J Syst Evol

• Research Article •    

Multi-omics provides insights into genome evolution and betacyanin biosynthesis in halophyte of Suaeda salsa

Xin Wang1,2†, Jiang‐Bao Xia1†*, Jun‐Hong Bai1,2*, Shuo Yin2, Wei Wang2, Da‐Wei Wang2, Xin‐Xin Yi3, and Sheng‐Hong Dai3   

  1. 1 Shandong Key Laboratory of Eco-Environmental Science for the Yellow River Delta, Binzhou University, Binzhou 256600, China;
    2 School of Environment, Beijing Normal University, Beijing 100875, China;
    3 Wuhan Frasergen Bioinformatics Co. Ltd., Wuhan 430070, China
    These authors contributed equally to this work and should be considered co-first authors.
    *Authors for correspondence. Jiang-Bao Xia. E-mail: xiajb@163.com; Jun-Hong Bai. E-mail: junhongbai@163.com
  • Received:2023-04-19 Accepted:2024-01-16 Online:2024-03-12

Abstract: As an important halophyte in the Yellow River Delta, the Amaranthaceae C3 Suaeda salsa (L.) Pall. has attracted much attention for the “red carpet” landscape, and could be simply divided into red and green phenotypes according to the betacyanin content in the fleshy leaves. However, S. salsa has not been sequenced yet, which limited people's understanding of this species at the molecular level. We constructed a high-quality chromosome-scale reference genome by combining high-throughput sequencing, PacBio single molecule real-time sequencing, and Hi-C sequencing techniques with a genome size of 445.10?Mb and contigs N50 of 2.94?Mb. Through the annotation of the S. salsa genome, 298.76?Mb of the repetitive sequences and 23?965 protein-coding genes were identified, of which the proportion of long terminal repeats type in the repetitive sequences was the most abundant, about 50.74% of the S. salsa genome. Comparative genomics indicated that S. salsa underwent a whole-genome duplication event about 146.15 million years ago (Ma), and the estimated divergence time between S. salsa and Suaeda aralocaspica was about 16.9?Ma. A total of four betacyanins including betanidin, celosianin II, amaranthin and 6′-O-malonyl-celosianin II were identified and purified in both phenotypes, while two significantly up-regulated betacyanins (celosianin II and amaranthin) may be the main reason for the red color in red phenotype. In addition, we also performed transcriptomics and metabolomics in both phenotypes to explore the molecular mechanisms of pigment synthesis, and a series of structural genes and transcription factors concerning with betacyanin production were selected in S. salsa.

Key words: betalain, genome assembly, genome evolution, halophyte, Suaeda salsa