Quantification of ortholog losses in insects and vertebrates

The increasing number of sequenced insect and vertebrate genomes of variable divergence enables refined comparative analyses to quantify the major modes of animal genome evolution and allows tracing of gene genealogy (orthology) and pinpointing of gene extinctions (losses), which can reveal lineage-...

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Veröffentlicht in:Genome biology Jg. 8; H. 11; S. R242
Hauptverfasser: Wyder, Stefan, Kriventseva, Evgenia V, Schröder, Reinhard, Kadowaki, Tatsuhiko, Zdobnov, Evgeny M
Format: Journal Article
Sprache:Englisch
Veröffentlicht: England BioMed Central 16.11.2007
Schlagworte:
Animals
Coleoptera
Diptera
Evolution, Molecular
genes
Genetic Variation
honey bees
Humans
Insecta - genetics
Likelihood Functions
Models, Genetic
Phylogeny
vertebrates
Vertebrates - genetics
ISSN:1474-760X, 1465-6906, 1474-760X, 1465-6914
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Zusammenfassung:The increasing number of sequenced insect and vertebrate genomes of variable divergence enables refined comparative analyses to quantify the major modes of animal genome evolution and allows tracing of gene genealogy (orthology) and pinpointing of gene extinctions (losses), which can reveal lineage-specific traits. To consistently quantify losses of orthologous groups of genes, we compared the gene repertoires of five vertebrates and five insects, including honeybee and Tribolium beetle, that represent insect orders outside the previously sequenced Diptera. We found hundreds of lost Urbilateria genes in each of the lineages and assessed their phylogenetic origin. The rate of losses correlates well with the species' rates of molecular evolution and radiation times, without distinction between insects and vertebrates, indicating their stochastic nature. Remarkably, this extends to the universal single-copy orthologs, losses of dozens of which have been tolerated in each species. Nevertheless, the propensity for loss differs substantially among genes, where roughly 20% of the orthologs have an 8-fold higher chance of becoming extinct. Extrapolation of our data also suggests that the Urbilateria genome contained more than 7,000 genes. Our results indicate that the seemingly higher number of observed gene losses in insects can be explained by their two- to three-fold higher evolutionary rate. Despite the profound effect of many losses on cellular machinery, overall, they seem to be guided by neutral evolution.
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ISSN:1474-760X
1465-6906
1474-760X
1465-6914
DOI:10.1186/gb-2007-8-11-r242