Cargando…

Bamboo Flowering from the Perspective of Comparative Genomics and Transcriptomics

Bamboos are an important member of the subfamily Bambusoideae, family Poaceae. The plant group exhibits wide variation with respect to the timing (1–120 years) and nature (sporadic vs. gregarious) of flowering among species. Usually flowering in woody bamboos is synchronous across culms growing over...

Descripción completa

Detalles Bibliográficos
Autores principales: Biswas, Prasun, Chakraborty, Sukanya, Dutta, Smritikana, Pal, Amita, Das, Malay
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5156695/
https://www.ncbi.nlm.nih.gov/pubmed/28018419
http://dx.doi.org/10.3389/fpls.2016.01900
_version_ 1782481303601414144
author Biswas, Prasun
Chakraborty, Sukanya
Dutta, Smritikana
Pal, Amita
Das, Malay
author_facet Biswas, Prasun
Chakraborty, Sukanya
Dutta, Smritikana
Pal, Amita
Das, Malay
author_sort Biswas, Prasun
collection PubMed
description Bamboos are an important member of the subfamily Bambusoideae, family Poaceae. The plant group exhibits wide variation with respect to the timing (1–120 years) and nature (sporadic vs. gregarious) of flowering among species. Usually flowering in woody bamboos is synchronous across culms growing over a large area, known as gregarious flowering. In many monocarpic bamboos this is followed by mass death and seed setting. While in sporadic flowering an isolated wild clump may flower, set little or no seed and remain alive. Such wide variation in flowering time and extent means that the plant group serves as repositories for genes and expression patterns that are unique to bamboo. Due to the dearth of available genomic and transcriptomic resources, limited studies have been undertaken to identify the potential molecular players in bamboo flowering. The public release of the first bamboo genome sequence Phyllostachys heterocycla, availability of related genomes Brachypodium distachyon and Oryza sativa provide us the opportunity to study this long-standing biological problem in a comparative and functional genomics framework. We identified bamboo genes homologous to those of Oryza and Brachypodium that are involved in established pathways such as vernalization, photoperiod, autonomous, and hormonal regulation of flowering. Additionally, we investigated triggers like stress (drought), physiological maturity and micro RNAs that may play crucial roles in flowering. We also analyzed available transcriptome datasets of different bamboo species to identify genes and their involvement in bamboo flowering. Finally, we summarize potential research hurdles that need to be addressed in future research.
format Online
Article
Text
id pubmed-5156695
institution National Center for Biotechnology Information
language English
publishDate 2016
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-51566952016-12-23 Bamboo Flowering from the Perspective of Comparative Genomics and Transcriptomics Biswas, Prasun Chakraborty, Sukanya Dutta, Smritikana Pal, Amita Das, Malay Front Plant Sci Plant Science Bamboos are an important member of the subfamily Bambusoideae, family Poaceae. The plant group exhibits wide variation with respect to the timing (1–120 years) and nature (sporadic vs. gregarious) of flowering among species. Usually flowering in woody bamboos is synchronous across culms growing over a large area, known as gregarious flowering. In many monocarpic bamboos this is followed by mass death and seed setting. While in sporadic flowering an isolated wild clump may flower, set little or no seed and remain alive. Such wide variation in flowering time and extent means that the plant group serves as repositories for genes and expression patterns that are unique to bamboo. Due to the dearth of available genomic and transcriptomic resources, limited studies have been undertaken to identify the potential molecular players in bamboo flowering. The public release of the first bamboo genome sequence Phyllostachys heterocycla, availability of related genomes Brachypodium distachyon and Oryza sativa provide us the opportunity to study this long-standing biological problem in a comparative and functional genomics framework. We identified bamboo genes homologous to those of Oryza and Brachypodium that are involved in established pathways such as vernalization, photoperiod, autonomous, and hormonal regulation of flowering. Additionally, we investigated triggers like stress (drought), physiological maturity and micro RNAs that may play crucial roles in flowering. We also analyzed available transcriptome datasets of different bamboo species to identify genes and their involvement in bamboo flowering. Finally, we summarize potential research hurdles that need to be addressed in future research. Frontiers Media S.A. 2016-12-15 /pmc/articles/PMC5156695/ /pubmed/28018419 http://dx.doi.org/10.3389/fpls.2016.01900 Text en Copyright © 2016 Biswas, Chakraborty, Dutta, Pal and Das. http://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) or licensor 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
Biswas, Prasun
Chakraborty, Sukanya
Dutta, Smritikana
Pal, Amita
Das, Malay
Bamboo Flowering from the Perspective of Comparative Genomics and Transcriptomics
title Bamboo Flowering from the Perspective of Comparative Genomics and Transcriptomics
title_full Bamboo Flowering from the Perspective of Comparative Genomics and Transcriptomics
title_fullStr Bamboo Flowering from the Perspective of Comparative Genomics and Transcriptomics
title_full_unstemmed Bamboo Flowering from the Perspective of Comparative Genomics and Transcriptomics
title_short Bamboo Flowering from the Perspective of Comparative Genomics and Transcriptomics
title_sort bamboo flowering from the perspective of comparative genomics and transcriptomics
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5156695/
https://www.ncbi.nlm.nih.gov/pubmed/28018419
http://dx.doi.org/10.3389/fpls.2016.01900
work_keys_str_mv AT biswasprasun bamboofloweringfromtheperspectiveofcomparativegenomicsandtranscriptomics
AT chakrabortysukanya bamboofloweringfromtheperspectiveofcomparativegenomicsandtranscriptomics
AT duttasmritikana bamboofloweringfromtheperspectiveofcomparativegenomicsandtranscriptomics
AT palamita bamboofloweringfromtheperspectiveofcomparativegenomicsandtranscriptomics
AT dasmalay bamboofloweringfromtheperspectiveofcomparativegenomicsandtranscriptomics