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Nanopore long-read RNAseq reveals transcriptional variations in citrus species

The number of studies on plant transcriptomes using ONT RNAseq technology is rapidly increasing in recent. It is a powerful method to decipher transcriptomic complexity, particularly alternative splicing (AS) event detection. Citrus plants are the most important widely grown fruit crops. Exploring d...

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Autores principales: Hu, Xiao-Li, You, Congjun, Zhu, Kaikai, Li, Xiaolong, Gong, Jinli, Ma, Haijie, Sun, Xuepeng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9845879/
https://www.ncbi.nlm.nih.gov/pubmed/36684788
http://dx.doi.org/10.3389/fpls.2022.1077797
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author Hu, Xiao-Li
You, Congjun
Zhu, Kaikai
Li, Xiaolong
Gong, Jinli
Ma, Haijie
Sun, Xuepeng
author_facet Hu, Xiao-Li
You, Congjun
Zhu, Kaikai
Li, Xiaolong
Gong, Jinli
Ma, Haijie
Sun, Xuepeng
author_sort Hu, Xiao-Li
collection PubMed
description The number of studies on plant transcriptomes using ONT RNAseq technology is rapidly increasing in recent. It is a powerful method to decipher transcriptomic complexity, particularly alternative splicing (AS) event detection. Citrus plants are the most important widely grown fruit crops. Exploring different AS events in citrus contributes to transcriptome improvement and functional genome study. Here, we performed ONT RNAseq in 9 species (Atalantia buxifolia, Citrus clementina, C. grandis, C. ichangensis, C. reticulata, C. sinensis, Clausena lansium, Fortunella hindsii, and Poncirus trifoliata), accompanied with Illumina sequencing. Non-redundant full-length isoforms were identified between 41,957 and 76,974 per species. Systematic analysis including different types of isoforms, number of isoforms per gene locus, isoform distribution, ORFs and lncRNA prediction and functional annotation were performed mainly focused on novel isoforms, unraveling the capability of novel isoforms detection and characterization. For AS events prediction, A3, RI, and AF were overwhelming types across 9 species. We analyzed isoform similarity and evolutionary relationships in all species. We identified that multiple isoforms derived from orthologous single copy genes among different species were annotated as enzymes, nuclear-related proteins or receptors. Isoforms with extending sequences on 5’, 3’, or both compared with reference genome were filtered out to provide information for transcriptome improvement. Our results provide novel insight into comprehending complex transcriptomes in citrus and valuable information for further investigation on the function of genes with diverse isoforms.
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spelling pubmed-98458792023-01-19 Nanopore long-read RNAseq reveals transcriptional variations in citrus species Hu, Xiao-Li You, Congjun Zhu, Kaikai Li, Xiaolong Gong, Jinli Ma, Haijie Sun, Xuepeng Front Plant Sci Plant Science The number of studies on plant transcriptomes using ONT RNAseq technology is rapidly increasing in recent. It is a powerful method to decipher transcriptomic complexity, particularly alternative splicing (AS) event detection. Citrus plants are the most important widely grown fruit crops. Exploring different AS events in citrus contributes to transcriptome improvement and functional genome study. Here, we performed ONT RNAseq in 9 species (Atalantia buxifolia, Citrus clementina, C. grandis, C. ichangensis, C. reticulata, C. sinensis, Clausena lansium, Fortunella hindsii, and Poncirus trifoliata), accompanied with Illumina sequencing. Non-redundant full-length isoforms were identified between 41,957 and 76,974 per species. Systematic analysis including different types of isoforms, number of isoforms per gene locus, isoform distribution, ORFs and lncRNA prediction and functional annotation were performed mainly focused on novel isoforms, unraveling the capability of novel isoforms detection and characterization. For AS events prediction, A3, RI, and AF were overwhelming types across 9 species. We analyzed isoform similarity and evolutionary relationships in all species. We identified that multiple isoforms derived from orthologous single copy genes among different species were annotated as enzymes, nuclear-related proteins or receptors. Isoforms with extending sequences on 5’, 3’, or both compared with reference genome were filtered out to provide information for transcriptome improvement. Our results provide novel insight into comprehending complex transcriptomes in citrus and valuable information for further investigation on the function of genes with diverse isoforms. Frontiers Media S.A. 2023-01-04 /pmc/articles/PMC9845879/ /pubmed/36684788 http://dx.doi.org/10.3389/fpls.2022.1077797 Text en Copyright © 2023 Hu, You, Zhu, Li, Gong, Ma and Sun 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
Hu, Xiao-Li
You, Congjun
Zhu, Kaikai
Li, Xiaolong
Gong, Jinli
Ma, Haijie
Sun, Xuepeng
Nanopore long-read RNAseq reveals transcriptional variations in citrus species
title Nanopore long-read RNAseq reveals transcriptional variations in citrus species
title_full Nanopore long-read RNAseq reveals transcriptional variations in citrus species
title_fullStr Nanopore long-read RNAseq reveals transcriptional variations in citrus species
title_full_unstemmed Nanopore long-read RNAseq reveals transcriptional variations in citrus species
title_short Nanopore long-read RNAseq reveals transcriptional variations in citrus species
title_sort nanopore long-read rnaseq reveals transcriptional variations in citrus species
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9845879/
https://www.ncbi.nlm.nih.gov/pubmed/36684788
http://dx.doi.org/10.3389/fpls.2022.1077797
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