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Article|15 Sep 2023|OPEN
The high-quality sequencing of the Brassica rapa ‘XiangQingCai’ genome and exploration of genome evolution and genes related to volatile aroma
Zhaokun Liu1 , ,† , Yanhong Fu2 ,† , Huan Wang1 , Yanping Zhang3 , Jianjun Han1 , Yingying Wang1 , Shaoqin Shen2 , Chunjin Li2 , Mingmin Jiang1 , Xuemei Yang1 and Xiaoming Song,2 ,
1Suzhou Academy of Agricultural Sciences, Suzhou, Jiangsu 215155, China
2College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
3Suzhou Polytechnic Institute of Agriculture, Suzhou, Jiangsu 215008, China
*Corresponding author. E-mail:,
Both authors contributed equally to the study.

Horticulture Research 10,
Article number: uhad187 (2023)
Views: 65

Received: 07 May 2023
Accepted: 08 Sep 2023
Published online: 15 Sep 2023


‘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.