| ECCB 2002 Poster sorted by: Author | Number Next | Previous poster (in order of the view you have selected) |
Title: Gene duplications at the base of chordate ancestry | P90 |
Leveugle, Magalie; Prat, Karine; Coulier, François; Birnbaum, Daniel leveugle@marseille.inserm.fr, prat@marseille.inserm.fr Laboratoire d'Oncologie Moléculaire, Unité 119 INSERM, Marseille France |
| One important mechanism for functional evolution is the duplication of genes and entire genomes. By increasing the number of genes, it provides a fertile ground to functional diversification and acquisition of new characters; duplicated copies undergo sequence modifications and acquire functional specificity, either by taking on a complete new function (neofunctionalization) or by each insuring part of the previous function (subfunctionalization) [1]. Two separate phases of extensive gene duplication were proposed to have occured early in vertebrate evolution. One phase of duplication is proposed on the vertebrate lineage after the divergence of cephalochordates, the second after the divergence of the jawless vertebrates (lampreys) [2] (figure 1). Tunicates, or sea squirts, are marine animals that spend most of their lives attached to docks, rocks or the undersides of boats. Tunicates are part of the Urochordate phylum, members of the Chordate phylum that includes all the vertebrates; and have a semi-rigide tail in their body which is called a notochord and can be compared to the spine of true vertebrates. In 1997, Simmen et al [3] estimated the total number of gene of the ascidian Ciona intestinalis to be ~ 15,000; far below the 30,000 estimated for vertebrate genomes. Therefore if the Ciona gene number is representative of basal chordates, all or most genes should have duplicated early in vertebrate evolution [4]. The aim of this study is to show whether specific duplications could also have occurred before separation of tunicates and vertebrates and to understand the evolution of several families of extant vertebrate genes in this context. We chose to work on proteins which play a role in cell communication and signalisation. Thus, for selected families such as receptor tyrosine kinases, forkhead and WNT proteins, sequence of known proteins were searched and retrieved from databases. Considering the phylogenetic position of Tunicates in chordate lineage, we searched and identified the homologous members of these families in the ascidian Ciona intestinalis and Ciona savignyi genomes. We aim at performing a phylogenetic study to identify the place of the ascidian genes in the evolution of the selected families. We processed in several steps, as shown in the figure 2: (For the figures see web representation of the poster abstract) - We first screened public databases to search all proteins belonging to the chosen families. Then, we blasted proteins against NCBI non redundant database to rescue all members of family that would have been missed in the first screening. Then, we aligned these proteins with Clustalx and built phylogenetic trees with Phylowin. - Then, we extracted in Ciona intestinalis genome the sequences that may belong to the chosen protein family. We blasted against Ciona reads database at JGI (DOE Joint Genome Institute : http://www.jgi.doe.gov/programs/ciona.htm). All selected clones found were classified and aligned. - Next, we tried to assemble clones to built putative sequences of Ciona proteins. All steps of this investigation were checked by continuous blast requests and by clustalX alignments. - Afterwards, we repeated the same procedure on Ciona savignyi genome. - Finally, we incorporated these extracted sequences in phylogenetic studies. Then, the same method was tested on several families of proteins of interest. |
| [1] Lynch, M. and Force, A., The probability of duplicate gene preservation by subfunctionalization. Genetics, 1999, 154: 459-473. [2] Ohno, S.; Evolution by Gene Duplication. Springer-Verlag Berlin, 1970. [3] Simmen, MW., Leitgeb ,S, Clark, VH, Jones, SJM, Bird, A; Gene number in an invertebrate chordate, Ciona intestinalis. Proc Natl Acad Sci USA,1997. 95: 4437-4440. [4] Holland ,PWH; Gene duplication: Past, present and future. Cell & Developmental Biology, 1999. 10: 541-547. |