the amphimdp expresses in the developing muscle. The amphimdp transcript is first detected in some vegetative pole cells of 4-hour gastrula and then it expresses in the mesentoderm of 6-hour gastrula. With the development, the gene expresses from anterior to posterior parts in the developing somites of neurula and early larva stages. The transcripts also show in the most posterior region where the tail bud is. No transcript is detected in 72-hour larva. The spacial and temporal characteristic of amphimdp expression suggests that this gene might function in the muscle development in amphioxus.
Supported by CNSF (No. 30070094, No. 30270693) and CSNSF (No. L2000D03).
P7. “Neuropeptide Y receptor genes support en bloc duplications in early vertebrate evolution”
Erik Salaneck, David H. Ardell*, Earl T. Larson & Dan Larhammar
Addresses: Department of Neuroscience, Unit of Pharmacology, Uppsala University, SE-751 24 Uppsala, Sweden, * Department of Molecular Evolution, Evolutionary Biology Center Uppsala University, SE-752 36 Uppsala, Sweden
Abstract:
Analyses of gene families in several chordate lineages has lead to the suggestion that the vertebrate genome underwent at least two large-scale duplication events early in vertebrate evolution, called the 2R theory. These events resulted in numerous gene families having orthologous genes on separate chromosomal segments, or paralogons, in humans and other mammals. The NPY receptor family in mammals consists of five subtypes called Y1, Y2, Y4, Y5 and Y6. The subtypes Y1, Y4 and Y6 exhibit a higher degree of sequence identity to each other and form a subfamily within the receptor family, the Y1 subfamily. These three genes have been mapped to three different paralogons in mammals, while Y1, Y2 and Y5 are located on the same chromosomal segment. This suggests that an ancient segment harboring the ancestral Y1, Y2 and Y5 genes was duplicated twice resulting in the Y1 subfamily. Subsequent gene loss appears to have eliminated the duplicates of Y2 and Y5 ancestors, as well as a fourth Y1 subfamily member, at least in mammals. In order to investigate when these duplication events occurred we cloned Y receptor genes from species that split from the vertebrate tree close to the time of these postulated duplication events. Three orthologs to the Y1 subfamily genes were cloned in the cartilagenous fish Squalus acanthias and a possible pro-orthologue to the Y4 subtype was cloned from an agnathan, the lamprey Lampetra fluviatilis. Phylogenetic analyses of these sequences clearly indicates that a duplication occurred between the split of cartilagenous fishes and that of agnathans from the vertebrate tree and support yet an earlier duplication, prior to the appearance of lampreys. Futher Y receptor genes cloned from teleost fish coroborate these results as there appears to be descendants of a lost Y1 subfamily gene in these species. Dating analyses revealed that the duplication events occurred 407 MYA, and > 450 MYA, in agreement with estimates from other gene families and the 2R hypothesis.
P8. “Chordates evolution and testing of their monophyly”
A. Vienne, A. Gilles and P. Pontarotti
Address: Laboratoire d'Hydrobiologie, EA Biodiversité 2202,Université de Provence, 3 place Victor Hugo 13331 Marseille, France.
Abstract:
Among the deuterostomes phylogeny, three phyla are distinguishable: Echinodermata (including sea stars, sea urchins, etc…), Hemichordata (including acorn worms and pterobranchs), and Chordata (including urochordates, cephalochordates and vertebrates). Inside the Chordata phylum, the position of species inside the vertebrates is quite unanimously defined. Nonetheless the position of urochordates in regard of vertebrates is still the purpose to debates and has been supposed by some authors to be a separate phylum from cephalochordates and vertebrates. As it was the case for the agnathes myxine and hagfish, for which more phylogenetic evidence were given for their controversial monophyly, the positioning of urochordates and cephalochordates in regard of vertebrates is still debated. Which raise the following question: which one of the Cephalochordata or Urochordata is the sister group of vertebrates? In the present analysis, using an approach consisting in a systematic screening of the urochordata Ciona intestinalis genome for 90 protein families, we focused on three points: 1) the identification of potential amphioxus orthologous genes for these 90 coding gene families and the estimation of the rate of gene loss between Urochordata and Cephalochordata, 2) to give a more accurate definition of positioning of Urochordata and Cephalochordata phyla in regard of vertebrates by testing chordates monophyly, 3) and the estimation of the divergence time between these.
P9. “Genetic diversity and conservation of Amphibian from french Guyana
Marie-Dominique Salducci, Christian Marty, Blanc Michel and André Gilles
Address: Laboratoire d'Hydrobiologie, EA Biodiversité 2202,Université de Provence, 3 place Victor Hugo 13331 Marseille, France.
Abstract:
L’étude de la biodiversité des Amphibiens de Guyane a permis l’élaboration d’un premier ouvrage faisant état des connaissances actuelles sur la taxonomie des Amphibiens de Guyane et d’Amazonie (1, 2, 3, 4). Le but de notre projet est d’appréhender la diversité génétique au sein de différentes espèces d’amphibiens de Guyane sur la base de caractères morphologiques et moléculaires, d’étudier si cette diversité est due à des processus de vicariances ou de spéciation allopatrique (i.e. isolement géographique) ou encore à des phénomènes de spéciations en sympatrie (i.e. dans un même milieu). Ce travail permettra d’établir une carte tenant compte de la répartition et de la diversité génétique des différentes espèces d’amphibiens étudiées.
L’objectif de ce projet est :
1) d’évaluer “ systématiquement ” la diversité génétique des unités morphologiques correspondant à une même espèce.
2) d’estimer la répartition géographique des différentes espèces (préalablement déterminées comme telles) sur le terrain.
3) de contribuer à la détermination des zones importantes pour la conservation des espèces considérées comme rares ou en danger (en complément des travaux effectués sur les ZNIEFF).
P10. “Cichlidae phylogeny of the Tanganyika lake”
C. Clabaut
Address: Institute of evolutionary biology. Department of Biology. P.O. Box M617. University Konstanz. D-78457 Konstanz, Germany.
Abstract:
The Great Lakes in the East African rift valley, and particularly the stunning diversity of their cichlid fishes, represent a prime model system for the study of explosive speciation and adaptive radiation. With an age of 9 to 12 million years, the Lake Tanganyika species assemblage is by far the oldest, and morphologically, ecologically and behaviorally the most complex assemblage with about 200 described species in 54 genera. Studies on the evolution of cichlids in Lake Tanganyika agree that several lineages arose with dramatic speed immediately after the formation of the lake. This is manifested in short branch lengths, which makes evolutionary reconstruction difficult. This study combines all available mitochondrial DNA sequences with newly generated nuclear DNA sequences in order to provide a more robust phylogeny of the Lake Tanganyika cichlid species flock.
P11. “The variation of Alu polymorphic elements and the prehistoric relationships between human populations in Western Mediterranean”
E. González-Pérez 1, E. Esteban1, M. Via1, N. Rodon1, N. Harich2, J.M. Dugoujon3 and P. Moral1.
Addresses: 1Universitat de Barcelona, Barcelona, Spain.
