@article{fe8240bfa0724dfead65538a5b131609,
title = "The Chimonanthus salicifolius genome provides insight into magnoliids evolution and flavonoids biosynthesis",
abstract = "Chimonanthus salicifolius, a member of the Calycanthaceae of magnoliids, is one of the most famous medicinal plants in Eastern China. Here, we report a chromosome-level genome assembly of C. salicifolius, comprising 820.1 Mb of genomic sequence with a contig N50 of 2.3 Mb and containing 36 651 annotated protein-coding genes. Phylogenetic analyses revealed that magnoliids were sister to the eudicots. Two rounds of ancient whole-genome duplication were inferred in the C. salicifolious genome. One is shared by Calycanthaceae after its divergence with Lauraceae, and the other is in the ancestry of Magnoliales and Laurales. Notably, long genes with > 20 kb in length were much more prevalent in the magnoliid genomes compared with other angiosperms, which could be caused by the length expansion of introns inserted by transposon elements. Homologous genes within the flavonoid pathway for C. salicifolius were identified, and correlation of the gene expression and the contents of flavonoid metabolites revealed potential critical genes involved in flavonoids biosynthesis. This study not only provides an additional whole-genome sequence from the magnoliids, but also opens the door to functional genomic research and molecular breeding of C. salicifolius.",
keywords = "Chimonanthus salicifolius, de novo genome assembly, evolution, gene expression, long genes, magnoliids",
author = "Qundan Lv and Jie Qiu and Jie Liu and Zheng Li and Wenting Zhang and Qin Wang and Jie Fang and Junjie Pan and Zhengdao Chen and Wenliang Cheng and Barker, {Michael S.} and Xuehui Huang and Xin Wei and Kejun Cheng",
note = "Funding Information: This work is financially supported by the Zhejiang Major Science & Technology Project of New Agricultural Varieties (2016C02058), the Zhejiang Province Major Science & Technology Project (2012C12014‐1), the National Natural Science Foundation of China (31671282), Shanghai Science and Technology Committee Rising‐Star Program (19QA1406500), and Shanghai Engineering Research Center of Plant Germplasm Resources (17DZ2252700). The authors thank Nextomics Biosciences Co., Ltd (Wuhan) for the help in genome assembly, Dr Qiang Zhao from National Center for Gene Research of Chinese Academy of Sciences for assistance in genome annotation, Dr Yunpeng Zhao (Zhejiang University), and Dr Jun Yang (Chinese Academy of Sciences) for the discussion and providing valuable suggestions to the manuscript. The authors gratefully acknowledge the support of the IBM high‐performance computing cluster of Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University. Funding Information: This work is financially supported by the Zhejiang Major Science & Technology Project of New Agricultural Varieties (2016C02058), the Zhejiang Province Major Science & Technology Project (2012C12014-1), the National Natural Science Foundation of China (31671282), Shanghai Science and Technology Committee Rising-Star Program (19QA1406500), and Shanghai Engineering Research Center of Plant Germplasm Resources (17DZ2252700). The authors thank Nextomics Biosciences Co., Ltd (Wuhan) for the help in genome assembly, Dr Qiang Zhao from National Center for Gene Research of Chinese Academy of Sciences for assistance in genome annotation, Dr Yunpeng Zhao (Zhejiang University), and Dr Jun Yang (Chinese Academy of Sciences) for the discussion and providing valuable suggestions to the manuscript. The authors gratefully acknowledge the support of the IBM high-performance computing cluster of Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University. Publisher Copyright: {\textcopyright} 2020 Society for Experimental Biology and John Wiley & Sons Ltd This article has been contributed to by US Government employees and their work is in the public domain in the USA",
year = "2020",
month = aug,
day = "1",
doi = "10.1111/tpj.14874",
language = "English (US)",
volume = "103",
pages = "1910--1923",
journal = "Plant Journal",
issn = "0960-7412",
publisher = "Wiley-Blackwell Publishing Ltd",
number = "5",
}