A phylogeny of caenorhabditis reveals frequent loss of introns during nematode evolution.
Since introns were discovered 26 years ago, people have wondered how changes in intron/exon structure occur, and what role these changes play in evolution. To answer these questions, we have begun studying gene structure in nematodes related to Caenorhabditis elegans. As a first step, we cloned a set of five genes from six different Caenorhabditis species, and used their amino acid sequences to construct the first detailed phylogeny of this genus. Our data indicate that nematode introns are lost at a very high rate during evolution, almost 400-fold higher than in mammals. These losses do not occur randomly, but instead, favor some introns and do not affect others. In contrast, intron gains are far less common than losses in these genes. On the basis of the sequences at each intron site, we suggest that several distinct mechanisms can cause introns to be lost. The small size of C. elegans introns should increase the rate at which each of these types of loss can occur, and might account for the dramatic difference in loss rate between nematodes and mammals.
Cho
Soochin
S
Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48864, USA.
Jin
Suk-Won
SW
Cohen
Adam
A
Ellis
Ronald E
RE
D000595:Amino Acid Sequence / Q000235:genetics; D000818:Animals; D001483:Base Sequence / Q000235:genetics; D002107:Caenorhabditis / Q000235:genetics*; D017173:Caenorhabditis elegans / Q000235:genetics*; D029742:Caenorhabditis elegans Proteins / Q000235:genetics; D002872:Chromosome Deletion; D017124:Conserved Sequence / Q000235:genetics; D019143:Evolution, Molecular; D005091:Exons / Q000235:genetics; D017238:Genes, Helminth / Q000235:genetics; D007438:Introns / Q000235:genetics*; D008969:Molecular Sequence Data; D009348:Nematoda / Q000235:genetics*; D009687:Nuclear Proteins / Q000235:genetics; D010802:Phylogeny; D019655:Quantitative Trait, Heritable; D016601:RNA-Binding Proteins / Q000235:genetics; D016415:Sequence Alignment; D013045:Species Specificity; D014157:Transcription Factors / Q000235:genetics; D039221:mRNA Cleavage and Polyadenylation Factors / Q000235:genetics
C416182:CPB-1 protein, C elegans; C416183:CPB-2 protein, C elegans; D029742:Caenorhabditis elegans Proteins; C403465:FOG-3 protein, C elegans; D009687:Nuclear Proteins; D016601:RNA-Binding Proteins; D014157:Transcription Factors; D039221:mRNA Cleavage and Polyadenylation Factors