Transcriptome analysis of the endangered Notopterygium incisum: Cold-tolerance gene discovery and identification of EST-SSR and SNP markers

doi:10.1016/j.pld.2019.01.001

Plant Diversity ›› 2019, Vol. 41 ›› Issue (01): 1-6.DOI: 10.1016/j.pld.2019.01.001

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Transcriptome analysis of the endangered Notopterygium incisum: Cold-tolerance gene discovery and identification of EST-SSR and SNP markers

Yun Jia^a, Ji-Qing Bai^b, Mi-Li Liu^a, Zhen-Fang Jiang^a, Yan Wu^a, Min-Feng Fang^a, Zhong-Hu Li^a

a Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China;
b Shaanxi University of Chinese Medicine, Xianyang 712046, China

收稿日期:2018-07-31 修回日期:2019-01-09 出版日期:2019-02-25 发布日期:2019-03-15
通讯作者: Min-Feng Fang, Zhong-Hu Li
基金资助:
This work was co-supported by the National Natural Science Foundation of China (31470400), Shaanxi Provincial Key Laboratory Project of Department of Education (grant no. 17JS135), the programme for the Key Research and Development Plan in Shaanxi province (grant no. 2018ZDXM-SF-014), the Shaanxi Provincial Education Department Serves Local Special Projects (grant no. 2018JC032) and Public health specialty in the Department of Traditional Chinese Medicine (grants no. 2011-76, 201207002, 2012- 13, 2013-135, 201407002, 2014-76, 2015-78, 2016-44, 2017-66).

Transcriptome analysis of the endangered Notopterygium incisum: Cold-tolerance gene discovery and identification of EST-SSR and SNP markers

Yun Jia^a, Ji-Qing Bai^b, Mi-Li Liu^a, Zhen-Fang Jiang^a, Yan Wu^a, Min-Feng Fang^a, Zhong-Hu Li^a

a Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China;
b Shaanxi University of Chinese Medicine, Xianyang 712046, China

Received:2018-07-31 Revised:2019-01-09 Online:2019-02-25 Published:2019-03-15
Contact: Min-Feng Fang, Zhong-Hu Li
Supported by:
This work was co-supported by the National Natural Science Foundation of China (31470400), Shaanxi Provincial Key Laboratory Project of Department of Education (grant no. 17JS135), the programme for the Key Research and Development Plan in Shaanxi province (grant no. 2018ZDXM-SF-014), the Shaanxi Provincial Education Department Serves Local Special Projects (grant no. 2018JC032) and Public health specialty in the Department of Traditional Chinese Medicine (grants no. 2011-76, 201207002, 2012- 13, 2013-135, 201407002, 2014-76, 2015-78, 2016-44, 2017-66).

摘要/Abstract

摘要： Notopterygium incisum C. C. Ting ex H. T. Chang (Apiaceae) is an endangered perennial herb in China. The lack of transcriptomic and genomic resources for N. incisum greatly hinders studies of its population genetics and conservation. In this study, we employed RNA-seq technology to characterize transcriptomes for the flowers, leaves, and stems of this endangered herb. A total of 56 million clean reads were assembled into 120,716 unigenes with an N50 length of 850 bp. Among these unigenes, 70,245 (58.19%) were successfully annotated and 65,965 (54.64%) were identified as coding sequences based on their similarities with sequences in public databases. We identified 21 unigenes that had significant relationships with cold tolerance in N. incisum according to gene ontology (GO) annotation analysis. In addition, 13,149 simple sequence repeats (SSRs) and 85,681 single nucleotide polymorphisms were detected as potential molecular genetic markers. Ninety-six primer pairs of SSRs were randomly selected to validate their amplification efficiency and polymorphism. Nineteen SSR loci exhibited polymorphism in three natural populations of N. incisum. These results provide valuable resources to facilitate future functional genomics and conservation genetics studies of N. incisum.

关键词: Endangered species, EST-SSR marker, Notopterygium incisum, Single nucleotide polymorphism, Transcriptome

Abstract: Notopterygium incisum C. C. Ting ex H. T. Chang (Apiaceae) is an endangered perennial herb in China. The lack of transcriptomic and genomic resources for N. incisum greatly hinders studies of its population genetics and conservation. In this study, we employed RNA-seq technology to characterize transcriptomes for the flowers, leaves, and stems of this endangered herb. A total of 56 million clean reads were assembled into 120,716 unigenes with an N50 length of 850 bp. Among these unigenes, 70,245 (58.19%) were successfully annotated and 65,965 (54.64%) were identified as coding sequences based on their similarities with sequences in public databases. We identified 21 unigenes that had significant relationships with cold tolerance in N. incisum according to gene ontology (GO) annotation analysis. In addition, 13,149 simple sequence repeats (SSRs) and 85,681 single nucleotide polymorphisms were detected as potential molecular genetic markers. Ninety-six primer pairs of SSRs were randomly selected to validate their amplification efficiency and polymorphism. Nineteen SSR loci exhibited polymorphism in three natural populations of N. incisum. These results provide valuable resources to facilitate future functional genomics and conservation genetics studies of N. incisum.

Key words: Endangered species, EST-SSR marker, Notopterygium incisum, Single nucleotide polymorphism, Transcriptome

Yun Jia, Ji-Qing Bai, Mi-Li Liu, Zhen-Fang Jiang, Yan Wu, Min-Feng Fang, Zhong-Hu Li. Transcriptome analysis of the endangered Notopterygium incisum: Cold-tolerance gene discovery and identification of EST-SSR and SNP markers[J]. Plant Diversity, 2019, 41(01): 1-6.

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Transcriptome analysis of the endangered Notopterygium incisum: Cold-tolerance gene discovery and identification of EST-SSR and SNP markers

Transcriptome analysis of the endangered Notopterygium incisum: Cold-tolerance gene discovery and identification of EST-SSR and SNP markers

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