Transcriptomic variation of hepatopancreas reveals the energy metabolism and biological processes associated with molting in Chinese mitten crab, Eriocheir sinensis

Huang, Shu; Yue, Wucheng; Chen, Jiao; Gaughan, Sarah; Lu, Wei; Lu, Guoqing; Wang, Chenghui

doi:10.1038/srep14015

Cited by 89 publications

(81 citation statements)

References 70 publications

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“…Most of previous genetic studies on the mitten crab were performed focusing on population genetics3839. In recent year, transcriptomic analysis using RNA-Seq technology was conducted on the immunity, molt, metamorphosis and reproduction38404142. A high-density linkage map of the mitten crab including 10,358 markers was developed on a northern population with 2b-RAD method32, but the markers identity is obscure because their sequences of the nucleotide have neither been described nor deposited in the data bank.…”

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confidence: 99%

A second generation SNP and SSR integrated linkage map and QTL mapping for the Chinese mitten crab Eriocheir sinensis

Qiu

Xiong

Han

et al. 2017

Sci Rep

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The Chinese mitten crab Eriocheir sinensis is the most economically important cultivated crab species in China, and its genome has a high number of chromosomes (2n = 146). To obtain sufficient markers for construction of a dense genetic map for this species, we employed the recently developed specific-locus amplified fragment sequencing (SLAF-seq) method for large-scale SNPs screening and genotyping in a F1 full-sib family of 149 individuals. SLAF-seq generated 127,677 polymorphic SNP markers, of which 20,803 valid markers were assigned into five segregation types and were used together with previous SSR markers for linkage map construction. The final integrated genetic map included 17,680 SNP and 629 SSR markers on the 73 linkage groups (LG), and spanned 14,894.9 cM with an average marker interval of 0.81 cM. QTL mapping localized three significant growth-related QTL to a 1.2 cM region in LG53 as well as 146 sex-linked markers in LG48. Genome-wide QTL-association analysis further identified four growth-related QTL genes named LNX2, PAK2, FMRFamide and octopamine receptors. These genes are involved in a variety of different signaling pathways including cell proliferation and growth. The map and SNP markers described here will be a valuable resource for the E. sinensis genome project and selective breeding programs.

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confidence: 99%

A second generation SNP and SSR integrated linkage map and QTL mapping for the Chinese mitten crab Eriocheir sinensis

Qiu

Xiong

Han

et al. 2017

Sci Rep

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“…Transcriptomics using NGS technology has revealed genes involved in stress response, reproduction, development, molting and growth, limb regeneration, immune response, endocrinology, and nutrition and digestion in decapod crustaceans (Sagi et al 2013; Tom et al 2013; Durica et al 2014; Ghaffari et al 2014; Hao et al 2014; Lv et al, 2014, 2015; Shen et al 2014; Song et al 2014; Tom et al 2014; Wei et al 2014a, 2014b; Abehsera et al 2015; Chandler et al 2015; Christiaens et al 2015; Huang et al 2015; Johnson et al 2015; Li et al 2015a, 2015b; Ventura et al 2014, 2015; Verbruggen et al 2015; Wang et al 2015; Das et al 2016a). It is clear from the input received at the SICB meeting and the ten symposium papers in this issue (Armstrong and Stillman 2016; Chandler et al 2016; Clark and Greenwood 2016; Das and Mykles 2016; Das et al 2016b; Havird and Santos 2016a, 2016b; Johnson et al 2016; Powell et al 2016; Tarrant et al 2016) that a greater understanding of the relationship between transcriptomic and phenotypic change in decapod crustaceans will not be achieved until more powerful and applicable “-omic” tools and resources are developed.…”

Section: Future Directions and Recommendationsmentioning

confidence: 99%

Resources and Recommendations for Using Transcriptomics to Address Grand Challenges in Comparative Biology

Mykles

Burnett

Durica

et al. 2016

Integr. Comp. Biol.

