2010
Journée Jean Chevaugeon, 8ème rencontres de phytopathologie-Mycologie, Aussois 25-29 janvier 2010
25 Jan 2010 Comparative genomics of Botrytis cinerea and related Ascomycota speciesNicolas Lapalu, Joelle Amselem, Hadi Quesneville, Marc-Henri Lebrun
The availability of a large number of complete and annotated fungal genome sequences allows the development of coherent comparative genomic studies that are helpful for structural and functional annotation. Protein sequence alignments “all against all” provide a resource to detect orthologous gene families as well as paralogs and multigenic families. In-depth analysis of the distribution of these families among genomes reveal species specific features (expansion, contraction of gene families) and help annotating protein functions for orthologous genes.
Here, we compared the complete set of proteins from Botrytis cinerea T4 isolate (BT4) to proteins from 11 other species of the Ascomycota Phylum. We defined protein families with OthoMCL (a Markov Clustering based tool) that detect orthologs from multiple sequences alignments. A total of 15184 families was found among the 11 genomes analysed, 3549 being shared by all species, and 2879 of them were assigned to single-copy orthologous gene clusters. Only few multigenic families with more than 6 genes per species were detected, most of them being open reading frames corresponding to transposons. Only 60 % of BT4 proteins were clustered in families with proteins shared with at least one other fungal species (40% of BT4 genes are specific to BT4). BT4 genome contains 492 multigenic families, including 12 species specific.
We have also shown that more than 1000 families are shared only by BT4 and Sclerotinia sclerotiorum (Ss). This is likely due to the fact that these 2 genomes are closely related (86% of protein identity) highlighting protein families that are apparently specific to this clade of the Ascomycetes.
We have used a set of protein families with phylogenetic performance according to Aguileta et al ( http://genome.jouy.inra.fr/funybase ) to obtain a phylogenetic tree of the 12 fungal species studied. Multiple alignments of the corresponding orthologs were performed with MUSCLE and cleaned with Gblocks. Recovered trees and orthologs families were supplied to CAFE. (Computational Analysis of gene Family), which implements a stochastic birth and death process, identifying gain and loss of families along the phylogenetic tree branches (expansion or contraction of gene families). This analysis emphasized 80 gene families (among the 15184 previously identified) with significant p-value, currently confirmed by manual inspection. These data will highlight some of the evolutionary trends that have shaped these genomes.
Keywords: Phylogeny, Comparative genomics
Creation date: 05 May 2010
eZ PublishPublication supervisor: A-F. Adam-Blondon
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