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The complexity of the Fragaria x ananassa (octoploid) transcriptome by single-molecule long-read sequencing
Strawberry (Fragaria x ananassa) is an allopolyploid species with diverse and complex transcripts. The regulatory mechanisms of fruit development and maturation have been extensively studied; however, little is known about the signaling mechanisms that direct this process in octoploid strawberry (Fr...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6441658/ https://www.ncbi.nlm.nih.gov/pubmed/30962939 http://dx.doi.org/10.1038/s41438-019-0126-6 |
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author | Yuan, Huazhao Yu, Hongmei Huang, Tao Shen, Xinjie Xia, Jin Pang, Fuhua Wang, Jing Zhao, Mizhen |
author_facet | Yuan, Huazhao Yu, Hongmei Huang, Tao Shen, Xinjie Xia, Jin Pang, Fuhua Wang, Jing Zhao, Mizhen |
author_sort | Yuan, Huazhao |
collection | PubMed |
description | Strawberry (Fragaria x ananassa) is an allopolyploid species with diverse and complex transcripts. The regulatory mechanisms of fruit development and maturation have been extensively studied; however, little is known about the signaling mechanisms that direct this process in octoploid strawberry (Fragaria x ananassa). Here, we used long-read sequencing (LRS) technology and RNA-seq analysis to investigate the diversity and complexity of the polyploid transcriptome and differentially expressed transcripts along four successive fruit developmental stages of cultivated strawberry. We obtained a reference transcriptome with 119,897 unique full-length isoforms, including 2017 new isoforms and 2510 long noncoding RNAs. Based on the genome of the plausible progenitor (Fragaria vesca), 20,229 alternative splicing (AS) events were identified. Using this transcriptome, we found 17,485 differentially expressed transcripts during strawberry fruit development, including 527 transcription factors (TFs) belonging to 41 families. The expression profiles of all members of the auxin, ABA pathway, and anthocyanin biosynthesis gene families were also examined, and many of them were highly expressed at the ripe fruit stage, strongly indicating that the role of those genes is in the regulation of fruit ripening. We produce a high-quality reference transcriptome for octoploid strawberry, including much of the full-length transcript diversity, to help understand the regulatory mechanisms of fruit development and maturation of polyploid species, particularly via elucidation of the biochemical pathways involved in auxin, ABA, and anthocyanin biosynthesis. |
format | Online Article Text |
id | pubmed-6441658 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-64416582019-04-08 The complexity of the Fragaria x ananassa (octoploid) transcriptome by single-molecule long-read sequencing Yuan, Huazhao Yu, Hongmei Huang, Tao Shen, Xinjie Xia, Jin Pang, Fuhua Wang, Jing Zhao, Mizhen Hortic Res Article Strawberry (Fragaria x ananassa) is an allopolyploid species with diverse and complex transcripts. The regulatory mechanisms of fruit development and maturation have been extensively studied; however, little is known about the signaling mechanisms that direct this process in octoploid strawberry (Fragaria x ananassa). Here, we used long-read sequencing (LRS) technology and RNA-seq analysis to investigate the diversity and complexity of the polyploid transcriptome and differentially expressed transcripts along four successive fruit developmental stages of cultivated strawberry. We obtained a reference transcriptome with 119,897 unique full-length isoforms, including 2017 new isoforms and 2510 long noncoding RNAs. Based on the genome of the plausible progenitor (Fragaria vesca), 20,229 alternative splicing (AS) events were identified. Using this transcriptome, we found 17,485 differentially expressed transcripts during strawberry fruit development, including 527 transcription factors (TFs) belonging to 41 families. The expression profiles of all members of the auxin, ABA pathway, and anthocyanin biosynthesis gene families were also examined, and many of them were highly expressed at the ripe fruit stage, strongly indicating that the role of those genes is in the regulation of fruit ripening. We produce a high-quality reference transcriptome for octoploid strawberry, including much of the full-length transcript diversity, to help understand the regulatory mechanisms of fruit development and maturation of polyploid species, particularly via elucidation of the biochemical pathways involved in auxin, ABA, and anthocyanin biosynthesis. Nature Publishing Group UK 2019-04-06 /pmc/articles/PMC6441658/ /pubmed/30962939 http://dx.doi.org/10.1038/s41438-019-0126-6 Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Yuan, Huazhao Yu, Hongmei Huang, Tao Shen, Xinjie Xia, Jin Pang, Fuhua Wang, Jing Zhao, Mizhen The complexity of the Fragaria x ananassa (octoploid) transcriptome by single-molecule long-read sequencing |
title | The complexity of the Fragaria x ananassa (octoploid) transcriptome by single-molecule long-read sequencing |
title_full | The complexity of the Fragaria x ananassa (octoploid) transcriptome by single-molecule long-read sequencing |
title_fullStr | The complexity of the Fragaria x ananassa (octoploid) transcriptome by single-molecule long-read sequencing |
title_full_unstemmed | The complexity of the Fragaria x ananassa (octoploid) transcriptome by single-molecule long-read sequencing |
title_short | The complexity of the Fragaria x ananassa (octoploid) transcriptome by single-molecule long-read sequencing |
title_sort | complexity of the fragaria x ananassa (octoploid) transcriptome by single-molecule long-read sequencing |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6441658/ https://www.ncbi.nlm.nih.gov/pubmed/30962939 http://dx.doi.org/10.1038/s41438-019-0126-6 |
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