A chromosome-level genome assembly provides insights into Cornus wilsoniana evolution, oil biosynthesis, and floral bud development

Abstract

Cornus wilsoniana W. is a woody oil plant with high oil content and strong hypolipidemic effects, making it a valuable species for medicinal, landscaping, and ecological purposes in China. To advance genetic research on this species, we employed PacBio together with Hi-C data to create a draft genome assembly for C. wilsoniana. Based on an 11-chromosome anchored chromosome-level assembly, the estimated genome size was determined to be 843.51 Mb. The N50 contig size and N50 scaffold size were calculated to be 4.49 and 78.00 Mb, respectively. Furthermore, 30 474 protein-coding genes were annotated. Comparative genomics analysis revealed that C. wilsoniana diverged from its closest species ∼12.46 million years ago (Mya). Furthermore, the divergence between Cornaceae and Nyssaceae occurred >62.22 Mya. We also found evidence of whole-genome duplication events and whole-genome triplication γ, occurring at ∼44.90 and 115.86 Mya. We further inferred the origins of chromosomes, which sheds light on the complex evolutionary history of the karyotype of C. wilsoniana. Through transcriptional and metabolic analysis, we identified two FAD2 homologous genes that may play a crucial role in controlling the oleic to linoleic acid ratio. We further investigated the correlation between metabolites and genes and identified 33 MADS-TF homologous genes that may affect flower morphology in C. wilsoniana. Overall, this study lays the groundwork for future research aimed at identifying the genetic basis of crucial traits in C. wilsoniana.

Acknowledgements

The authors would like to express their gratitude to the Hunan Academy of Forestry, Guangdong Academy of Forestry, Longshan Forest Farm in Lechang City of Guangdong Province, Xishan Forest Farm in Dazu District of Chongqing Municipality, and Yangkou State-owned Forest Farm in Fujian Province for their efforts in selecting superior resources and collecting, preserving, and propagating C. wilsoniana materials. The authors would also like to thank Yicun Chen from the Subtropical Forestry Research Institute of the Chinese Academy of Forestry for providing the Litsea cubeba genome data. The authors are also grateful to the members of Ming Chen’s laboratory for helpful discussions and valuable comments. This work was supported by the National Natural Science Foundation of China (31770767, 32070656, 32070677 and 32270709); Foundation of State Key Laboratory of Utilization of Woody Oil Resource (GZKF202201); Hunan Province Key Research and Development Program Project (2018NK2044); Jiangsu Collaborative Innovation Center for Modern Crop Production and Collaborative Innovation Center for Modern Crop Production co-sponsored by province and ministry.

Author contributions

Z.H., L.Z., M.C., and D.C. conceived the study and provided data. H.C. performed the data analyses, visualization, and manuscript writing. H.C., Q.N., Y.H., and R.Y. performed the data interpretation. X.Z. established the databases. Z.H., L.Z., M.C., and D.C. supervised the work and provided scientific advice. M.W., C.L., J.C., Yunzhu C., Yong C., and C.C. contributed significantly to the selection of superior resources, collecting, preserving, and propagating C. wilsoniana materials. All authors contributed to writing and editing the final manuscript.

Data availability

The raw genome and transcriptome sequencing data of C. wilsoniana have been deposited in the Genome Sequence Archive (https://ngdc.cncb.ac.cn/gsa: accession no. CRA010376) [125]. The raw metabolome data has been deposited in OMIX (https://ngdc.cncb.ac.cn/omix/releaseList: accession no. OMIX003453), and the chromosome-level genome assembly and annotation files have been deposited in GWH (https://ngdc.cncb.ac.cn/gwh: accession no. GWHCAYR00000000) at the National Genomics Data Center, China National Center for Bioinformation/Beijing Institute of Genomics, Chinese Academy of Sciences [126]. The reference genome assembly and annotation files of C. wilsoniana at contig and scaffold level are also available for free download on our website (https://biobigdata.nju.edu.cn/cornus).

Conflict of interest

The authors declare that they have no conflict of interests.

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