Chromosome-scale reference genome of broccoli (Brassica oleracea var. italica Plenck) provides insights into glucosinolate biosynthesis

Abstract

Broccoli (Brassica oleracea var. italica Plenck) is an important vegetable crop, as it is rich in health-beneficial glucosinolates (GSLs). However, the genetic basis of the GSL diversity in Brassicaceae remains unclear. Here we report a chromosome-level genome assembly of broccoli generated using PacBio HiFi reads and Hi-C technology. The final genome assembly is 613.79 Mb in size, with a contig N50 of 14.70 Mb. The GSL profile and content analysis of different B. oleracea varieties, combined with a phylogenetic tree analysis, sequence alignment, and the construction of a 3D model of the methylthioalkylmalate synthase 1 (MAM1) protein, revealed that the gene copy number and amino acid sequence variation both contributed to the diversity of GSL biosynthesis in B. oleracea. The overexpression of BoMAM1 (BolI0108790) in broccoli resulted in high accumulation and a high ratio of C4-GSLs, demonstrating that BoMAM1 is the key enzyme in C4-GSL biosynthesis. These results provide valuable insights for future genetic studies and nutritive component applications of Brassica crops.

Acknowledgements

This work was supported by the National Key Research and Development Program of China (2022YFF1003000), the National Natural Science Foundation of China (32372682, 32272747, 32072585, 32072568), the International Cooperation Projects of National Key R&D Program of China (2022YFE0108300), the Graduate Research Innovation Project of Hunan (2023XC103), and the innovation and entrepreneurship training program for college students (S202310537006X). We thank Qian Liu ([e-mail]) for the methodology and validation of the comparative genomic analysis.

Author contributions

Q.Y.W. and S.X.M. contributed equally to the work. S.X.M., Q.Y.W., and J.W.W. wrote the original draft and conceptualization; S.X.M., Y.S.W., H.P.H., J.L., X.C., L.H.H., and Y.X.T. performed data curation and investigation; Y.S.W. and J.H.Z. provided methodology and validation; Q.Y.W. and K.H. reviewed and edited the writing and acquired funding.

Data availability

All raw sequencing data generated in this study have been deposited in figshare (https://figshare.com/) with the DOI number 10.6084/m9.figshare.24935037. Sequences of other species involved in this study were downloaded from the NCBI database (https://www.ncbi.nlm.nih.gov/), Brassicaceae Database (BRAD, http://brassicadb.cn), and the related references.

Conflict of interest statement

No conflict of interest is declared.

Supplementary data

Supplementary data are available at Horticulture Research online.

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