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.
abstract: 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, and 1,846 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Tianjin Center for Control and Prevention of Aquatic Animal Infectious Disease, Tianjin, People's Republic of China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Sun
authors.affiliation: Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, People's Republic of China.
authors.forename: Yichen
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, People's Republic of China.
authors.forename: Yichen
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Tianjin Center for Control and Prevention of Aquatic Animal Infectious Disease, Tianjin, People's Republic of China.
authors.forename: Shuxia
authors.initials: S
authors.lastname: Xue
authors.affiliation: Tianjin Center for Control and Prevention of Aquatic Animal Infectious Disease, Tianjin, People's Republic of China.
authors.forename: Xuyun
authors.initials: X
authors.lastname: Geng
authors.affiliation: Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, People's Republic of China.
authors.forename: Tong
authors.initials: T
authors.lastname: Hao
authors.affiliation: Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, People's Republic of China; Tianjin Center for Control and Prevention of Aquatic Animal Infectious Disease, Tianjin, People's Republic of China.
authors.forename: Jinsheng
authors.initials: J
authors.lastname: Sun
mesh_terms: D000818:Animals; D060829:Arthropod Proteins / Q000235:genetics* / Q000378:metabolism; D003386:Brachyura / Q000235:genetics / Q000378:metabolism*; D005123:Eye / Q000378:metabolism* / Q000473:pathology; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D063990:Gene Ontology; D043143:Hepatopancreas / Q000378:metabolism*; D053858:Metabolic Networks and Pathways / Q000235:genetics; D058977:Molecular Sequence Annotation; D060888:Real-Time Polymerase Chain Reaction; D059467:Transcriptome
chemical_list: D060829:Arthropod Proteins
references.citation: PLoS One. 2012;7(8):e43447
references.pmid: 22952684
references.citation: Science. 2008 Aug 15;321(5891):956-60
references.pmid: 18599741
references.citation: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W293-7
references.pmid: 16845012
references.citation: Gen Comp Endocrinol. 2011 Jun 1;172(2):293-304
references.pmid: 21447337
references.citation: PLoS One. 2013 Jun 19;8(6):e65176
references.pmid: 23840318
references.citation: Nucleic Acids Res. 2001 Jan 1;29(1):22-8
references.pmid: 11125040
references.citation: Nat Methods. 2008 Jul;5(7):621-8
references.pmid: 18516045
references.citation: Biol Bull. 2001 Aug;201(1):17-25
references.pmid: 11526059
references.citation: Science. 2007 Jul 20;317(5836):338-42
references.pmid: 17641193
references.citation: BMC Genomics. 2010 Sep 22;11:506
references.pmid: 20858287
references.citation: Comp Biochem Physiol B Biochem Mol Biol. 2003 Aug;135(4):707-19
references.pmid: 12892763
references.citation: BMC Genomics. 2012 Sep 17;13:484
references.pmid: 22985019
references.citation: Peptides. 2009 Mar;30(3):507-17
references.pmid: 18722490
references.citation: Indian J Exp Biol. 2004 Apr;42(4):403-12
references.pmid: 15088691
references.citation: Nat Biotechnol. 2011 May 15;29(7):644-52
references.pmid: 21572440
references.citation: Biol Rev Camb Philos Soc. 1970 May;45(2):121-65
references.pmid: 4915582
references.citation: Bioinformatics. 2009 Aug 1;25(15):1966-7
references.pmid: 19497933
references.citation: Comp Biochem Physiol B Biochem Mol Biol. 2011 Mar;158(3):242-9
references.pmid: 21199679
references.citation: Physiol Zool. 1997 Jul-Aug;70(4):415-20
references.pmid: 9237301
references.citation: Arch Int Physiol Biochim Biophys. 1992 May-Jun;100(3):281-3
references.pmid: 1382680
references.citation: Biotechniques. 2002 Jun;32(6):1372-4, 1376, 1378-9
references.pmid: 12074169
references.citation: Peptides. 1993 Jan-Feb;14(1):103-8
references.pmid: 8382808
references.citation: Bioinformatics. 2005 Sep 15;21(18):3674-6
references.pmid: 16081474
references.citation: BMC Genomics. 2009 Nov 16;10:531
references.pmid: 19917133
references.citation: Mol Immunol. 2009 Sep;46(15):2918-30
references.pmid: 19631987
references.citation: Comp Biochem Physiol A Mol Integr Physiol. 2001 Jul;129(4):909-17
references.pmid: 11440876
references.citation: Proc Int Conf Intell Syst Mol Biol. 1999;:138-48
references.pmid: 10786296
references.citation: PLoS One. 2012;7(10):e47442
references.pmid: 23071809
references.citation: Comp Biochem Physiol A Mol Integr Physiol. 2005 Jan;140(1):29-39
references.pmid: 15664310
references.citation: Comp Biochem Physiol C Toxicol Pharmacol. 2006 Mar-Apr;142(3-4):390-400
references.pmid: 16403679