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Transcriptional Landscapes of Long Non-coding RNAs and Alternative Splicing in Pyricularia oryzae Revealed by RNA-Seq

Pyricularia oryzae causes the rice blast, which is one of the most devastating crop diseases worldwide, and is a model fungal pathogen widely used for dissecting the molecular mechanisms underlying fungal virulence/pathogenicity. Although the whole genome sequence of P. oryzae is publicly available,...

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Autores principales: Li, Zhigang, Yang, Jun, Peng, Junbo, Cheng, Zhihua, Liu, Xinsen, Zhang, Ziding, Bhadauria, Vijai, Zhao, Wensheng, Peng, You-Liang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8475275/
https://www.ncbi.nlm.nih.gov/pubmed/34589103
http://dx.doi.org/10.3389/fpls.2021.723636
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author Li, Zhigang
Yang, Jun
Peng, Junbo
Cheng, Zhihua
Liu, Xinsen
Zhang, Ziding
Bhadauria, Vijai
Zhao, Wensheng
Peng, You-Liang
author_facet Li, Zhigang
Yang, Jun
Peng, Junbo
Cheng, Zhihua
Liu, Xinsen
Zhang, Ziding
Bhadauria, Vijai
Zhao, Wensheng
Peng, You-Liang
author_sort Li, Zhigang
collection PubMed
description Pyricularia oryzae causes the rice blast, which is one of the most devastating crop diseases worldwide, and is a model fungal pathogen widely used for dissecting the molecular mechanisms underlying fungal virulence/pathogenicity. Although the whole genome sequence of P. oryzae is publicly available, its current transcriptomes remain incomplete, lacking the information on non-protein coding genes and alternative splicing. Here, we performed and analyzed RNA-Seq of conidia and hyphae, resulting in the identification of 3,374 novel genes. Interestingly, the vast majority of these novel genes likely transcribed long non-coding RNAs (lncRNAs), and most of them were localized in the intergenic regions. Notably, their expressions were concomitant with the transcription of neighboring genes thereof in conidia and hyphae. In addition, 2,358 genes were found to undergo alternative splicing events. Furthermore, we exemplified that a lncRNA was important for hyphal growth likely by regulating the neighboring protein-coding gene and that alternative splicing of the transcription factor gene CON7 was required for appressorium formation. In summary, results from this study indicate that lncRNA transcripts and alternative splicing events are two important mechanisms for regulating the expression of genes important for conidiation, hyphal growth, and pathogenesis, and provide new insights into transcriptomes and gene regulation in the rice blast fungus.
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spelling pubmed-84752752021-09-28 Transcriptional Landscapes of Long Non-coding RNAs and Alternative Splicing in Pyricularia oryzae Revealed by RNA-Seq Li, Zhigang Yang, Jun Peng, Junbo Cheng, Zhihua Liu, Xinsen Zhang, Ziding Bhadauria, Vijai Zhao, Wensheng Peng, You-Liang Front Plant Sci Plant Science Pyricularia oryzae causes the rice blast, which is one of the most devastating crop diseases worldwide, and is a model fungal pathogen widely used for dissecting the molecular mechanisms underlying fungal virulence/pathogenicity. Although the whole genome sequence of P. oryzae is publicly available, its current transcriptomes remain incomplete, lacking the information on non-protein coding genes and alternative splicing. Here, we performed and analyzed RNA-Seq of conidia and hyphae, resulting in the identification of 3,374 novel genes. Interestingly, the vast majority of these novel genes likely transcribed long non-coding RNAs (lncRNAs), and most of them were localized in the intergenic regions. Notably, their expressions were concomitant with the transcription of neighboring genes thereof in conidia and hyphae. In addition, 2,358 genes were found to undergo alternative splicing events. Furthermore, we exemplified that a lncRNA was important for hyphal growth likely by regulating the neighboring protein-coding gene and that alternative splicing of the transcription factor gene CON7 was required for appressorium formation. In summary, results from this study indicate that lncRNA transcripts and alternative splicing events are two important mechanisms for regulating the expression of genes important for conidiation, hyphal growth, and pathogenesis, and provide new insights into transcriptomes and gene regulation in the rice blast fungus. Frontiers Media S.A. 2021-09-08 /pmc/articles/PMC8475275/ /pubmed/34589103 http://dx.doi.org/10.3389/fpls.2021.723636 Text en Copyright © 2021 Li, Yang, Peng, Cheng, Liu, Zhang, Bhadauria, Zhao and Peng. 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
Li, Zhigang
Yang, Jun
Peng, Junbo
Cheng, Zhihua
Liu, Xinsen
Zhang, Ziding
Bhadauria, Vijai
Zhao, Wensheng
Peng, You-Liang
Transcriptional Landscapes of Long Non-coding RNAs and Alternative Splicing in Pyricularia oryzae Revealed by RNA-Seq
title Transcriptional Landscapes of Long Non-coding RNAs and Alternative Splicing in Pyricularia oryzae Revealed by RNA-Seq
title_full Transcriptional Landscapes of Long Non-coding RNAs and Alternative Splicing in Pyricularia oryzae Revealed by RNA-Seq
title_fullStr Transcriptional Landscapes of Long Non-coding RNAs and Alternative Splicing in Pyricularia oryzae Revealed by RNA-Seq
title_full_unstemmed Transcriptional Landscapes of Long Non-coding RNAs and Alternative Splicing in Pyricularia oryzae Revealed by RNA-Seq
title_short Transcriptional Landscapes of Long Non-coding RNAs and Alternative Splicing in Pyricularia oryzae Revealed by RNA-Seq
title_sort transcriptional landscapes of long non-coding rnas and alternative splicing in pyricularia oryzae revealed by rna-seq
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8475275/
https://www.ncbi.nlm.nih.gov/pubmed/34589103
http://dx.doi.org/10.3389/fpls.2021.723636
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