2Université Chouaib-Doukkali, El Jadida, Morocco.
3Université Paul Sabatier, Toulouse, France.
Abstract:
In the NW Africa region, the Berbers are the autochthonous population wich derive from an ancient pre-neolithic population that received a number of influences from other human groups: the Arab populations who invaded Northwestern Africa imposing the Islamic rules, the sub-Saharan populations, and even a possible genetic contact with iberian human groups. In this particular case, human population genetics will contribute to the clarification of the arabization process in NW Africa, the relationships between Berber groups and their neighbours and to test the genetic influx of sub-saharans in this particular human populations.
The aim of this work is to present preliminary results on a survey of polymorphic Alu elements in different human populations from NW Africa and the Iberian Peninsula. Recent Alu subfamilies of SINE’s include a significant number of polymorphic Alu insertions in humans. Polymorphic Alu elements are neutral genetic markers of identical descent with known ancestral state. This fact turn Alu insertions into useful markers for the study of human population genetics. A total number of 17 Alu insertions were analyzed in five Iberian populations, three Berber groups from NW Africa, an Arab-speaker population from Morocco and a sub-Saharan ethnic group from Ivory Coast.
The results of this study allow the genetic characterization of Berber populations from Northwestern Africa, which shows a certain degree of differentiation from Arab-speaker groups of the same geographic area. Besides, a particular position of the Algerian Berbers is observed. Furthermore, a closer genetic distance between Spaniards and Moroccan Berbers as compared with other Berber populations support a certain degree of genetic influx consistent with some previous studies, as well as a substantial sub-saharan genetic contribution into the NW African groups.
P12. “Chemotaxonomy of some Artemisia species on the basis of volatile compouds”
V. Masotti, F. Juteau, J.M. Bessiere and J. Viano.
Address: Université Aix-Marseille I, 3 place Victor Hugo, 13331 Marseille, France.
Abstract:
The genus Artemisia is one of the largest and most widely distribute of the nearly 100 genera of the Asteraceae. This family is very distinctive in its morphological characters (capitulum and cypsela) and in its chemical attributes. The subdivision of family into 13 tribes by Bentham (1873) has been largely accepted, but the recent classification of the Asteraceae, according to Bremer (1994), divided the family into 17 tribes, split into 2 subfamilies. The genus Artemisia is related to the Anthemidae tribe. The Anthemideae is the seventh largest tribe in the Asteraceae, it is monophyletic and composed of 109 genera and 1740 species. Following Watson (1996) and morphophylogenic datas (Bremer & Humphries, 1993), Artemisia, Seriphidium and Dendrathemna form a monophyletic clade in the Anthemidae, corresponding to the subtribe Artemisineae.
Artemisia genus, that represent about 400 species, is mainly diversified in Asia and ex-USSR. The genus is highly evolved, with a wide range of life forms, from tall shrubs to dwarf herbaceous alpine plants, occurring in a variety of habitats between arctic alpine environments to the dry deserts. Many species are not always well known and a world revision of the genus from a systematic point of view is needed (Heywood et al., 1977).
The first rational and natural arrangement of Artemisia was given by Besser (1829), that has divided the genus in four sections on the basis of floral structure. Phylogenetically, it has been admitted that Abrotanum and Absinthium represent the more primitive sections, while Dracunculus and Seriphidium are the most advanced (Clements and Hall, 1923). Some taxonomists have elevated Besser’s section to subgenus, and reduced the taxa number by combining Absinthium with Abrotanum to form Artemisia subgenus (Poljakov, 1961, Kelsey and Shafizadeh, 1979). Some of these authors (Kelsey and Shafizadeh, 1979) were working on chemosystematic of the Artemisia genus, using sesquiterpene lactones as markers, and a chemotaxonomic section Vulgares arose from this work, closely related to New world Abrotanum species.
Flavonoid datas (Belenovskaja, 1996) support subdivision of the genus into three subgenera : Artemisia, Dracunculus and Seriphidium, and assessed the advanced position of the entire genus in the Asteraceae.
As almost all classes of compounds are present in the genus, other chemical datas are required to resolve taxonomic relationships at the intrageneric and interspecific level of the genus Artemisia, as well as phenotypic variations (Mucciarelli and Maffei, 2002).
Within this context, our work deals with morphological characters and volatile compounds of eight species of Artemisia, growing wild in Mediterranean area. The analysis of capitulas, flowers and achenes, using SEM, as lead us to link these species to the sections described by Besser (1829). Chemical analysis has taken into account some parameters as phenology and/or ecology. A link has been done with Anthemideae by the presence of camphenes, bisabolenes and cadinenes. At an infrageneric level, chemical analysis assess the combination of Absinthium and Abrotanum, when Dracunculus and Seriphidium are clearly separated by original compounds (polyacetylenes for example). A set of chemical markers have been identified in order to characterize each species.
References:
Bentham, 1873, J. Linn. Soc. Bot., 13, pp. 335-577
Watson L.E., 1996, Proceedings of the international compositae conference, Royal Botanic gardens, Kew, vol I, ch. 23 pp. 341-348.
Bremer K., 1994, Asteraceae : Cladistics and Classification, Timber press, Portland.
Bremer K., & Humphries B., 1993, Bull. Nat. Hist. Mus. (London), 23, pp. 71-177
Belenovskaja L., 1996, Proceedings of the international compositae conference, Royal Botanic gardens, Kew, vol I, ch. 18, pp. 253-259.
Heywood V.H. et al, 1977, in Heywood V.H. et al The Biology and chemistry of the Compositae, Academic press, London, vol I, chap I, pp. 1-19
Besser, W.S., 1829, Bull. Soc. Imp. Natl. Mosc., 1, 219.
Mucciarelli M. & Maffei M., 2002, in Wright C., Artemisia, ch. I, Taylor & Francis, London, pp. 1-50.
Kelsey R.G. & Shafizadeh F., 1979, Phytochemistry, 18, 1591-1611.
Clements, F.E. & Hall H.M., 1923 The phylogenetic methods in taxonomy. The North american species of Artemisia, Chrysothamnus and Atriplex, Publs Carnegie Inst., New York.
Poljakov P.P., 1961, in Komarov V.L., Flora of the USSR, Izdatelstvo Akad. NauK SSSR, Leningrad, vol XXVI, pp. 425-631.
