Comparative Transcriptome Analysis Reveals Sex-Biased Gene Expression in Juvenile Chinese Mitten Crab Eriocheir sinensis.
ABSTRACT: Sex-biased genes are considered to account for most of phenotypic differences between males and females. In order to explore the sex-biased gene expression in crab, we performed the whole-body transcriptome analysis in male and female juveniles of the Chinese mitten crab Eriocheir sinensis using next-generation sequencing technology. Of the 23,349 annotated unigenes, 148 were identified as sex-related genes. A total of 29 candidate genes involved in primary sex determination pathways were detected, indicating the sex determination cascade of the mitten crab might be more complex than previously supposed. Differential expression analysis showed 448 differentially expressed genes (DEGs) between the two transcriptomes. Most of DEGs were involved in processes such as metabolism and immunity, and not associated with obvious sexual function. The pathway predominantly enriched for DEGs were related to lysosome, which might reflect the differences in metabolism between males and females. Of the immune DGEs, 18 up-regulated genes in females were humoral immune factors, and eight up-regulated genes in males were pattern recognition receptors, suggesting sex differences of immune defense might exist in the mitten crab. In addition, two reproduction-related genes, vitellogenin and insulin-like androgenic gland factor, were identified to express in both sexes but with significantly higher level in males. Our research provides the first whole-body RNA sequencing of sex-specific transcriptomes for juvenile E. sinensis and will facilitate further studies on molecular mechanisms of crab sexual dimorphism.
Project description:Hepatopancreatic necrosis disease (HPND) is a newly emerging disease in the Chinese mitten crab, Eriocheir sinensis, which has resulted in large economic losses. However, the underlying cause of this disease remains unclear. To better understand the pathogenesis and pathogenic mechanism of HPND, we compared the transcriptome differences of the hepatopancreas of E. sinensis with and without HPND. The analysis yielded > 30 million reads for each sample of three test (with HPND) and three control groups (without HPND). We observed 978 downregulated genes and 644 upregulated genes. Among the gene ontology categories "biological process," "cellular component," and "molecular function", the subcategories cellular process, single-organism process, biological regulation, metabolic process, cell part, organelle, organelle part, binding, and catalytic were enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that "metabolism of xenobiotics by cytochrome P450," "drug metabolism-cytochrome P450," "chemical carcinogenesis," and "material metabolism" were the "five" most significantly enriched pathways in the hepatopancreas of E. sinensis with HPND. The results revealed that material metabolic abnormalities and drug effects from the external environment might be associated with HPND in the Chinese mitten crab. Considering the wide use of pyrethroids for pond cleaning in Xinghua city, we speculated that pyrethroids might cause HPND in the Chinese mitten crab. Our study provided useful information about the cause and pathogenetic mechanisms of HPND and could help to prevent this disease in production practice.
Project description:The carnitine palmitoyltransferase (CPT) family includes CPT 1 and CPT 2 that transport long-chain fatty acids into the mitochondrial compartment for ?-oxidation. In this study, three isoforms (CPT 1?, CPT 1? and CPT 2) of the CPT family were cloned from Chinese mitten crab (Eriocheir sinensis) and their complete coding sequences (CDS) were obtained. Sequence analysis revealed deduced amino acid sequences of 915, 775 and 683 amino acids, respectively. Gene expression analysis revealed a broad tissue distribution for all three isoforms, with high CPT 1? and CPT 2 mRNA levels in the hepatopancreas of males and females. In males, CPT 1? was highly expressed in gill, heart, brain ganglia and muscle, while in females, CPT 1?-mRNA levels were relatively high in muscle, hepatopancreas and ovary tissue. The effects of dietary fish oil replacement on the expression of the three CPT isoforms in the hepatopancreas during gonadal development were investigated using five experimental diets formulated with replacement of 0, 25, 50, 75 and 100% fish oil by 1:1 rapeseed oil: soybean oil. The results showed that Diets 2# and 5# yielded higher CPT 1? and CPT 2 mRNA expression in males (P < 0.05), while in females, expression of all three CPT isoforms increased then declined in the hepatopancreas with increasing dietary fish oil replacement. The observed changes in CPT gene expression varied in different isoforms and gender, suggesting the three CPT genes might play different roles in fatty acid ?-oxidation in E. sinensis.
Project description:Phenotypic differences between males and females of sexually dimorphic species are caused in large part by differences in gene expression between the sexes, most of which occurs in the gonads. To accurately identify genes differentially expressed between males and females in Drosophila, we sequenced the testis and ovary transcriptomes of D. yakuba, D. pseudoobscura, and D. ananassae and used them to identify sex-biased genes in the latter two species. We highlight the increased sensitivity and improved power of sex-biased gene detection methods when using our testis/ovary data versus male and female whole body transcriptome data. We thus provide a resource specifically designed to accurately identify and characterize sex-biased genes across Drosophila. This dataset is available through NCBI GEO accession GSE52058.
