Megabase-scale presence-absence variation with Tripsacum origin was under selection during maize domestication and adaptation.
Megabase-scale presence-absence variation with Tripsacum origin was under selection during maize domestication and adaptation.
复制标题
玉米驯化和适应过程中选择了来自 Tripsacum 的兆碱基规模存在-不存在变异
DOI：
10.1186/s13059-021-02448-2
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发表时间：
2021-08-20
期刊：
影响因子：
12.3
通讯作者：
Jin W
中科院分区：
文献类型：
--
作者：
Huang Y;Huang W;Meng Z;Braz GT;Li Y;Wang K;Wang H;Lai J;Jiang J;Dong Z;Jin W
背景
结构变异(SVS)极大地推动了不同物种的基因组多样性和环境适应。与高等真核生物中普遍存在的小SVS不同，大尺寸SVS在基因组中很少存在，但它们是物种形成和适应的关键进化力量之一。
结果
在这项研究中，我们发现并表征了玉米基因组中的几个百万碱基尺度的存在-不存在变异(PAV)。令人惊讶的是，我们发现了一个3.2Mb的PAV片段，它显示出高度的完整性，并在自然多样性小组中以完全存在或不存在的形式存在。这种PAV嵌入在核仁组织者区域(NOR)，在那里被发现抑制的重组维持PAV对抗进化变异。有趣的是，通过分析这个PAV的序列，我们不仅揭示了从teosinte到现代玉米的驯化痕迹，而且还揭示了它起源于Tripsaum的足迹，从而揭示了Tripsaum对玉米物种形成的一个以前未知的贡献。此外，还研究了Tripsaum片段迁移的功能后果，PAV所赋予的环境适合度可能解释了整个片段作为玉米驯化和改良的选择目标。
结论
这些发现提供了一个新的视角，即三七对玉米物种形成有贡献，也为基因组进化和物种形成过程中的“化石”结构变异的进化和功能分析提供了一种策略。
Background
Structural variants (SVs) significantly drive genome diversity and environmental adaptation for diverse species. Unlike the prevalent small SVs ( kilobase-scale) in higher eukaryotes, large-size SVs rarely exist in the genome, but they function as one of the key evolutionary forces for speciation and adaptation.
Results
In this study, we discover and characterize several megabase-scale presence-absence variations (PAVs) in the maize genome. Surprisingly, we identify a 3.2 Mb PAV fragment that shows high integrity and is present as complete presence or absence in the natural diversity panel. This PAV is embedded within the nucleolus organizer region (NOR), where the suppressed recombination is found to maintain the PAV against the evolutionary variation. Interestingly, by analyzing the sequence of this PAV, we not only reveal the domestication trace from teosinte to modern maize, but also the footprints of its origin from Tripsacum, shedding light on a previously unknown contribution from Tripsacum to the speciation of Zea species. The functional consequence of the Tripsacum segment migration is also investigated, and environmental fitness conferred by the PAV may explain the whole segment as a selection target during maize domestication and improvement.
Conclusions
These findings provide a novel perspective that Tripsacum contributes to Zea speciation, and also instantiate a strategy for evolutionary and functional analysis of the “fossil” structure variations during genome evolution and speciation.
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影响因子：
12.3
作者：
Bauer E;Falque M;Walter H;Bauland C;Camisan C;Campo L;Meyer N;Ranc N;Rincent R;Schipprack W;Altmann T;Flament P;Melchinger AE;Menz M;Moreno-González J;Ouzunova M;Revilla P;Charcosset A;Martin OC;Schön CC
通讯作者：
Schön CC
影响因子：
5.8
作者：
Bradbury, Peter J.;Zhang, Zhiwu;Buckler, Edward S.
通讯作者：
Buckler, Edward S.
影响因子：
30.8
作者：
Chia, Jer-Ming;Song, Chi;Ware, Doreen
通讯作者：
Ware, Doreen
影响因子：
4.5
作者：
Bilinski, Paul;Albert, Patrice S.;Ross-Ibarra, Jeffrey
通讯作者：
Ross-Ibarra, Jeffrey
影响因子：
5.4
作者：
Belo, Andre;Beatty, Mary K.;Rafalski, Antoni
通讯作者：
Rafalski, Antoni