Genome survey and identification of key genes associated with freezing tolerance in genomic draft of hexaploid wild Camellia oleifera

ABSTRACT

Camellia oleifera Abel. is the dominant woody oil crop under significant development in China. Wild C. oleifera in Lu Mountain is a valuable genetic resource with strong freezing tolerance. With high-throughput sequencing, the genome of wild C. oleifera in Lu Mountain was analysed and 700.3 Gb clean reads were obtained. The genome of wild C. oleifera was estimated as allohexaploid, and its haplotype genome size was about 2.69 Gb-2.79 Gb, with repeat content of 63.01%-73.02% and heterozygosity of 6.30%-7.43%, belonging to a very complex genome. The genomic draft was assembled that contained a total of 6,952,303 scaffolds with N50 length of 1.23 kb, and the overall length was 2.39 Gb with GC content of 40.87%. In the genomic draft, 1,104,618 SSRs were identified; scaffold1096012 and scaffold1779458 were identified as key genes associated with freezing tolerance combined with the transcriptome data of field plus lab experiments. In this study, the genomic background of hexaploid wild C. oleifera in Lu Mountain was revealed. This lays the foundation for obtaining the high-quality chromosome-level reference genome of wild C. oleifera. The identification of SSRs and key genes associated with freezing tolerance may contribute to the efficient exploration and utilisation of this genetic resource.

KEYWORDS:

• Camellia oleifera
• high-throughput sequencing
• genome survey
• genomic draft
• simple sequence repeat
• freezing tolerance

Acknowledgements

This research was funded by the National Natural Science Foundation of China (grant no. 32270238).

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The data that support the findings in this research are deposited in the short read archive (SRA) databank (https://www.ncbi.nlm.nih.gov/sra) with the accession number PRJNA984951.

Author’s contribution

XH and RJ designed the experiments. XH conducted the experiments with helps from XK, ZJ, ZY and RJ. XH, XK, ZJ, ZY and RJ participated in data analyses. All authors contributed to writing of the manuscript.

Consent for publication

All the authors have read and consented to submit the manuscript.

Ethical approval

The article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/14620316.2023.2272155

Additional information

Funding

This work was supported by the National Natural Science Foundation of China (32270238).