The Chromosome-Based Rubber Tree Genome Provides New Insights into Spurge Genome Evolution and Rubber Biosynthesis
The Chromosome-Based Rubber Tree Genome Provides New Insights into Spurge Genome Evolution and Rubber Biosynthesis
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DOI：
10.1016/j.molp.2019.10.017
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发表时间：
2020-02-03
期刊：
影响因子：
27.5
通讯作者：
Gao, Li-Zhi
中科院分区：
文献类型：
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作者：
Liu, Jin;Shi, Cong;Gao, Li-Zhi
橡胶树巴西橡胶树生产的天然橡胶是一种重要的工业原料。本研究利用单分子实时测序（SMRT）和Hi-C技术，构建了橡胶树品种GT1的高质量参考基因组，将1.47 gb的基因组组装固定在18条假染色体上。由于共同的古多倍体事件发生在Hevea和Manihot分裂之前，基于染色体的基因组分析使我们能够建立一个spurge染色体进化模型。在过去的1000万年里，我们发现了三个橡胶树特异性ltr -反转录转座子家族的快速爆发，导致整个橡胶树基因组自Manihot分化以来大规模扩展了65.88%（约970 Mbp）。我们发现与整个橡胶生物合成过程相关的基因大规模扩增，如基础代谢过程、乙烯生物合成、多糖和糖蛋白凝集素的激活，这些都是乳胶生产的重要特性。获得了栽培橡胶树和野生橡胶树之间的基因组变异图谱，其中包含1570万个高质量的单核苷酸多态性。我们发现了数百个候选驯化基因，尽管橡胶树的驯化历史相对较短，但在栽培橡胶树而不是野生橡胶树中，这些基因的基因组多样性急剧降低，其中一些基因与橡胶的生物合成有关。该基因组组合代表了未来橡胶树研究和育种的关键资源，为提高植物的生物和非生物耐受性和橡胶产量提供了新的靶点。
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 similar to 1.47-Gb genome assembly into 18 pseudochromosomes. 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 10 million years, leading to the massive expansion by similar to 65.88% (similar to 970 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 and glycoprotein lectin, which are important properties for latex production. A map of genomic variation between the cultivated and wild rubber trees was obtained, which contains similar to 15.7 million high-quality single-nucleotide polymorphisms. 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 of rubber tree, some of which are involved in rubber biosynthesis. This genome assembly represents key resources for future rubber tree research and breeding, providing novel targets for improving plant biotic and abiotic tolerance and rubber production.