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Genomics, Proteomics & Bioinformatics:油桐基因组揭示油脂高产的遗传基础

已有 3552 次阅读 2020-4-7 07:43 |个人分类:每日摘要|系统分类:论文交流

Tung Tree (Vernicia fordii) Genome Provides A Resource for Understanding Genome Evolution and Improved Oil Production


First author: Lin Zhang; Affiliations: Central South University of Forestry and Technology (中南林业科技大学): Changsha, China

Corresponding author: Xiaofeng Tan


Tung tree (Vernicia fordii) is an economically important woody oil plant that produces tung oil rich in eleostearic acid. Here, we report a high-quality chromosome-scale genome sequence of tung tree. The genome sequence was assembled by combining Illumina short reads, Pacific Biosciences single-molecule real-time long reads, and Hi-C sequencing data. The size of tung tree genome is 1.12 Gb, with 28,422 predicted genes and over 73% repeat sequences. The V. fordii underwent an ancient genome triplication event shared by core eudicots but no further whole-genome duplication in the subsequent ca. 34.55 million years of evolutionary history of the tung tree lineage. Insertion time analysis revealed that repeat-driven genome expansion might have arisen as a result of long-standing long terminal repeat retrotransposon bursts and lack of efficient DNA deletion mechanisms. The genome harbors 88 resistance genes encoding nucleotide-binding sites; 17 of these genes may be involved in early-infection stage of Fusarium wilt resistance. Further, 651 oil-related genes were identified, 88 of which are predicted to be directly involved in tung oil biosynthesis. Relatively few phosphoenolpyruvate carboxykinase genes, and synergistic effects between transcription factors and oil biosynthesis-related genes might contribute to the high oil content of tung seed. The tung tree genome constitutes a valuable resource for understanding genome evolution, as well as for molecular breeding and genetic improvements for oil production.




油桐(学名:Vernicia fordii)是一种经济性的木本产油植物,能够生产富含硬脂酸(eleostearic acid)的桐油。本文中,作者报道了一个高质量的、染色体级别的油桐参考基因组。作者通过结合Illumina短reads、PacBio单分子实时长reads以及Hi-C测序数据组装了油桐的基因组。油桐基因组大小约为1.12Gb,包含28422个蛋白编码基因,其中基因组的73%由重复序列构成。油桐基因组经历了一次古老的、由所有核心真双子叶植物共享的全基因组复制事件,而后在约3455万年的演化时间里,桐树这一支系再未发生过全基因组复制事件。插入时间分析显示由重复序列所驱动的基因组扩张主要是由长久以来LTR逆转座子的爆发所导致的,并且油桐基因组缺少有效的DNA删除机制。油桐基因组包含88个编码核苷酸结合位点的抗性基因,其中17个可能参与了镰刀菌侵染早期阶段的枯萎病抗性。另外,作者还鉴定了651个油脂相关的基因,其中88个可能直接参与了桐油的生物合成。相对较少的磷酸烯醇式丙酮酸羧激酶(phosphoenolpyruvate carboxykinase,PEPCK)基因以及转录因子与油脂生物合成相关基因之间的协同效应可能作用于油桐种子中较高的油含量。油桐基因组的报道为理解基因组演化、以及油脂产量的分子育种与遗传改良都提供了宝贵的遗传资源。


p.s. 磷酸烯醇式丙酮酸羧激酶PEPCK作用于将草酰乙酸(Oxalacetic acid)催化形成磷酸烯醇式丙酮酸(Phosphoenolpyruvic acid),后者会进一步被催化成丙酮酸(Pyruvic acid)。而丙酮酸会在有氧时进入线粒体,在丙酮酸脱氢酶复合体的催化下氧化脱羧产生乙酰辅酶A(Acetyl-CoA)。乙酰辅酶A会在乙酰辅酶A羧化酶(ACCase)的催化下形成丙二酰辅酶A(Malonyl-CoA),后者进入脂肪酸生物合成通路(Fatty acid biosynthesis)。油桐中,ACCase数目与大豆相当,分别是9个和10个;但大豆中有16个PEPCK,而油桐中仅有3个PEPC。已有研究发现,抑制或干扰PEPCK的表达,可以调节油脂和蛋白质生物合成的共同底物丙酮酸(PEP)的流向,从而促进油脂的合成。所以,PEPCK基因家族的收缩或是导致油桐种子中油脂合成活跃的一个比较重要的原因。



通讯:谭晓风 (https://zhxy.csuft.edu.cn/szdw/jsml/201006/t20100601_34193.html)


个人简介:1984年,中南林业科技大学,硕士;1997年,中南林业科技大学,博士。


研究方向:森林培育、经济林学。



doi: https://doi.org/10.1016/j.gpb.2019.03.006


Journal: Genomics, Proteomics & Bioinformatics

Published date: March 26, 2020



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