De novo transcriptomic analysis and identification of EST-SSR markers in Stephanandra incisa
Abstract Stephanandra incisa is a wild-type shrub with beautiful leaves and white flowers and is commonly used as a garden decoration accessory. However, the limited availability of genomic data of S. incisa has restricted its breeding process. Here, we identified EST-SSR markers using de novo trans...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2021-01-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-020-80329-7 |
| _version_ | 1818858356264140800 |
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| author | Cuiping Zhang Zhonglan Wu Xinqiang Jiang Wei Li Yizeng Lu Kuiling Wang |
| author_facet | Cuiping Zhang Zhonglan Wu Xinqiang Jiang Wei Li Yizeng Lu Kuiling Wang |
| author_sort | Cuiping Zhang |
| collection | DOAJ |
| description | Abstract Stephanandra incisa is a wild-type shrub with beautiful leaves and white flowers and is commonly used as a garden decoration accessory. However, the limited availability of genomic data of S. incisa has restricted its breeding process. Here, we identified EST-SSR markers using de novo transcriptome sequencing. In this study, a transcriptome database containing 35,251 unigenes, having an average length of 985 bp, was obtained from S. incisa. From these unigene sequences, we identified 5,555 EST-SSRs, with a distribution density of one SSR per 1.60 kb. Dinucleotides (52.96%) were the most detected SSRs, followed by trinucleotides (34.64%). From the EST-SSR loci, we randomly selected 100 sites for designing primer and used the DNA of 60 samples to verify the polymorphism. The average value of the effective number of alleles (Ne), Shannon’s information index (I), and expective heterozygosity (He) was 1.969, 0.728, and 0.434, respectively. The polymorphism information content (PIC) value was in the range of 0.108 to 0.669, averaging 0.406, which represented a middle polymorphism level. Cluster analysis of S. incisa were also performed based on the obtained EST-SSR data in our work. As shown by structure analysis, 60 individuals could be classified into two groups. Thus, the identification of these novel EST-SSR markers provided valuable sequence information for analyzing the population structure, genetic diversity, and genetic resource assessment of S. incisa and other related species. |
| first_indexed | 2024-12-19T08:54:59Z |
| format | Article |
| id | doaj.art-ce478119f0fe4bbd9d0dcddfdcac6c30 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-19T08:54:59Z |
| publishDate | 2021-01-01 |
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| series | Scientific Reports |
| spelling | doaj.art-ce478119f0fe4bbd9d0dcddfdcac6c302022-12-21T20:28:38ZengNature PortfolioScientific Reports2045-23222021-01-0111111010.1038/s41598-020-80329-7De novo transcriptomic analysis and identification of EST-SSR markers in Stephanandra incisaCuiping Zhang0Zhonglan Wu1Xinqiang Jiang2Wei Li3Yizeng Lu4Kuiling Wang5College of Landscape Architecture and Forestry, Qingdao Agricultural UniversityCollege of Landscape Architecture and Forestry, Qingdao Agricultural UniversityCollege of Landscape Architecture and Forestry, Qingdao Agricultural UniversityCollege of Landscape Architecture and Forestry, Qingdao Agricultural UniversityShandong Provincial Center of Forest Tree Germplasm ResourcesCollege of Landscape Architecture and Forestry, Qingdao Agricultural UniversityAbstract Stephanandra incisa is a wild-type shrub with beautiful leaves and white flowers and is commonly used as a garden decoration accessory. However, the limited availability of genomic data of S. incisa has restricted its breeding process. Here, we identified EST-SSR markers using de novo transcriptome sequencing. In this study, a transcriptome database containing 35,251 unigenes, having an average length of 985 bp, was obtained from S. incisa. From these unigene sequences, we identified 5,555 EST-SSRs, with a distribution density of one SSR per 1.60 kb. Dinucleotides (52.96%) were the most detected SSRs, followed by trinucleotides (34.64%). From the EST-SSR loci, we randomly selected 100 sites for designing primer and used the DNA of 60 samples to verify the polymorphism. The average value of the effective number of alleles (Ne), Shannon’s information index (I), and expective heterozygosity (He) was 1.969, 0.728, and 0.434, respectively. The polymorphism information content (PIC) value was in the range of 0.108 to 0.669, averaging 0.406, which represented a middle polymorphism level. Cluster analysis of S. incisa were also performed based on the obtained EST-SSR data in our work. As shown by structure analysis, 60 individuals could be classified into two groups. Thus, the identification of these novel EST-SSR markers provided valuable sequence information for analyzing the population structure, genetic diversity, and genetic resource assessment of S. incisa and other related species.https://doi.org/10.1038/s41598-020-80329-7 |
| spellingShingle | Cuiping Zhang Zhonglan Wu Xinqiang Jiang Wei Li Yizeng Lu Kuiling Wang De novo transcriptomic analysis and identification of EST-SSR markers in Stephanandra incisa Scientific Reports |
| title | De novo transcriptomic analysis and identification of EST-SSR markers in Stephanandra incisa |
| title_full | De novo transcriptomic analysis and identification of EST-SSR markers in Stephanandra incisa |
| title_fullStr | De novo transcriptomic analysis and identification of EST-SSR markers in Stephanandra incisa |
| title_full_unstemmed | De novo transcriptomic analysis and identification of EST-SSR markers in Stephanandra incisa |
| title_short | De novo transcriptomic analysis and identification of EST-SSR markers in Stephanandra incisa |
| title_sort | de novo transcriptomic analysis and identification of est ssr markers in stephanandra incisa |
| url | https://doi.org/10.1038/s41598-020-80329-7 |
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