Cargando…

A transcriptomic scan for potential candidate genes involved in osmoregulation in an obligate freshwater palaemonid prawn (Macrobrachium australiense)

BACKGROUND: Understanding the genomic basis of osmoregulation (candidate genes and/or molecular mechanisms controlling the phenotype) addresses one of the fundamental questions in evolutionary ecology. Species distributions and adaptive radiations are thought to be controlled by environmental salini...

Descripción completa

Detalles Bibliográficos
Autores principales: Moshtaghi, Azam, Rahi, Md. Lifat, Nguyen, Viet Tuan, Mather, Peter B., Hurwood, David A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5068373/
https://www.ncbi.nlm.nih.gov/pubmed/27761323
http://dx.doi.org/10.7717/peerj.2520
_version_ 1782460787189612544
author Moshtaghi, Azam
Rahi, Md. Lifat
Nguyen, Viet Tuan
Mather, Peter B.
Hurwood, David A.
author_facet Moshtaghi, Azam
Rahi, Md. Lifat
Nguyen, Viet Tuan
Mather, Peter B.
Hurwood, David A.
author_sort Moshtaghi, Azam
collection PubMed
description BACKGROUND: Understanding the genomic basis of osmoregulation (candidate genes and/or molecular mechanisms controlling the phenotype) addresses one of the fundamental questions in evolutionary ecology. Species distributions and adaptive radiations are thought to be controlled by environmental salinity levels, and efficient osmoregulatory (ionic balance) ability is the main mechanism to overcome the problems related to environmental salinity gradients. METHODS: To better understand how osmoregulatory performance in freshwater (FW) crustaceans allow individuals to acclimate and adapt to raised salinity conditions, here we (i), reviewed the literature on genes that have been identified to be associated with osmoregulation in FW crustaceans, and (ii), performed a transcriptomic analysis using cDNA libraries developed from mRNA isolated from three important osmoregulatory tissues (gill, antennal gland, hepatopancreas) and total mRNA from post larvae taken from the freshwater prawn, Macrobrachium australiense using Illumina deep sequencing technology. This species was targeted because it can complete its life cycle totally in freshwater but, like many Macrobrachium sp., can also tolerate brackish water conditions and hence should have genes associated with tolerance of both FW and saline conditions. RESULTS: We obtained between 55.4 and 65.2 million Illumina read pairs from four cDNA libraries. Overall, paired end sequences assembled into a total of 125,196 non-redundant contigs (≥200 bp) with an N50 length of 2,282 bp and an average contig length of 968 bp. Transcriptomic analysis of M. australiense identified 32 different gene families that were potentially involved with osmoregulatory capacity. A total of 32,597 transcripts were specified with gene ontology (GO) terms identified on the basis of GO categories. Abundance estimation of expressed genes based on TPM (transcript per million) ≥20 showed 1625 transcripts commonly expressed in all four libraries. Among the top 10 genes expressed in four tissue libraries associated with osmoregulation, arginine kinase and Na+/K+- ATPase showed the highest transcript copy number with 7098 and 660, respectively in gill which is considered to be the most important organ involved in osmoregulation. DISCUSSION: The current study provides the first broad transcriptome from M. australiense using next generation sequencing and identifies potential candidate genes involved in salinity tolerance and osmoregulation that can provide a foundation for investigating osmoregulatory capacity in a wide variety of freshwater crustaceans.
format Online
Article
Text
id pubmed-5068373
institution National Center for Biotechnology Information
language English
publishDate 2016
publisher PeerJ Inc.
record_format MEDLINE/PubMed
spelling pubmed-50683732016-10-19 A transcriptomic scan for potential candidate genes involved in osmoregulation in an obligate freshwater palaemonid prawn (Macrobrachium australiense) Moshtaghi, Azam Rahi, Md. Lifat Nguyen, Viet Tuan Mather, Peter B. Hurwood, David A. PeerJ Evolutionary Studies BACKGROUND: Understanding the genomic basis of osmoregulation (candidate genes and/or molecular mechanisms controlling the phenotype) addresses one of the fundamental questions in evolutionary ecology. Species distributions and adaptive radiations are thought to be controlled by environmental salinity levels, and efficient osmoregulatory (ionic balance) ability is the main mechanism to overcome the problems related to environmental salinity gradients. METHODS: To better understand how osmoregulatory performance in freshwater (FW) crustaceans allow individuals to acclimate and adapt to raised salinity conditions, here we (i), reviewed the literature on genes that have been identified to be associated with osmoregulation in FW crustaceans, and (ii), performed a transcriptomic