Characterization of new microsatellite markers based on the transcriptome sequencing of Clematis finetiana
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...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2018-05-01
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| Series: | Hereditas |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s41065-018-0060-x |
| _version_ | 1819032086783197184 |
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| author | Zhigao Liu Weili Shao Yamei Shen Mengcheng Ji Wenchao Chen Ying Ye Yongbao Shen |
| author_facet | Zhigao Liu Weili Shao Yamei Shen Mengcheng Ji Wenchao Chen Ying Ye Yongbao Shen |
| author_sort | Zhigao Liu |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-21T06:56:21Z |
| format | Article |
| id | doaj.art-d9e904e7e9884d7a801725f9cfde8152 |
| institution | Directory Open Access Journal |
| issn | 1601-5223 |
| language | English |
| last_indexed | 2024-12-21T06:56:21Z |
| publishDate | 2018-05-01 |
| publisher | BMC |
| record_format | Article |
| series | Hereditas |
| spelling | doaj.art-d9e904e7e9884d7a801725f9cfde81522022-12-21T19:12:20ZengBMCHereditas1601-52232018-05-0115511910.1186/s41065-018-0060-xCharacterization of new microsatellite markers based on the transcriptome sequencing of Clematis finetianaZhigao Liu0Weili Shao1Yamei Shen2Mengcheng Ji3Wenchao Chen4Ying Ye5Yongbao Shen6College of Landscape Architecture, Nanjing Forestry UniversityCollege of Landscape Architecture, Zhejiang A & F UniversityCollege of Landscape Architecture, Zhejiang A & F UniversityCollege of Landscape Architecture, Zhejiang A & F UniversityCollege of Landscape Architecture, Zhejiang A & F UniversityCollege of Landscape Architecture, Zhejiang A & F UniversityCollege of Landscape Architecture, Nanjing Forestry UniversityAbstract 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.http://link.springer.com/article/10.1186/s41065-018-0060-xClematis finetianaMarker development,Transcriptome sequencingSSRs |
| spellingShingle | Zhigao Liu Weili Shao Yamei Shen Mengcheng Ji Wenchao Chen Ying Ye Yongbao Shen Characterization of new microsatellite markers based on the transcriptome sequencing of Clematis finetiana Hereditas Clematis finetiana Marker development,Transcriptome sequencing SSRs |
| title | Characterization of new microsatellite markers based on the transcriptome sequencing of Clematis finetiana |
| title_full | Characterization of new microsatellite markers based on the transcriptome sequencing of Clematis finetiana |
| title_fullStr | Characterization of new microsatellite markers based on the transcriptome sequencing of Clematis finetiana |
| title_full_unstemmed | Characterization of new microsatellite markers based on the transcriptome sequencing of Clematis finetiana |
| title_short | Characterization of new microsatellite markers based on the transcriptome sequencing of Clematis finetiana |
| title_sort | characterization of new microsatellite markers based on the transcriptome sequencing of clematis finetiana |
| topic | Clematis finetiana Marker development,Transcriptome sequencing SSRs |
| url | http://link.springer.com/article/10.1186/s41065-018-0060-x |
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