P13. “Evolutionary biology as a tool towards a more customized biological control strategy of weeds: Hoary cress as a case study”
Fumanal B.1, Martin J.F.2, Sobhian R.1 , Quimby P.C.1, Gaskin J. 3 and Bon M.C.1
Addresses: 1 EBCL-ARS, Campus International de Baillarguet, 34980 Montferrier Le Lez, France. bfumanal@ars-ebcl.org;rsobhian@ars-ebcl.org;mcbon@ars-ebcl.org; cquimby@ars-ebcl.org
2 Centre de Biologie et de Gestion des Populations, Campus International de Baillarguet, 34980 Montferrier sur Lez, France. martinjf@ensam.inra.fr
3 USDA-ARS, Northern Plains Agricultural Research Laboratory, Sidney, Montana, USA. JGaskin@sidney.ars.usda.gov
Abstract:
Invasive weeds negatively impact ecosystems by reducing biodiversity and quality of wildlife habitats in open range and in natural resource areas. In this context, biological control - an ecologically sensitive strategy using natural enemies - represents an alternative approach to chemical use in exotic weed management. While conceptually it is agreed that a sound understanding of the genetic structure and history of the populations of both the target and the biological control agent will lead to a more customized biological control strategy, there is a surprising lack of such approach using molecular markers in the literature. This is in particular the case for hoary cress, Cardaria draba (Brassicaceae), one of the most invasive noxious weeds on North American rangelands and croplands and native to Eurasia. Among the current projects undertaken for the evaluation and introduction of biological control agents targeted against the hoary cress, the program related to a potential biological control agent, a collar gall weevil Ceutorhynchus assimilis (Coleoptera: Curculionidae) is still in its infancy. The genetic variability of this weevil, which is widely distributed in Eurasia and North Africa, was investigated using Cytochrome Oxidase subunit I (mitochondrial DNA gene) variation in populations found on Cardaria draba and other host plants throughout the distribution area. Results clearly suggested the splitting of this single taxonomic species into two distinct genetic clades in the haplotype network. Furthermore, all host plant specificity tests converge to suggest that only populations displaying haplotypes of one of these clades are specific to C. draba with regard to the larval development. These populations are restricted to the South of France and surroundings. Breeding experiments are being carried out to assess the level of reproductive isolation of these entities. Likewise, a study was jointly undertaken to trace the origin of the C. draba American populations and to evaluate the phylogeography of the species in its native range in comparison to the weevil. Our first results tend to show a pattern of genetic variation similar to the one observed for the weevil in Europe. Ultimately, such information will provide valuable insights for both studies of the mechanisms of differentiation through specialization and of the weed- insect evolution that are of particular interest in biological control strategy in general and in the risk assessment in particular.
P14. “Systématique du genre Ophrys”
Errol Vela
Address: Institut Méditerranéen d'Ecologie et de Paléoécologie (CNRS), Université d'Aix-MArseille 3
Abstract:
The genus Ophrys L. emend. Swartz is an eurymediterranean taxa which is rich-specific, in active evolution and that capacities of quick speciation are dues to a very rare fact : exclusive entomogamy with sexual-deceptive attraction (acting on males of several Hymenoptera), associated with a strong natural morphological and genetic variability.
In addition to teachings of classical morphology, sectioning the genus has beneficed of study on pollination by insects from 1920’s, and the comprehension of aggregates, species and subspecies has beneficed of real birth of this discipline during 1980’s.
Last tentative of infrageneric classification only based on morphology have used cladistic tools during 1990’s, and so first results in genetic (DNA characterization) arrived. In our days a best comprehension of sections and aggregates is possible, but many works are to purchase.
Complementarily, utilization of caryology and also pheromone’s chemistry (plants / insects communication) could allow a best comprehension of specific and subspecific variability role within the most complex aggregates.
Systematic classification and phylogenetic or phylogeographic reconstruction of this Mediterranean genus history with full of species (most of them endemic of a small area and more or less threatened), could take a best perception of conservation priorities. To be efficient this global strategy should take a care of population and biological status of each specific pollinator (at this time too much unknown), and equally of habitat characteristics of both plant and insect.
P15. “Regional differentiation among populations of Pinus nigra detected by chloroplast SSRs”
Addresses: 1IMEP, Université d’Aix-Marseille III, Faculté de St. Jérôme, 13397 Marseille, France
2Department of Environmental Science Policy and Management, University of California, Berkeley, CA 94720, U.S.A.
Abstract:
European black pine (Pinus nigra) is a widespread species ranging from Northwest Africa around the northern Mediterranean to the Black Sea. It is highly variable morpohologically that has led to taxonomic confusion. In western Europe, foresters have planted exotic provenances, selected for their higher growth rates and their better stem form. In southern France this has led to confusion as to the composition of black pine forests and to the existence of native gene pools. Our earlier work using foliar terpenoids detected differences between black pines from the Cevennes in France and those attributed to ssp. nigra from Italy, Austria and Slovenia and those attributed to laricio from Corsica. Recently, highly polymorphic microsatellites of the chloroplast genome have proved to be excellent markers for the detection of evolutionary lineages and are providing information on possible re-colonization routes following glacial retreats. Since the chloroplast genome is passed un-recombined through the paternal line in conifers, it is treated as a single locus and the combination of alleles at different microsatellite loci are characterized as a haplotype. We have examined haplotypic variation using 10 cpDNA microsatellites among 280 trees from continental France, from Corsica, from Sicily and Calabria and from north eastern Italy, representing the three putative subspecies salzmannii, laricio and nigra. Our data show that the populations from continental France include a mix of haplotypes attributable to nigra and laricio, but also haplotype lineages that are well distinct confirming the presence of a gene pool that is presumably native to this region. We are looking further at the possible evolutionary lineage of these populations that may have re-colonized the area from an Iberian peninsular route.
P16. “Complementarity of molecular data for understanding phylogenetic relationships in the section Mentha”
Virginie Gobert*, Michael Wink**, Pierre Taberlet***, Sandrine Moja*
Addresses: *Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales, EA 3061, Facultés des Sciences et Techniques, UJM Saint-Etienne.
**Institut fur Pharmazie and molecular Biotechnologie IPMB, Univertät Heidelberg
***Laboratoire de Biologie des Populations d’Altitudes, UMR 5553, Grenoble.
Abstract:
The taxonomy of mints is complex because of their high morphological polymorphism, their ability to hybridize and their domestication. The genetic diversity assessed by AFLP and ISSR markers showed strong links between parental species and their hybrids but the phylogenetic relationships between polyploids and diploids remained not clear. In order to find responses to this question, non-coding chloroplastic DNA (tnrL intron, intergenic spacers (tnrL-tnrF, psbA-tnrH) and ITS (internal Transcribed Spacers 1 and 2) were sequenced.
Cladisdic and phenetic analyses were performed independently for chloroplastic and genomic sequences. No strict congruence was observed between data and no monophyletic group was found. Nevertheless, the complementary level of information could be used to find phylogenetic relationship between species, and then close links appeared between polyploid (M. aquatica) and diploid (M. longifolia). The chloroplastic DNA results gave the maternal lineage of hybrids and showed several haplotypes at inter and intra species levels. The ITS sequences polymorphism was studied at intra-individual level by cloning and multicopies were detected in several species, mainly in polyploid ones. The confrontation of the AFLP-ISSR data to the non-coding chloroplastic and ITS ones is very interesting to show that in the section Mentha, the evolutionary history is complex because of introgression probably due to domestication.
