Origin and evolution of new exons in rodents
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Origin and evolution of new exons in rodents. / Wang, Wen; Zheng, Hongkun; Yang, Shuang; Yu, Haijing; Li, Jun; Jiang, Huifeng; Su, Jianning; Yang, Lei; Zhang, Jianguo; McDermott, Jason; Samudrala, Ram; Wang, Jian; Yang, Huanming; Yu, Jun; Kristiansen, Karsten; Wong, Gane Ka-Shu; Wang, Jun.
In: Genome Research, Vol. 15, No. 9, 2005, p. 1258-64.Research output: Contribution to journal › Journal article › Research › peer-review
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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
VL - 15
SP - 1258
EP - 1264
JO - Genome Research
JF - Genome Research
SN - 1088-9051
IS - 9
ER -
ID: 11230832