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Transcriptome Analysis of the Endangered Notopterygium incisum: Cold-tolerance Gene Discovery and Identification of EST-SSR and SNP Markers

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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 et al. Plant Divers.

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.

Keywords: EST-SSR marker; Endangered species; Notopterygium incisum; Single nucleotide polymorphism; Transcriptome.

Figures

Fig. 1
Fig. 1
Geographic distributions of the Notopterygium incisum samples. The yellow dots show the sampled natural populations of N. incisum. The green dots show the natural geographic distribution sites of N. incisum.
Fig. 2
Fig. 2
Length distributions of Notopterygium incisum transcripts and unigenes.
Fig. 3
Fig. 3
The information of 47 highly represented candidate functional categories in Notopterygium incisum.
Fig. 4
Fig. 4
Clusters of enKaryotic Ortholog Groups (KOG) classification. In total, 21,343 sequences were grouped into 26 KOG classifications.
Fig. 5
Fig. 5
The numbers of different SSR types detected in the Notopterygium incisum transcriptome.

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