The high-quality sequencing of the Brassica rapa ‘XiangQingCai’ genome and exploration of genome evolution and genes related to volatile aroma

Abstract

‘Vanilla’ (XQC, brassica variety chinensis) is an important vegetable crop in the Brassica family, named for its strong volatile fragrance. In this study, we report the high-quality chromosome-level genome sequence of XQC. The assembled genome length was determined as 466.11 Mb, with an N50 scaffold of 46.20 Mb. A total of 59.50% repetitive sequences were detected in the XQC genome, including 47 570 genes. Among all examined Brassicaceae species, XQC had the closest relationship with B. rapa QGC (‘QingGengCai’) and B. rapa Pakchoi. Two whole-genome duplication (WGD) events and one recent whole-genome triplication (WGT) event occurred in the XQC genome in addition to an ancient WGT event. The recent WGT was observed to occur during 21.59–24.40 Mya (after evolution rate corrections). Our findings indicate that XQC experienced gene losses and chromosome rearrangements during the genome evolution of XQC. The results of the integrated genomic and transcriptomic analyses revealed critical genes involved in the terpenoid biosynthesis pathway and terpene synthase (TPS) family genes. In summary, we determined a chromosome-level genome of B. rapa XQC and identified the key candidate genes involved in volatile fragrance synthesis. This work can act as a basis for the comparative and functional genomic analysis and molecular breeding of B. rapa in the future.

Acknowledgements

This work was supported by the Suzhou Agricultural Science and Technology Innovation project (SNG2020065; SNG2020045), Suzhou Municipal Bureau of Agriculture and Rural Affairs, the National Natural Science Foundation of China (32172583), and the Natural Science Foundation of Hebei (C2021209005). The genome sequencing was performed in the Novogene Corporation.

Author contributions

Z.L. was responsible for the project initiation. Z.L. and X.S. supervised and managed the project and research. Experiments and analyses were designed by Z.L., X.S., H.W., and Y.Z. Bioinformatic analyses were led by X.S., Z.L., Y.F., Y.Z., and S.S. The manuscript was written and revised by Z.L., X. S., Y.F., H.W., and Y.Z. All authors read and revised the manuscript.

Data availability

The XQC genome sequence and RNA-seq datasets have been deposited in the Genome Sequence Archive [85] of the BIG Data Center [86], under accession numbers CRA010486 and CRA010488. They are publicly accessible at http://bigd.big.ac.cn/gsa. The genome sequences and annotation of XQC can be downloaded from the TBGR database (http://www.tbgr.org.cn) with the Genome ID of Pakchoi-XQC-v1.0 [30].

Conflict of interest statement

The authors declare no competing interests.

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