A genome triplication associated with early diversification of the core eudicots.
A genome triplication associated with early diversification of the core eudicots.
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DOI：
10.1186/gb-2012-13-1-r3
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发表时间：
2012-01-26
期刊：
影响因子：
12.3
通讯作者：
Depamphilis CW
中科院分区：
文献类型：
--
作者：
Jiao Y;Leebens-Mack J;Ayyampalayam S;Bowers JE;McKain MR;McNeal J;Rolf M;Ruzicka DR;Wafula E;Wickett NJ;Wu X;Zhang Y;Wang J;Zhang Y;Carpenter EJ;Deyholos MK;Kutchan TM;Chanderbali AS;Soltis PS;Stevenson DW;McCombie R;Pires JC;Wong GK;Soltis DE;Depamphilis CW
虽然人们一致认为在真雄蕊中发生了一个重要的多倍体事件--伽马，但该事件的系统发育位置仍然不清楚。为了确定这种多倍化发生的时间相对于被子植物历史上的物种形成事件，我们使用了系统基因组学的方法来研究位于共线伽马区块上的基因集复制的时间。我们用从基础被子植物、木兰科植物、海星类植物的公共转录获得的大组同源基因以及超过91.8千兆碱基的非草单子叶植物和基础优生植物的新一代转录组序列填充了769个推定基因家族。绝大多数(95%)分辨率良好的伽马复制发生在玫瑰石和小行星分离之前，以及单子叶和优子叶分裂之后，这提供了伽马多倍体事件发生在优树演化早期的有力证据。此外，大多数基因复制发生在毛滴目和核心优化点的分化之后，这表明伽马似乎仅限于核心优化点。分子测年估计表明，重复事件集中在1.17亿年前。近75%被子植物物种的核心优生植物谱系的快速辐射似乎是在伽马三倍体事件之后或不久发生的。基因树与物种系统发育的一致性可以阐明基因组进化中主要事件的时间，即使基因组序列只适用于基因树中所代表的物种的子集。全面的转录组数据集是基因组序列的宝贵补充，用于高分辨率的系统基因组分析。
Although it is agreed that a major polyploidy event, gamma, occurred within the eudicots, the phylogenetic placement of the event remains unclear. To determine when this polyploidization occurred relative to speciation events in angiosperm history, we employed a phylogenomic approach to investigate the timing of gene set duplications located on syntenic gamma blocks. We populated 769 putative gene families with large sets of homologs obtained from public transcriptomes of basal angiosperms, magnoliids, asterids, and more than 91.8 gigabases of new next-generation transcriptome sequences of non-grass monocots and basal eudicots. The overwhelming majority (95%) of well-resolved gamma duplications was placed before the separation of rosids and asterids and after the split of monocots and eudicots, providing strong evidence that the gamma polyploidy event occurred early in eudicot evolution. Further, the majority of gene duplications was placed after the divergence of the Ranunculales and core eudicots, indicating that the gamma appears to be restricted to core eudicots. Molecular dating estimates indicate that the duplication events were intensely concentrated around 117 million years ago. The rapid radiation of core eudicot lineages that gave rise to nearly 75% of angiosperm species appears to have occurred coincidentally or shortly following the gamma triplication event. Reconciliation of gene trees with a species phylogeny can elucidate the timing of major events in genome evolution, even when genome sequences are only available for a subset of species represented in the gene trees. Comprehensive transcriptome datasets are valuable complements to genome sequences for high-resolution phylogenomic analysis.
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影响因子：
7
作者：
Blanc, G;Hokamp, K;Wolfe, KH
通讯作者：
Wolfe, KH
DOI：
10.1073/pnas.0900906106
发表时间：
2009-04-07
影响因子：
11.1
作者：
Fawcett, Jeffrey A.;Maere, Steven;Van de Peer, Yves
通讯作者：
Van de Peer, Yves
影响因子：
10.7
作者：
Johnson, Deborah A.;Thomas, Michael A.
通讯作者：
Thomas, Michael A.
影响因子：
64.8
作者：
Aury, Jean-Marc;Jaillon, Olivier;Wincker, Patrick
通讯作者：
Wincker, Patrick
影响因子：
64.8
作者：
Jaillon, Olivier;Aury, Jean-Marc;Wincker, Patrick
通讯作者：
Wincker, Patrick