Abstract
BackgroundClematis is the biggest genus in the family Ranunculaceae with about 300 species. Clematis is also a globally important commercial group of flowers, especially in the United States and European countries. Their petals with different colors and shapes make the genus the “Queen of the Vines”. However, the genomic information and phylogeny of Clematis based on existing molecular studies are limited. In this paper, new microsatellites (SSR) markers were identified from the transcriptome data of C. finetiana obtained using the Illumina paired-end sequencing technology.ResultsSequences on a total of 71,900 high-quality unigenes with the mean length of 865 bp were produced in this study. There were 6192unigenes annotated and classified into 49 functional sub-groups in three main ontology categories in GO (Gen Ontology) database,14,022 unigenes mapped to COGs (Clusters of Orthologous Groups) database and classified into 25 functional categories, and 21,494 unigenes obtained and divided into 128 pathways of KEGG (Kyoto Encyclopedia of Genes) Database. A total of 7532 SSRs were discovered from 6337 unigenes. We randomly tested 210 primer pairs, of which 52 primer pairs were able to generate specific products, and 19 possessed polymorphism in the 13 wild populations of six species from Clematis, which were used as a test material.ConclusionsThe dataset of C. finetiana transcriptome and the identified new SSR markers will promote genetic research and breeding effort in Clematis.
Highlights
Clematis is the biggest genus in the family Ranunculaceae with about 300 species
To improve precision in genetic analyses on Clematis, we developed such as microsatellite (SSR) markers based on the transcriptome sequencing of C. finetiana and utilized them to investigate inter- and intraspecific diversity and differentiation and genetic relationships among Clematis samples
RNA-seq sequencing and de novo assembly A total of 11.12 Gb clean bases were produced from the transcriptome sequencing of C. finetiana. 111.18 Mb (99.91%) clean reads with 97.56% Q20 and 93.66% Q30 were collected through data filtering. 71,900 unigenes were generated when all high-quality reads were assembled
Summary
Clematis is a globally important commercial group of flowers, especially in the United States and European countries. Their petals with different colors and shapes make the genus the “Queen of the Vines”. C. finetianais widely distributed in south China, in Zhejiang Fujian, Guangxi, Sichuan and Yunnan provinces. It is exploited and used as a medicinal plant because of Microsatellite (SSR) markers are an important tool for the evaluation of genetic diversity and differentiation between species and populations [6, 7]. Only few molecular marker studies and DNA sequencing-based investigations have
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