Chenghui Wang

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

Molting is a critical developmental process for crustaceans, yet the underlying molecular mechanism is unknown. In this study, we used RNA-Seq to investigate transcriptomic profiles of the hepatopancreas and identified differentially expressed genes at four molting stages of Chinese mitten crab (Eriocheir sinensis). A total of 97,398 transcripts were assembled, with 31,900 transcripts annotated. Transcriptomic comparison revealed 1,189 genes differentially expressed amongst different molting stages. We observed a pattern associated with energy metabolism and physiological responses during a molting cycle. In specific, differentially expressed genes enriched in postmolt were linked to energy consumption whereas genes enriched in intermolt were related to carbohydrates, lipids metabolic and biosynthetic processes. In premolt, a preparation stage for upcoming molting and energy consumption, highly expressed genes were enriched in response to steroid hormone stimulus and immune system development. The expression profiles of twelve functional genes detected via RNA-Seq were corroborated through real-time RT-PCR assay. Together, our results, including assembled transcriptomes, annotated functional elements and enriched differentially expressed genes amongst different molting stages, provide novel insights into the functions of the hepatopancreas in energy metabolism and biological processes pertaining to molting in crustaceans.

Hepatopancreas transcriptome analysis of Chinese mitten crab (Eriocheir sinensis) with white hepatopancreas syndrome

ABSTRACT White hepatopancreas is a syndrome that has recently emerged in aquaculture of Chinese mitten crab (Eriocheir sinensis). High lethality of the disease caused large economic loss, which drew considerable attention of fish farmers and scientific researchers. In this study, hepatopancreas reference transcriptome was de novo assembled and differential expression analysis was conducted between white hepatopancreas and normal (yellow) hepatopancreas of E. sinensis. A total of 90,687 transcripts were assembled, and 27,387 were annotated. Transcriptomic comparison revealed 69 differentially expressed genes between individuals featuring white hepatopancreas and yellow hepatopancreas. Genes associated with immune response and cell death, include thioredoxin‐related transmembrane protein 1, hemocytin, methuselah‐like 1, and E3 ubiquitin‐protein ligase, and they were up‐regulated, whereas titin and 5‐formyltetrahydrofolate cyclo‐ligase, which are genes related to cell proliferation, were down‐regulated in E. sinensis with white hepatopancreas syndrome. Our study provides novel insights into genetic causes of formation and novel gene markers for detection of white hepatopancreas syndrome in aquaculture of E. sinensis. HighlightsGene expression profiles of hepatopancreas with white hepatopancreas syndrome were firstly generated in this study.Our research provides insights into the formation and biological response to white hepatopancreas syndrome of E. sinensis.Our research provides novel gene markers for detection of white hepatopancreas syndrome in aquaculture of E. sinensis.

Domestication drive the changes of immune and digestive system of Eurasian perch (Perca fluviatilis)

Domestication has altered a variety of traits within the Eurasian perch (Perca fluviatilis), including phenotypic, physiological and behavioral traits of Eurasian perch (Perca fluviatilis). Little is known, however, about the genetic changes between domesticated and wild Eurasian perch. In this study, we assembled a high-quality de novo reference transcriptome and identified differentially expressed genes between wild and domesticated Eurasian perch. A total of 113,709 transcripts were assembled, and 58,380 transcripts were annotated. Transcriptomic comparison revealed 630 differentially expressed genes between domesticated and wild Eurasian perch. Within domesticated Eurasian perch there were 412 genes that were up-regulated including MHCI, MHCII, chia, ighm within immune system development. There were 218 genes including try1, ctrl, ctrb, cela3b, cpa1 and cpb1, which were down-regulated that were associated with digestive processes. Our results indicated domestication drives the changes of immune and digestive system of Eurasian perch. Our study not only provide valuable genetic resources for further studies in Eurasian perch, but also provide novel insights into the genetic basis of physiological changes in Eurasian perch during domestication process.

Transcriptomic comparison of invasive bigheaded carps ( Hypophthalmichthys nobilis and Hypophthalmichthys molitrix ) and their hybrids

Abstract Bighead carp (Hypophthalmichthys nobilis) and silver carp (Hypophthalmichthys molitrix), collectively called bigheaded carps, are invasive species in the Mississippi River Basin (MRB). Interspecific hybridization between bigheaded carps has been considered rare within their native rivers in China; however, it is prevalent in the MRB. We conducted de novo transcriptome analysis of pure and hybrid bigheaded carps and obtained 40,759 to 51,706 transcripts for pure, F1 hybrid, and backcross bigheaded carps. The search against protein databases resulted in 20,336–28,133 annotated transcripts (over 50% of the transcriptome) with over 13,000 transcripts mapped to 23 Gene Ontology biological processes and 127 KEGG metabolic pathways. More transcripts were detected in silver carp than in bighead carp; however, comparable numbers of transcripts were annotated. Transcriptomic variation detected between two F1 hybrids may indicate a potential loss of fitness in hybrids. The neighbor‐joining distance tree constructed using over 2,500 one‐to‐one orthologous sequences suggests transcriptomes could be used to infer the history of introgression and hybridization. Moreover, we detected 24,792 candidate SNPs that can be used to identify different species. The transcriptomes, orthologous sequences, and candidate SNPs obtained in this study should provide further knowledge of interspecific hybridization and introgression.

