A reference-grade genome assembly for Gossypium bickii and insights into its genome evolution and formation of pigment glands and gossypol

Kuang Sheng; Yue Sun; Meng Liu; Yuefen Cao; Yifei Han; Cheng Li; Uzair Muhammad; Muhammad Khan Daud; Wanru Wang; Huazu Li; Samrana Samrana; Yixuan Hui; Shuijin Zhu; Jinhong Chen; Tianlun Zhao

doi:10.1016/j.xplc.2022.100421

A reference-grade genome assembly for Gossypium bickii and insights into its genome evolution and formation of pigment glands and gossypol

Plant Commun. 2023 Jan 9;4(1):100421. doi: 10.1016/j.xplc.2022.100421. Epub 2022 Aug 10.

Authors

Kuang Sheng¹, Yue Sun¹, Meng Liu², Yuefen Cao¹, Yifei Han¹, Cheng Li³, Uzair Muhammad¹, Muhammad Khan Daud⁴, Wanru Wang¹, Huazu Li¹, Samrana Samrana¹, Yixuan Hui¹, Shuijin Zhu⁵, Jinhong Chen⁶, Tianlun Zhao⁷

Affiliations

¹ Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
² Novogene Bioinformatics Institute, Beijing, China.
³ Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
⁴ Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Pakistan.
⁵ Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China; Hainan Institute, Zhejiang University, Sanya, China. Electronic address: tlzhao@zju.edu.cn.
⁶ Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China; Hainan Institute, Zhejiang University, Sanya, China. Electronic address: jinhongchen@zju.edu.cn.
⁷ Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China; Hainan Institute, Zhejiang University, Sanya, China. Electronic address: shjzhu@zju.edu.cn.

Abstract

The pigment gland is a morphological characteristic of Gossypium and its related genera. Gossypium bickii (G₁) is characterized by delayed pigment gland morphogenesis in the cotyledons. In this study, a reference-grade genome of G₁ was generated, and comparative genomics analysis showed that G₁ was closest to Gossypium australe (G₂), followed by A- and D-genome species. Two large fragment translocations in chromosomes 5 and 13 were detected between the G genome and other Gossypium genomes and were unique to the G₁ and G₂ genomes. Compared with the G₂ genome, two large fragment inversions in chromosomes 12 and 13 were detected in G₁. According to the phylogeny, divergence time, and similarity analysis of nuclear and chloroplast genomes, G₁ was formed by hybridization between Gossypium sturtianum (C₁) and a common ancestor of G₂ and Gossypium nelsonii (G₃). The coordinated expression patterns of pigment gland formation (GoPGF) and gossypol biosynthesis genes in G₁ were verified to be consistent with its phenotype, and nine genes that were related to the process of pigment gland formation were identified. A novel gene, GbiCYP76B6, regulated by GoPGF, was found to affect gossypol biosynthesis. These findings offer insights into the origin and evolution of G₁ and its mechanism of pigment gland formation and gossypol biosynthesis.

Keywords: Gossypium bickii; evolution; genome; gossypol; pigment glands.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cell Nucleus
Evolution, Molecular
Gossypium* / genetics
Gossypol*
Hybridization, Genetic

Substances

Gossypol