Karyotype and gene order evolution from reconstructed extinct ancestors highlight contrasts in genome plasticity of modern rosid crops.
Karyotype and gene order evolution from reconstructed extinct ancestors highlight contrasts in genome plasticity of modern rosid crops.
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DOI：
10.1093/gbe/evv014
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发表时间：
2015-01-29
影响因子：
3.3
通讯作者：
Salse J
中科院分区：
文献类型：
--
作者：
Murat F;Zhang R;Guizard S;Gavranović H;Flores R;Steinbach D;Quesneville H;Tannier E;Salse J
利用葡萄、杨树、拟南芥、大豆、荷花、苹果、草莓、可可、木瓜等9个品种的全基因组序列，对蔷薇类作物的古代史进行了研究。我们描述了一个祖先蔷薇的核型，结构为7/21个原染色体，具有最小的6250个有序原基因集和最小的物理编码基因空间为50兆碱基。我们还提出了加花科、芸苔科、锦葵科、豆科、蔷薇科、水杨科和Vitaceae家族的祖先核型，分别具有9、8、10、6、12、9、12和19条原染色体。在这些祖先核型和现代物种比较的基础上，我们提出了一个基于异源六倍化的两步进化情景，涉及新特征的a， B和C二倍体祖先，导致任何现代玫瑰作物的显性（稳定）和敏感（塑性）基因组区室。最后，一个新的用户友好的在线工具，“DicotSyntenyViewer”（可从http://urgi.versailles.inra.fr/synteny-dicot获得），已经可以用于精确的道路翻译基因组学。
We used nine complete genome sequences, from grape, poplar, Arabidopsis, soybean, lotus, apple, strawberry, cacao, and papaya, to investigate the paleohistory of rosid crops. We characterized an ancestral rosid karyotype, structured into 7/21 protochomosomes, with a minimal set of 6,250 ordered protogenes and a minimum physical coding gene space of 50 megabases. We also proposed ancestral karyotypes for the Caricaceae, Brassicaceae, Malvaceae, Fabaceae, Rosaceae, Salicaceae, and Vitaceae families with 9, 8, 10, 6, 12, 9, 12, and 19 protochromosomes, respectively. On the basis of these ancestral karyotypes and present-day species comparisons, we proposed a two-step evolutionary scenario based on allohexaploidization involving the newly characterized A, B, and C diploid progenitors leading to dominant (stable) and sensitive (plastic) genomic compartments in any modern rosid crops. Finally, a new user-friendly online tool, “DicotSyntenyViewer” (available from http://urgi.versailles.inra.fr/synteny-dicot), has been made available for accurate translational genomics in rosids.