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Changes in the Organics Metabolism in the Hepatopancreas Induced by Eyestalk Ablation of the Chinese Mitten Crab Eriocheir sinensis Determined via Transcriptome and DGE Analysis
BACKGROUND: To understand the regulation mechanism of eyestalk ablation on the activities of hepatopancreas, Illumina RNA-Seq and digital gene expression (DGE) analyses were performed to investigate the transcriptome of the eyestalk, Y-organ, and hepatopancreas of E. sinensis and to identify the gen...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3995808/ https://www.ncbi.nlm.nih.gov/pubmed/24755618 http://dx.doi.org/10.1371/journal.pone.0095827 |
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author | Sun, Yan Zhang, Yichen Liu, Yichen Xue, Shuxia Geng, Xuyun Hao, Tong Sun, Jinsheng |
author_facet | Sun, Yan Zhang, Yichen Liu, Yichen Xue, Shuxia Geng, Xuyun Hao, Tong Sun, Jinsheng |
author_sort | Sun, Yan |
collection | PubMed |
description | BACKGROUND: To understand the regulation mechanism of eyestalk ablation on the activities of hepatopancreas, Illumina RNA-Seq and digital gene expression (DGE) analyses were performed to investigate the transcriptome of the eyestalk, Y-organ, and hepatopancreas of E. sinensis and to identify the genes associated with the hepatopancreas metabolism that are differentially expressed under eyestalk ablation conditions. RESULTS: A total of 58,582 unigenes were constructed from 157,168 contigs with SOAPdenovo. A BlastX search against the NCBI Nr database identified 21,678 unigenes with an E-value higher than 10(−5). Using the BLAST2Go and BlastAll software programs, 6,883 unigenes (11.75% of the total) were annotated to the Gene Ontology (GO) database, 7,386 (12.6%) unigenes were classified into 25 Clusters of Orthologous Groups of Proteins (COGs), 16,200 (27.7%) unigenes were assigned to 242 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and1,846 unigenes were matched to “metabolism pathways”. The DGE analysis revealed that 1,416 unigenes were significantly differentially expressed in the hepatopancreas, of which 890 unigenes were up-regulated and 526 unigenes were down-regulated. Of the differentially expressed genes, 382 unigenes were annotated and 63 were classified into metabolism pathways. The results of the real-time polymerase chain reaction (PCR) analysis of four unigenes related to carbohydrate metabolism were consistent with those obtained from the DGE analysis, which demonstrates that the sequencing data were satisfactory for further gene expression analyses. CONCLUSION: This paper reported the transcriptom of the eyestalk, Y-organ, and hepatopancreas from E. sinensis. DGE analysis provided the different expressed genes of the metabolism processes in hepatopancreas that are affected by eyestalk ablation. These findings will facilitate further investigations on the mechanisms of the metabolism of organic substances during development and reproduction in crustaceans. |
format | Online Article Text |
id | pubmed-3995808 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-39958082014-04-25 Changes in the Organics Metabolism in the Hepatopancreas Induced by Eyestalk Ablation of the Chinese Mitten Crab Eriocheir sinensis Determined via Transcriptome and DGE Analysis Sun, Yan Zhang, Yichen Liu, Yichen Xue, Shuxia Geng, Xuyun Hao, Tong Sun, Jinsheng PLoS One Research Article BACKGROUND: To understand the regulation mechanism of eyestalk ablation on the activities of hepatopancreas, Illumina RNA-Seq and digital gene expression (DGE) analyses were performed to investigate the transcriptome of the eyestalk, Y-organ, and hepatopancreas of E. sinensis and to identify the genes associated with the hepatopancreas metabolism that are differentially expressed under eyestalk ablation conditions. RESULTS: A total of 58,582 unigenes were constructed from 157,168 contigs with SOAPdenovo. A BlastX search against the NCBI Nr database identified 21,678 unigenes with an E-value higher than 10(−5). Using the BLAST2Go and BlastAll software programs, 6,883 unigenes (11.75% of the total) were annotated to the Gene Ontology (GO) database, 7,386 (12.6%) unigenes were classified into 25 Clusters of Orthologous Groups of Proteins (COGs), 16,200 (27.7%) unigenes were assigned to 242 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and1,846 unigenes were matched to “metabolism pathways”. The DGE analysis revealed that 1,416 unigenes were significantly differentially expressed in the hepatopancreas, of which 890 unigenes were up-regulated and 526 unigenes were down-regulated. Of the differentially expressed genes, 382 unigenes were annotated and 63 were classified into metabolism pathways. The results of the real-time polymerase chain reaction (PCR) analysis of four unigenes related to carbohydrate metabolism were consistent with those obtained from the DGE analysis, which demonstrates that the sequencing data were satisfactory for further gene expression analyses. CONCLUSION: This paper reported the transcriptom of the eyestalk, Y-organ, and hepatopancreas from E. sinensis. DGE analysis provided the different expressed genes of the metabolism processes in hepatopancreas that are affected by eyestalk ablation. These findings will facilitate further investigations on the mechanisms of the metabolism of organic substances during development and reproduction in crustaceans. Public Library of Science 2014-04-22 /pmc/articles/PMC3995808/ /pubmed/24755618 http://dx.doi.org/10.1371/journal.pone.0095827 Text en © 2014 Sun 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 Sun, Yan Zhang, Yichen Liu, Yichen Xue, Shuxia Geng, Xuyun Hao, Tong Sun, Jinsheng Changes in the Organics Metabolism in the Hepatopancreas Induced by Eyestalk Ablation of the Chinese Mitten Crab Eriocheir sinensis Determined via Transcriptome and DGE Analysis |
title | Changes in the Organics Metabolism in the Hepatopancreas Induced by Eyestalk Ablation of the Chinese Mitten Crab Eriocheir sinensis Determined via Transcriptome and DGE Analysis |
title_full | Changes in the Organics Metabolism in the Hepatopancreas Induced by Eyestalk Ablation of the Chinese Mitten Crab Eriocheir sinensis Determined via Transcriptome and DGE Analysis |
title_fullStr | Changes in the Organics Metabolism in the Hepatopancreas Induced by Eyestalk Ablation of the Chinese Mitten Crab Eriocheir sinensis Determined via Transcriptome and DGE Analysis |
title_full_unstemmed | Changes in the Organics Metabolism in the Hepatopancreas Induced by Eyestalk Ablation of the Chinese Mitten Crab Eriocheir sinensis Determined via Transcriptome and DGE Analysis |
title_short | Changes in the Organics Metabolism in the Hepatopancreas Induced by Eyestalk Ablation of the Chinese Mitten Crab Eriocheir sinensis Determined via Transcriptome and DGE Analysis |
title_sort | changes in the organics metabolism in the hepatopancreas induced by eyestalk ablation of the chinese mitten crab eriocheir sinensis determined via transcriptome and dge analysis |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3995808/ https://www.ncbi.nlm.nih.gov/pubmed/24755618 http://dx.doi.org/10.1371/journal.pone.0095827 |
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