P17. “Molecular evidence for hybridization and introgression in the section Mentha using AFLP and ISSR markers”
Addresses: *Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales, EA 3061, Facultés des Sciences et Techniques, UJM Saint-Etienne.
**Laboratoire de Biologie des Populations d’Altitudes, UMR 5553, Grenoble.
Keywords: Mentha, AFLP, Lamiaceae, DNA fingerprinting, genetic diversity, polyploid, hybridization
Abstract:
Amplified Fragment Length Polymorphism (AFLP) and ISSR (Inter Simple Sequence Repeat) methods were used to evaluate genetic diversity and to assess genetic relationships within section Mentha in order to clarify taxonomy of several interspecific mint hybrids with molecular markers. To this end, genetic diversity of 62 Mentha accessions from different geographic origins, representing five species and three hybrids, was assessed. The range of genetic similarity coefficients (0.11 to 0.98) showed that our collection is composed of genetically diverse accessions. The ISSR and AFLP data sets were analysed separately in a first time. According to phenetic and cladistic analysis, the congruence between data was evident and combined analysis was performed giving higher boostrap values. The 62 mint accessions were grouped into two major clusters. Principal Coordinates analysis separated species into well defined groups and clear relationships between species and hybrids could be described. Our AFLP-ISSR analysis supports taxonomic classification established among Mentha species by conventional (morphological, cytological and chemical) methods. It allows the assessment of phenetic relationships between species and the hybrids M. spicata and M. x piperita, largely cultivated all over the world for their menthol source, and provides new insights about the subdivision of M. spicata, based for the first time on molecular markers.
Reference
V. GOBERT, S. MOJA, M. COLSON, AND P. TABERLET. Hybridization in the section Mentha (Lamiaceae) inferred from AFLP markers. American Journal of Botany 89(12): 2017–2023. 2002.
P18. “When the collections dead recount by the way of the DNA molecules : molecular systematics and evolutionary history of the Melanoplinae subfamily (Insecta, Orthoptera, Caelifera)”
Ioana C. Chintauan-Marquier¹, F. Pompanon² and C. Amedegnato³
Addresses: 1,2 Laboratoire d'Ecologie Alpine, Genomique des Populations et Biodiversite, UMR CNRS-UJF 5553, 38041 Grenoble ; 3 Laboratoire d’Entomologie, Museum National d’Histoire Naturelle, 45 Rue de Buffon, 75005 Paris
Abstract:
The Melanoplinae grasshoppers constitute the largest subfamily of Acrididae in the Americas, including important pest species and having a Holarctic-Neotropical distribution. The opacity of the origin and of the melanoploid relationships was favoured by the lack of fossil records and the homoplasious morphological classifications. Three historical biogeographic scenarios for the intercontinental conjectures have emerged from earlier studies: one is a variation of the Halffter’s Holarcticist Hypothesis, a second have suggested an out of South America origin for a northward bulk of migrations, and the third viewed the Nearctic region as center from whence colonists emerged, establishing the Eurasiatic and the Neotropical taxa. This is the first study in which nuclear markers (18S, ITS1 and 28S) are used, individually or combined with mitochondrial genes (12S), to (1) test the monophyly of the Melanoplinae subfamily and of its tribes, in relation with ancestors from Africa and Americas, (2) verify which of the scenarios best describe the subfamily’s origins and the patterns of intercontinental movements, (3) date the events inferred from the phylogenetical analyses and (4) propose a systematic position for doubtful and new described morphological melano pline taxa. These goals were achieved with the parsimony, minimum evolution, maximum likelihood and bayesian methods applied in the analyses of the DNA sequences of twenty five museum collections specimens representing five Melanoplinae tribes (from seven mentioned by Otte, 1995). The feasibility of the results was tested with parametrical and non-parametrical techniques and the timing of species divergence are discussed within a geological context.
P19. “Utilising Retrotransposons as a tool for Analyzing Genetic Diversity and Phylogeny in Lycopersicon and Capsicum (Solanaceae)”
Sheh May Tam
Address: INRA, Biologie Cellulaire, 78026, Versailles ceadex, FRANCE
Abstract:
Retrotransposons are mobile genetic elements that are ubiquitous in eukaryotic organisms and co-exist in the genome as several different families, being variable in copy number and in chromosomal dispersion. Due to their replicative transposition mode, they are capable of generating stable insertions. We present results of our work generated using SSAP (Sequence Specific Amplified Polymorphism) that show retrotransposons as useful genetic markers that can help us better understand the genetic diversity and phylogeny in species of tomato and pepper.
P20. “Hypervariable regions of self-incompatibility RNases and phylogeny inference”
Addresses: Northern Caucasus Research Institute for Horticulture and Viticulture, Russia
And: Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden)
Abstract:
Self-incompatibility (SI) is an important property of higher plants to prevent fertilization with their own pollen and, thus, to force outbreeding. Being switched off in many self-compatible species (presumably well adapted to the environment conditions), SI persists in most others. Three plant families considered in this research (Rosaceae, Veronicaceae and Solanaceae) possess gametophytic SI that is determined by a gaploid genotype of the pollen grain interacting with diploid one of the pollinated plant. Dozens of self-incompatibility alleles have been characterized in last decade and provided a vast material for investigation of molecular evolution of self-incompatibility system. However, there is a functionally determined allelic variability among the protein sequences. Hypervariable regions of S-gene convene not only the molecular clock or evolutional fitness but also specific selection pressure that drives them to diverge excessively inside the species, while the rate of the species evolution can be usual.
Since S-gene is highly desirable to be used in the research, a special procedure for purifying relevant datasets had to be developed. It is proposed to take the variability into account. Only the regions (or positions) showing low uncertainty inside the species are adequate in comparisons of different taxa.
The problem of material for phylogeny inference appears to be solved if only those positions selected for the analysis that are not subject of allelic variability. Information content of a particular position of the sequence can be characterized using the uncertainty measure. The well-known measure of uncertainty (Shannon and Weaver, 1949; Schneider, 1986) can be used. This procedure has to be applied after alignment and deals with inserted gaps. For this reason, it is worth modifying the formula to imply a penalty for positions with gaps.
The program PHYLHYP implemented this procedure to discriminate between hypervariable and conserved regions. To make more relevant the decision about a particular position, inside-species (allelic) positional uncertainty scores are compared with between-species ones. The inside-species uncertainties are calculated separately for all alleles of a species and combined into the mean. To produce between-species value, a series of bootstraps from the set is used: one allele per species per sample for a given position. A part of amino acid positions is extracted forming a consensus sequence for the species. This is used for the further work, which can be done with common methods and software tools.
The source code of PHYLHYP program written in ANSI C will be available via the personal web page of author.
