Different Modes of Gene Duplication Show Divergent Evolutionary Patterns and Contribute Differently to the Expansion of Gene Families Involved in Important Fruit Traits in Pear (Pyrus bretschneideri).
Different Modes of Gene Duplication Show Divergent Evolutionary Patterns and Contribute Differently to the Expansion of Gene Families Involved in Important Fruit Traits in Pear (Pyrus bretschneideri).
复制标题
不同的基因复制模式表现出不同的进化模式，并且对梨（Pyrus bretschneideri）重要果实性状相关基因家族的扩展有不同的贡献
DOI：
10.3389/fpls.2018.00161
复制
发表时间：
2018
影响因子：
5.6
通讯作者：
Zhang S
中科院分区：
文献类型：
--
作者：
Qiao X;Yin H;Li L;Wang R;Wu J;Wu J;Zhang S
梨是蔷薇科重要的水果作物，经历了两轮古老的全基因组复制（WGD）。然而，在梨基因组中，不同类型的基因复制是否在复制后进化不同仍不清楚。在这项研究中，我们确定了梨基因复制的不同模式。来自WGD、串联、近端、反转录转座、基于DNA的转座或分散重复的重复基因在基因组分布、基因特征、选择压力、表达分歧、调控分歧和生物学作用方面不同。梨基因组复制后，在3000 - 4500万年的进化过程中，复制基因之间发生了广泛的序列、表达和调控差异。与其他基因复制模式相比，反转录转座基因表现出相对较高的表达和调控差异。相比之下，WGD基因经历了较慢的序列分歧，并可能受到丰富的基因转换事件。此外，不同类别的重复基因表现出偏见的功能作用。研究了与梨果实品质和口感密切相关的糖和有机酸代谢途径基因家族的进化和扩展模式。单基因重复在很大程度上解释了梨中山梨醇代谢途径相关基因家族的广泛扩展。在蔗糖代谢途径和三羧酸循环途径中也检测到基因家族扩展。因此，这项研究提供了深入了解重复基因的进化命运。
Pear is an important fruit crop of the Rosaceae family and has experienced two rounds of ancient whole-genome duplications (WGDs). However, whether different types of gene duplications evolved differently after duplication remains unclear in the pear genome. In this study, we identified the different modes of gene duplication in pear. Duplicate genes derived from WGD, tandem, proximal, retrotransposed, DNA-based transposed or dispersed duplications differ in genomic distribution, gene features, selection pressure, expression divergence, regulatory divergence and biological roles. Widespread sequence, expression and regulatory divergence have occurred between duplicate genes over the 30–45 million years of evolution after the recent genome duplication in pear. The retrotransposed genes show relatively higher expression and regulatory divergence than other gene duplication modes. In contrast, WGD genes underwent a slower sequence divergence and may be influenced by abundant gene conversion events. Moreover, the different classes of duplicate genes exhibited biased functional roles. We also investigated the evolution and expansion patterns of the gene families involved in sugar and organic acid metabolism pathways, which are closely related to the fruit quality and taste in pear. Single-gene duplications largely account for the extensive expansion of gene families involved in the sorbitol metabolism pathway in pear. Gene family expansion was also detected in the sucrose metabolism pathway and tricarboxylic acid cycle pathways. Thus, this study provides insights into the evolutionary fates of duplicated genes.
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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：
7
作者：
Grishkevich V;Yanai I
通讯作者：
Yanai I
影响因子：
7.4
作者：
Arsovski, Andrej A.;Pradinuk, Julian;Adams, Keith L.
通讯作者：
Adams, Keith L.
影响因子：
46.9
作者：
Bray, Nicolas L.;Pimentel, Harold;Pachter, Lior
通讯作者：
Pachter, Lior
影响因子：
10.7
作者：
Gout, Jean-Francois;Lynch, Michael
通讯作者：
Lynch, Michael