Genome sequences provide insights into the reticulate origin and unique traits of woody bamboos

First author: Zhen-Hua Guo; Affiliations: CAS Kunming Institute of Botany (中科院昆明植物研究所): Kunming, China

Corresponding author: De-Zhu Li

Polyploidization is a major driver of speciation and its importance to plant evolution has been well recognized. Bamboos comprise of one diploid herbaceous and three polyploid woody lineages, and are the only major subfamily in grasses which diversified in forests with tree-like lignified culm for its woody members. Here we generated four draft genomes of major bamboo lineages at three different ploidy levels (diploid, tetraploid and hexaploid). We also constructed a high-density genetic linkage map of bamboo for a hexaploid species, providing a linkage-map-based strategy for assembly and identification of subgenomes in polyploids. Further phylogenomic analyses based on a large dataset of syntenic genes with expected copies revealed that woody bamboos originated subsequent to the divergence of the herbaceous bamboo lineage, and experienced complex reticulate evolution by three independent allopolyploid events involving four extinct diploid ancestors. A shared but distinct subgenome was identified in all polyploid forms, and its progenitor could be critical in ancient polyploidizations and origin of woody bamboos. We also found important genetic clues to the unique flowering behavior and woody trait in bamboos. Taken together, our study provides significant insights into ancient reticulate evolution at the subgenome level in the absence of extant donor species, and offers a potential model scenario for a broad-scale study of plant origins by allopolyploidization in angiosperms.

多倍化是物种形成的主要驱动因素，对于植物的演化十分重要。竹子这一支包括一个二倍体的草本和三个多倍体木本，是草本植物中唯一一个拥有木质化秆物种的亚家族。本文中，作者报道了三种不同倍性的竹子基因组草图，包括二倍体、四倍体和六倍体竹子。作者还构建了一个六倍体竹子的高密度遗传连锁图谱，为基于遗传图谱的组装策略提供了可能，同时也能够进一步鉴定多倍体中的亚基因组。进一步基于大量共线性基因的系统基因组分析显示六倍体的竹子起源于草本竹子分化之后，并且通过三次独立的异源多倍化事件经历了复杂的网状演化，这三次异源多倍化事件涉及了四个已灭绝的二倍体祖先。作者在所有多倍体竹子中鉴定到了共享但又不同的亚基因组，该亚基因组的祖先对于古老的多倍化以及木本竹子的起源可能是非常重要的。综上，本文的研究在没有现存供体物种情况下揭示了亚基因组水平上的古老网状演化，并为大范围探索被子植物异源多倍化作用于植物起源提供了研究模型。

通讯：李德铢（http://english.kib.cas.cn/OurTearms/KLOBB/PPRG_14279/rw/201208/t20120809_89712.html）

个人简介：1983年，江西农业大学，林学学士；1986年，西南林学院，硕士；1990年，中国科学院昆明植物研究所，博士；1993年，英国爱丁堡皇家植物园，博士后；1994年，剑桥大学植物科学系暨植物园，博士后。

研究方向：植物系统演化、群体遗传、生物地理、生态适应、种质资源保存及DNA条形码开发等。

doi: https://doi.org/10.1016/j.molp.2019.05.009

Journal: Molecular Plant

Published date: May 27, 2019