Dataset Information

The complete chloroplast genome of Epimedium sagittatum (Sieb. Et Zucc.) Maxim. (Berberidaceae), a traditional Chinese herb.

ABSTRACT: Epimedium sagittatum is an important traditional medicinal plant in China. In this study, we assembled the complete chloroplast (cp) genome of E. sagittatum. The whole cp genome of E. sagittatum is 157,114?bp in length, comprising a pair of inverted repeat (IR) regions (25,775?bp) separated by a large single copy (LSC) region (88,507?bp) and a small single copy (SSC) region (17,057?bp). The E. sagittatum cp genome contains 133 genes, of which 82 protein-coding genes, 38 tRNA genes, 8 rRNA genes and 5 pseudogenes. Phylogenetic analysis shows that E. sagittatumis closely clustered with E. lishihchenii. This genome provides a wealth of information for distinguishing of Epimedium species.

SUBMITTER: Liu X

PROVIDER: S-EPMC7706818 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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The complete chloroplast genome of Epimedium sagittatum (Sieb. Et Zucc.) Maxim. (Berberidaceae), a traditional Chinese herb.

Liu Xiang X Yang Qianru Q Zhang Cheng C Shen Guoan G Guo Baolin B

Mitochondrial DNA. Part B, Resources 20190716 2

Epimedium sagittatum is an important traditional medicinal plant in China. In this study, we assembled the complete chloroplast (cp) genome of E. sagittatum. The whole cp genome of E. sagittatum is 157,114 bp in length, comprising a pair of inverted repeat (IR) regions (25,775 bp) separated by a large single copy (LSC) region (88,507 bp) and a small single copy (SSC) region (17,057 bp). The E. sagittatum cp genome contains 133 genes, of which 82 protein-coding genes, ...[more]

PMID: 33365631

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Project description:BACKGROUND: Epimedium sagittatum (Sieb. Et Zucc.) Maxim, a traditional Chinese medicinal plant species, has been used extensively as genuine medicinal materials. Certain Epimedium species are endangered due to commercial overexploition, while sustainable application studies, conservation genetics, systematics, and marker-assisted selection (MAS) of Epimedium is less-studied due to the lack of molecular markers. Here, we report a set of expressed sequence tags (ESTs) and simple sequence repeats (SSRs) identified in these ESTs for E. sagittatum. RESULTS: cDNAs of E. sagittatum are sequenced using 454 GS-FLX pyrosequencing technology. The raw reads are cleaned and assembled into a total of 76,459 consensus sequences comprising of 17,231 contigs and 59,228 singlets. About 38.5% (29,466) of the consensus sequences significantly match to the non-redundant protein database (E-value < 1e-10), 22,295 of which are further annotated using Gene Ontology (GO) terms. A total of 2,810 EST-SSRs is identified from the Epimedium EST dataset. Trinucleotide SSR is the dominant repeat type (55.2%) followed by dinucleotide (30.4%), tetranuleotide (7.3%), hexanucleotide (4.9%), and pentanucleotide (2.2%) SSR. The dominant repeat motif is AAG/CTT (23.6%) followed by AG/CT (19.3%), ACC/GGT (11.1%), AT/AT (7.5%), and AAC/GTT (5.9%). Thirty-two SSR-ESTs are randomly selected and primer pairs are synthesized for testing the transferability across 52 Epimedium species. Eighteen primer pairs (85.7%) could be successfully transferred to Epimedium species and sixteen of those show high genetic diversity with 0.35 of observed heterozygosity (Ho) and 0.65 of expected heterozygosity (He) and high number of alleles per locus (11.9). CONCLUSION: A large EST dataset with a total of 76,459 consensus sequences is generated, aiming to provide sequence information for deciphering secondary metabolism, especially for flavonoid pathway in Epimedium. A total of 2,810 EST-SSRs is identified from EST dataset and approximately 1580 EST-SSR markers are transferable. E. sagittatum EST-SSR transferability to the major Epimedium germplasm is up to 85.7%. Therefore, this EST dataset and EST-SSRs will be a powerful resource for further studies such as taxonomy, molecular breeding, genetics, genomics, and secondary metabolism in Epimedium species.

Dataset Information

The complete chloroplast genome of Epimedium sagittatum (Sieb. Et Zucc.) Maxim. (Berberidaceae), a traditional Chinese herb.

Publications

The complete chloroplast genome of <i>Epimedium sagittatum</i> (Sieb. Et Zucc.) Maxim. (Berberidaceae), a traditional Chinese herb.

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