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

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.

Acknowledgements

This study was supported by the National Natural Science Foundation of China (grants. 32171843, 32230073), and the Science and Technology Innovation Program of Hunan Province (2022RC3055). We thank Tao Ma, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China, for providing suggestions on the research design of the study. We thank PubBio-Tech, Wuhan, for providing suggestions on the phylogenetic and genome-wide association analysis.

Author contributions

L.Z. and W.L. contributed to the conception and design of the study. Field and lab experiments, plant materials collection, and data analysis were performed by W.L., X.D., J.C., M.L., X.Z., H.L., and L.Z. The first draft of the manuscript was written by L.Z. and W.L.. X.Z., H.C., and H.L. gave some useful comments and revised the manuscript. All authors read and commented on the manuscript.

Data Availability Statement

The PacBio sequencing data, Hi-C data, ISO-seq data, and resequencing short reads have been deposited in the Genome Sequence Archive (Genomics, Proteomics & Bioinformatics 2021) in the National Genomics Data Center (Nucleic Acids Res 2022), China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences (GSA: CRA007017 and CRA009450) that are publicly accessible at https://ngdc.cncb.ac.cn/gsa.

Conflict of Interests

The authors declare that they have no conflicts of interest associated with this work.

Supplementary Information

Supplementary data is available at Horticulture Research online.

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