Abstract
BackgroundEpimedium 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.ResultscDNAs 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).ConclusionA 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 ~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.
Highlights
A large-scale expressed sequence tags (ESTs) dataset with 76,459 consensuses derived from E. sagittatum is reported in this study
A total of 22,295 sequences has been successfully annotated with Gene Ontology (GO) terms based on the known sequences, and part of unique sequences are involved in the flavonoid metabolic pathway, which would facilitate deciphering the molecular mechanism of secondary metabolism in Epimedium
Ho and He range from 0.04 to 0.6 and from 0.17 to 0.94 with an average of 0.35 and 0.65, respectively, and the number of alleles per locus ranges from 3 to 27 with an average of 11.9 alleles. These results suggest that the major germplasm of Epimedium show high genetic diversity
Summary
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. A traditional Chinese medicinal herb, is prepared from the aerial parts of Epimedium species of Berberidaceae, which is a basal eudicot family containing enormous medicinal plants. Only a few of genomic markers have been exploited, so far, in our lab for studying genetic diversity of natural populations, including 14, 19, and 12 SSRs for E. sagittatum [9], E. koreanum [10], and E. brevicornu [11], respectively. According to our knowledge, the novel gene discovery and molecular breeding of Epimedium new cultivars haven’t been started yet due to the lack of genetic and genomic information
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