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

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 at the molecular level. We adopted PacBio-SMRT, Illumina HiSeq paired-end and Hi-C technique to provide a chromosome-level genome of S. salsa (2n = 2x = 18 chromosomes), and the size of this high-quality genome assembly was 445.10 Mb with scaffold N50 of 47.37 Mb. The assembled genome was reported to have 19,580 genes, of which 99.52% were functionally annotated. Genome annotation showed 67.12% as the repetitive sequences, with long terminal repeats (LTR) being the richest (50.74%). Comparative genomics indicated that S. salsa undergone a WGD event about 146.15 million years ago (Mya), and the estimated divergence time between S. salsa and S. aralocaspica was about 16.9 Mya. 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 concerned with betacyanin production were selected in S. salsa .