Recursive paleohexaploidization shapes the durian genome

First author: Jinpeng Wang; Affiliations: North China University of Science and Technology (华北理工大学): Tangshan, China

Corresponding author: Xiyin Wang (王希胤)

Durian (榴莲) genome becomes available recently and revealed two paleopolyploidization events, which were inferred to share with cotton. Here, we reanalyzed the durian genome in comparison with other well-characterized genomes. We found that durian and cotton were actually affected by different polyploidization events: hexaploidization in durian lineage ~19-21 million years ago (mya) and decaploidization in cotton ~13-14 mya. Previous problematic interpretation (理解) might be caused by elevated evolutionary rates in cotton genes due to the decaploidization, and insufficient consideration of the complexity of plant genomes. The decaploidization considerably elevated evolutionary rates so that cotton genes evolve ~64% faster than durian ones, and explained a previous ~4 times over dating of the event. In contrast, the hexaploidization has not prominently elevated durian gene rates likely due to the negative correlation with its long generation time. Moreover, divergent evolutionary rates should also be responsible for 98.4% of reconstructed phylogenetic trees of homologous genes being incongruent with expected topolopy. These findings provided further insight into the roles played by polypoidization to the evolution of genomes and genes and raised necessity to revisit existing reconstructed phylogenetic trees.

最近，榴莲的基因组公布，揭示了榴莲基因组上发生过两次古多倍化事件，被认为是与棉花共享的。本文中，作者重新分析了榴莲的基因组，并与其它质量较好的基因组进行了比较分析。作者发现榴莲和棉花中的古多倍化事件不是同一个，榴莲基因组大约在19-21个百万年前发生过一次古六倍化事件，而棉花在13-14个百万年前发生过一次古十倍化事件。先前研究的错误结论可能是由于低估了棉花基因的演化速率，并且并未充分考虑到植物基因组的复杂性。棉花基因组的古十倍化事件极大的提升了棉花基因的演化速率，所以棉花基因的演化速率约比榴莲快64%，因此也解释了之前计算的多倍化时间多4倍的差距。相反，榴莲基因组中的古六倍化事件由于榴莲的世代周期较长而并未显著提升榴莲基因的演化速率。此外，不同的演化速率也导致了98.4%的同源基因所构建的系统发育树与期望拓扑结构不一致。本文的研究发现为多倍化事件对于基因组和基因的演化提供了新的视野，同时说明了现有系统发育树需要重新被审视。

p.s. Teh et al., (2017) The draft genome of tropical fruit durian (Durio zibethinus). Nature Genetics 49: 1633-1641

通讯：王希胤  (http://bio.ncst.edu.cn/col/1460771460061/2016/04/19/1461037268201.html)

个人简介：1991-1995年，吉林大学，数学学士；2000-2005年，北京大学，生物信息学博士；2006-2009年，美国乔治亚大学，博士后。

研究方向：生物信息学软件和数据库开发；染色体进化理论创新；基因组多倍化与稳定性研究；重要经济作物全基因组比对算法和应用研究；基因家族和调控网络研究。

doi: https://doi.org/10.1104/pp.18.00921

Journal: Plant Physiology

First Published: 01 November, 2018