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High quality genome of Erigeron breviscapus provides a reference for herbal plants in Asteraceae
Author(s) -
He Simei,
Dong Xiao,
Zhang Guanghui,
Fan Wei,
Duan Shengchang,
Shi Hong,
Li Dawei,
Li Rui,
Chen Geng,
Long Guangqiang,
Zhao Yan,
Chen Mo,
Yan Mi,
Yang Jianli,
Lu Yingchun,
Zhou Yanli,
Chen Wei,
Dong Yang,
Yang Shengchao
Publication year - 2021
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.13257
Subject(s) - biology , contig , genome , candidate gene , gene , sequence assembly , genetics , transcriptome , gene expression
Erigeron breviscapus is an important medicinal plant in Compositae and the first species to realize the whole process from the decoding of the draft genome sequence to scutellarin biosynthesis in yeast. However, the previous low‐quality genome assembly has hindered the optimization of candidate genes involved in scutellarin synthesis and the development of molecular‐assisted breeding based on the genome. Here, the E. breviscapus genome was updated using PacBio RSII sequencing data and Hi‐C data, and increased in size from 1.2 Gb to 1.43 Gb, with a scaffold N50 of 156.82 Mb and contig N50 of 140.95 kb, and a total of 43,514 protein‐coding genes were obtained and oriented onto nine pseudo‐chromosomes, thus becoming the third plant species assembled to chromosome level after sunflower and lettuce in Compositae. Fourteen genes with evidence for positive selection were identified and found to be related to leaf morphology, flowering and secondary metabolism. The number of genes in some gene families involved in flavonoid biosynthesis in E. breviscapus have been significantly expanded. In particular, additional candidate genes involved in scutellarin biosynthesis, such as flavonoid‐7‐ O ‐glucuronosyltransferase genes ( F7GATs ) were identified using updated genome. In addition, three candidate genes encoding indole‐3‐pyruvate monooxygenase YUCCA2 (YUC2), serine carboxypeptidase‐like 18 (SCPL18), and F‐box protein (FBP), respectively, were identified to be probably related to leaf development and flowering by resequencing 99 individuals. These results provided a substantial genetic basis for improving agronomic and quality traits of E. breviscapus , and provided a platform for improving other draft genome assemblies to chromosome‐level.