Transcriptome analysis of mud crab ( Scylla paramamosain ) gills in response to Mud crab reovirus (MCRV)

Liu, Shanshan; Chen, Guanxing; Xu, Huailiang; Zou, Wei-Bin; Yan, Wen-Rui; Wang, Qianqian; Deng, Hengwei; Zhang, Heqian; Yu, Guojiao; He, Jianguo; Weng, Shaoping

doi:10.1016/j.fsi.2016.07.033

Cited by 43 publications

(17 citation statements)

References 58 publications

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“…Transcriptomics approaches have been widely applied to study osmotic adjustment in aquatic animals [12, 27, 28, 29]. Advances in transcriptome technology have greatly improved our ability to analyse non-model species.…”

Section: Introductionmentioning

confidence: 99%

Comparative transcriptome analysis reveals osmotic-regulated genes in the gill of Chinese mitten crab (Eriocheir sinensis)

et al. 2019

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Salinity is one of the most important abiotic factors directly affecting the reproduction, molting, growth, immune, physiological and metabolic activities of Chinese mitten crab (Eriocheir sinensis). This species has strong osmoregulatory capacity and can maintain stringent internal homeostasis. However, the mechanisms conferring tolerance to salinity fluctuations are not well understood. To reveal the genes and pathways involved in osmoregulation, adult male crabs (body weight = 110 ± 5 g) were acclimated for 144 h in freshwater (FW, 0 ppt) or seawater (SW, 25 ppt). Changes in the transcriptome of crab gills were then analysed by RNA-Seq, and 174,903 unigenes were obtained. Comparison of genes between FW- SW-acclimated groups identified 932 genes that were significantly differentially expressed in the gill, comprising 433 and 499 up- and downregulated transcripts. Gene Ontology functional enrichment analysis revealed that important biological processes related to salt stress were significantly enriched, including energy metabolism, ion transport, signal transduction and antioxidant activity. Kyoto Encyclopaedia of Genes and Genomes enrichment analysis mapped the differentially expressed genes to 241 specific metabolic pathways, and pathways related to energy metabolism, oxidative phosphorylation and the tricarboxylic acid (TCA)/citrate cycle were significantly enriched. Salinity stress altered the expression of many enzymes involved in energy metabolism, ion transport, signal transduction and antioxidant pathways, including citrate synthase (CS), Na+/K+-ATPase (NKA), Na+-K+-2Cl cotransporter-1 (NKCC1), dopamine receptor D1 (DRD1), synaptic binding protein 1 (STXBP1), Cu2+/Zn2+ superoxide dismutase (SOD1) and glutathione S-transferase (GST). Additionally, the obtained transcriptomic sequencing data provided a useful resource for identification of novel genes, and further physiological analysis of Chinese mitten crab.

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Section: Introductionmentioning

confidence: 99%

Comparative transcriptome analysis reveals osmotic-regulated genes in the gill of Chinese mitten crab (Eriocheir sinensis)

et al. 2019

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“…This is mainly because there has been a general lack of appropriate tools able to identify and characterize viruses collected from environmental samples. However, the emergence of high throughput next generation sequencing (NSG) in recent years has not only enhanced our understanding of host responses to viral infections (Chu et al, 2015; Dahle et al, 2015; Xu et al, 2015, 2016a,b; Liu et al, 2016), but it has opened a great avenue for identification of viruses found in different aquatic environments using metagenomics analyses (Suttle, 2005, 2007; Djikeng et al, 2009; Kim et al, 2015). Viral metagenomics is a culture independent sequencing tool able to identify a large number of viral genomes from the same sample at the same time without prior knowledge of genomic sequences of the viruses to be identified (Handelsman, 2004; Bibby, 2013).…”

Section: Introductionmentioning

confidence: 99%

Environmental Viral Metagenomics Analyses in Aquaculture: Applications in Epidemiology and Disease Control

Munang’andu

2016

Front. Microbiol.