P21. “Analyse de l’ADN ancien extrait à partir de momies naturelles du site archeologique de FOSTAT (Egypte)”
E. Bouzaïd £, R. Kéfi £, F. Paris # , R-P. Gayraud§ et E. Béraud-Colomb£
Addresses : £: Unité 387 INSERM Hôpital Sainte Marguerite BP.29- 13277 Marseille CEDEX 9
# : Représentant de l'IRD (ex Orstom) en Egypte, P.O. Box 26, 12211 GIZA, République Arabe d'Egypte
§ :UMR 6572 CNRS, Laboratoire d'Archéologie Médiévale Méditerranéenne, 5 rue du château de l'horloge, BP647, 13094 Aix en Provence Cedex 02, France
Abstract :
Au sud de la capitale égyptienne, les archéologues fouillent la nécropole de Fostat où ont été inhumés, il y a 1000 ans, les membres de la dynastie chiite des Fatimides. En 969, ces conquérants fondèrent la ville d’Al-Qâhira, le Caire actuel, qui devint grâce à eux un important centre intellectuel et commercial. A Fostat, dans de somptueux mausolées, ils inhumèrent pour la seconde fois leurs morts, qu'ils avaient transportés depuis la Tunisie.
L’ADN de 18 spécimens a été extrait par la méthode Phénol/Chlorodiméthane, puis l’utilisation de la technique de PCR en temps réel a été testée pour la première fois dans l’étude de l’ADN de momies naturelles. Les conditions optimales d’amplification déterminées ont permis d’obtenir, en une seule PCR, un produit d’amplification en quantité suffisante pour être directement séquencé. Toutes les analyses étant réalisées en double (deux PCR indépendantes), nous pourrons discuter la reproductibilité des séquences obtenues.
P22. “HSPs expression in Branchiopods (crustacea) : biomarker of stress adaptation and witness of evolution”
S. Jean, L. De Jong, X. Moreau, A. Thiéry
Address : EA 2202 "Biodiversité", Laboratoire de Biologie Animale (Plancton), Université de Provence, 3 Place Victor Hugo, 13331 Marseille, France.
Abstract:
In all organisms examined so far, hyperthermia induces the rapid and transient synthesis of a set of proteins known as Heat Shock Proteins (HSPs). These are highly conserved throughout evolution and are believed to unable cells to cope with heat and other environmental stresses as anoxia. These proteins can be grouped into three families according to their molecular weight: HSP90-100, HSP70 and small HSPs. In unstressed cells, they have constitutive functions that are essential in various aspects of protein metabolism. The major role of HSPs is to protect the cells from environmental stress damages. They act by binding to partially denatured proteins and by dissociating protein aggregates to regulate their correct folding and to limit cell death. HSP70 are often the most abundant products of protein synthesis in stressed cells and have been proposed as general biomarker for environmental biomonitoring. Moreover, the HSP70 family probably includes the most conserved genes/proteins as yet known in nature.
Branchiopods are considered as archaic crustaceans and have conserved the same morphological aspect since the Paleozoïc (morphological stasis). Thereby, they are believed to be panchronic organisms. Most Branchiopods (Anostraca, Notostraca…) inhabit the continental stagnant freshwaters and especially temporary ponds. In such habitat, most of them produce resting eggs (cysts) which are able to survive to the drying of their habitat. This progressive drying induces anoxia which constitutes a major stress before their death.
The present study deals with HSP70 expression in Branchiopods. Our topic is to investigate how these organisms react to such drastic abiotic conditions and if this reaction could be related to their panchronic evolution.
P23. “Deciphering the evolutionary biology of freshwater fish using multiple approaches - insights for the biological conservation of Leuciscus souffia souffia (Teleostei: Cyprinidae) as a case study”
M. D. Salducci #, J.-F. Martin†, N. Pech #, R. Chappaz #, C. Costedoat # & A. Gilles #*
Addresses: # Equipe d’Accueil Biodiversité 2202 - Université de Provence – Case 36 - 3, Place Victor Hugo, 13331 Marseille cedex 3, France.
† Centre de Biologie et de Gestion des Populations – Campus International de Baillarguet, CS 30016, 34988 Montferrier-sur-Lez cedex, France.
Abstract:
The organisation of genetic variability is of primary importance in designing conservation strategies. In this context, the conservation units are often defined using the concept of Evolutionary Significant Units (ESUs) what could appear as a useful guide. The main issue with this approach is that the plethora of definitions for this concept highlight different aspects of evolutionary biology and are thereby not always congruent. Another difficulty arises when species hybridise as it is the case in Cyprinid fishes for which the debate joins discussions on the species definitions. For exemple, the vairone, Leuciscus souffia (Teleostei: Cyprinidae) is a protected species (IUCN, Bern convention, Habitat directive) but current legislation does not take into account its ambiguous taxonomic status, neither its genetic variability nor its ecological preferences. In this paper, we examine the genetic structure and phylogeography of the subspecies Leuciscus souffia souffia in its distribution area (France) with a combination of morphology, allozymes and mitochondrial DNA sequences using analyses mainly based on AMOVA and nested clade analysis. We then decipher the evolutionary biology of this fish and evaluate the practical utility of the most often-used definitions of ESUs. The combined analysis displays decoupling between morphological homogeneity and moderate genetic differentiation, suggesting that Management Units (following Moritz’ definition) should be designed. We conclude in proposing directions both for the protection of endangered populations and for the conservation of evolutionary potential based on the evolutionary dynamics found for the examined populations.
P24. “High similarity between flanking regions of different microsatellites in Parnassius apollo and Euphydryas aurinia (Lepidoptera)”
Emese Meglécz*, Frederic Petenian*, Etienne Danchin** , Jean-Yves Rasplus***, Eric Faure* *
Addresses: Evolutionary Systematics Laboratory, CASE 5, UPRES Biodiversité 2202, Université de Provence, 3 place Victor Hugo, F-13331, Marseille Cedex 3, France
** Phylogenomics Laboratory, UPRES Biodiversité 2202, Université de Provence, 3 place Victor Hugo, F-13331, Marseille Cedex 3, France.
*** Centre de Biologie et Gestion des Populations (CBGP), Campus International de Baillarguet, CS 30 016, 34 988 Montferrier, France
Abstract:
Microsatellites flanking regions have been compared within two butterfly species. Several microsatellite flanking regions showed high similarity to one another indicating probable duplication/multiplication events involving large regions containing microsatellites. The multiplication of microsatellites might also be linked to mobile elements. Furthermore, crossing over between non-homologous microsatellites can lead to the exchange of the flanking regions between microsatellites. The same phenomenon was observed in both species but its extent was different in Parnassius apollo and Euphydryas aurinia. These findings explain at least partially why microsatellite isolation in Lepidoptera has been relatively unsuccessful so far.
