The genome of okra (Abelmoschus esculentus) provides insights into its genome evolution and high nutrient content

Abstract

Okra (Abelmoschus esculentus) is an important vegetable crop with high nutritional value. However, the mechanism underlying its high nutrient content remains poorly understood. Here, we present a chromosome-scale genome of okra with a size of 1.19 Gb. Comparative genomics analysis revealed the phylogenetic status of A. esculentus, as well as whole-genome duplication (WGD) events that have occurred widely across the Malvaceae species. We found that okra has experienced three additional WGDs compared with the diploid cotton Gossypium raimondii, resulting in a large chromosome number (2n = 130). After three WGDs, okra has undergone extensive genomic deletions and retained substantial numbers of genes related to secondary metabolite biosynthesis and environmental adaptation, resulting in significant differences between okra and G. raimondii in the gene families related to cellulose synthesis. Combining transcriptomic and metabolomic analysis, we revealed the relationship between gene expression and metabolite content change across different okra developmental stages. Furthermore, the sinapic acid/S-lignin biosynthesis-related gene families have experienced remarkable expansion in okra, and the expression of key enzymes involved in the sinapic acid/S-lignin biosynthesis pathway vary greatly across developmental periods, which partially explains the differences in metabolite content across the different stages. Our study gains insights into the comprehensive evolutionary history of Malvaceae species and the genetic basis that underlies the nutrient content changes in okra, which will facilitate the functional study and genetic improvement of okra varieties.

Acknowledgements

This work was supported by the Natural Science Foundation of Hebei Province (Grant No. C2021201048) and the Interdisciplinary Research Program of Natural Science of Hebei University (Grant No. 513201422004). We thank Catherine Perfect, MA (Cantab), from Liwen Bianji (Edanz) (www.liwenbianji.cn), for editing the English text of a draft of this manuscript.

Author contributions

H.D. and L.X. conceived and supervised the project; L.X. and H.D. designed the paper; L.X., R.W., and H.D. wrote the paper; R.W., W.L., Q.H., H.Z., and X.Z. sequenced and processed the raw data; R.W., L.X., W.L., Q.H., and Z.L. assembled and annotated the genome; L.X., R.W., and Y.W. performed the phylogenetic and genome evolution analysis; R.W., L.X., and C.D. analysed the metabolome data; R.W., L.X., M.W., and W.L. conducted the transcriptome analysis.

Data availability

The whole genome sequencing data reported in this study have been deposited in the Genome Warehouse in the National Genomics Data Center [83, 84], Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, under accession number GWHBWBG00000000, and are publicly accessible at https://ngdc.cncb.ac.cn/gwh.

Conflict of interest statement

The authors have declared no competing interests.

Supplementary data

Supplementary data is available at Horticulture Research online.

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