通过全基因组测序探索番茄（Solanum section Lycopersicon）分支的遗传变异
摘要
通过对代表 Lycopersicon、Arcanum、Eriopersicon 和 Neolycopersicon 组的 84 个番茄种质及相关野生物种进行测序，我们探索了番茄分支的遗传变异。我们重建了三个新的参考基因组以支持我们的比较基因组分析。商业育种系中的序列多样性极低，表明栽培番茄经历了剧烈的遗传侵蚀。这一点反映在野生物种的 SNP 数量上，其可超过 1000 万，即栽培种质的 20 倍。比较序列比对揭示了组、物种和种质特异性的多态性，这些多态性解释了番茄种质中特有的果实性状和生长习性。利用注释后的 Heinz 参考基因组的基因模型，我们观察到果实多样化和生长相关基因与非随机基因集相比，其 dN/dS 比率存在偏差，这可能是正向选择的结果。我们在野生 S. lycopersicum 物种中检测到高度分歧的片段，并在源自共同供体种质的栽培种质中检测到渐渗足迹。来自栽培种质的果实多样化和生长特异性基因的系统发育关系显示分辨率不完全，且依赖于渐渗供体。相比之下，全基因组 SNP 信息具有足够的效力，可通过最大似然分析解析 Lycopersicon 分支四个主要组中每个种质的系统发育位置。系统发育关系似乎与栖息地和交配类型相关，并指出这些组内存在地理种族，因此对渐渗杂交育种具有实际意义。我们的研究说明了在支持番茄比较基因组学和 Solanum 基因组进化研究中需要多个参考基因组。
引用
@article{arxiv.1504.05610,
title = {Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing},
author = {Saulo A. Aflitos and Elio Schijlen and Richard Finkers and Sandra Smit and Jun Wang and Gengyun Zhang and Ning Li and Likai Mao and Hans de Jong and Freek Bakker and Barbara Gravendeel and Timo Breit and Rob Dirks and Henk Huits and Darush Struss and Ruth Wagner and Hans van Leeuwen and Roeland van Ham and Laia Fito and Laëtitia Guigner and Myrna Sevilla and Philippe Ellul and Eric W. Ganko and Arvind Kapur and Emmanuel Reclus and Bernard de Geus and Henri van de Geest and Bas te Lintel Hekkert and Jan C. Van Haarst and Lars Smits and Andries Koops and Gabino Sanchez Perez and Dick de Ridder and Sjaak van Heusden and Richard Visser and Zhiwu Quan and Jiumeng Min and Li Liao and Xiaoli Wang and Guangbiao Wang and Zhen Yue and Xinhua Yang and Na Xu and Eric Schranz and Eric F. Smets and Rutger A. Vos and Han Rauwerda and Remco Ursem and Cees Schuit and Mike Kerns and Jan van den Berg and Wim H. Vriezen and Antoine Janssen and Torben Jahrman and Frederic Moquet and Julien Bonnet and Sander A. Peters},
journal= {arXiv preprint arXiv:1504.05610},
year = {2015}
}
备注
4 Figure, 10 Supplementary Figures, 2 Supplementary Figures This is the pre-peer reviewed version of the following article: The Plant Journal 80.1 (2014): 136-148, which has been published in final form at http://doi.org/10.1111/tpj.12616