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

作　　者：Xin Wang Jiang-Bao Xia Jun-Hong Bai Shuo Yin Wei Wang Da-Wei Wang Xin-Xin Yi Sheng-Hong Dai 

机构地区：[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

出　　处：《Journal of Systematics and Evolution》2024年第6期1150-1164,共15页植物分类学报（英文版）

基　　金：Our research was financially supported by the Funds for International Cooperation and Exchange of the National Natural Science Foundation of China-CONICYT(51961125201);the Joint Funds of the National Natural Science Foundation of China(U2006215);the Introduction and Cultivation Plan of Youth Innovative Talent in Shandong Province Colleges,Research and Innovation Team of Coastal Wetland Ecological Protection and Restoration in the Yellow River Delta.

摘　　要：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.

关 键 词：BETALAIN genome assembly genome evolution HALOPHYTE Suaeda salsa 

分 类 号：Q94[生物学—植物学]