On the origin of new genes in Drosophila Export

@article{citeulike:3112167, abstract = {10.1101/gr.076588.108 Several mechanisms have been proposed to account for the origination of new genes. Despite extensive case studies, the general principles governing this fundamental process are still unclear at the whole-genome level. Here, we unveil genome-wide patterns for the mutational mechanisms leading to new genes and their subsequent lineage-specific evolution at different time nodes in the species subgroup. We find that (1) tandem gene duplication has generated \^{a}ˆ¼80\% of the nascent duplicates that are limited to single species ( or ); (2) the most abundant new genes shared by multiple species (44.1\%) are dispersed duplicates, and are more likely to be retained and be functional; (3) de novo gene origination from noncoding sequences plays an unexpectedly important role during the origin of new genes, and is responsible for 11.9\% of the new genes; (4) retroposition is also an important mechanism, and had generated \^{a}ˆ¼10\% of the new genes; (5) \^{a}ˆ¼30\% of the new genes in the species complex recruited various genomic sequences and formed chimeric gene structures, suggesting structure innovation as an important way to help fixation of new genes; and (6) the rate of the origin of new functional genes is estimated to be five to 11 genes per million years in the subgroup. Finally, we survey gene frequencies among 19 globally derived strains for -specific new genes and reveal that 44.4\% of them show copy number polymorphisms within a population. In conclusion, we provide a panoramic picture for the origin of new genes in species.}, address = {CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China;}, author = {Zhou, Qi and Zhang, Guojie and Zhang, Yue and Xu, Shiyu and Zhao, Ruoping and Zhan, Zubing and Li, Xin and Ding, Yun and Yang, Shuang and Wang, Wen}, citeulike-article-id = {3112167}, citeulike-linkout-0 = {http://dx.doi.org/10.1101/gr.076588.108}, citeulike-linkout-1 = {http://genome.cshlp.org/content/18/9/1446.abstract}, citeulike-linkout-2 = {http://genome.cshlp.org/content/18/9/1446.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/18550802}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=18550802}, day = {30}, doi = {10.1101/gr.076588.108}, issn = {1088-9051}, journal = {Genome Research}, keywords = {evolution, genomics, rearrangements}, month = {September}, number = {9}, pages = {1446--1455}, posted-at = {2009-08-29 20:03:15}, priority = {2}, title = {On the origin of new genes in Drosophila}, url = {http://dx.doi.org/10.1101/gr.076588.108}, volume = {18}, year = {2008} }

TY - JOUR ID - citeulike:3112167 L3 - citeulike-article-id:3112167 N2 - 10.1101/gr.076588.108 Several mechanisms have been proposed to account for the origination of new genes. Despite extensive case studies, the general principles governing this fundamental process are still unclear at the whole-genome level. Here, we unveil genome-wide patterns for the mutational mechanisms leading to new genes and their subsequent lineage-specific evolution at different time nodes in the species subgroup. We find that (1) tandem gene duplication has generated ∼80% of the nascent duplicates that are limited to single species ( or ); (2) the most abundant new genes shared by multiple species (44.1%) are dispersed duplicates, and are more likely to be retained and be functional; (3) de novo gene origination from noncoding sequences plays an unexpectedly important role during the origin of new genes, and is responsible for 11.9% of the new genes; (4) retroposition is also an important mechanism, and had generated ∼10% of the new genes; (5) ∼30% of the new genes in the species complex recruited various genomic sequences and formed chimeric gene structures, suggesting structure innovation as an important way to help fixation of new genes; and (6) the rate of the origin of new functional genes is estimated to be five to 11 genes per million years in the subgroup. Finally, we survey gene frequencies among 19 globally derived strains for -specific new genes and reveal that 44.4% of them show copy number polymorphisms within a population. In conclusion, we provide a panoramic picture for the origin of new genes in species. IS - 9 JF - Genome Research SN - 1088-9051 AD - CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; EP - 1455 TI - On the origin of new genes in Drosophila VL - 18 SP - 1446 KW - evolution KW - genomics KW - rearrangements AU - Zhou, Qi AU - Zhang, Guojie AU - Zhang, Yue AU - Xu, Shiyu AU - Zhao, Ruoping AU - Zhan, Zubing AU - Li, Xin AU - Ding, Yun AU - Yang, Shuang AU - Wang, Wen PY - 2008/09/30/ UR - http://dx.doi.org/10.1101/gr.076588.108 ER -