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High-throughput RNA sequencing (RNA-seq) technology has become an important tool for studying physiological responses of organisms to changes in their environment. De novo assembly of RNA-seq data has allowed researchers to create a comprehensive catalog of genes expressed in a tissue and to quantify their expression without a complete genome sequence. The contributions from the “Tapping the Power of Crustacean Transcriptomics to Address Grand Challenges in Comparative Biology” symposium in this issue show the successes and limitations of using RNA-seq in the study of crustaceans. In conjunction with the symposium, the Animal Genome to Phenome Research Coordination Network collated comments from participants at the meeting regarding the challenges encountered when using transcriptomics in their research. Input came from novices and experts ranging from graduate students to principal investigators. Many were unaware of the bioinformatics analysis resources currently available on the CyVerse platform. Our analysis of community responses led to three recommendations for advancing the field: (1) integration of genomic and RNA-seq sequence assemblies for crustacean gene annotation and comparative expression; (2) development of methodologies for the functional analysis of genes; and (3) information and training exchange among laboratories for transmission of best practices. The field lacks the methods for manipulating tissue-specific gene expression. The decapod crustacean research community should consider the cherry shrimp, Neocaridina denticulata, as a decapod model for the application of transgenic tools for functional genomics. This would require a multi-investigator effort.

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“…Therefore, it was not surprising that there were little energy metabolism processes or pathways enriched in DEGs in this study. But it is worth noting that a number of neuromodulator-related pathways were enriched including the dopaminergic, serotonergic, cholinergic and glutamatergic pathways, which were not found in previous research [12, 13, 42]. Hormones from the XO-SG complex appear to be controlled by the neurotransmitters/neuromodulators dopamine, serotonin, and enkephalin [43–47].…”

Section: Discussionmentioning

confidence: 99%

Transcriptomic variation of eyestalk reveals the genes and biological processes associated with molting in Portunus trituberculatus

Zhang

Liu

et al. 2017

PLoS ONE

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BackgroundMolting is an essential biological process throughout the life history of crustaceans, which is regulated by many neuropeptide hormones expressed in the eyestalk. To better understand the molting mechanism in Portunus trituberculatus, we used digital gene expression (DGE) to analyze single eyestalk samples during the molting cycle by high-throughput sequencing.ResultsWe obtained 14,387,942, 12,631,508 and 13,060,062 clean sequence reads from inter-molt (InM), pre-molt (PrM) and post-molt (PoM) cDNA libraries, respectively. A total of 1,394 molt-related differentially expressed genes (DEGs) were identified. GO and KEGG enrichment analysis identified some important processes and pathways with key roles in molting regulation, such as chitin metabolism, peptidase inhibitor activity, and the ribosome. We first observed a pattern associated with the neuromodulator-related pathways during the molting cycle, which were up-regulated in PrM and down-regulated in PoM. Four categories of important molting-related transcripts were clustered and most of them had similar expression patterns, which suggests that there is a connection between these genes throughout the molt cycle.ConclusionOur work is the first molt-related investigation of P. trituberculatus focusing on the eyestalk at the whole transcriptome level. Together, our results, including DEGs, identification of molting-related biological processes and pathways, and observed expression patterns of important genes, provide a novel insight into the function of the eyestalk in molting regulation.

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Transcriptomic variation of hepatopancreas reveals the energy metabolism and biological processes associated with molting in Chinese mitten crab, Eriocheir sinensis

Cited by 89 publications

References 70 publications

A second generation SNP and SSR integrated linkage map and QTL mapping for the Chinese mitten crab Eriocheir sinensis

A second generation SNP and SSR integrated linkage map and QTL mapping for the Chinese mitten crab Eriocheir sinensis

Resources and Recommendations for Using Transcriptomics to Address Grand Challenges in Comparative Biology

Transcriptomic variation of eyestalk reveals the genes and biological processes associated with molting in Portunus trituberculatus

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