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Characterization of New Microsatellite Markers Based on the Transcriptome Liu et al. Hereditas (2018) 155:23 https://doi.org/10.1186/s41065-018-0060-x RESEARCH Open Access Characterization of new microsatellite markers based on the transcriptome sequencing of Clematis finetiana Zhigao Liu1,2, Weili Shao2, Yamei Shen2, Mengcheng Ji2, Wenchao Chen2, Ying Ye2 and Yongbao Shen1* Abstract Background: Clematis 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. Results: Sequences 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. Conclusions: The dataset of C. finetiana transcriptome and the identified new SSR markers will promote genetic research and breeding effort in Clematis. Keywords: Clematis finetiana, Marker development,Transcriptome sequencing, SSRs Background triterpenoid saponins, flavonoids and many other com- There are about 300 species [1] in the genus Clematis L., pounds present in roots and leaves [5]. C. finetiana is an mainly distributed in the temperate zone of the northern evergreen species, which enhances its use in balconies and hemisphere [2].China has abundant germplasm resources for fences. It can keep growing vigorously in hot summer of Clematis, 147 species (49%) were distributed through- conditions, which makes it different from many other cul- out the country, especially in the southwestern area [3]. tivars and species of Clematis. C. finetiana is loved by Clematis is the largest genus in the family Ranunculaceae, home gardening enthusiasts for its lovely white flowers consists of typically vigorous, woody, climbing vines, and and excellent heat-resistance properties. It is a good is famous for its diverse flower shapes and colors [4]; hun- resource for heat tolerance breeding of ornamental dreds of cultivars make it the “Queen of the Vines”. C. Clematis. finetianais widely distributed in south China, in Zhejiang Microsatellite (SSR) markers are an important tool for Fujian, Guangxi, Sichuan and Yunnan provinces. It is the evaluation of genetic diversity and differentiation exploited and used as a medicinal plant because of between species and populations [6, 7]. This marker type has a generally good transferability between closely * Correspondence: [email protected] 1 related species and it is a useful tool in genetic mapping College of Landscape Architecture, Nanjing Forestry University, Nanjing – 210037, Jiangsu, People’s Republic of China as well [8 10]. Previously, only few molecular marker Full list of author information is available at the end of the article studies and DNA sequencing-based investigations have © The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Liu et al. Hereditas (2018) 155:23 Page 2 of 9 been reported on Clematis, including the use of ISSR Data filtering, de novo assembly and unigene function primers [11], randomly amplified polymorphic DNA annotation [12], ITS sequencing [13, 14], and single nucleotide poly- SeqPreq (https://github.com/jstjohn/SeqPrep)and sickle morphisms (SNP) analyses of chloroplast regions accD, (https://github.com/najoshi/sickle) were used to remove rps16, rpl16, trnS-trnG,atpB-rbcL, trnV-atpE and matK sequencing adapters and trim low-quality sequences. [15, 16]. Currently, there is a lack of SSR markers cap- After that, Trinity [18] software was used to assemble all able of effectively detecting polymorphisms in Clematis. clean high-quality reads. The expression level of transcripts Transcriptome sequencing has been widely used for wasmeasuredbyRSEM,andtheresultwasreportedby characterizing transcriptional events in a specific tissue units of TPM (transcripts per million).BLASTX was or during a given period. It is a very useful tool also for employed to annotate the function of unigene sequences research on non-model species that lack sequenced gen- using no redundant (Nr) protein database (NCBI), Swiss ome information. The high-throughput character and Prot database, KEGG (Kyoto Encyclopedia of Genes and low cost makes RNA-seq a good choice for genetic Genomes), COG (Clusters of Orthologous Groups) and − investigations. The data resulting from transcriptome se- InterPro database with an E-value<10 5.Blast2GO quencing is valuable also for molecular marker develop- software was used for gene ontology (GO) annotation. ment, such as microsatellite (SSR) and single nucleotide polymorphism (SNP) markers. To the best of our know- Real-time quantitative RT-PCR for verifying gene expression ledge, very few research reports are available about the profiles application of RNA-seqin studies on Clematis [17] and The equivalent mixed RNA samples (young leaves, stems no information of SSR markers in Clematis has been and roots) from three individuals of C. finetiana which published. To improve precision in genetic analyses on used for transcriptome sequencing were used as three Clematis, we developed SSR markers based on the tran- biological replicates for the qRT-PCR experiment. And 12 scriptome sequencing of C. finetiana and utilized them to genes with different expression levels were randomly investigate inter- and intraspecific diversity and differenti- selected for validating the expression results of RNA-seq ation and genetic relationships among Clematis samples. sequencing. Primers (Additional file 2)weredesignedby Primer Premier 5(http://downloads.fyxm.net/download- Methods now-Primer-Premier-Others-Home-&-Education-101178. Materials and methods html) based on the selected unigene sequences. PCR reac- Plant materials tion mixture was consisted of 7 μlddH2O, 1 μlcDNA, Young leaves, stems and roots of C. finetiana were 10 μl 2 × SYBR® Select Master Mix (Applied Biosystems, collected from three individuals. All samples were frozen VIC, Australia), and 1 μl each primer. qRT-PCR was carried in liquid nitrogen immediately and stored at − 80 °C out on ABI ViiA™ 7 Real-Time PCR system (Applied Bio- until RNA extraction. Young leaves of wild Clematis systems, CA, USA) followed the cycling conditions: 95 °C germplasm of six species including112 individuals for 2 min, 50 cycles at 95 °C for 10 s, 60 °C for 10 s and (Additional file 1) were also harvested and dried with 72 °C for 40 s. GAPDH [19] was used as an internal control silica gel prior to DNA extraction. for normalizing the expression level of the 12 genes used for qRT-PCR testing. The specific primers of GAPDH were RNA extraction, cDNA library contraction and RNA-seq listed in (Additional file 2). The relative expression level of –Δ sequencing the selected gene was calculated via the 2 Ct. Total RNA was isolated using the TRIzol reagent (Invitro- gen, Carlsbad, CA, USA) and RNeasy® mini kit (Qiagen, SSR detection and primer design Valencia, CA) according to the manufacturer’sprotocol. SSR discovery was performed using the MISA software The quality and concentration of RNA were assessed by (http://pgrc.ipk-gatersleben.de/misa) with the parameters electrophoresis on a 1.2% agarose gel and using Nano- (unit size-min repeats) as follows: 1–12, 2–6, 3–5, 4–5, photometer Pearl/P360 (Implen, Munich, Germany). 5–4, 6–4. Primer pairs of each detected SSR locus were Equal amounts of purified RNA from different tissues designed by Primer3 (http://bioinfo.ut.ee/primer3) with were pooled together for cDNA library construction default parameters. A total of 210 primer pairs and transcriptome sequencing. TransCript cDNA sam- (Additional file 3) were randomly chosen and syn- ple prep kit (TransGen Biotech, China) was used for thesized for the validation of SSR markers. cDNA library construction. Agilent 2100 Bioanaylzer (Agilent Technologies, Palo Alto, CA, USA) and1.2% DNA extraction, validation of SSR markers and genetic agarose gel electrophoresis were used in qualification of analysis the cDNA library. Then the library was sequenced Total genomic DNA was extracted from dry leaf tissue using Illumina HiSeq™2000(Illumina). of 112 wild individuals from 13
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