Origin and evolution of new exons in rodents

TY - JOUR

T1 - Origin and evolution of new exons in rodents

AU - Wang, Wen

AU - Zheng, Hongkun

AU - Yang, Shuang

AU - Yu, Haijing

AU - Li, Jun

AU - Jiang, Huifeng

AU - Su, Jianning

AU - Yang, Lei

AU - Zhang, Jianguo

AU - McDermott, Jason

AU - Samudrala, Ram

AU - Wang, Jian

AU - Yang, Huanming

AU - Yu, Jun

AU - Kristiansen, Karsten

AU - Wong, Gane Ka-Shu

AU - Wang, Jun

N1 - Keywords: Alternative Splicing; Animals; Base Sequence; DNA; Evolution, Molecular; Exons; Expressed Sequence Tags; Humans; Introns; Mice; Phylogeny; Rats; Rodentia; Sequence Deletion; Sequence Homology, Nucleic Acid; Species Specificity; Time Factors

PY - 2005

Y1 - 2005

N2 - Gene number difference among organisms demonstrates that new gene origination is a fundamental biological process in evolution. Exon shuffling has been universally observed in the formation of new genes. Yet to be learned are the ways new exons originate and evolve, and how often new exons appear. To address these questions, we identified 2695 newly evolved exons in the mouse and rat by comparing the expressed sequences of 12,419 orthologous genes between human and mouse, using 743,856 pig ESTs as the outgroup. The new exon origination rate is about 2.71 x 10(-3) per gene per million years. These new exons have markedly accelerated rates both of nonsynonymous substitutions and of insertions/deletions (indels). A much higher proportion of new exons have K(a)/K(s) ratios >1 (where K(a) is the nonsynonymous substitution rate and K(s) is the synonymous substitution rate) than do the old exons shared by human and mouse, implying a role of positive selection in the rapid evolution. The majority of these new exons have sequences unique in the genome, suggesting that most new exons might originate through "exonization" of intronic sequences. Most of the new exons appear to be alternative exons that are expressed at low levels.

AB - Gene number difference among organisms demonstrates that new gene origination is a fundamental biological process in evolution. Exon shuffling has been universally observed in the formation of new genes. Yet to be learned are the ways new exons originate and evolve, and how often new exons appear. To address these questions, we identified 2695 newly evolved exons in the mouse and rat by comparing the expressed sequences of 12,419 orthologous genes between human and mouse, using 743,856 pig ESTs as the outgroup. The new exon origination rate is about 2.71 x 10(-3) per gene per million years. These new exons have markedly accelerated rates both of nonsynonymous substitutions and of insertions/deletions (indels). A much higher proportion of new exons have K(a)/K(s) ratios >1 (where K(a) is the nonsynonymous substitution rate and K(s) is the synonymous substitution rate) than do the old exons shared by human and mouse, implying a role of positive selection in the rapid evolution. The majority of these new exons have sequences unique in the genome, suggesting that most new exons might originate through "exonization" of intronic sequences. Most of the new exons appear to be alternative exons that are expressed at low levels.

U2 - 10.1101/gr.3929705

DO - 10.1101/gr.3929705

M3 - Journal article

C2 - 16109974

SN - 1088-9051

VL - 15

SP - 1258

EP - 1264

JO - Genome Research

JF - Genome Research

IS - 9

ER -