A Microarray Based Genomic Hybridization Method for Identification of New Genes in Plants:Case Analyses of Arabidopsis and Oryza |
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作者姓名: | Chuanzhu Fan Maria D. Vibranovski Ying Chen Manyuan Long |
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作者单位: | Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA |
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摘 要: | 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.
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关 键 词: | 拟南芥 水稻 植物基因 新基因 鉴定 微阵列基因组杂交法 |
修稿时间: | 2007-01-09 |
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