Structure and function of the alternatively spliced isoforms of the ecdysone receptor gene in the Chinese mitten crab, Eriocheir sinensis

Alternative splicing is an essential molecular mechanism that increase the protein diversity of a species to regulate important biological processes. Ecdysone receptor (EcR), an essential nuclear receptor, is essential in the molting, growth, development, reproduction, and regeneration of crustaceans. In this study, the whole sequence of EcR gene from Eriocheir sinensis was obtained. The sequence was 45,481 bp in length with 9 exons. Moreover, four alternatively spliced EcR isoforms (Es-EcR-1, Es-EcR-2, Es-EcR-3 and Es-EcR-4) were identified. The four isoforms harbored a common A/B domain and a DNA-binding region but different D domains and ligand-binding regions. Three alternative splicing patterns (alternative 5′ splice site, exon skipping, and intron retention) were identified in the four isoforms. Functional studies indicated that the four isoforms have specific functions. Es-EcR-3 may play essential roles in regulating periodic molting. Es-EcR-2 may participate in the regulation of ovarian development. Our results indicated that Es-EcR has broad regulatory functions in molting and development and established the molecular basis for the investigation of ecdysteroid signaling related pathways in E. sinensis.

Tissue-expression profiles unveils the gene interaction of hepatopancreas, eyestalk, and ovary in precocious female Chinese mitten crab, Eriocheir sinensis

Sexual precocity is a serious and common biological phenomenon in animal species. Large amount of precocity individuals was identified in Chinese mitten crab, Eriocheir sinensis, which caused huge economical loss every year. However, the underlying genetic basis of precocity in E. sinensis is still lack. In this study, histology observation, comparative transcriptome was conducted among different stages of precocious one-year old and normal two-year old E. sinensis, tissue-expression profiles of ovary, hepatopancreas, and eyestalk tissues were presented and compared. Genes associated with lipid metabolic process, lipid transport, vitelline membrane formation, vitelline synthesis and neuropeptide hormone related genes were upregulated in the ovary, hepatopancreas and eyestalk of precocious E. sinensis. Our results indicated eyestalk involved in neuroendocrine system providing neuropeptide hormone that may induce vitellogenesis in hepatopancreas and further stimulate ovary development. Hepatopancreas is a site for energy storage, vitellogenin synthesis and may assist to induce oogenesis through lipid transport in precocious E. sinensis. The genetic basis of precocity in E. sinensis is an integrated gene regulatory network of eyestalk, hepatopancreas, and ovary tissues. Our study provides effective convenient phenotype measurement method for identification of potential precocious E. sinensis detection, and valuable genetic resources and novel insights into the research of molecular mechanism of precocity in E. sinensis.

Genetic admixture of mitten crabs in the Northeast Asia hybrid zones

Hybridization and genetic admixture in hybrid zones promote phenotypic and genotypic adaptive changes in organisms. Hybrids between Chinese mitten crab (Eriocheir sinensis) and Japanese mitten crab (Eriocheir japonica) have been reported in the Vladivostok region of Russia. However, the direction and extent of hybridization remains unknown in Northeast Asia. In this paper, genetic variation and admixture were investigated by examining a mitochondrial NADH dehydrogenase subunit II gene (ND2) and 10 microsatellite DNA loci in mitten crabs from the Tumen River in China and Vladivostok in Russia. In addition, the adjacent distributions of E. sinensis in China and E. japonica in Japan were analyzed. The Tumen River and Vladivostok were both identified as hybrid zones of E. sinensis and E. japonica. As indicated by ND2 sequences analysis, the mitten crabs in the Tumen River and Vladivostok displayed 5–10 times higher nucleotide diversity and more mixed haplotypes than pure E. sinensis and E. japonica. Meanwhile, approximately 31.25% of the mitten crabs in Vladivostok and 30.00% in the Tumen River were identified as potential hybrids, indicating strong genetic admixture between the two mitten crabs in these hybrid zones. Our results provide quantitative evidence of genetic admixture of E. sinensis and E. japonica in Northeast Asia.

Comparative skin transcriptome of two Oujiang color common carp (Cyprinus carpio var. color) varieties

Body color variation has long been a hot research topic in evolutionary and functional biology. Oujiang color common carp (Cyprinus carpio var. color) is a well-known economical and ornamental fish. Three main types of pigments and four distinct color patterns are typical characters of Oujiang color common carp, which makes it an excellent fish model to study body coloration. In this study, skin transcriptome assembly and comparisons were conducted in two Oujiang color common carp varieties: whole red and whole white. Transcriptome comparison revealed that more differentially expressed energy metabolism genes were upregulated in whole white compared to whole red. The results indicated that energy metabolism genes might be strongly associated with environmental adaption and growth performance and likely affect the red and white color formation in Oujiang color common carp. Our study provided direct guidance for the aquaculture industrials of Oujiang color common carp and presented valuable genetic resources for body color research in fish.

Selection of appropriate reference genes for qPCR in the Chinese mitten crab, Eriocheir sinensis (Decapoda, Varunidae)

The accuracy of qPCR depends on the stability of the reference gene used for data normalization. However, the stably expressed reference genes in the Chinese mitten crab, Eriocheir sinensis , have not been well identified under different experimental conditions. In this study, the stabilities of the expressions of 10 candidate reference genes were evaluated in different developmental stages, tissues, and moulting stages of E. sinensis . Our results indicated that UBE and S27 were the most stable reference genes. To validate the suitability of the reference genes, the EcR (ecdysone receptor) gene was analysed among different moulting stages. The results showed that the expression level of EcR was elevated using the least stable reference gene, GST , compared with using the three most stable reference genes. Taken together, our results indicate that reference genes should be assessed and selected in accordance with the experimental conditions, and more than one reference gene should be selected.