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

Authors: LI, WENYING - Central South University Of Forestry And Technology; DONG, XIANG - Central South University Of Forestry And Technology; ZHANG, XINGTAN - Chinese Academy Of Agricultural Sciences; CAO, JIE - Central South University Of Forestry And Technology; LIU, MEILAN - Central South University Of Forestry And Technology; ZHOU, XU - Central South University Of Forestry And Technology; LONG, HONGXU - Central South University Of Forestry And Technology; Cao, Heping; LIN, HAI - Central South University Of Forestry And Technology; ZHANG, LIN - Central South University Of Forestry And Technology

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/8/2024
Publication Date: 5/18/2024
Citation: Li, W., Dong, X., Zhang, X., Cao, J., Liu, M., Zhou, X., Long, H., Cao, H., Lin, H., Zhang, L. 2024. Genome assembly and resequencing shed light on evolution, population selection, and sex identification in Vernicia montana. Horticulture Research. 11(7). Article uhae141. https://doi.org/10.1093/hr/uhae141.
DOI: https://doi.org/10.1093/hr/uhae141

Interpretive Summary: Vernicia montana and Vernicia fordii are the two most representative tree species of the genus Vernicia in the Euphorbiaceae family. Both species are commonly referred to as “tung oil trees” or “tung trees” and are economically important for the production of high-value tung oil from seeds and have important ornamental values in landscaping, due to their flower-related traits such as flower color, aroma, and abundant inflorescence phenotypes. Tung oil consists of approximately 80% a-eleostearic acid, which is highly susceptible to oxidation due to its three conjugated double bonds, and is thus widely used in various industrial fields, such as protective waterproof finishes, electrical insulating materials, environmentally friendly ink, biodiesel. In comparison with V. fordii, V. montana is a dioecious plant with female trees having higher fruit yields, and male trees displaying higher ornamental values due to large inflorescences. V. montana has been introduced to America, Argentina, Australia, Southeast Asia, and East Asia from southern China since the Qing dynasty for tung oil production. However, 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. 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.

Technical 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.