Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy
Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy
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DOI：
10.1105/tpc.106.041665
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发表时间：
2006-06-01
期刊：
影响因子：
11.6
通讯作者：
Bancroft, Ian
中科院分区：
文献类型：
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作者：
Town, Christopher D.;Cheung, Foo;Bancroft, Ian
我们测序了2.2 Mb，代表了甘蓝的三个复制的基因组片段，它们彼此相邻，并与拟南芥基因组的一个片段复制区域同源。序列注释鉴定出甘蓝基因组片段中共线保守基因177个。同义碱基替换率分析表明，拟南芥和芸苔系分化后不久，三倍的芸苔基因组片段从一个共同祖先分化而来。蛋白质家族的系统发育分析证实了这一结论。以拟南芥为外群，推测在芸苔系发生基因组三倍复制时存在的35%的基因已经丢失，最有可能是通过缺失机制，以分散的模式丢失。编码参与信号转导或转录的蛋白质的基因没有发现比编码其他功能的蛋白质的基因保留得更广泛，但在拟南芥基因组中预测的推定蛋白质在甘蓝中代表性不足。我们从拟南芥谱系中发现了一个基因丢失的例子。我们发现了核基因组起源基因片段频繁插入的证据，并在甘蓝和拟南芥基因组的非共线位置发现了四个明显完整的基因。
We sequenced 2.2 Mb representing triplicated genome segments of Brassica oleracea, which are each paralogous with one another and homologous with a segmentally duplicated region of the Arabidopsis thaliana genome. Sequence annotation identified 177 conserved collinear genes in the B. oleracea genome segments. Analysis of synonymous base substitution rates indicated that the triplicated Brassica genome segments diverged from a common ancestor soon after divergence of the Arabidopsis and Brassica lineages. This conclusion was corroborated by phylogenetic analysis of protein families. Using A. thaliana as an outgroup, 35% of the genes inferred to be present when genome triplication occurred in the Brassica lineage have been lost, most likely via a deletion mechanism, in an interspersed pattern. Genes encoding proteins involved in signal transduction or transcription were not found to be significantly more extensively retained than those encoding proteins classified with other functions, but putative proteins predicted in the A. thaliana genome were underrepresented in B. oleracea. We identified one example of gene loss from the Arabidopsis lineage. We found evidence for the frequent insertion of gene fragments of nuclear genomic origin and identified four apparently intact genes in noncollinear positions in the B. oleracea and A. thaliana genomes.