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High-quality reference transcriptome construction improves RNA-seq quantification in Oryza sativa indica
The Reference Transcriptomic Dataset (RTD) is an accurate and comprehensive collection of transcripts originating from a given organism. It holds the key to precise transcript quantification and downstream analysis of differential expressions and regulations. Currently, transcriptome annotations for...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9558114/ https://www.ncbi.nlm.nih.gov/pubmed/36246658 http://dx.doi.org/10.3389/fgene.2022.995072 |
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author | Srikakulam, Nagesh Sridevi, Ganapathi Pandi, Gopal |
author_facet | Srikakulam, Nagesh Sridevi, Ganapathi Pandi, Gopal |
author_sort | Srikakulam, Nagesh |
collection | PubMed |
description | The Reference Transcriptomic Dataset (RTD) is an accurate and comprehensive collection of transcripts originating from a given organism. It holds the key to precise transcript quantification and downstream analysis of differential expressions and regulations. Currently, transcriptome annotations for most crop plants are far from complete. For example, Oryza sativa indica (O. sativa indica) is reported to have 40,759 transcripts in the Ensembl database without alternative transcript isoforms and alternative splicing (AS) events. To generate a high-quality RTD, we conducted RNA sequencing of rice leaf samples collected at various time points during Rhizoctonia solani infection. The obtained reads were analyzed by adopting the recently developed computational analysis pipeline to assemble the RTD with increased transcript and AS diversity for O. sativa indica (IndicaRTD). After stringent quality filtering, the newly constructed transcriptome annotation was comprised of 122,968 non-redundant transcripts from 53,695 genes. This study identified many novel transcripts compared to Ensembl deposited data that are important for regulating molecular and physiological processes in the plant system. Currently, the assembled IndicaRTD must allow fast quantification of transcript and gene expression with high precision. |
format | Online Article Text |
id | pubmed-9558114 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-95581142022-10-14 High-quality reference transcriptome construction improves RNA-seq quantification in Oryza sativa indica Srikakulam, Nagesh Sridevi, Ganapathi Pandi, Gopal Front Genet Genetics The Reference Transcriptomic Dataset (RTD) is an accurate and comprehensive collection of transcripts originating from a given organism. It holds the key to precise transcript quantification and downstream analysis of differential expressions and regulations. Currently, transcriptome annotations for most crop plants are far from complete. For example, Oryza sativa indica (O. sativa indica) is reported to have 40,759 transcripts in the Ensembl database without alternative transcript isoforms and alternative splicing (AS) events. To generate a high-quality RTD, we conducted RNA sequencing of rice leaf samples collected at various time points during Rhizoctonia solani infection. The obtained reads were analyzed by adopting the recently developed computational analysis pipeline to assemble the RTD with increased transcript and AS diversity for O. sativa indica (IndicaRTD). After stringent quality filtering, the newly constructed transcriptome annotation was comprised of 122,968 non-redundant transcripts from 53,695 genes. This study identified many novel transcripts compared to Ensembl deposited data that are important for regulating molecular and physiological processes in the plant system. Currently, the assembled IndicaRTD must allow fast quantification of transcript and gene expression with high precision. Frontiers Media S.A. 2022-09-29 /pmc/articles/PMC9558114/ /pubmed/36246658 http://dx.doi.org/10.3389/fgene.2022.995072 Text en Copyright © 2022 Srikakulam, Sridevi and Pandi. 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 | Genetics Srikakulam, Nagesh Sridevi, Ganapathi Pandi, Gopal High-quality reference transcriptome construction improves RNA-seq quantification in Oryza sativa indica |
title | High-quality reference transcriptome construction improves RNA-seq quantification in Oryza sativa indica |
title_full | High-quality reference transcriptome construction improves RNA-seq quantification in Oryza sativa indica |
title_fullStr | High-quality reference transcriptome construction improves RNA-seq quantification in Oryza sativa indica |
title_full_unstemmed | High-quality reference transcriptome construction improves RNA-seq quantification in Oryza sativa indica |
title_short | High-quality reference transcriptome construction improves RNA-seq quantification in Oryza sativa indica |
title_sort | high-quality reference transcriptome construction improves rna-seq quantification in oryza sativa indica |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9558114/ https://www.ncbi.nlm.nih.gov/pubmed/36246658 http://dx.doi.org/10.3389/fgene.2022.995072 |
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