To systematically estimate the gene duplication events In closely related species, we have to use comparative genomlc approaches, either through genomlc sequence comparison or comparative genomlc hybridization （CGH）...To systematically estimate the gene duplication events In closely related species, we have to use comparative genomlc approaches, either through genomlc sequence comparison or comparative genomlc hybridization （CGH）. Given the scarcity of complete genomlc sequences of plant species, in the present study we adopted an array based CGH to Investigate gene duplications In the genus Arabldopsls. Fragment genomlc DNA from four species, namely Arabidopsls thallana, A. lyrata subsp, lyrata, A. lyrata subsp, petraea, and A. halleri, was hybridized to Affymetrlx （Santa Clara, CA, USA） tiling arrays that are designed from the genomlc sequences of A. thallana. Pairwlse comparisons of signal intensity were made to infer the potential duplicated candidates along each phylogenetic branch. Ninety-four potential candidates of gene duplication along the genus were Identified. Among them, the majority （69 of 94） were A. thallana lineage specific. This result indicates that the array based CGH approach may be used to Identify candidates of duplication In other plant genera containing closely related species, such as Oryza, particularly for the AA genome species. We compared the degree of gene duplication through retrotransposon between O. satlva and A. thallana and found a strikingly higher number of chimera retroposed genes In rice. The higher rate of gene duplication through retroposltlon and other mechanisms may Indicate that the grass species Is able to adapt to more diverse environments.展开更多
基金Supported by Fellowships from the Pew Latin American Fellows Program and Conselho Nacional de Desenvolvimento Cientfico e Tecnologico （to MDV）, the USA National Science Foundation CAREER award （MCB0238168） and USA National Institutes of Health R01 grants （R01GM065429-01A1 and GM078070-01A1） to ML at the University of Chicago. Publication of this paper is supported by the National Natural Science Foundation of China （30624808）.Acknowledgements The authors thank Dr Hedibert F. Lopes （University of Chicago, Graduate School of Business, Chicago, USA） for his discussions regarding the statistical methods, Noboru Jo Sakabe （IQ- USP/LICR-Sao Paulo Branch, Sao Paulo, Brazil） for critical reading of the manuscript. The authors also thank those people who provided seed samples of Arabidopsis： ABRC Stock Center （The 0hio State University, Columbus, 0H 43210, USA）, Justin Borevitz （Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois 60637, USA）, Daphne Preuss （Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois 60637, USA）, Joy Bergelson （Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois 60637, USA）, and Mark MacNair （Department of Biological Sciences, University of Exeter, Exeter, EX4 6EZ, UK）.
文摘To systematically estimate the gene duplication events In closely related species, we have to use comparative genomlc approaches, either through genomlc sequence comparison or comparative genomlc hybridization （CGH）. Given the scarcity of complete genomlc sequences of plant species, in the present study we adopted an array based CGH to Investigate gene duplications In the genus Arabldopsls. Fragment genomlc DNA from four species, namely Arabidopsls thallana, A. lyrata subsp, lyrata, A. lyrata subsp, petraea, and A. halleri, was hybridized to Affymetrlx （Santa Clara, CA, USA） tiling arrays that are designed from the genomlc sequences of A. thallana. Pairwlse comparisons of signal intensity were made to infer the potential duplicated candidates along each phylogenetic branch. Ninety-four potential candidates of gene duplication along the genus were Identified. Among them, the majority （69 of 94） were A. thallana lineage specific. This result indicates that the array based CGH approach may be used to Identify candidates of duplication In other plant genera containing closely related species, such as Oryza, particularly for the AA genome species. We compared the degree of gene duplication through retrotransposon between O. satlva and A. thallana and found a strikingly higher number of chimera retroposed genes In rice. The higher rate of gene duplication through retroposltlon and other mechanisms may Indicate that the grass species Is able to adapt to more diverse environments.
