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Transcriptomic Complexity of Culm Growth and Development in Different Types of Moso Bamboo

Moso bamboo is capable of both sexual and asexual reproduction during natural growth, resulting in four distinct types of culms: the bamboo shoot-culm, the seedling stem, the leptomorph rhizome, and a long-ignored culm—the outward-rhizome. Sometimes, when the outward rhizomes break through the soil,...

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Autores principales: Li, Long, Zhou, Binao, Liu, Dong, Wu, Hongyu, Shi, Qianqian, Lin, Shuyan, Yao, Wenjing
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10138756/
https://www.ncbi.nlm.nih.gov/pubmed/37108588
http://dx.doi.org/10.3390/ijms24087425
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author Li, Long
Zhou, Binao
Liu, Dong
Wu, Hongyu
Shi, Qianqian
Lin, Shuyan
Yao, Wenjing
author_facet Li, Long
Zhou, Binao
Liu, Dong
Wu, Hongyu
Shi, Qianqian
Lin, Shuyan
Yao, Wenjing
author_sort Li, Long
collection PubMed
description Moso bamboo is capable of both sexual and asexual reproduction during natural growth, resulting in four distinct types of culms: the bamboo shoot-culm, the seedling stem, the leptomorph rhizome, and a long-ignored culm—the outward-rhizome. Sometimes, when the outward rhizomes break through the soil, they continue to grow longitudinally and develop into a new individual. However, the roles of alternative transcription start sites (aTSS) or termination sites (aTTS) as well as alternative splicing (AS) have not been comprehensively studied for their development. To re-annotate the moso bamboo genome and identify genome-wide aTSS, aTTS, and AS in growing culms, we utilized single-molecule long-read sequencing technology. In total, 169,433 non-redundant isoforms and 14,840 new gene loci were identified. Among 1311 lncRNAs, most of which showed a positive correlation with their target mRNAs, one-third of these IncRNAs were preferentially expressed in winter bamboo shoots. In addition, the predominant AS type observed in moso bamboo was intron retention, while aTSS and aTTS events occurred more frequently than AS. Notably, most genes with AS events were also accompanied by aTSS and aTTS events. Outward rhizome growth in moso bamboo was associated with a significant increase in intron retention, possibly due to changes in the growth environment. As different types of moso bamboo culms grow and develop, a significant number of isoforms undergo changes in their conserved domains due to the regulation of aTSS, aTTS, and AS. As a result, these isoforms may play different roles than their original functions. These isoforms then performed different functions from their original roles, contributing to the transcriptomic complexity of moso bamboo. Overall, this study provided a comprehensive overview of the transcriptomic changes underlying different types of moso bamboo culm growth and development.
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spelling pubmed-101387562023-04-28 Transcriptomic Complexity of Culm Growth and Development in Different Types of Moso Bamboo Li, Long Zhou, Binao Liu, Dong Wu, Hongyu Shi, Qianqian Lin, Shuyan Yao, Wenjing Int J Mol Sci Article Moso bamboo is capable of both sexual and asexual reproduction during natural growth, resulting in four distinct types of culms: the bamboo shoot-culm, the seedling stem, the leptomorph rhizome, and a long-ignored culm—the outward-rhizome. Sometimes, when the outward rhizomes break through the soil, they continue to grow longitudinally and develop into a new individual. However, the roles of alternative transcription start sites (aTSS) or termination sites (aTTS) as well as alternative splicing (AS) have not been comprehensively studied for their development. To re-annotate the moso bamboo genome and identify genome-wide aTSS, aTTS, and AS in growing culms, we utilized single-molecule long-read sequencing technology. In total, 169,433 non-redundant isoforms and 14,840 new gene loci were identified. Among 1311 lncRNAs, most of which showed a positive correlation with their target mRNAs, one-third of these IncRNAs were preferentially expressed in winter bamboo shoots. In addition, the predominant AS type observed in moso bamboo was intron retention, while aTSS and aTTS events occurred more frequently than AS. Notably, most genes with AS events were also accompanied by aTSS and aTTS events. Outward rhizome growth in moso bamboo was associated with a significant increase in intron retention, possibly due to changes in the growth environment. As different types of moso bamboo culms grow and develop, a significant number of isoforms undergo changes in their conserved domains due to the regulation of aTSS, aTTS, and AS. As a result, these isoforms may play different roles than their original functions. These isoforms then performed different functions from their original roles, contributing to the transcriptomic complexity of moso bamboo. Overall, this study provided a comprehensive overview of the transcriptomic changes underlying different types of moso bamboo culm growth and development. MDPI 2023-04-18 /pmc/articles/PMC10138756/ /pubmed/37108588 http://dx.doi.org/10.3390/ijms24087425 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Li, Long
Zhou, Binao
Liu, Dong
Wu, Hongyu
Shi, Qianqian
Lin, Shuyan
Yao, Wenjing
Transcriptomic Complexity of Culm Growth and Development in Different Types of Moso Bamboo
title Transcriptomic Complexity of Culm Growth and Development in Different Types of Moso Bamboo
title_full Transcriptomic Complexity of Culm Growth and Development in Different Types of Moso Bamboo
title_fullStr Transcriptomic Complexity of Culm Growth and Development in Different Types of Moso Bamboo
title_full_unstemmed Transcriptomic Complexity of Culm Growth and Development in Different Types of Moso Bamboo
title_short Transcriptomic Complexity of Culm Growth and Development in Different Types of Moso Bamboo
title_sort transcriptomic complexity of culm growth and development in different types of moso bamboo
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10138756/
https://www.ncbi.nlm.nih.gov/pubmed/37108588
http://dx.doi.org/10.3390/ijms24087425
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