P25. “Sex-ratio drive and Y chromosome evolution”
C. Montchamp-Moreau1, D. Jutier1 and A. Atlan2
Addresses: 1CNRS UPR 9034, Populations, génétique et Evolution, Avenue de la terrasse, F91198 Gif sur Yvette Cedex
2CNRS UMR6556, Ecobio, université Rennes 1, F35042 Rennes Cedex
Abstract:
The sex-ratio trait, known in natural populations of several drosophila species, results from meiotic drive of the X chromosome against the Y chromosome. The males that express the trait produce strongly femal-biased progeny. The emergence of sex-ratio X chromosome is expected to lower the polymorphism of the Y chromosome through selective sweep of Y-linked suppressors, because a drive-resistant Y has a strong transmission advantage over a drive-sensitive one. We addressed this question through the study of Y chromosomes sampled in natural populations of Drosophila simulans, a species where drive suppressors have evolved and maintain a roughly equal sex ratio in the populations, even when driving X chromosome are at high frequency. We found that these Y chromosomes were highly polymorphic with regard to their ability to suppress drive, thus suggesting that the evolution of sex-ratio drive could on the contrary increase the polymorphism of the Y chromosome. However, sequence analysis of Y-linked genes did not reveal any variation among the suppressor Y chromosomes, which supports the selective sweep hypothesis.
P26. “Comparative genomics of sunflower and Arabidopsis and insight into synteny across time”
A. Cibrian Jaramillo
Adress: Center for environmental research and conservation. Columbia university. Schermernhorn Extension 10th floor, 1200 Amsterdam ave, MC 5557. New-York, NY 10027.
P27. “Conserved synteny and evolution of chiken fucosyltransferase genes compared to human and mouse”
Philippe Coullina, Rafael Oriolb, Richard PMA Crooijmansc, Rosella Molliconeb, Martien AM Groenenc, Valérie Fillond, Charlotte Adrien-Dehaisa, A. Bernheima, Rima Zoorobe and Jean-Jacques Candelierb 1
Addresses: INSERM U 504 16, Avenue Paul Vaillant-Couturier 94807 Villejuif Cedex, France
UMR 8125, Cytogénétique et génomique des cancers, Institut Gustave Roussy, 94807 Villejuif Cedex, France
Animal Breeding and Genetics group, Wageningen Institute of Animal Sciences, Wageningen University, Wageningen, The Netherlands
Laboratoire de Genetique Cellulaire, Centre INRA de Toulouse-Auzeville, BP27, 31326 Castanet Tolosan. France
CNRS FRE 2376, 19 rue Guy Moquet BP8 94801 Villejuif France
Short title: Chicken fucosyltransferase genes compared to human
Key Words: fucosyltransferase, evolution, chicken, man, synteny, cytogenetic, chromosome, gene location
Abstract:
The fucosyltransferases are a subfamily of glycosyltransferases responsible of the biosynthesis of H and Lewis antigens implicated in various biological functions. Fucosyltrasferase genes are rather well conserved through evolution and sequence similarities among the 2-fucosyltransferases and the 3/4-fucosyltransferases suggested a common genetic origin for each of these two families followed by duplication and divergent evolution. The identification of three conserved peptide motifs shared by 2-, 6- and protein-O-fucosyltransferases strongly suggests a common ancestor for these three families.
Since the chromosomal structure in the ancestral vertebrate groups is a footprint of the gene organization it is interesting to follow their chromosomal localisation. Birds and mammals diverged approximately 300millions years ago, and the chicken represented a particular point of interest.
In human, 12 genes and a pseudogene dispatched on 8 chromosomes are presently identified. In the chichen we have evidenced 3 families of fucosyltransferases: 2/6, 3/4, and protein-O-fucosyltransferase. We have localized the corresponding genes in the chicken and in some other galliforms. The bird to human comparison shows a general preservation of the synteny yet described (which appeared better preserved than with mouse). An exception appeared for the human cluster of FUT3, FUT5 and FUT6 genes. This cluster corresponds to an insertion on the chicken chromosome 1 of a unique gene FUT3/5/6 ancestor of the three human genes. The FUT4 gene was assigned to the same chicken chromosome 1. This fact suggests the possible existence of a duplication of an ancestral gene and a moving on this chromosome that gave the bird FUT3/5/6 sequence and the bird FUT4 gene before the bird/mammalian separation. Finally, other works on the syntenies between HSA19 and GGA1 seem to indicate that the orthologous genes of different fucosyltransferases were associated on the same portion of chromosome at a given moment of evolution.
A Grimaldi , S Roetynsk and P Pontarotti
Address: Equipe Phylogénomique Université Aix Marseille I 3 place Victor Hugo, 13331 Marseille Cedex 3, France
Abstract:
Olfactory receptor (OR) genes are under positive selective pressure. One consequence of this is that OR duplicates tend to be fixed in populations, if the neo duplicate gene gives a selective advantage . This could explain the presence of thousands of OR genes found scattered in our genome as well as in other mammalian genomes. A duplication concerns a region and not a single gene. So when a region containing at least one OR duplicates, and if the OR are fixed due to positive selective pressure, we presume that the surrounding region which includes other genes families is also fixed (hitchhiking effect). The first family we identified to be linked physically to the OR is the B30 multigenic family. Actually, the distribution of OR genes and B30 genes in the human genome is not random : the physical link is statistically significant. So these families could have co-duplicated and have been co-fixed during evolution as well as the other gene families located in the original region. To further test this hypothesis, we started a phylogenomic study, which includes localizations and phylogenies of these families. When we found two regions of the human genome containing at least one OR and one B30 which are paralogs , we built phylogenetic trees, one for each family, looked for duplications which occurred during the same period of time and tested the statistical significance of our observations. The results obtained this way provide several arguments in favor of a "bloc duplication" of chromosome regions including OR associated with B30. This is the first step of our demonstration that olfaction plays an important role in the genome evolution.
P29. “Fitness costs of Doc expression are insufficient to stabilize its copy number in Drosophila melanogaster “
Hsiao-Pei Yang and Sergey V. Nuzhdin
Address: Section of Evolution and Ecology , UC Davis, Davis, CA 95616, USA.
Abstract:
The stable coexistence of transposable elements (TEs) with their host genome over long period of time suggests TEs have to impose some deleterious effect upon their host fitness. Three mechanisms have been proposed to account for the deleterious effect caused by TEs: host gene interruptions by TE insertions, chromosomal rearrangements by TE induced ectopic recombination, and costly TE expression. But, the relative importance of these mechanisms controlling TE abundance in the host genome remains controversial. Here we test specifically if TE expression accounts for the host fitness cost imposed by TE insertions. In retrotransposons, Doc, expression requires binding of the host RNA polymerase to the internal promoter. If expression of Doc elements is deleterious to their host, Doc copies with promoters would be more strongly selected against and would persist in the population for shorter periods of time in comparison with Docs lacking promotors. We tested this prediction using sequence specific amplified polymorphism (SSAP) analyses. We compared the populations of these two types of Doc elements in two sets of lines of Drosophila melanogaster, selection-free isogenic lines accumulating new Doc insertions, and isogenized isofemale lines sampled from a natural population. We found that (1) there is no difference in the proportion of promoter-bearing and promoter-lacking copies between sets of lines, and (2) the distributions of occupation frequency across sites in samples from a natural population are not significantly different between these two types of copies. Our results show that expression is not playing a major role in stabilizing Doc copy numbers.
