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\begin{document}

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



\author[1]{Xin Wang}%
\author[1]{Jiangbao Xia}%
\author[2]{Junhong Bai}%
\author[2]{Shuo Yin}%
\author[2]{Wei Wang}%
\author[2]{Dawei Wang}%
\author[3]{Xinxin Yi}%
\author[3]{Shenghong Dai}%
\affil[1]{Binzhou University}%
\affil[2]{Beijing Normal University}%
\affil[3]{Wuhan Frasergen Bioinformatics Co., Ltd.}%


\vspace{-1em}



  
  \date{June 07, 2024}


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\begin{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 at the molecular level. We constructed a high-quality
chromosome-level reference genome by combining high-throughput
sequencing, PacBio Single Molecule Real-Time (SMRT) sequencing, and Hi-C
sequencing techniques with a genome size of 445 MB and contigs N50 of
2.94 Mb. Through the annotation of the reference genome, a total of
288.23 Mb of the repeating elements (64.76\% of the total genome size)
and 23,965 protein-coding genes were identified. 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.%
\end{abstract}%



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\verb`20221223manuscript.doc`  available at \url{https://authorea.com/users/451940/articles/614974-multi-omics-provides-insights-into-genome-evolution-and-betacyanin-biosynthesis-in-halophyte-of-suaeda-salsa}

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