Evolutionary history and functional divergence of the cytochrome P450 gene superfamily between Arabidopsis thaliana and Brassica species uncover effects of whole genome and tandem duplications.
Evolutionary history and functional divergence of the cytochrome P450 gene superfamily between Arabidopsis thaliana and Brassica species uncover effects of whole genome and tandem duplications.
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DOI：
10.1186/s12864-017-4094-7
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发表时间：
2017-09-18
期刊：
影响因子：
4.4
通讯作者：
Liao B
中科院分区：
文献类型：
--
作者：
Yu J;Tehrim S;Wang L;Dossa K;Zhang X;Ke T;Liao B
细胞色素P450单加氧酶（P450）超家族参与多种初级和次级代谢产物的生物合成。然而，对于芸苔属p450基因从拟南芥的共同祖先中分离出来后，全基因组重复（WGD）和串联重复（TD）事件对其进化史和功能分化的影响知之甚少。通过隐马尔可夫模型搜索和人工筛选，我们发现芸苔属植物的P450成员数量是拟南芥的近1.4倍。拟南芥和芸苔属植物的大部分p450位于假染色体上。推断的系统发育表明，所有p450都聚集在两个不同的亚群中。WGD事件分析表明，不同的P450基因家族在物种进化事件后出现。在TD事件分析中，芸苔属植物TD事件的p450可分为古代和近代两个部分。我们比较了WGD和TD事件对拟南芥和芸苔属植物P450超基因家族的影响，结果表明，芸苔系的家族特异性进化可归因于WGD和TD，而WGD被认为是P450超基因家族近期进化的主要机制。对拟南芥和芸苔属植物p4500s的表达分析表明，wgd型p4500s与td型p4500s在芸苔属植物不同组织中的表达模式相同，但表达完全不同。选择力分析表明拟南芥和芸苔属植物之间存在P450同源基因对负选择，但拟南芥- b中P450同源基因对间无显著差异。rapa和A. thaliana。与拟南芥相比，油菜甘蓝和甘蓝甘蓝不同亚基因组的差异。本研究首次探讨了WGD和TD对拟南芥和芸苔属植物P450基因家族进化史和功能分化的影响。本研究为研究被子植物基因家族形成机制提供了生物学模型，特别是在被子植物进化史的背景下，并为被子植物基因组研究提供了新的见解。本文的在线版本（10.1186/s12864-017-4094-7）包含补充材料，授权用户可使用。
The cytochrome P450 monooxygenase (P450) superfamily is involved in the biosynthesis of various primary and secondary metabolites. However, little is known about the effects of whole genome duplication (WGD) and tandem duplication (TD) events on the evolutionary history and functional divergence of P450s in Brassica after splitting from a common ancestor with Arabidopsis thaliana. Using Hidden Markov Model search and manual curation, we detected that Brassica species have nearly 1.4-fold as many P450 members as A. thaliana. Most P450s in A. thaliana and Brassica species were located on pseudo-chromosomes. The inferred phylogeny indicated that all P450s were clustered into two different subgroups. Analysis of WGD event revealed that different P450 gene families had appeared after evolutionary events of species. For the TD event analyses, the P450s from TD events in Brassica species can be divided into ancient and recent parts. Our comparison of influence of WGD and TD events on the P450 gene superfamily between A. thaliana and Brassica species indicated that the family-specific evolution in the Brassica lineage can be attributed to both WGD and TD, whereas WGD was recognized as the major mechanism for the recent evolution of the P450 super gene family. Expression analysis of P450s from A. thaliana and Brassica species indicated that WGD-type P450s showed the same expression pattern but completely different expression with TD-type P450s across different tissues in Brassica species. Selection force analysis suggested that P450 orthologous gene pairs between A. thaliana and Brassica species underwent negative selection, but no significant differences were found between P450 orthologous gene pairs in A. thaliana–B. rapa and A. thaliana–B. oleracea lineages, as well as in different subgenomes in B. rapa or B. oleracea compared with A. thaliana. This study is the first to investigate the effects of WGD and TD on the evolutionary history and functional divergence of P450 gene families in A. thaliana and Brassica species. This study provides a biology model to study the mechanism of gene family formation, particularly in the context of the evolutionary history of angiosperms, and offers novel insights for the study of angiosperm genomes. The online version of this article (10.1186/s12864-017-4094-7) contains supplementary material, which is available to authorized users.
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影响因子：
7
作者：
Blanc, G;Hokamp, K;Wolfe, KH
通讯作者：
Wolfe, KH
影响因子：
5.6
作者：
Le Roy J;Huss B;Creach A;Hawkins S;Neutelings G
通讯作者：
Neutelings G
影响因子：
14.9
作者：
Huala, E;Dickerman, AW;Rhee, SY
通讯作者：
Rhee, SY
影响因子：
7
作者：
Lysak, MA;Koch, MA;Schubert, I
通讯作者：
Schubert, I
DOI：
10.1073/pnas.0909766107
发表时间：
2010-10-26
影响因子：
11.1
作者：
Beilstein, Mark A.;Nagalingum, Nathalie S.;Mathews, Sarah
通讯作者：
Mathews, Sarah