Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
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
_version_ 1784757287244529664
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
work_keys_str_mv AT chenqing transcriptomiccomplexityinstrawberryfruitdevelopmentandmaturationrevealedbynanoporesequencing
AT linximeng transcriptomiccomplexityinstrawberryfruitdevelopmentandmaturationrevealedbynanoporesequencing
AT tangwenlu transcriptomiccomplexityinstrawberryfruitdevelopmentandmaturationrevealedbynanoporesequencing
AT dengqian transcriptomiccomplexityinstrawberryfruitdevelopmentandmaturationrevealedbynanoporesequencing
AT wangyan transcriptomiccomplexityinstrawberryfruitdevelopmentandmaturationrevealedbynanoporesequencing
AT linyuanxiu transcriptomiccomplexityinstrawberryfruitdevelopmentandmaturationrevealedbynanoporesequencing
AT hewen transcriptomiccomplexityinstrawberryfruitdevelopmentandmaturationrevealedbynanoporesequencing
AT zhangyunting transcriptomiccomplexityinstrawberryfruitdevelopmentandmaturationrevealedbynanoporesequencing
AT limengyao transcriptomiccomplexityinstrawberryfruitdevelopmentandmaturationrevealedbynanoporesequencing
AT luoya transcriptomiccomplexityinstrawberryfruitdevelopmentandmaturationrevealedbynanoporesequencing
AT zhangyong transcriptomiccomplexityinstrawberryfruitdevelopmentandmaturationrevealedbynanoporesequencing
AT wangxiaorong transcriptomiccomplexityinstrawberryfruitdevelopmentandmaturationrevealedbynanoporesequencing
AT tanghaoru transcriptomiccomplexityinstrawberryfruitdevelopmentandmaturationrevealedbynanoporesequencing