Convergent evolution of AP2/ERF III and IX subfamilies through recurrent polyploidization and tandem duplication during eudicot adaptation to paleoenvironmental changes.
Convergent evolution of AP2/ERF III and IX subfamilies through recurrent polyploidization and tandem duplication during eudicot adaptation to paleoenvironmental changes.
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AP2/ERF III 和 IX 亚科在双子叶植物适应古环境变化过程中通过反复多倍化和串联复制的趋同进化
DOI：
10.1016/j.xplc.2022.100420
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发表时间：
2022-11-14
影响因子：
10.5
通讯作者：
Wu, Wenwu
中科院分区：
文献类型：
--
作者：
Guo, Liangyu;Wang, Shuo;Nie, Yuqi;Shen, Yirong;Ye, Xiaoxue;Wu, Wenwu
全基因组复制（WGD或多倍化）已被认为是被子植物适应环境变化的遗传贡献者。然而，许多真双子叶植物谱系没有经历最近的WGD（R-WGD）周围和/或之后的白垩纪-古近纪（K-Pg）边界，严重的环境变化的时间;这些植物如何生存在很大程度上被忽视。在此，我们从真双子叶植物的主要分支收集了22株植物，并根据R-WGD的出现或不存在将它们分为两组：12株含R-WGD的植物（R-WGD-Y）和10株R-WGD-缺乏的植物（R-WGD-N）。随后，我们在R-WGD-Y中鉴定了496个基因丰富的家族，并揭示了AP 2/ERF转录因子家族的成员在R-WGD后会聚地过度保留，并显示出异常的冷刺激。通过比较R-WGD-Y和R-WGD-N的AP 2/ERF家族的进化轨迹，揭示了辐射后AP 2/ERF III和IX亚家族通过反复的独立WGD和串联重复（TD）的收敛扩展。的扩张表现出一致的富集时间周围和/或K-Pg边界后，当全球变冷是一个主要的环境压力。因此，在不同的真双子叶植物谱系中，AP 2/ERF III C-重复结合因子（CBF）重复序列及其调节子的会聚扩增和共保留有助于冷特异性调控网络的重新布线。此外，启动子分析的冷响应AP 2/ERF基因揭示了一个潜在的顺式调控代码（G框：CACGTG）。我们提出了一个跷跷板模型的WGD和TD的收敛扩展的AP 2/ERF III和IX基因，有助于真双子叶植物的适应在古环境的变化，我们认为，TD可能是一个互惠/替代机制的遗传创新的植物，缺乏WGD。这项研究表明，收敛扩展的AP 2/ERF III和IX亚家族通过经常性的独立重复的WGD在WGD含植物与串联重复（TD）在WGD缺乏植物在全球冷却周围和/或之后的古近纪（K-Pg）边界。提出了WGDs和TDs在真双子叶植物适应严重环境变化的AP 2/ERF III和IX基因趋同扩增中的跷跷板模型。
Whole-genome duplication (WGD or polyploidization) has been suggested as a genetic contributor to angiosperm adaptation to environmental changes. However, many eudicot lineages did not undergo recent WGD (R-WGD) around and/or after the Cretaceous-Paleogene (K-Pg) boundary, times of severe environmental changes; how those plants survived has been largely ignored. Here, we collected 22 plants from major branches of the eudicot phylogeny and classified them into two groups according to the occurrence or absence of R-WGD: 12 R-WGD-containing plants (R-WGD-Y) and 10 R-WGD-lacking plants (R-WGD-N). Subsequently, we identified 496 gene-rich families in R-WGD-Y and revealed that members of the AP2/ERF transcription factor family were convergently over-retained after R-WGDs and showed exceptional cold stimulation. The evolutionary trajectories of the AP2/ERF family were then compared between R-WGD-Y and R-WGD-N to reveal convergent expansions of the AP2/ERF III and IX subfamilies through recurrent independent WGDs and tandem duplications (TDs) after the radiation of the plants. The expansions showed coincident enrichments in- times around and/or after the K-Pg boundary, when global cooling was a major environmental stressor. Consequently, convergent expansions and co-retentions of AP2/ERF III C-repeat binding factor (CBF) duplicates and their regulons in different eudicot lineages contributed to the rewiring of cold-specific regulatory networks. Moreover, promoter analysis of cold-responsive AP2/ERF genes revealed an underlying cis-regulatory code (G-box: CACGTG). We propose a seesaw model of WGDs and TDs in the convergent expansion of AP2/ERF III and IX genes that has contributed to eudicot adaptation during paleoenvironmental changes, and we suggest that TD may be a reciprocal/alternative mechanism for genetic innovation in plants that lack WGD. This study shows convergent expansions of AP2/ERF III and IX subfamilies through recurrent independent duplications of WGDs in WGD-containing plants versus tandem duplications (TDs) in WGD-lacking plants during global cooling around and/or after the Cretaceous-Paleogene (K-Pg) boundary. It proposes a seesaw model of WGDs and TDs in the convergent expansion of AP2/ERF III and IX genes in eudicot adaptation to severe environmental changes.
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DOI：
10.1093/bioinformatics/btr064
发表时间：
2011-04-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Grant CE;Bailey TL;Noble WS
通讯作者：
Noble WS
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
DOI：
10.1073/pnas.1316278111
发表时间：
2014-02-11
影响因子：
11.1
作者：
Franco-Zorrilla, Jose M.;Lopez-Vidriero, Irene;Solano, Roberto
通讯作者：
Solano, Roberto
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：
11.6
作者：
Kagale, Sateesh;Robinson, Stephen J.;Parkin, Isobel A. P.
通讯作者：
Parkin, Isobel A. P.