The Cissus quadrangularis genome reveals its adaptive features in an arid habitat

Abstract

Cissus quadrangularis is a tetraploid species belonging to the Vitaceae family and is known for the Crassulacean acid metabolism (CAM) pathway in the succulent stem, while the leaves perform C₃ photosynthesis. Here, we report a high-quality genome of C. quadrangularis comprising a total size of 679.2 Mb which was phased into two subgenomes. Genome annotation identified 51 857 protein-coding genes, while approximately 47.75% of the genome was composed of repetitive sequences. Gene expression ratios of two subgenomes demonstrated that the sub-A genome as the dominant subgenome played a vital role during the drought tolerance. Genome divergence analysis suggests that the tetraploidization event occurred around 8.9 million years ago. Transcriptome data revealed that pathways related to cutin, suberine, and wax metabolism were enriched in the stem during drought treatment, suggesting that these genes contributed to the drought adaption. Additionally, a subset of CAM-related genes displayed diurnal expression patterns in the succulent stems but not in leaves, indicating that stem-biased expression of existing genes contributed to the CAM evolution. Our findings provide insights into the mechanisms of drought adaptation and photosynthesis transition in plants.

Acknowledgements

This work was supported by the National Science Foundation of China (31961143026) and Scientific Research Program of Sino-Africa Joint Research Center (SAJC201614, SAJL201607 and SAJC202101).

Author contributions

H.X. and Q.W. initiated the study of the C. quadrangularis genome sequencing project. Q.L. and Y.W. are joint first authors. G.H provided plant materials. D.K.G. and H.Z. isolated DNAs, H.Z., Q.L., and Y.L. collected all samples and extracted their RNA. Q.L. and Y.W. carried out the genome assembly, annotation, and transcriptome analysis with the help of J.Z. Y.W. carried out the subgenome dominance analyses with the help of T.W., H.Z., Y.L, and Y.H. detected the diel acid fluctuation in the leaves and stems of C. quadrangularis. Q.L. identified the CAM pathway related genes. Q.L., Y.W., and H.X. wrote the initial manuscript. T.W., R.A., S.G.A., and R.W.G. contributed to the discussion of the project at different stages. All authors revised and contributed to the final version of the text.

Data availability statement

All data used and generated in this study have been deposited on the National Genomics Data Center (NGDC, https://ngdc.cncb.ac.cn/) with the project number PRJCA020539. All data is available from the corresponding author upon reasonable request.

Conflict of interests

The authors declare no competing interests.

Supplementary information

Supplementary data is available at Horticulture Research online.

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