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Studies on the epidemiology of viral diseases in aquaculture have for a long time depended on isolation of viruses from infected aquatic organisms. The role of aquatic environments in the epidemiology of viral diseases in aquaculture has not been extensively expounded mainly because of the lack of appropriate tools for environmental studies on aquatic viruses. However, the upcoming of metagenomics analyses opens great avenues in which environmental samples can be used to study the epidemiology of viral diseases outside their host species. Hence, in this review I have shown that epidemiological factors that influence the composition of viruses in different aquatic environments include ecological factors, anthropogenic activities and stocking densities of cultured organisms based on environmental metagenomics studies carried out this far. Ballast water transportation and global trade of aquatic organisms are the most common virus dispersal process identified this far. In terms of disease control for outdoor aquaculture systems, baseline data on viruses found in different environments intended for aquaculture use can be obtained to enable the design of effective disease control strategies. And as such, high-risk areas having a high specter of pathogenic viruses can be identified as an early warning system. As for the control of viral diseases for indoor recirculation aquaculture systems (RAS), the most effective disinfection methods able to eliminate pathogenic viruses from water used in RAS can be identified. Overall, the synopsis I have put forth in this review shows that environmental samples can be used to study the epidemiology of viral diseases in aquaculture using viral metagenomics analysis as an overture for the design of rational disease control strategies.

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“…Previous study has shown 21,791 isotigs in the testis and ovary of the same crab species [ 8 ]. In addition, the gills of this crab species challenged with mud crab reovirus was analyzed, producing 67,279 assembled unigenes [ 9 ]. The unigenes identified in the study not only enrich transcriptomes data of S .…”

Section: Discussionmentioning

confidence: 99%

“…The transcriptomes of various tissues have been reported in S . paramamosain , such as hemolymph, gonads, cerebral ganglia, gill and mixture of the muscle, hepatopancreas, eyestalk [ 4 , 7 – 9 ], while the transcriptome of muscle is still unclear. This paper reported the results of next-generation sequencing (Illumina sequencing) which pay attention to claw muscle growth during mud crab fattening.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome profiling of claw muscle of the mud crab (Scylla paramamosain) at different fattening stages

et al. 2017

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In crustaceans, muscle growth and development is complicated, and to date substantial knowledge gaps exist. In this study, the claw muscle, hepatopancreas and nervous tissue of the mud crab (Scylla paramamosain) were collected at three fattening stages for sequence by the Illumina sequencing. A total of 127.87 Gb clean data with no less than 3.94 Gb generated for each sample and the cycleQ30 percentages were more than 86.13% for all samples. De Bruijn assembly of these clean data produced 94,853 unigenes, thereinto, 50,059 unigenes were found in claw muscle. A total of 121 differentially expressed genes (DEGs) were revealed in claw muscle from the three fattening stages with a Padj value < 0.01, including 63 genes with annotation. Functional annotation and enrichment analysis showed that the DEGs clusters represented the predominant gene catalog with roles in biochemical processes (glycolysis, phosphorylation and regulation of transcription), molecular function (ATP binding, 6-phosphofructokinase activity, and sequence-specific DNA binding) and cellular component (6-phosphofructokinase complex, plasma membrane, and integral component of membrane). qRT-PCR was employed to further validate certain DEGs. Single nucleotide polymorphism (SNP) analysis obtained 159,322, 125,963 and 166,279 potential SNPs from the muscle transcriptome at stage B, stage C and stage D, respectively. In addition, there were sixteen neuropeptide transcripts being predicted in the claw muscle. The present study provides a comprehensive transcriptome of claw muscle of S. paramamosain during fattening, providing a basis for screening the functional genes that may affect muscle growth of S. paramamosain.

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Transcriptome analysis of mud crab ( Scylla paramamosain ) gills in response to Mud crab reovirus (MCRV)

Cited by 43 publications

References 58 publications

Comparative transcriptome analysis reveals osmotic-regulated genes in the gill of Chinese mitten crab (Eriocheir sinensis)

Comparative transcriptome analysis reveals osmotic-regulated genes in the gill of Chinese mitten crab (Eriocheir sinensis)

Environmental Viral Metagenomics Analyses in Aquaculture: Applications in Epidemiology and Disease Control

Transcriptome profiling of claw muscle of the mud crab (Scylla paramamosain) at different fattening stages

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