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Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis

Populus wulianensis is an endangered species endemic to Shandong Province, China. Despite the economic and ornamental value of this species, few genomics and genetic studies have been performed. In this study, we performed a relevant analysis of the full-length transcriptome sequencing data of P. wu...

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Autores principales: Wu, Qichao, Zang, Fengqi, Xie, Xiaoman, Ma, Yan, Zheng, Yongqi, Zang, Dekui
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7530656/
https://www.ncbi.nlm.nih.gov/pubmed/33004908
http://dx.doi.org/10.1038/s41598-020-73289-5
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author Wu, Qichao
Zang, Fengqi
Xie, Xiaoman
Ma, Yan
Zheng, Yongqi
Zang, Dekui
author_facet Wu, Qichao
Zang, Fengqi
Xie, Xiaoman
Ma, Yan
Zheng, Yongqi
Zang, Dekui
author_sort Wu, Qichao
collection PubMed
description Populus wulianensis is an endangered species endemic to Shandong Province, China. Despite the economic and ornamental value of this species, few genomics and genetic studies have been performed. In this study, we performed a relevant analysis of the full-length transcriptome sequencing data of P. wulianensis and obtained expressed sequence tag (EST)-simple sequence repeat (SSR) markers with polymorphisms that can be used for further genetic research. In total, 8.18 Gb (3,521,665) clean reads with an average GC content of 42.12% were obtained. From the corrected 64,737 high-quality isoforms, 42,323 transcript sequences were obtained after redundancy analysis with CD-HIT. Among these transcript sequences, 41,876 sequences were annotated successfully. A total of 23,539 potential EST-SSRs were identified from 16,057 sequences. Excluding mononucleotides, the most abundant motifs were trinucleotide SSRs (47.80%), followed by di- (46.80%), tetra- (2.98%), hexa- (1.58%) and pentanucleotide SSRs (0.84%). Among the 100 designed EST-SSRs, 18 were polymorphic with high PIC values (0.721 and 0.683) and could be used for analyses of the genetic diversity and population structure of P. wulianensis. These full-length transcriptome sequencing data will facilitate gene discovery and functional genomics research in P. wulianensis, and the novel EST-SSRs developed in our study will promote molecular-assisted breeding, genetic diversity and conservation biology research in this species.
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spelling pubmed-75306562020-10-02 Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis Wu, Qichao Zang, Fengqi Xie, Xiaoman Ma, Yan Zheng, Yongqi Zang, Dekui Sci Rep Article Populus wulianensis is an endangered species endemic to Shandong Province, China. Despite the economic and ornamental value of this species, few genomics and genetic studies have been performed. In this study, we performed a relevant analysis of the full-length transcriptome sequencing data of P. wulianensis and obtained expressed sequence tag (EST)-simple sequence repeat (SSR) markers with polymorphisms that can be used for further genetic research. In total, 8.18 Gb (3,521,665) clean reads with an average GC content of 42.12% were obtained. From the corrected 64,737 high-quality isoforms, 42,323 transcript sequences were obtained after redundancy analysis with CD-HIT. Among these transcript sequences, 41,876 sequences were annotated successfully. A total of 23,539 potential EST-SSRs were identified from 16,057 sequences. Excluding mononucleotides, the most abundant motifs were trinucleotide SSRs (47.80%), followed by di- (46.80%), tetra- (2.98%), hexa- (1.58%) and pentanucleotide SSRs (0.84%). Among the 100 designed EST-SSRs, 18 were polymorphic with high PIC values (0.721 and 0.683) and could be used for analyses of the genetic diversity and population structure of P. wulianensis. These full-length transcriptome sequencing data will facilitate gene discovery and functional genomics research in P. wulianensis, and the novel EST-SSRs developed in our study will promote molecular-assisted breeding, genetic diversity and conservation biology research in this species. Nature Publishing Group UK 2020-10-01 /pmc/articles/PMC7530656/ /pubmed/33004908 http://dx.doi.org/10.1038/s41598-020-73289-5 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Wu, Qichao
Zang, Fengqi
Xie, Xiaoman
Ma, Yan
Zheng, Yongqi
Zang, Dekui
Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis
title Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis
title_full Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis
title_fullStr Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis
title_full_unstemmed Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis
title_short Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis
title_sort full-length transcriptome sequencing analysis and development of est-ssr markers for the endangered species populus wulianensis
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7530656/
https://www.ncbi.nlm.nih.gov/pubmed/33004908
http://dx.doi.org/10.1038/s41598-020-73289-5
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