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PacBio and Illumina RNA Sequencing Identify Alternative Splicing Events in Response to Cold Stress in Two Poplar Species

In eukaryotes, alternative splicing (AS) is a crucial regulatory mechanism that modulates mRNA diversity and stability. The contribution of AS to stress is known in many species related to stress, but the posttranscriptional mechanism in poplar under cold stress is still unclear. Recent studies have...

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Autores principales: Yang, Jingli, Lv, Wanqiu, Shao, Liying, Fu, Yanrui, Liu, Haimei, Yang, Chengjun, Chen, Aihua, Xie, Xieyu, Wang, Zhiwei, Li, Chenghao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8529222/
https://www.ncbi.nlm.nih.gov/pubmed/34691113
http://dx.doi.org/10.3389/fpls.2021.737004
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author Yang, Jingli
Lv, Wanqiu
Shao, Liying
Fu, Yanrui
Liu, Haimei
Yang, Chengjun
Chen, Aihua
Xie, Xieyu
Wang, Zhiwei
Li, Chenghao
author_facet Yang, Jingli
Lv, Wanqiu
Shao, Liying
Fu, Yanrui
Liu, Haimei
Yang, Chengjun
Chen, Aihua
Xie, Xieyu
Wang, Zhiwei
Li, Chenghao
author_sort Yang, Jingli
collection PubMed
description In eukaryotes, alternative splicing (AS) is a crucial regulatory mechanism that modulates mRNA diversity and stability. The contribution of AS to stress is known in many species related to stress, but the posttranscriptional mechanism in poplar under cold stress is still unclear. Recent studies have utilized the advantages of single molecular real-time (SMRT) sequencing technology from Pacific Bioscience (PacBio) to identify full-length transcripts. We, therefore, used a combination of single-molecule long-read sequencing and Illumina RNA sequencing (RNA-Seq) for a global analysis of AS in two poplar species (Populus trichocarpa and P. ussuriensis) under cold stress. We further identified 1,261 AS events in P. trichocarpa and 2,101 in P. ussuriensis among which intron retention, with a frequency of more than 30%, was the most prominent type under cold stress. RNA-Seq data analysis and annotation revealed the importance of calcium, abscisic acid, and reactive oxygen species signaling in cold stress response. Besides, the low temperature rapidly induced multiple splicing factors, transcription factors, and differentially expressed genes through AS. In P. ussuriensis, there was a rapid occurrence of AS events, which provided a new insight into the complexity and regulation of AS during cold stress response in different poplar species for the first time.
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spelling pubmed-85292222021-10-22 PacBio and Illumina RNA Sequencing Identify Alternative Splicing Events in Response to Cold Stress in Two Poplar Species Yang, Jingli Lv, Wanqiu Shao, Liying Fu, Yanrui Liu, Haimei Yang, Chengjun Chen, Aihua Xie, Xieyu Wang, Zhiwei Li, Chenghao Front Plant Sci Plant Science In eukaryotes, alternative splicing (AS) is a crucial regulatory mechanism that modulates mRNA diversity and stability. The contribution of AS to stress is known in many species related to stress, but the posttranscriptional mechanism in poplar under cold stress is still unclear. Recent studies have utilized the advantages of single molecular real-time (SMRT) sequencing technology from Pacific Bioscience (PacBio) to identify full-length transcripts. We, therefore, used a combination of single-molecule long-read sequencing and Illumina RNA sequencing (RNA-Seq) for a global analysis of AS in two poplar species (Populus trichocarpa and P. ussuriensis) under cold stress. We further identified 1,261 AS events in P. trichocarpa and 2,101 in P. ussuriensis among which intron retention, with a frequency of more than 30%, was the most prominent type under cold stress. RNA-Seq data analysis and annotation revealed the importance of calcium, abscisic acid, and reactive oxygen species signaling in cold stress response. Besides, the low temperature rapidly induced multiple splicing factors, transcription factors, and differentially expressed genes through AS. In P. ussuriensis, there was a rapid occurrence of AS events, which provided a new insight into the complexity and regulation of AS during cold stress response in different poplar species for the first time. Frontiers Media S.A. 2021-10-07 /pmc/articles/PMC8529222/ /pubmed/34691113 http://dx.doi.org/10.3389/fpls.2021.737004 Text en Copyright © 2021 Yang, Lv, Shao, Fu, Liu, Yang, Chen, Xie, Wang and Li. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Yang, Jingli
Lv, Wanqiu
Shao, Liying
Fu, Yanrui
Liu, Haimei
Yang, Chengjun
Chen, Aihua
Xie, Xieyu
Wang, Zhiwei
Li, Chenghao
PacBio and Illumina RNA Sequencing Identify Alternative Splicing Events in Response to Cold Stress in Two Poplar Species
title PacBio and Illumina RNA Sequencing Identify Alternative Splicing Events in Response to Cold Stress in Two Poplar Species
title_full PacBio and Illumina RNA Sequencing Identify Alternative Splicing Events in Response to Cold Stress in Two Poplar Species
title_fullStr PacBio and Illumina RNA Sequencing Identify Alternative Splicing Events in Response to Cold Stress in Two Poplar Species
title_full_unstemmed PacBio and Illumina RNA Sequencing Identify Alternative Splicing Events in Response to Cold Stress in Two Poplar Species
title_short PacBio and Illumina RNA Sequencing Identify Alternative Splicing Events in Response to Cold Stress in Two Poplar Species
title_sort pacbio and illumina rna sequencing identify alternative splicing events in response to cold stress in two poplar species
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8529222/
https://www.ncbi.nlm.nih.gov/pubmed/34691113
http://dx.doi.org/10.3389/fpls.2021.737004
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