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Transcriptomic analysis of ‘Suli’ pear (Pyrus pyrifolia white pear group) buds during the dormancy by RNA-Seq
BACKGROUND: Bud dormancy is a critical developmental process that allows perennial plants to survive unfavorable environmental conditions. Pear is one of the most important deciduous fruit trees in the world, but the mechanisms regulating bud dormancy in this species are unknown. Because genomic inf...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3562153/ https://www.ncbi.nlm.nih.gov/pubmed/23234335 http://dx.doi.org/10.1186/1471-2164-13-700 |
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author | Liu, Guoqin Li, Wanshun Zheng, Penghua Xu, Tong Chen, Lijuan Liu, Dongfeng Hussain, Sayed Teng, Yuanwen |
author_facet | Liu, Guoqin Li, Wanshun Zheng, Penghua Xu, Tong Chen, Lijuan Liu, Dongfeng Hussain, Sayed Teng, Yuanwen |
author_sort | Liu, Guoqin |
collection | PubMed |
description | BACKGROUND: Bud dormancy is a critical developmental process that allows perennial plants to survive unfavorable environmental conditions. Pear is one of the most important deciduous fruit trees in the world, but the mechanisms regulating bud dormancy in this species are unknown. Because genomic information for pear is currently unavailable, transcriptome and digital gene expression data for this species would be valuable resources to better understand the molecular and biological mechanisms regulating its bud dormancy. RESULTS: We performed de novo transcriptome assembly and digital gene expression (DGE) profiling analyses of ‘Suli’ pear (Pyrus pyrifolia white pear group) using the Illumina RNA-seq system. RNA-Seq generated approximately 100 M high-quality reads that were assembled into 69,393 unigenes (mean length = 853 bp), including 14,531 clusters and 34,194 singletons. A total of 51,448 (74.1%) unigenes were annotated using public protein databases with a cut-off E-value above 10(-5). We mainly compared gene expression levels at four time-points during bud dormancy. Between Nov. 15 and Dec. 15, Dec. 15 and Jan. 15, and Jan. 15 and Feb. 15, 1,978, 1,024, and 3,468 genes were differentially expressed, respectively. Hierarchical clustering analysis arranged 190 significantly differentially-expressed genes into seven groups. Seven genes were randomly selected to confirm their expression levels using quantitative real-time PCR. CONCLUSIONS: The new transcriptomes offer comprehensive sequence and DGE profiling data for a dynamic view of transcriptomic variation during bud dormancy in pear. These data provided a basis for future studies of metabolism during bud dormancy in non-model but economically-important perennial species. |
format | Online Article Text |
id | pubmed-3562153 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-35621532013-02-05 Transcriptomic analysis of ‘Suli’ pear (Pyrus pyrifolia white pear group) buds during the dormancy by RNA-Seq Liu, Guoqin Li, Wanshun Zheng, Penghua Xu, Tong Chen, Lijuan Liu, Dongfeng Hussain, Sayed Teng, Yuanwen BMC Genomics Research Article BACKGROUND: Bud dormancy is a critical developmental process that allows perennial plants to survive unfavorable environmental conditions. Pear is one of the most important deciduous fruit trees in the world, but the mechanisms regulating bud dormancy in this species are unknown. Because genomic information for pear is currently unavailable, transcriptome and digital gene expression data for this species would be valuable resources to better understand the molecular and biological mechanisms regulating its bud dormancy. RESULTS: We performed de novo transcriptome assembly and digital gene expression (DGE) profiling analyses of ‘Suli’ pear (Pyrus pyrifolia white pear group) using the Illumina RNA-seq system. RNA-Seq generated approximately 100 M high-quality reads that were assembled into 69,393 unigenes (mean length = 853 bp), including 14,531 clusters and 34,194 singletons. A total of 51,448 (74.1%) unigenes were annotated using public protein databases with a cut-off E-value above 10(-5). We mainly compared gene expression levels at four time-points during bud dormancy. Between Nov. 15 and Dec. 15, Dec. 15 and Jan. 15, and Jan. 15 and Feb. 15, 1,978, 1,024, and 3,468 genes were differentially expressed, respectively. Hierarchical clustering analysis arranged 190 significantly differentially-expressed genes into seven groups. Seven genes were randomly selected to confirm their expression levels using quantitative real-time PCR. CONCLUSIONS: The new transcriptomes offer comprehensive sequence and DGE profiling data for a dynamic view of transcriptomic variation during bud dormancy in pear. These data provided a basis for future studies of metabolism during bud dormancy in non-model but economically-important perennial species. BioMed Central 2012-12-12 /pmc/articles/PMC3562153/ /pubmed/23234335 http://dx.doi.org/10.1186/1471-2164-13-700 Text en Copyright ©2012 Liu et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Liu, Guoqin Li, Wanshun Zheng, Penghua Xu, Tong Chen, Lijuan Liu, Dongfeng Hussain, Sayed Teng, Yuanwen Transcriptomic analysis of ‘Suli’ pear (Pyrus pyrifolia white pear group) buds during the dormancy by RNA-Seq |
title | Transcriptomic analysis of ‘Suli’ pear (Pyrus pyrifolia white pear group) buds during the dormancy by RNA-Seq |
title_full | Transcriptomic analysis of ‘Suli’ pear (Pyrus pyrifolia white pear group) buds during the dormancy by RNA-Seq |
title_fullStr | Transcriptomic analysis of ‘Suli’ pear (Pyrus pyrifolia white pear group) buds during the dormancy by RNA-Seq |
title_full_unstemmed | Transcriptomic analysis of ‘Suli’ pear (Pyrus pyrifolia white pear group) buds during the dormancy by RNA-Seq |
title_short | Transcriptomic analysis of ‘Suli’ pear (Pyrus pyrifolia white pear group) buds during the dormancy by RNA-Seq |
title_sort | transcriptomic analysis of ‘suli’ pear (pyrus pyrifolia white pear group) buds during the dormancy by rna-seq |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3562153/ https://www.ncbi.nlm.nih.gov/pubmed/23234335 http://dx.doi.org/10.1186/1471-2164-13-700 |
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