Large-scale trends in the evolution of gene structures within 11 animal genomes.
We have used the annotations of six animal genomes (Homo sapiens, Mus musculus, Ciona intestinalis, Drosophila melanogaster, Anopheles gambiae, and Caenorhabditis elegans) together with the sequences of five unannotated Drosophila genomes to survey changes in protein sequence and gene structure over a variety of timescales--from the less than 5 million years since the divergence of D. simulans and D. melanogaster to the more than 500 million years that have elapsed since the Cambrian explosion. To do so, we have developed a new open-source software library called CGL (for "Comparative Genomics Library"). Our results demonstrate that change in intron-exon structure is gradual, clock-like, and largely independent of coding-sequence evolution. This means that genome annotations can be used in new ways to inform, corroborate, and test conclusions drawn from comparative genomics analyses that are based upon protein and nucleotide sequence similarities.
Yandell
Mark
M
Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, USA. myandell@genetics.utah
Mungall
Chris J
CJ
Smith
Chris
C
Prochnik
Simon
S
Kaminker
Joshua
J
Hartzell
George
G
Lewis
Suzanna
S
Rubin
Gerald M
GM
D000818:Animals; D000852:Anopheles / Q000235:genetics; D017173:Caenorhabditis elegans / Q000235:genetics; D002938:Ciona intestinalis / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D004331:Drosophila melanogaster / Q000235:genetics; D019143:Evolution, Molecular; D016678:Genome; D006801:Humans; D051379:Mice; D010802:Phylogeny; D040901:Proteomics / Q000379:methods; D013045:Species Specificity