Full-length SMRT transcriptome sequencing and microsatellite characterization in Paulownia catalpifolia

Abstract Paulownia catalpifolia is an important, fast-growing timber species known for its high density, color and texture. However, few transcriptomic and genetic studies have been conducted in P. catalpifolia. In this study, single-molecule real-time sequencing technology was applied to obtain the...

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Autores principales:	Yanzhi Feng, Yang Zhao, Jiajia Zhang, Baoping Wang, Chaowei Yang, Haijiang Zhou, Jie Qiao
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/f6a28d88a4df426294f6890f5447bf13
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spelling	oai:doaj.org-article:f6a28d88a4df426294f6890f5447bf132021-12-02T16:45:11ZFull-length SMRT transcriptome sequencing and microsatellite characterization in Paulownia catalpifolia10.1038/s41598-021-87538-82045-2322https://doaj.org/article/f6a28d88a4df426294f6890f5447bf132021-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-87538-8https://doaj.org/toc/2045-2322Abstract Paulownia catalpifolia is an important, fast-growing timber species known for its high density, color and texture. However, few transcriptomic and genetic studies have been conducted in P. catalpifolia. In this study, single-molecule real-time sequencing technology was applied to obtain the full-length transcriptome of P. catalpifolia leaves treated with varying degrees of drought stress. The sequencing data were then used to search for microsatellites, or simple sequence repeats (SSRs). A total of 28.83 Gb data were generated, 25,969 high-quality (HQ) transcripts with an average length of 1624 bp were acquired after removing the redundant reads, and 25,602 HQ transcripts (98.59%) were annotated using public databases. Among the HQ transcripts, 16,722 intact coding sequences, 149 long non-coding RNAs and 179 alternative splicing events were predicted, respectively. A total of 7367 SSR loci were distributed throughout 6293 HQ transcripts, of which 763 complex SSRs and 6604 complete SSRs. The SSR appearance frequency was 28.37%, and the average distribution distance was 5.59 kb. Among the 6604 complete SSR loci, 1–3 nucleotide repeats were dominant, occupying 97.85% of the total SSR loci, of which mono-, di- and tri-nucleotide repeats were 44.68%, 33.86% and 19.31%, respectively. We detected 112 repeat motifs, of which A/T (42.64%), AG/CT (12.22%), GA/TC (9.63%), GAA/TTC (1.57%) and CCA/TGG (1.54%) were most common in mono-, di- and tri-nucleotide repeats, respectively. The length of the repeat SSR motifs was 10–88 bp, and 4997 (75.67%) were ≤ 20 bp. This study provides a novel full-length transcriptome reference for P. catalpifolia and will facilitate the identification of germplasm resources and breeding of new drought-resistant P. catalpifolia varieties.Yanzhi FengYang ZhaoJiajia ZhangBaoping WangChaowei YangHaijiang ZhouJie QiaoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Yanzhi Feng Yang Zhao Jiajia Zhang Baoping Wang Chaowei Yang Haijiang Zhou Jie Qiao Full-length SMRT transcriptome sequencing and microsatellite characterization in Paulownia catalpifolia
description	Abstract Paulownia catalpifolia is an important, fast-growing timber species known for its high density, color and texture. However, few transcriptomic and genetic studies have been conducted in P. catalpifolia. In this study, single-molecule real-time sequencing technology was applied to obtain the full-length transcriptome of P. catalpifolia leaves treated with varying degrees of drought stress. The sequencing data were then used to search for microsatellites, or simple sequence repeats (SSRs). A total of 28.83 Gb data were generated, 25,969 high-quality (HQ) transcripts with an average length of 1624 bp were acquired after removing the redundant reads, and 25,602 HQ transcripts (98.59%) were annotated using public databases. Among the HQ transcripts, 16,722 intact coding sequences, 149 long non-coding RNAs and 179 alternative splicing events were predicted, respectively. A total of 7367 SSR loci were distributed throughout 6293 HQ transcripts, of which 763 complex SSRs and 6604 complete SSRs. The SSR appearance frequency was 28.37%, and the average distribution distance was 5.59 kb. Among the 6604 complete SSR loci, 1–3 nucleotide repeats were dominant, occupying 97.85% of the total SSR loci, of which mono-, di- and tri-nucleotide repeats were 44.68%, 33.86% and 19.31%, respectively. We detected 112 repeat motifs, of which A/T (42.64%), AG/CT (12.22%), GA/TC (9.63%), GAA/TTC (1.57%) and CCA/TGG (1.54%) were most common in mono-, di- and tri-nucleotide repeats, respectively. The length of the repeat SSR motifs was 10–88 bp, and 4997 (75.67%) were ≤ 20 bp. This study provides a novel full-length transcriptome reference for P. catalpifolia and will facilitate the identification of germplasm resources and breeding of new drought-resistant P. catalpifolia varieties.
format	article
author	Yanzhi Feng Yang Zhao Jiajia Zhang Baoping Wang Chaowei Yang Haijiang Zhou Jie Qiao
author_facet	Yanzhi Feng Yang Zhao Jiajia Zhang Baoping Wang Chaowei Yang Haijiang Zhou Jie Qiao
author_sort	Yanzhi Feng
title	Full-length SMRT transcriptome sequencing and microsatellite characterization in Paulownia catalpifolia
title_short	Full-length SMRT transcriptome sequencing and microsatellite characterization in Paulownia catalpifolia
title_full	Full-length SMRT transcriptome sequencing and microsatellite characterization in Paulownia catalpifolia
title_fullStr	Full-length SMRT transcriptome sequencing and microsatellite characterization in Paulownia catalpifolia
title_full_unstemmed	Full-length SMRT transcriptome sequencing and microsatellite characterization in Paulownia catalpifolia
title_sort	full-length smrt transcriptome sequencing and microsatellite characterization in paulownia catalpifolia
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/f6a28d88a4df426294f6890f5447bf13
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Full-length SMRT transcriptome sequencing and microsatellite characterization in Paulownia catalpifolia

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