Chromosome-level genome assembly and population genomics reveals crucial selection for subgynoecy development in chieh-qua

Abstract

Chieh-qua is an important cucurbit crop and very popular in South China and Southeast Asia. Despite its significance, its genetic basis and domestication history are unclear. In this study, we have successfully generated a chromosome-level reference genome assembly for the chieh-qua ‘A36’ using a hybrid assembly strategy that combines PacBio long reads and Illumina short reads. The assembled genome of chieh-qua is approximately 953.3 Mb in size and is organized into 12 chromosomes, with contig N50 of 6.9 Mb and scaffold N50 of 68.2 Mb. Notably, the chieh-qua genome is comparable in size to the wax gourd genome. Through gene prediction analysis, we have identified a total of 24 593 protein-coding genes in the A36 genome. Additionally, approximately 56.6% (539.3 Mb) of the chieh-qua genome consists of repetitive sequences. Comparative genome analysis revealed that chieh-qua and wax gourd are closely related, indicating a close evolutionary relationship between the two species. Population genomic analysis, employing 129 chieh-qua accessions and 146 wax gourd accessions, demonstrated that chieh-qua exhibits greater genetic diversity compared to wax gourd. We also employed the GWAS method to identify related QTLs associated with subgynoecy, an interested and important trait in chieh-qua. The MYB59 (BhiCQ0880026447) exhibited relatively high expression levels in the shoot apex of four subgynoecious varieties compared with monoecious varieties. Overall, this research provides insights into the domestication history of chieh-qua and offers valuable genomic resources for further molecular research.

Acknowledgements

This work was funded by the National Natural Science Foundation of China (32002038), Special Fund for Scientific Innovation Strategy-construction of High-Level Academy of Agricultural Science (R2021PY-QF008), Agricultural Competitive Industry Discipline Team Building Project of Guangdong Academy of Agricultural Sciences (202114TD, 202103TD). The authors also appreciate Yueqin Heng from South China Agricultural University and Shulin Liu from Institute of Genetics and Developmental Biology, Chinese Academy of Sciences for their help in polishing the language of manuscript.

Author contributions

M.W., S.Y., and H.L. designed the experiment and managed the project. Z.C., B.J., D.X., L.C., and S.S. collected samples, extracted genetic materials, and performed the experiments. K.W. and H.L. performed the genome assembly, annotation, and data analysis. M.W. and Q.P. performed population and agronomic trait investigation. M.W. wrote the manuscript. H.L., S.Y., and Q.P. revised the manuscript.

Data availability

The data used to support the study results are included within the article and all the original sequencing data is uploading in the Central Authentication Service (PRJCA022068).

Conflict of interest statement

The authors declare no conflict of interest.

Supplementary data

Supplementary data is available at Horticulture Research online.

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