analysis using cDNA libraries developed from mRNA isolated from three important osmoregulatory tissues (gill, antennal gland, hepatopancreas) and total mRNA from post larvae taken from the freshwater prawn, Macrobrachium australiense using Illumina deep sequencing technology. This species was targeted because it can complete its life cycle totally in freshwater but, like many Macrobrachium sp., can also tolerate brackish water conditions and hence should have genes associated with tolerance of both FW and saline conditions. RESULTS: We obtained between 55.4 and 65.2 million Illumina read pairs from four cDNA libraries. Overall, paired end sequences assembled into a total of 125,196 non-redundant contigs (≥200 bp) with an N50 length of 2,282 bp and an average contig length of 968 bp. Transcriptomic analysis of M. australiense identified 32 different gene families that were potentially involved with osmoregulatory capacity. A total of 32,597 transcripts were specified with gene ontology (GO) terms identified on the basis of GO categories. Abundance estimation of expressed genes based on TPM (transcript per million) ≥20 showed 1625 transcripts commonly expressed in all four libraries. Among the top 10 genes expressed in four tissue libraries associated with osmoregulation, arginine kinase and Na+/K+- ATPase showed the highest transcript copy number with 7098 and 660, respectively in gill which is considered to be the most important organ involved in osmoregulation. DISCUSSION: The current study provides the first broad transcriptome from M. australiense using next generation sequencing and identifies potential candidate genes involved in salinity tolerance and osmoregulation that can provide a foundation for investigating osmoregulatory capacity in a wide variety of freshwater crustaceans. PeerJ Inc. 2016-10-05 /pmc/articles/PMC5068373/ /pubmed/27761323 http://dx.doi.org/10.7717/peerj.2520 Text en ©2016 Moshtaghi et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Evolutionary Studies
Moshtaghi, Azam
Rahi, Md. Lifat
Nguyen, Viet Tuan
Mather, Peter B.
Hurwood, David A.
A transcriptomic scan for potential candidate genes involved in osmoregulation in an obligate freshwater palaemonid prawn (Macrobrachium australiense)
title A transcriptomic scan for potential candidate genes involved in osmoregulation in an obligate freshwater palaemonid prawn (Macrobrachium australiense)
title_full A transcriptomic scan for potential candidate genes involved in osmoregulation in an obligate freshwater palaemonid prawn (Macrobrachium australiense)
title_fullStr A transcriptomic scan for potential candidate genes involved in osmoregulation in an obligate freshwater palaemonid prawn (Macrobrachium australiense)
title_full_unstemmed A transcriptomic scan for potential candidate genes involved in osmoregulation in an obligate freshwater palaemonid prawn (Macrobrachium australiense)
title_short A transcriptomic scan for potential candidate genes involved in osmoregulation in an obligate freshwater palaemonid prawn (Macrobrachium australiense)
title_sort transcriptomic scan for potential candidate genes involved in osmoregulation in an obligate freshwater palaemonid prawn (macrobrachium australiense)
topic Evolutionary Studies
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5068373/
https://www.ncbi.nlm.nih.gov/pubmed/27761323
http://dx.doi.org/10.7717/peerj.2520
work_keys_str_mv AT moshtaghiazam atranscriptomicscanforpotentialcandidategenesinvolvedinosmoregulationinanobligatefreshwaterpalaemonidprawnmacrobrachiumaustraliense
AT rahimdlifat atranscriptomicscanforpotentialcandidategenesinvolvedinosmoregulationinanobligatefreshwaterpalaemonidprawnmacrobrachiumaustraliense
AT nguyenviettuan atranscriptomicscanforpotentialcandidategenesinvolvedinosmoregulationinanobligatefreshwaterpalaemonidprawnmacrobrachiumaustraliense
AT matherpeterb atranscriptomicscanforpotentialcandidategenesinvolvedinosmoregulationinanobligatefreshwaterpalaemonidprawnmacrobrachiumaustraliense
AT hurwooddavida atranscriptomicscanforpotentialcandidategenesinvolvedinosmoregulationinanobligatefreshwaterpalaemonidprawnmacrobrachiumaustraliense
AT moshtaghiazam transcriptomicscanforpotentialcandidategenesinvolvedinosmoregulationinanobligatefreshwaterpalaemonidprawnmacrobrachiumaustraliense
AT rahimdlifat transcriptomicscanforpotentialcandidategenesinvolvedinosmoregulationinanobligatefreshwaterpalaemonidprawnmacrobrachiumaustraliense
AT nguyenviettuan transcriptomicscanforpotentialcandidategenesinvolvedinosmoregulationinanobligatefreshwaterpalaemonidprawnmacrobrachiumaustraliense
AT matherpeterb transcriptomicscanforpotentialcandidategenesinvolvedinosmoregulationinanobligatefreshwaterpalaemonidprawnmacrobrachiumaustraliense
AT hurwooddavida transcriptomicscanforpotentialcandidategenesinvolvedinosmoregulationinanobligatefreshwaterpalaemonidprawnmacrobrachiumaustraliense