Cargando…

RNA-seq analysis reveals extensive transcriptional plasticity to temperature stress in a freshwater fish species

BACKGROUND: Identifying genes of adaptive significance in a changing environment is a major focus of ecological genomics. Such efforts were restricted, until recently, to researchers studying a small group of model organisms or closely related taxa. With the advent of next generation sequencing (NGS...

Descripción completa

Detalles Bibliográficos
Autores principales: Smith, Steve, Bernatchez, Louis, Beheregaray, Luciano B
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3680095/
https://www.ncbi.nlm.nih.gov/pubmed/23738713
http://dx.doi.org/10.1186/1471-2164-14-375
_version_ 1782273074366775296
author Smith, Steve
Bernatchez, Louis
Beheregaray, Luciano B
author_facet Smith, Steve
Bernatchez, Louis
Beheregaray, Luciano B
author_sort Smith, Steve
collection PubMed
description BACKGROUND: Identifying genes of adaptive significance in a changing environment is a major focus of ecological genomics. Such efforts were restricted, until recently, to researchers studying a small group of model organisms or closely related taxa. With the advent of next generation sequencing (NGS), genomes and transcriptomes of virtually any species are now available for studies of adaptive evolution. We experimentally manipulated temperature conditions for two groups of crimson spotted rainbowfish (Melanotaenia duboulayi) and measured differences in RNA transcription between them. This non-migratory species is found across a latitudinal thermal gradient in eastern Australia and is predicted to be negatively impacted by ongoing environmental and climatic change. RESULTS: Using next generation RNA-seq technologies on an Illumina HiSeq2000 platform, we assembled a de novo transcriptome and tested for differential expression across the treatment groups. Quality of the assembly was high with a N50 length of 1856 bases. Of the 107,749 assembled contigs, we identified 4251 that were differentially expressed according to a consensus of four different mapping and significance testing approaches. Once duplicate isoforms were removed, we were able to annotate 614 up-regulated transfrags and 349 that showed reduced expression in the higher temperature group. CONCLUSIONS: Annotated blast matches reveal that differentially expressed genes correspond to critical metabolic pathways previously shown to be important for temperature tolerance in other fish species. Our results indicate that rainbowfish exhibit predictable plastic regulatory responses to temperature stress and the genes we identified provide excellent candidates for further investigations of population adaptation to increasing temperatures.
format Online
Article
Text
id pubmed-3680095
institution National Center for Biotechnology Information
language English
publishDate 2013
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-36800952013-06-13 RNA-seq analysis reveals extensive transcriptional plasticity to temperature stress in a freshwater fish species Smith, Steve Bernatchez, Louis Beheregaray, Luciano B BMC Genomics Research Article BACKGROUND: Identifying genes of adaptive significance in a changing environment is a major focus of ecological genomics. Such efforts were restricted, until recently, to researchers studying a small group of model organisms or closely related taxa. With the advent of next generation sequencing (NGS), genomes and transcriptomes of virtually any species are now available for studies of adaptive evolution. We experimentally manipulated temperature conditions for two groups of crimson spotted rainbowfish (Melanotaenia duboulayi) and measured differences in RNA transcription between them. This non-migratory species is found across a latitudinal thermal gradient in eastern Australia and is predicted to be negatively impacted by ongoing environmental and climatic change. RESULTS: Using next generation RNA-seq technologies on an Illumina HiSeq2000 platform, we assembled a de novo transcriptome and tested for differential expression across the treatment groups. Quality of the assembly was high with a N50 length of 1856 bases. Of the 107,749 assembled contigs, we identified 4251 that were differentially expressed according to a consensus of four different mapping and significance testing approaches. Once duplicate isoforms were removed, we were able to annotate 614 up-regulated transfrags and 349 that showed reduced expression in the higher temperature group. CONCLUSIONS: Annotated blast matches reveal that differentially expressed genes correspond to critical metabolic pathways previously shown to be important for temperature tolerance in other fish species. Our results indicate that rainbowfish exhibit predictable plastic regulatory responses to temperature stress and the genes we identified provide excellent candidates for further investigations of population adaptation to increasing temperatures. BioMed Central 2013-06-05 /pmc/articles/PMC3680095/ /pubmed/23738713 http://dx.doi.org/10.1186/1471-2164-14-375 Text en Copyright © 2013 Smith 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
Smith, Steve
Bernatchez, Louis
Beheregaray, Luciano B
RNA-seq analysis reveals extensive transcriptional plasticity to temperature stress in a freshwater fish species
title RNA-seq analysis reveals extensive transcriptional plasticity to temperature stress in a freshwater fish species
title_full RNA-seq analysis reveals extensive transcriptional plasticity to temperature stress in a freshwater fish species
title_fullStr RNA-seq analysis reveals extensive transcriptional plasticity to temperature stress in a freshwater fish species
title_full_unstemmed RNA-seq analysis reveals extensive transcriptional plasticity to temperature stress in a freshwater fish species
title_short RNA-seq analysis reveals extensive transcriptional plasticity to temperature stress in a freshwater fish species
title_sort rna-seq analysis reveals extensive transcriptional plasticity to temperature stress in a freshwater fish species
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3680095/
https://www.ncbi.nlm.nih.gov/pubmed/23738713
http://dx.doi.org/10.1186/1471-2164-14-375
work_keys_str_mv AT smithsteve rnaseqanalysisrevealsextensivetranscriptionalplasticitytotemperaturestressinafreshwaterfishspecies
AT bernatchezlouis rnaseqanalysisrevealsextensivetranscriptionalplasticitytotemperaturestressinafreshwaterfishspecies
AT beheregaraylucianob rnaseqanalysisrevealsextensivetranscriptionalplasticitytotemperaturestressinafreshwaterfishspecies