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Transcriptomic Complexity in Strawberry Fruit Development and Maturation Revealed by Nanopore Sequencing
The use of alternative transcription start or termination sites (aTSS or aTTS) as well as alternative splicing (AS) produce diverse transcript isoforms, playing indispensable roles in the plant development and environmental adaptations. Despite the advances in the finding of the genome-wide alternat...
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/PMC9326444/ https://www.ncbi.nlm.nih.gov/pubmed/35909727 http://dx.doi.org/10.3389/fpls.2022.872054 |
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author | Chen, Qing Lin, Ximeng Tang, Wenlu Deng, Qian Wang, Yan Lin, Yuanxiu He, Wen Zhang, Yunting Li, Mengyao Luo, Ya Zhang, Yong Wang, Xiaorong Tang, Haoru |
author_facet | Chen, Qing Lin, Ximeng Tang, Wenlu Deng, Qian Wang, Yan Lin, Yuanxiu He, Wen Zhang, Yunting Li, Mengyao Luo, Ya Zhang, Yong Wang, Xiaorong Tang, Haoru |
author_sort | Chen, Qing |
collection | PubMed |
description | The use of alternative transcription start or termination sites (aTSS or aTTS) as well as alternative splicing (AS) produce diverse transcript isoforms, playing indispensable roles in the plant development and environmental adaptations. Despite the advances in the finding of the genome-wide alternatively spliced genes in strawberry, it remains unexplored how AS responds to the developmental cues and what relevance do these outcomes have to the gene function. In this study, we have systematically investigated the transcriptome complexity using long-read Oxford Nanopore Technologies along the four successive developmental stages. The full-length cDNA sequencing results unraveled thousands of previously unexplored transcript isoforms raised from aTSS, aTTS, and AS. The relative contributions of these three processes to the complexity of strawberry fruit transcripts were compared. The aTSS and aTTS were more abundant than the AS. Differentially expressed transcripts unraveled the key transitional role of the white fruit stage. Isoform switches of transcripts from 757 genes were observed. They were associated with protein-coding potential change and domain gain or loss as the main consequences. Those genes with switched isoforms take part in the key processes of maturation in the late stages. A case study using yeast two hybrid analysis supported the functional divergence of the two isoforms of the B-box protein 22. Our results provided a new comprehensive overview of the dynamic transcriptomic landscape during strawberry fruit development and maturation. |
format | Online Article Text |
id | pubmed-9326444 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-93264442022-07-28 Transcriptomic Complexity in Strawberry Fruit Development and Maturation Revealed by Nanopore Sequencing Chen, Qing Lin, Ximeng Tang, Wenlu Deng, Qian Wang, Yan Lin, Yuanxiu He, Wen Zhang, Yunting Li, Mengyao Luo, Ya Zhang, Yong Wang, Xiaorong Tang, Haoru Front Plant Sci Plant Science The use of alternative transcription start or termination sites (aTSS or aTTS) as well as alternative splicing (AS) produce diverse transcript isoforms, playing indispensable roles in the plant development and environmental adaptations. Despite the advances in the finding of the genome-wide alternatively spliced genes in strawberry, it remains unexplored how AS responds to the developmental cues and what relevance do these outcomes have to the gene function. In this study, we have systematically investigated the transcriptome complexity using long-read Oxford Nanopore Technologies along the four successive developmental stages. The full-length cDNA sequencing results unraveled thousands of previously unexplored transcript isoforms raised from aTSS, aTTS, and AS. The relative contributions of these three processes to the complexity of strawberry fruit transcripts were compared. The aTSS and aTTS were more abundant than the AS. Differentially expressed transcripts unraveled the key transitional role of the white fruit stage. Isoform switches of transcripts from 757 genes were observed. They were associated with protein-coding potential change and domain gain or loss as the main consequences. Those genes with switched isoforms take part in the key processes of maturation in the late stages. A case study using yeast two hybrid analysis supported the functional divergence of the two isoforms of the B-box protein 22. Our results provided a new comprehensive overview of the dynamic transcriptomic landscape during strawberry fruit development and maturation. Frontiers Media S.A. 2022-07-13 /pmc/articles/PMC9326444/ /pubmed/35909727 http://dx.doi.org/10.3389/fpls.2022.872054 Text en Copyright © 2022 Chen, Lin, Tang, Deng, Wang, Lin, He, Zhang, Li, Luo, Zhang, Wang and Tang. 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 Chen, Qing Lin, Ximeng Tang, Wenlu Deng, Qian Wang, Yan Lin, Yuanxiu He, Wen Zhang, Yunting Li, Mengyao Luo, Ya Zhang, Yong Wang, Xiaorong Tang, Haoru Transcriptomic Complexity in Strawberry Fruit Development and Maturation Revealed by Nanopore Sequencing |
title | Transcriptomic Complexity in Strawberry Fruit Development and Maturation Revealed by Nanopore Sequencing |
title_full | Transcriptomic Complexity in Strawberry Fruit Development and Maturation Revealed by Nanopore Sequencing |
title_fullStr | Transcriptomic Complexity in Strawberry Fruit Development and Maturation Revealed by Nanopore Sequencing |
title_full_unstemmed | Transcriptomic Complexity in Strawberry Fruit Development and Maturation Revealed by Nanopore Sequencing |
title_short | Transcriptomic Complexity in Strawberry Fruit Development and Maturation Revealed by Nanopore Sequencing |
title_sort | transcriptomic complexity in strawberry fruit development and maturation revealed by nanopore sequencing |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9326444/ https://www.ncbi.nlm.nih.gov/pubmed/35909727 http://dx.doi.org/10.3389/fpls.2022.872054 |
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