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...

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Autores principales:	Cuiping Zhang, Zhonglan Wu, Xinqiang Jiang, Wei Li, Yizeng Lu, Kuiling Wang
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/ce478119f0fe4bbd9d0dcddfdcac6c30
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spelling	oai:doaj.org-article:ce478119f0fe4bbd9d0dcddfdcac6c302021-12-02T14:12:47ZDe novo transcriptomic analysis and identification of EST-SSR markers in Stephanandra incisa10.1038/s41598-020-80329-72045-2322https://doaj.org/article/ce478119f0fe4bbd9d0dcddfdcac6c302021-01-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-80329-7https://doaj.org/toc/2045-2322Abstract 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.Cuiping ZhangZhonglan WuXinqiang JiangWei LiYizeng LuKuiling WangNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q 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
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.
format	article
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
title	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_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_sort	de novo transcriptomic analysis and identification of est-ssr markers in stephanandra incisa
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/ce478119f0fe4bbd9d0dcddfdcac6c30
work_keys_str_mv	AT cuipingzhang denovotranscriptomicanalysisandidentificationofestssrmarkersinstephanandraincisa AT zhonglanwu denovotranscriptomicanalysisandidentificationofestssrmarkersinstephanandraincisa AT xinqiangjiang denovotranscriptomicanalysisandidentificationofestssrmarkersinstephanandraincisa AT weili denovotranscriptomicanalysisandidentificationofestssrmarkersinstephanandraincisa AT yizenglu denovotranscriptomicanalysisandidentificationofestssrmarkersinstephanandraincisa AT kuilingwang denovotranscriptomicanalysisandidentificationofestssrmarkersinstephanandraincisa
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De novo transcriptomic analysis and identification of EST-SSR markers in Stephanandra incisa

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