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Genome-wide transcriptome analysis of gametophyte development in Physcomitrella patens

BACKGROUND: Regulation of gene expression plays a pivotal role in controlling the development of multicellular plants. To explore the molecular mechanism of plant developmental-stage transition and cell-fate determination, a genome-wide analysis was undertaken of sequential developmental time-points...

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Autores principales: Xiao, Lihong, Wang, Hui, Wan, Ping, Kuang, Tingyun, He, Yikun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3264550/
https://www.ncbi.nlm.nih.gov/pubmed/22168156
http://dx.doi.org/10.1186/1471-2229-11-177
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author Xiao, Lihong
Wang, Hui
Wan, Ping
Kuang, Tingyun
He, Yikun
author_facet Xiao, Lihong
Wang, Hui
Wan, Ping
Kuang, Tingyun
He, Yikun
author_sort Xiao, Lihong
collection PubMed
description BACKGROUND: Regulation of gene expression plays a pivotal role in controlling the development of multicellular plants. To explore the molecular mechanism of plant developmental-stage transition and cell-fate determination, a genome-wide analysis was undertaken of sequential developmental time-points and individual tissue types in the model moss Physcomitrella patens because of the short life cycle and relative structural simplicity of this plant. RESULTS: Gene expression was analyzed by digital gene expression tag profiling of samples taken from P. patens protonema at 3, 14 and 24 days, and from leafy shoot tissues at 30 days, after protoplast isolation, and from 14-day-old caulonemal and chloronemal tissues. In total, 4333 genes were identified as differentially displayed. Among these genes, 4129 were developmental-stage specific and 423 were preferentially expressed in either chloronemal or caulonemal tissues. Most of the differentially displayed genes were assigned to functions in organic substance and energy metabolism or macromolecule biosynthetic and catabolic processes based on gene ontology descriptions. In addition, some regulatory genes identified as candidates might be involved in controlling the developmental-stage transition and cell differentiation, namely MYB-like, HB-8, AL3, zinc finger family proteins, bHLH superfamily, GATA superfamily, GATA and bZIP transcription factors, protein kinases, genes related to protein/amino acid methylation, and auxin, ethylene, and cytokinin signaling pathways. CONCLUSIONS: These genes that show highly dynamic changes in expression during development in P. patens are potential targets for further functional characterization and evolutionary developmental biology studies.
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spelling pubmed-32645502012-01-24 Genome-wide transcriptome analysis of gametophyte development in Physcomitrella patens Xiao, Lihong Wang, Hui Wan, Ping Kuang, Tingyun He, Yikun BMC Plant Biol Research Article BACKGROUND: Regulation of gene expression plays a pivotal role in controlling the development of multicellular plants. To explore the molecular mechanism of plant developmental-stage transition and cell-fate determination, a genome-wide analysis was undertaken of sequential developmental time-points and individual tissue types in the model moss Physcomitrella patens because of the short life cycle and relative structural simplicity of this plant. RESULTS: Gene expression was analyzed by digital gene expression tag profiling of samples taken from P. patens protonema at 3, 14 and 24 days, and from leafy shoot tissues at 30 days, after protoplast isolation, and from 14-day-old caulonemal and chloronemal tissues. In total, 4333 genes were identified as differentially displayed. Among these genes, 4129 were developmental-stage specific and 423 were preferentially expressed in either chloronemal or caulonemal tissues. Most of the differentially displayed genes were assigned to functions in organic substance and energy metabolism or macromolecule biosynthetic and catabolic processes based on gene ontology descriptions. In addition, some regulatory genes identified as candidates might be involved in controlling the developmental-stage transition and cell differentiation, namely MYB-like, HB-8, AL3, zinc finger family proteins, bHLH superfamily, GATA superfamily, GATA and bZIP transcription factors, protein kinases, genes related to protein/amino acid methylation, and auxin, ethylene, and cytokinin signaling pathways. CONCLUSIONS: These genes that show highly dynamic changes in expression during development in P. patens are potential targets for further functional characterization and evolutionary developmental biology studies. BioMed Central 2011-12-15 /pmc/articles/PMC3264550/ /pubmed/22168156 http://dx.doi.org/10.1186/1471-2229-11-177 Text en Copyright ©2011 Xiao 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
Xiao, Lihong
Wang, Hui
Wan, Ping
Kuang, Tingyun
He, Yikun
Genome-wide transcriptome analysis of gametophyte development in Physcomitrella patens
title Genome-wide transcriptome analysis of gametophyte development in Physcomitrella patens
title_full Genome-wide transcriptome analysis of gametophyte development in Physcomitrella patens
title_fullStr Genome-wide transcriptome analysis of gametophyte development in Physcomitrella patens
title_full_unstemmed Genome-wide transcriptome analysis of gametophyte development in Physcomitrella patens
title_short Genome-wide transcriptome analysis of gametophyte development in Physcomitrella patens
title_sort genome-wide transcriptome analysis of gametophyte development in physcomitrella patens
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3264550/
https://www.ncbi.nlm.nih.gov/pubmed/22168156
http://dx.doi.org/10.1186/1471-2229-11-177
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