The Chromosome-based Rubber Tree Genome Provides New Insights into Spurge Genome Evolution and Rubber Biosynthesis

First author: Jin Liu; Affiliations: Yunnan Institute of Tropical Crops (云南热带作物研究所): Jinghong, China

Corresponding author: Li-Zhi Gao

The rubber tree, Hevea brasiliensis, produces natural rubber that serves as an essential industrial raw material. Here, we present a high-quality reference genome for a rubber tree cultivar GT1 using single-molecule real-time sequencing (SMRT) and Hi-C technologies to anchor the ～1.47-Gb genome assembly into 18 pseudo-chromosomes. The chromosome-based genome analysis enabled us to establish a model of spurge chromosome evolution since the common paleopolyploid event occurred before the split of Hevea and Manihot. We show recent and rapid bursts of the three Hevea-specific LTR-retrotransposon families during the last ten million years (MYR), leading to the massive expansion ～60.44% (～890 Mbp) of the whole rubber tree genome since the divergence from Manihot. We identify large-scale expansion of genes associated with whole rubber biosynthesis processes, such as basal metabolic processes, ethylene biosynthesis, and the activation of polysaccharide (多糖) and glycoprotein lectin, which are important properties for the latex production. We report the first map of genomic variation between the cultivated and wild rubber trees and obtained ～15.7 million high-quality single nucleotide polymorphisms (SNPs). We identified hundreds of candidate domestication genes with drastically lowered genomic diversity in the cultivated but not wild rubber trees despite a relatively short domestication history, some of which are involved in the rubber biosynthesis. This genome assembly represents key resources for future rubber tree breeding programs providing novel gene targets to improve biotic and abiotic tolerance and rubber production.

橡胶树Hevea brasiliensis生产自然的橡胶，作为一种重要的工业原材料。本文中，作者利用单分子实时测序SMRT和Hi-C技术报道了一个高质量的橡胶树栽培种GT1的参考基因组，大小约为1.47 Gb，挂载到了18个假染色体上。在木薯属与橡胶属分化之前，二者共同的祖先发生过古多倍化事件，作者通过染色体层面的基因组分析建立起了染色体演化模型。作者发现在与木薯属分化之后，橡胶树基因组在最近10个百万年左右中有三个特异的LTR逆转录转座子家族发生了快速爆发，约使得橡胶树基因组扩张了60.44%，即890 Mbp。作者鉴定了与橡胶生物合成相关的基因家族的大范围扩张，比如乙烯生物合成等基础代谢进程以及作用于乳胶生产的多糖和糖蛋白凝集素的激活。作者还构建了野生和栽培种橡胶之间第一张基因组变异图谱，共获得约1570万个高质量SNPs。作者鉴定到了数百个驯化相关的候选基因，尽管橡胶的驯化历史不长，但很明显这些基因在栽培种橡胶中具有极低的多态性，而在野生种中则相反，其中一些基因参与了橡胶的生物合成。本文所报道的基因组为未来橡胶树育种项目提供了珍贵的遗产资源，同时也为橡胶树的生物/非生物胁迫育种以及橡胶产量提升提供了新的靶基因。

通讯：高立志 (http://groups.kib.cas.cn/gbows/glz/)

个人简介：1987-1991年，云南大学，学士；1991-1994年，云南大学，硕士；1994-1997年，中科院植物研究所，博士。

研究方向：主要利用基因组学、生态学和生物信息学等方法手段，研究兴趣涵盖分子进化、理论群体遗传学、分子生态学和保护生物学等诸多领域的一些重要科学问题。

doi: https://doi.org/10.1016/j.molp.2019.10.017

Journal: Molecular Plants

Published online: December 12, 2019