Acknowledgments:This work is supported by a NSF grant (#DEB-9815621) to SVN.
P30. “Genome-wide
analysis of orthologous proteins in worm, fly, and human”
Abstract:
The sequencing of the human genome and the genomes of the invertebrates C. elegans (worm), and D. melanogaster (fly) have given biologists unprecedented possibilities to find orthologous counterparts of human genes that descend from very ancient ancestors in order to accelerate gene function discovery. As predicting detailed function (substrate or pathway specificity) from the sequence is beyond today's technology, it is most useful to consider orthologs as defined by Fitch (1970): genes that derive from a single gene in the last common ancestor of the species. Such genes are most likely to be functional counterparts, although this is not guaranteed. Genes that derive from a duplication were defined as paralogs.
Invertebrates and higher organisms are notorious for high numbers of gene duplications and/or gene losses. It is important to know if two genes derive from a duplication that preceded the speciation between to organisms. If the duplication has occurred first, the genes are paralogs spread across different species, and must not be confused with orthologs. If the speciation came first, the duplicated genes should be considered co-orthologs. We call such co-orthologs inparalogs, while the other type of paralog is called outparalog (Remm et al, 2001). A simplification of the problem would be to only consider the most similar inparalog but in many cases there is not clear distinction among them. We therefore consider it very important to find all inparalogs of a cluster while avoiding outparalogs.
Orthology analysis over such timespans faces many challenges due to gene duplications and losses, and few comprehensive surveys have been reported to date. We prefer the manual methods of reviewing gene trees to ensure high quality, but automated methods have to be applied as they enable genome-scale analysis of several species.
We present the first large-scale analysis of orthologous proteins in human, worm, and fly. The analysis has been made in three parts:
HMM models were utilized to retrieve all the possible transmembrane genes from the three genomes. A subset of transmembrane proteins was selected and used to manually produce clusters of orthologs among the three species. Then the program Inparanoid was used. It performs pairwise genome comparisons looking for main orthologs (defined as pairs of genes with the mutually best matches) using BLAST output. After that, additional orthologs (inparalogs) for this pair are clustered in each species. Another program combines the pairwise outputs of Inparanoid trying to merge the orthologs from all the species where it is possible. The merges of particular homologs are done under the procedure of average linkage clustering.
The manual clusters were compared with the results automated procedure.
The automated procedure has been used in comparison of all the proteins of human, fly, and worm.
Finally, the resulting ortholog groups were used to investigate on a large scale the relations observed between the three species in this study. A database containing all the clustered orthologs will be publicly available.
P31. “Modeling evolution after gene duplication”
F.N. Braun, A.C. Berglund, and D.A. Liberles*
Addresses: Stockholm Bioinformatics Center, Stockholm University, 10691 Stockholm,
Sweden and Computational Biology Unit, University of Bergen, 5020 Bergen, Norway
Abstract:
A simple model of an enzyme neutrally evolving under structural constraints is aimed at understanding the role of duplication events in shaping homolog distributions. The simple model incorporates an idealized account of enzyme-substrate binding, focusing on hydrophobic vs. polar (HP) amino acid composition of tertiary structure about the cleft. We simulate function-constrained evolution of the cleft via random HP substitution, modulated by birth/death of a gene duplicate. Other aspects of the modeling incorporate parameters to deal more explicitly with amino acid substitution properties, to examine the effects of directional selection applied according to a punctuated equilibrium model, and to examine the effects of specific secondary and tertiary structural constraints. These simulations predict homolog distribution statistics and illustrate the potential role of subfunctionalization in enhancing duplicate gene retention, ultimately relating to the evolution of novel function.
P32. Molecular evolution of the TCP gene family in some Angiosperm taxa.
2 Groupe Développement et Evolution, Université Pierre et Marie Curie /CNRS UMR 7622, 9 quai Saint-Bernard, case 241, 75252 Paris, France – address from 10/2001 to 10/2002
3Service Commun de Biosystématique, Université Pierre et Marie Curie, 9 quai Saint-Bernard, case 241, 75252 Paris, France
Abstract:
The TCP family of putative transcriptional factors is characterized by a specific basic helix loop helix domain (TCP domain, Cubas et al. 1999). The founding members of the family are Teosinte-branched1 from maize that represses growth of secondary branches, Cycloidea from Antirrhinum majus that is involved in floral symmetry, PCFs from Oryza sativa that bind promoter sequences of a gene involved in DNA replication and cell cycle control. When analyzed, gene expression occurrs in developping meristems, suggesting a role in growth and development.
Both Cyc and Dichtoma, a paralogue of Cyc are required for a zygomorphic flower in A. majus. Lcyc, an orthologue of Cyc in Linaria is also involved in zygomorphy. Both A. majus. and Linaria belong to the same family, Veronicaceae. Our interest is in a putative role of Cyc orthologues, or other independently recruited genes of the TCP family in the establishment of an asymetric flower in other Angiosperm groups. We present here results of an extensive phylogenetic analysis of TCP sequences from databases and of our experimental work on few species of Ranunculales.
P. Cubas, N. Lauter, J. Doebley, E. Coen, The TCP domain : a motif found in proteins regulating plant growth and development. The Plant Journal 18 (1999) 215-222.
P33. “A new method that improves structural annotation”
V. Vitiello
Address: Phylogenix, Technopole de Chateau Gombert, Marseille, France.
Abstract:
We developed a new software of structural annotation : Phygenix. A comparative study was carried out between this software and 2 others: Hmmgene and Genscan.
We decided to test software by using the HMR195 data base made up of 195 nucleotidic sequences and 195 corresponding proteins ( Rogic S., et al.). DNA sequences were extracted from GenBank . Some of the basic requirements in sequence selection were:
-the source organism is Homo sapiens, Mus musculus or Rattus norvegicus
-only genomic sequences that contain exactly one gene were considered
-mRNA sequences and sequences containing pseudo genes or alternatively spliced genes were excluded. Sequences that passed the filtering steps were further subjected to non-redundancy testing.
The final restriction of the dataset was done to confirm exon locations annotated in the GenBank records. For each sequence in the dataset they used the BLAST to find a corresponding mRNA sequence that had been independently sequenced and not derived from the genomic sequence.
If such an mRNA sequence existed, they used the sim4 program to align the genomic sequence and the mRNA sequence.
Only those sequences whose exon annotation perfectly matched the sim4 results were selected for the final version of their dataset.
The resulting dataset contain 195 sequences with exactly one complete, either single-exon or multi-exon, gene.
