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In-Depth Tanscriptomic Analysis on Giant Freshwater Prawns

Gene discovery in the Malaysian giant freshwater prawn (Macrobrachium rosenbergii) has been limited to small scale data collection, despite great interest in various research fields related to the commercial significance of this species. Next generation sequencing technologies that have been develop...

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Autores principales: Mohd-Shamsudin, Maizatul Izzah, Kang, Yi, Lili, Zhao, Tan, Tian Tian, Kwong, Qi Bin, Liu, Hang, Zhang, Guojie, Othman, Rofina Yasmin, Bhassu, Subha
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3667022/
https://www.ncbi.nlm.nih.gov/pubmed/23734171
http://dx.doi.org/10.1371/journal.pone.0060839
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author Mohd-Shamsudin, Maizatul Izzah
Kang, Yi
Lili, Zhao
Tan, Tian Tian
Kwong, Qi Bin
Liu, Hang
Zhang, Guojie
Othman, Rofina Yasmin
Bhassu, Subha
author_facet Mohd-Shamsudin, Maizatul Izzah
Kang, Yi
Lili, Zhao
Tan, Tian Tian
Kwong, Qi Bin
Liu, Hang
Zhang, Guojie
Othman, Rofina Yasmin
Bhassu, Subha
author_sort Mohd-Shamsudin, Maizatul Izzah
collection PubMed
description Gene discovery in the Malaysian giant freshwater prawn (Macrobrachium rosenbergii) has been limited to small scale data collection, despite great interest in various research fields related to the commercial significance of this species. Next generation sequencing technologies that have been developed recently and enabled whole transcriptome sequencing (RNA-seq), have allowed generation of large scale functional genomics data sets in a shorter time than was previously possible. Using this technology, transcriptome sequencing of three tissue types: hepatopancreas, gill and muscle, has been undertaken to generate functional genomics data for M. rosenbergii at a massive scale. De novo assembly of 75-bp paired end Ilumina reads has generated 102,230 unigenes. Sequence homology search and in silico prediction have identified known and novel protein coding candidate genes (∼24%), non-coding RNA, and repetitive elements in the transcriptome. Potential markers consisting of simple sequence repeats associated with known protein coding genes have been successfully identified. Using KEGG pathway enrichment, differentially expressed genes in different tissues were systematically represented. The functions of gill and hepatopancreas in the context of neuroactive regulation, metabolism, reproduction, environmental stress and disease responses are described and support relevant experimental studies conducted previously in M. rosenbergii and other crustaceans. This large scale gene discovery represents the most extensive transcriptome data for freshwater prawn. Comparison with model organisms has paved the path to address the possible conserved biological entities shared between vertebrates and crustaceans. The functional genomics resources generated from this study provide the basis for constructing hypotheses for future molecular research in the freshwater shrimp.
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spelling pubmed-36670222013-06-03 In-Depth Tanscriptomic Analysis on Giant Freshwater Prawns Mohd-Shamsudin, Maizatul Izzah Kang, Yi Lili, Zhao Tan, Tian Tian Kwong, Qi Bin Liu, Hang Zhang, Guojie Othman, Rofina Yasmin Bhassu, Subha PLoS One Research Article Gene discovery in the Malaysian giant freshwater prawn (Macrobrachium rosenbergii) has been limited to small scale data collection, despite great interest in various research fields related to the commercial significance of this species. Next generation sequencing technologies that have been developed recently and enabled whole transcriptome sequencing (RNA-seq), have allowed generation of large scale functional genomics data sets in a shorter time than was previously possible. Using this technology, transcriptome sequencing of three tissue types: hepatopancreas, gill and muscle, has been undertaken to generate functional genomics data for M. rosenbergii at a massive scale. De novo assembly of 75-bp paired end Ilumina reads has generated 102,230 unigenes. Sequence homology search and in silico prediction have identified known and novel protein coding candidate genes (∼24%), non-coding RNA, and repetitive elements in the transcriptome. Potential markers consisting of simple sequence repeats associated with known protein coding genes have been successfully identified. Using KEGG pathway enrichment, differentially expressed genes in different tissues were systematically represented. The functions of gill and hepatopancreas in the context of neuroactive regulation, metabolism, reproduction, environmental stress and disease responses are described and support relevant experimental studies conducted previously in M. rosenbergii and other crustaceans. This large scale gene discovery represents the most extensive transcriptome data for freshwater prawn. Comparison with model organisms has paved the path to address the possible conserved biological entities shared between vertebrates and crustaceans. The functional genomics resources generated from this study provide the basis for constructing hypotheses for future molecular research in the freshwater shrimp. Public Library of Science 2013-05-29 /pmc/articles/PMC3667022/ /pubmed/23734171 http://dx.doi.org/10.1371/journal.pone.0060839 Text en © 2013 Mohd-Shamsudin 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, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Mohd-Shamsudin, Maizatul Izzah
Kang, Yi
Lili, Zhao
Tan, Tian Tian
Kwong, Qi Bin
Liu, Hang
Zhang, Guojie
Othman, Rofina Yasmin
Bhassu, Subha
In-Depth Tanscriptomic Analysis on Giant Freshwater Prawns
title In-Depth Tanscriptomic Analysis on Giant Freshwater Prawns
title_full In-Depth Tanscriptomic Analysis on Giant Freshwater Prawns
title_fullStr In-Depth Tanscriptomic Analysis on Giant Freshwater Prawns
title_full_unstemmed In-Depth Tanscriptomic Analysis on Giant Freshwater Prawns
title_short In-Depth Tanscriptomic Analysis on Giant Freshwater Prawns
title_sort in-depth tanscriptomic analysis on giant freshwater prawns
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3667022/
https://www.ncbi.nlm.nih.gov/pubmed/23734171
http://dx.doi.org/10.1371/journal.pone.0060839
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