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Gigascience. 2017 Jun 1;6(6):1-7. doi: 10.1093/gigascience/gix028.

Hybrid de novo genome assembly of the Chinese herbal fleabane Erigeron breviscapus.

Yang J1, Zhang G2, Zhang J3, Liu H4,5, Chen W1,6, Wang X4,5, Li Y7, Dong Y1,6,8, Yang S2.

Author information

1
Biological Big Data College, Yunnan Agricultural University, Kunming 650201, China.
2
National-Local Joint Engineering Research Center on Germplasm Utilization and Innovation of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming 650201, China.
3
NOWBIO Technology Co. Ltd, Kunming 650202, China.
4
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
5
University of Chinese Academy of Sciences, Beijing 100049, China.
6
Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China.
7
Longjin Pharmaceutical Co. Ltd, Kunming 650228, China.
8
College of Life Science, Kunming University of Science and Technology, Kunming 650500, China.

Abstract

The plants in the Erigeron genus of the Compositae (Asteraceae) family are commonly called fleabanes, possibly due to the belief that certain chemicals in these plants repel fleas. In the traditional Chinese medicine, Erigeron breviscapus , which is native to China, was widely used in the treatment of cerebrovascular disease. A handful of bioactive compounds, including scutellarin, 3,5-dicaffeoylquinic acid, and 3,4-dicaffeoylquinic acid, have been isolated from the plant. With the purpose of finding novel medicinal compounds and understanding their biosynthetic pathways, we propose to sequence the genome of E. breviscapus . We assembled the highly heterozygous E. breviscapus genome using a combination of PacBio single-molecular real-time sequencing and next-generation sequencing methods on the Illumina HiSeq platform. The final draft genome is approximately 1.2 Gb, with contig and scaffold N50 sizes of 18.8 kb and 31.5 kb, respectively. Further analyses predicted 37 504 protein-coding genes in the E. breviscapus genome and 8172 shared gene families among Compositae species. The E. breviscapus genome provides a valuable resource for the investigation of novel bioactive compounds in this Chinese herb.

KEYWORDS:

Erigeron breviscapus; Illumina sequencing; PacBio sequencing

PMID:
28431028
PMCID:
PMC5449645
DOI:
10.1093/gigascience/gix028
[Indexed for MEDLINE]
Free PMC Article

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