On these 195 sequences, 103 are human sequences, 82 are mise and 10 are rat . The human sequences were removed, for this test, to be able to annotate the sequences compared to others different sequences in the human division of swissprot, which one studies, in the data base used. The goal of this test is to compare the result of each software, for each predicted protein, with the proteins of the HMR195 data base.
In 87% of the cases, the PhyGenix software predicts the same protein that in the HMR195 data base. Whereas Genscan and Hmmgene predict only in 31% and 38% of the cases, respectively, the correct protein. Furthermore the over prediction problem is less important in the case of PhyGenix than Hmmgene and Genscan: 5 % for PhyGenix, 15% for Hmmgene and 22% for Genscan .
References
Sanja Rogic, Alan K. Mackworth, Francis B.F. Ouellette. Evaluation of Gene-Finding Programs on Mammalian Sequences
Genome Research.11 : 817-832 ,2001
http://www.cs.ubc.ca/~rogic/evaluation/
P34. “Automatisation of the phylogenetic analysis”
P. Gouret
Address: Phylogenix, Technopole de Chateau Gombert, Marseille, France.
Abstract:
We will present the PhyGenix software which is able to performe automatically phylogenetic analysis. To validate this tool, comparative studies were realized between « hand-made » phylogeny (on the genes RXR for example) and automated phylogeny.These comparative studies were made on 9 multigenic families (Abi-Rached L., et al.) and the results will be presented at the meeting .
Furthermore, phylogenetic analysis allows to put evidence problems of functional annotation in data bases. The corresponding result will be presented at the meeting.
References
Laurent Abi-Rached, André Gilles,Takashi Shiina, Pierre Pontarotti, Hidetoshi Inoko
Evidence of en bloc duplication in vertebrate genomes.
Nature genetics, volume31 :100-105, May 2002
P35. “Serotonin-like immunoreactive neurons in the brain and the visual system of Euphausiacea (Crustacea, Eucarida)”
D. Benzid, X. Moreau, L. De Jong, J.-P. Casanova
Address : EA 2202 "Biodiversité", Laboratoire de Biologie Animale (Plancton), Université de Provence, 3 place V. Hugo, 13331 Marseille, France.
Abstract:
In crustaceans, the neurotransmitter serotonin (5-hydroxytryptamine, 5-HT) is involved in the control of many biological functions and behaviours, e.g. release of hormones, regulation of cardiac rhythm, feeding and social behaviours. Besides, it has been suggested that the development of the 5-HT system and the localisation of 5-HT neurons can be useful markers to better understand and to precise some controversial phylogenetic relationships between crustacean taxa. Until now, the presence of 5-HT and a mapping of serotoninergic nervous system have not been investigated in Euphausiacea (Crustacea, Eucarida). The aim of this study was to evidence the presence of this neuromodulator in two Euphausiacea species, Nematoscelis megalops (Sars, 1883) and Stylocheiron longicorne (Sars, 1883) using an immuno-histo-fluorescent technique. Frozen sections of entire animals were incubated with a primary antibody raised against 5-HT and revealed with a TRITC-labelled secondary antibody and then observed under an epifluorescence microscope. 5-HT was present in the neuropiles of the eyestalk, in the crystalline cones and in the rhabdom area. Pyramidal cells bodies and 5-HT immunoreactive structures were observed in different part of the supraoesophageal ganglion. In the thorax and the abdomen, 5-HT ganglia and projections were also found. The features of 5-HT immunoreactivity in Euphausiacea nervous system show strong similarities with that of recently investigated in Mysidacea, and that of Decapoda. These similarities and some differences will be discussed in view to enlarge the debate concerning the phylogenetic relationships between these taxa. Our results will also allow providing helpful informations about some biological functions mediated by 5-HT in these crustaceans.
P36. “A new tool to search and Blast the Gene Ontology network”
Olivier Richard and David Roussel
Address: Université de la Méditerranée, Faculté des Sciences de Luminy – Case 901
13288 Marseille, Cedex 9, France.
Abstract:
The objective of Gene Ontology (1,2) is to provide controlled vocabularies for the description of the molecular functions, biological processes and cellular components of gene products. These terms are to be used as attributes of gene products by collaborating databases, facilitating uniform queries across them. They may also provide new ways for functionnal annotation (3) and text-based knowledge discovery tools and methods (4).
The controlled vocabularies of terms are structured to allow both attribution and querying to be at different levels of granularity. GO is a database independant of any other, but databases external to GO collaborate with GO by making database cross-links between GO terms and objects in their databases.
The web tools available to search or Blast (5) the GO network are often slow, limited for many parameters and or not suited to users. This project aimed at building a local, adaptable and easy-to-use tool in Java language (6,7) to search gene products in the GO network (using the GO database from the GO Consortium), or to Blast a protein (blastp) or DNA (blastx) sequence against it. The results page shows terms obtained from GO, and links to AmiGO (8) for visualisation of terms in the GO network as well as links to entries in external databases.
Search tools for biology-related databases may be more and more rapid and accurate, but problems related to functionnal annotation and evidence sources in databases should be discussed.
The Gene Ontology Consortium - www.geneontology.org
Gene Ontology: tool for the unification of biology.
The Gene Ontology Consortium. 2000. Nature Genetics 25:25-29.
Large-Scale Protein Annotation through Gene Ontology.
Xie H, Wasserman A, Levine Z, Novik A, Grebinskiy V, Shoshan A, Mintz L.
Genome Res. 2002 May;12(5):785-94.
Association of genes to genetically inherited diseases using data mining.
Perez-Iratxeta C, Bork P, Andrade MA.
Nat Genet. 2002 Jul;31(3):316-9.
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C. Brochier
Address: Atelier de BioInformatique Université Pierre et Marie Curie (Paris 6) 12, rue Cuvier Escalier A, 3ième Etage 75005 Paris France
Abstract:
The first emerging phyla in the tree of life based on the small subunit ribosomal RNA (16S rRNA) are hyperthermophilic. The most parsimonious explanation for this result is that the ability to live in a hot environment is an ancestral character inherited from the Last Universal Common Ancestor (LUCA). The adaptation to a mesophilic lifestyle will appear later and independently in the three domains of life. This hypothesis is widely accepted because it is in agreement with the popular scenario of the emergence of life in a hot environment. The reanalysis of the eubacterial phylogeny based on the 16S rRNA from 19 phyla (95 taxa) using a more reliable approach fails to find the early emergence of hyperthermophilic eubacteria (such as Aquificales and Thermotogales). Those phyla branch in the apical part of the tree among mesophilic groups. This important result suggests that eubacteria derive from a non-hyperthermophilic ancestor and seriously questions the validity of the hypothesis of a hyperthermophilic LUCA. In our tree the most basal phylum is the Planctomycetales. This unstudied group possesses numerous unique features as the existence of single or double membranes, analogous to the eukaryotic nucleus, isolating the DNA from the rest of the cytoplasm. An early emergence of the Planctomycetales have to be confirmed by a careful phylogenetic analysis of different alternative markers from the complete genome sequencing projects that will be available soon.