High quality genome of Erigeron breviscapus provides a reference for herbal plants in Asteraceae

doi:10.1111/1755-0998.13257

KIB OpenIR

	High quality genome of Erigeron breviscapus provides a reference for herbal plants in Asteraceae
	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
	2021
发表期刊	MOLECULAR ECOLOGY RESOURCES
ISSN	1755-098X
卷号	21 期号:1 页码:153-169
摘要	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.
关键词	Erigeron breviscapus genome GWAS scutellarin FLAVONOIDS-BIOSYNTHESIS WIDE ASSOCIATION AGRONOMIC TRAITS HIGH-ACCURACY GENE FAMILY PREDICTION ALIGNMENT PATHWAY IDENTIFICATION ACCUMULATION
DOI	10.1111/1755-0998.13257
WOS记录号	WOS:000581806900001
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/73153
专题	中国科学院昆明植物研究所
作者单位	1.Yunnan Agr Univ, Natl & Local Joint Engn Res Ctr Germplasm Innovat, Key Lab Med Plant Biol Yunnan Prov, State Key Lab Conservat & Utilizat BioResources Y, Kunming, Yunnan, Peoples R China 2.Yunnan Agr Univ, Biol Big Data Coll, Prov Key Lab, Kunming, Yunnan, Peoples R China 3.Kunming Univ Sci & Technol, Inst Primate Translat Med, Kunming, Yunnan, Peoples R China 4.Zhejiang Univ, Coll Life Sci, State Key Lab Plant Physiol & Biochem, Hangzhou, Peoples R China 5.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, Plant Germplasm & Genom Ctr, Kunming, Yunnan, Peoples R China
推荐引用方式 GB/T 7714	He,Simei,Dong,Xiao,Zhang,Guanghui,et al. High quality genome of Erigeron breviscapus provides a reference for herbal plants in Asteraceae[J]. MOLECULAR ECOLOGY RESOURCES,2021,21(1):153-169.
APA	He,Simei.,Dong,Xiao.,Zhang,Guanghui.,Fan,Wei.,Duan,Shengchang.,...&Yang,Shengchao.(2021).High quality genome of Erigeron breviscapus provides a reference for herbal plants in Asteraceae.MOLECULAR ECOLOGY RESOURCES,21(1),153-169.
MLA	He,Simei,et al."High quality genome of Erigeron breviscapus provides a reference for herbal plants in Asteraceae".MOLECULAR ECOLOGY RESOURCES 21.1(2021):153-169.