Characterization of new microsatellite markers based on the transcriptome sequencing of Clematis finetiana

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.Electronic supplementary materialThe online version of this article (10.1186/s41065-018-0060-x) contains supplementary material, which is available to authorized users.

Genetic Divergence and Relationship Among Opisthopappus Species Identified by Development of EST-SSR Markers

“…The SSRs frequency and distribution density were higher than some species, such as Argyranthemum broussonetii (2.3%, 27 kb) (White et al, 2016) and Zingiber officinale (2.7%, 25.2 kb) (Awasthi et al, 2017), and lower than Arachis hypogaea (17.7%, 3.3 kb) (Wang et al, 2018), Curcuma longa (14.6%, 5.3 kb; 14.9%, 5.2 kb; 20.5%, 4.8 kb) (Annadurai et al, 2013), and Curcuma alismatifolia (12.5%, 6.6 kb) (Taheri et al, 2019). Differences in the frequency of SSRs in ESTs could be partially attributed to the different genetic basis of various plant species, the size of the unigene assembly dataset, SSR search criteria, sequence redundancy, as well as the mining tools utilized (Kumpatla and Mukhopadhyay, 2005;Chen et al, 2015;Wei et al, 2016;Liu et al, 2018;Taheri et al, 2019).…”

Comprehensive analysis of a novel lncRNA profile reveals potential prognostic biomarkers in clear cell renal cell carcinoma

“…To analyze the biological features of target lncRNAs, the genes that were highly correlated with the expression of these lncRNAs (Pearson |R|>0.5) in the TCGA database were investigated. Through the application of the Database for Annotation, Visualization and Integrated Discovery (https://david.ncifcrf.gov/), the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses of these lncRNAs were conducted (25,26). P<0.05 was considered to indicate a statistically significant difference.…”

Physiological and Gene Expression Changes of Clematis crassifolia and Clematis cadmia in Response to Heat Stress

“…Clematis also has a certain medicinal value, which can be used as anti-inflammatory, antirheumatism, and analgesic agents (Hao et al, 2013;Li et al, 2017). There are approximately 355 species of Clematis in the world and 147 species in China (Pringle, 1971;Liu et al, 2018). In terms of adaptability to the environment, Clematis prefers a cool climate and is often associated with shrubs in the wild.…”