A near complete genome assembly of chia assists in identification of key fatty acid desaturases in developing seeds

Leiting Li; Jingjing Song; Meiling Zhang; Shahid Iqbal; Yuanyuan Li; Heng Zhang; Hui Zhang

doi:10.3389/fpls.2023.1102715

A near complete genome assembly of chia assists in identification of key fatty acid desaturases in developing seeds

Front Plant Sci. 2023 Mar 20:14:1102715. doi: 10.3389/fpls.2023.1102715. eCollection 2023.

Authors

Leiting Li¹, Jingjing Song¹, Meiling Zhang², Shahid Iqbal³, Yuanyuan Li⁴, Heng Zhang¹, Hui Zhang⁵

Affiliations

¹ National Key Laboratory of Molecular Plant Genetics, Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.
² Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, China.
³ Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef University of Agriculture, Multan, Pakistan.
⁴ Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.
⁵ Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, Shandong, China.

Abstract

Chia is an annual crop whose seeds have the highest content of α-linolenic acid (ALA) of any plant known to date. We generated a high-quality assembly of the chia genome using circular consensus sequencing (CCS) of PacBio. The assembled six chromosomes are composed of 21 contigs and have a total length of 361.7 Mb. Genome annotation revealed a 53.5% repeat content and 35,850 protein-coding genes. Chia shared a common ancestor with Salvia splendens ~6.1 million years ago. Utilizing the reference genome and two transcriptome datasets, we identified candidate fatty acid desaturases responsible for ALA biosynthesis during chia seed development. Because the seed of S. splendens contains significantly lower proportion of ALA but similar total contents of unsaturated fatty acids, we suggest that strong expression of two ShFAD3 genes are critical for the high ALA content of chia seeds. This genome assembly will serve as a valuable resource for breeding, comparative genomics, and functional genomics studies of chia.

Keywords: FAD; HiFi; chia; polyunsaturated fatty acids; transcriptome.

Associated data

figshare/10.6084/m9.figshare.21976526

Grants and funding

This work was supported by the National Natural Science Foundation of China (31922008 to HeZ and 31900189 to LL), the Strategic Priority Research Program of CAS (XDB27040108 to HeZ), the Belt and Road Program of CAS (131965KYSB20190083-03 to HeZ), the Youth Innovation Promotion Association CAS (Y201844 to HeZ), and Central Guided Local Science and Technology Development Fund Project (YDZX2021079 to HuZ).