Genome assembly and resequencing shed light on evolution, population selection, and sex identification in Vernicia montana.

IF 7.6 Q1 GENETICS & HEREDITY 园艺研究(英文) Pub Date : 2024-05-18 eCollection Date: 2024-07-01 DOI:10.1093/hr/uhae141
Wenying Li, Xiang Dong, Xingtan Zhang, Jie Cao, Meilan Liu, Xu Zhou, Hongxu Long, Heping Cao, Hai Lin, Lin Zhang
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Abstract

Vernicia montana is a dioecious plant widely cultivated for high-quality tung oil production and ornamental purposes in the Euphorbiaceae family. The lack of genomic information has severely hindered molecular breeding for genetic improvement and early sex identification in V. montana. Here, we present a chromosome-level reference genome of a male V. montana with a total size of 1.29 Gb and a contig N50 of 3.69 Mb. Genome analysis revealed that different repeat lineages drove the expansion of genome size. The model of chromosome evolution in the Euphorbiaceae family suggests that polyploidization-induced genomic structural variation reshaped the chromosome structure, giving rise to the diverse modern chromosomes. Based on whole-genome resequencing data and analyses of selective sweep and genetic diversity, several genes associated with stress resistance and flavonoid synthesis such as CYP450 genes and members of the LRR-RLK family, were identified and presumed to have been selected during the evolutionary process. Genome-wide association studies were conducted and a putative sex-linked insertion and deletion (InDel) (Chr 2: 102 799 917-102 799 933 bp) was identified and developed as a polymorphic molecular marker capable of effectively detecting the gender of V. montana. This InDel is located in the second intron of VmBASS4, suggesting a possible role of VmBASS4 in sex determination in V. montana. This study sheds light on the genome evolution and sex identification of V. montana, which will facilitate research on the development of agronomically important traits and genomics-assisted breeding.

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基因组组装和重新测序揭示了 Vernicia montana 的进化、种群选择和性别鉴定。
鹅掌楸是一种雌雄异株的植物,广泛栽培用于生产优质桐油和观赏。基因组信息的缺乏严重阻碍了Vernicia montana的分子育种遗传改良和早期性别鉴定。在此,我们展示了一个染色体水平的雄性 V. montana 参考基因组,其总大小为 1.29 Gb,等位基因 N50 为 3.69 Mb。基因组分析表明,不同的重复系推动了基因组规模的扩大。大戟科染色体进化模型表明,多倍体化引起的基因组结构变异重塑了染色体结构,从而产生了多样的现代染色体。根据全基因组重测序数据以及选择性扫描和遗传多样性分析,确定了几个与抗逆性和黄酮类化合物合成相关的基因,如 CYP450 基因和 LRR-RLK 家族成员,并推测这些基因在进化过程中经过了选择。研究人员进行了全基因组关联研究,发现了一个假定的与性别相关的插入和缺失(InDel)(Chr 2: 102 799 917-102 799 933 bp),并将其开发为一种多态性分子标记,能够有效检测蒙大拿藤黄属植物的性别。该 InDel 位于 VmBASS4 的第二个内含子上,表明 VmBASS4 可能在 V. montana 的性别决定中发挥作用。这项研究揭示了V. montana的基因组进化和性别鉴定,将有助于重要农艺性状的开发和基因组辅助育种的研究。
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来源期刊
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