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

Background: 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...

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Autores principales: Yang, Jing, Zhang, Guanghui, Zhang, Jing, Liu, Hui, Chen, Wei, Wang, Xiao, Li, Yahe, Dong, Yang, Yang, Shengchao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5449645/
https://www.ncbi.nlm.nih.gov/pubmed/28431028
http://dx.doi.org/10.1093/gigascience/gix028
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author Yang, Jing
Zhang, Guanghui
Zhang, Jing
Liu, Hui
Chen, Wei
Wang, Xiao
Li, Yahe
Dong, Yang
Yang, Shengchao
author_facet Yang, Jing
Zhang, Guanghui
Zhang, Jing
Liu, Hui
Chen, Wei
Wang, Xiao
Li, Yahe
Dong, Yang
Yang, Shengchao
author_sort Yang, Jing
collection PubMed
description Background: 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. Findings: 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. Conclusions: The E. breviscapus genome provides a valuable resource for the investigation of novel bioactive compounds in this Chinese herb.
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spelling pubmed-54496452017-07-31 Hybrid de novo genome assembly of the Chinese herbal fleabane Erigeron breviscapus Yang, Jing Zhang, Guanghui Zhang, Jing Liu, Hui Chen, Wei Wang, Xiao Li, Yahe Dong, Yang Yang, Shengchao Gigascience Data Note Background: 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. Findings: 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. Conclusions: The E. breviscapus genome provides a valuable resource for the investigation of novel bioactive compounds in this Chinese herb. Oxford University Press 2017-04-18 /pmc/articles/PMC5449645/ /pubmed/28431028 http://dx.doi.org/10.1093/gigascience/gix028 Text en © The Authors 2017. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Data Note
Yang, Jing
Zhang, Guanghui
Zhang, Jing
Liu, Hui
Chen, Wei
Wang, Xiao
Li, Yahe
Dong, Yang
Yang, Shengchao
Hybrid de novo genome assembly of the Chinese herbal fleabane Erigeron breviscapus
title Hybrid de novo genome assembly of the Chinese herbal fleabane Erigeron breviscapus
title_full Hybrid de novo genome assembly of the Chinese herbal fleabane Erigeron breviscapus
title_fullStr Hybrid de novo genome assembly of the Chinese herbal fleabane Erigeron breviscapus
title_full_unstemmed Hybrid de novo genome assembly of the Chinese herbal fleabane Erigeron breviscapus
title_short Hybrid de novo genome assembly of the Chinese herbal fleabane Erigeron breviscapus
title_sort hybrid de novo genome assembly of the chinese herbal fleabane erigeron breviscapus
topic Data Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5449645/
https://www.ncbi.nlm.nih.gov/pubmed/28431028
http://dx.doi.org/10.1093/gigascience/gix028
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