Project description:As an important freshwater aquaculture species in China, the Chinese mitten crab (Eriocheir japonica sinensis) has high economic and nutritional value. However, limited genomic information is currently available for studying its basic development and genetic diversity. Here, we performed whole-genome sequencing on Oxford Nanopore Technologies Limited's platform using promethION. The assembled size of E. j.sinensis genome was approximately 1.27 Gb, which is close to the estimated size (1.19 Gb). Furthermore, based on assessment using Benchmarking Universal Single-Copy Orthologs (BUSCO) (Simao et al., 2015), 94.00% of the expected eukaryotic genes were completely present in the genome assembly. In addition, repetitive sequences accounted for ~61.42% of the assembled genome, and 22,619 protein-coding genes were annotated. Comparative genomics analysis demonstrated that the Chinese mitten crab diverged from Penaeus vannamei ~373.6 million years ago, with a faster evolution rate than shrimp. We anticipate that the annotated high-quality genome of E. j. sinensis will promote research on its basic development and evolution and make substantial contributions to comparative genomic analyses of crustaceans.
Project description:The Chinese mitten crab Eriocheir sinensis lives in saline or fresh water during different life stages and exhibits a complex life history, making it an ideal model to study the salinity adaptation of euryhaline animals. In this study, RNA-seq techniques, and determinations of free amino acids (FAAs), monoamine neurotransmitters, and Na+/K+ pump activity, were employed to understand the osmoregulatory mechanism in Chinese mitten crab. A total of 15,138 differentially expressed genes were obtained from 12 transcriptome libraries. GO enrichment analysis revealed that the mRNA expression profiles were completely remodeled from 12 to 24 h after salinity stress. The neuroendocrine system was activated under stimulation, and the monoamine neurotransmitters including dopamine (DA) and serotonin (5-HT) were released to modulate osmoregulation. Furthermore, the Na+/K+ pump in crab hemocytes was significantly inhibited post salinity stress, resulting in increased intracellular ion concentrations and osmotic pressure to sustain the osmotic balance. Moreover, six key FAAs, including alanine (Ala), proline (Pro), glycine (Gly), glutamate (Glu), arginine (Arg), and aspartate (Asp), were overexpressed to modulate the extracellular osmotic balance during salinity adaptation. Interestingly, the immune genes were not enriched in the GO analysis, implying that the immune system might not contribute fundamentally to the tolerance upon fluctuating ambient salinity in the Chinese mitten crab. These results collectively demonstrated that the Chinese mitten crab had evolved an efficient regulation mechanism by modulating the FAAs production and Na+/K+ pump activity to sustain the osmotic balance independent of the immune system, in which the neuroendocrine modulation, especially generated by the monoamine neurotransmitter, played an indispensable role.
Project description:BACKGROUND:The Chinese mitten crab, Eriocheir sinensis, is one of the most studied and economically important crustaceans in China. Its transition from a swimming to a crawling method of movement during early development, anadromous migration during growth, and catadromous migration during breeding have been attractive features for research. However, knowledge of the underlying molecular mechanisms that regulate these processes is still very limited. FINDINGS:A total of 258.8 gigabases (Gb) of raw reads from whole-genome sequencing of the crab were generated by the Illumina HiSeq2000 platform. The final genome assembly (1.12 Gb), about 67.5 % of the estimated genome size (1.66 Gb), is composed of 17,553 scaffolds (>2 kb) with an N50 of 224 kb. We identified 14,436 genes using AUGUSTUS, of which 7,549 were shown to have significant supporting evidence using the GLEAN pipeline. This gene number is much greater than that of the horseshoe crab, and the annotation completeness, as evaluated by CEGMA, reached 66.9 %. CONCLUSIONS:We report the first genome sequencing, assembly, and annotation of the Chinese mitten crab. The assembled draft genome will provide a valuable resource for the study of essential developmental processes and genetic determination of important traits of the Chinese mitten crab, and also for investigating crustacean evolution.
Project description:Chinese mitten crab (Eriocheir sinensis) is one of the most commercially important aquaculture species in China. The androgenic gland (AG) of crustaceans plays pivotal roles in the regulation of male differentiation and in maintaining the male sexual characteristics. In order to reveal related mechanisms in AG, we compared transcriptomes of AG between proliferation and secretion phase. A total of 72,000 unigenes and 4,027 differentially expressed genes were obtained. Gene ontology enrichment analysis indicated that biological processes and metabolic pathways related to protein synthesis and secretion such as transcription, translation, and signal transduction were significantly enriched. Critical genes such as IAG, SXL, TRA-2, SRY, FTZ-F1, FOXL2, and FEM-1 were identified and potentially involved in maintaining the testis development and spermatogenesis. Ribosomes pathway revealed the cause of insulin-like androgenic gland hormone secretion increase. Three insulin-like receptors were thought to be associated with growth and spermatogenesis. In the neuroactive ligand-receptor interaction pathway, the expression of octopamine receptor, 5-HT receptor 1, and melatonin receptor was significantly changed, which revealed the key regulation mechanism of aggressive and mating behavior of males. Comparative transcriptome analysis provided new insights into the genome-wide molecular mechanisms of AG development and the regulatory mechanisms of male development.
Project description:Identifying sex differences in gene expression within the brain is critical for determining why multiple neurological and behavioural disorders differentially affect males and females. Several are more common or severe in males (e.g., autism and schizophrenia) or females (e.g., Alzheimer’s disease and depression). We analyzed transcriptomic data from the mouse hippocampus of six inbred strains (129S1/SvImJ, A/J, C57BL/6J, DBA/1J, DBA/2J and PWD/Ph), to provide a perspective on differences between male and female gene expression. Our data show that: 1) significant gene expression differences in males versus females varies substantially across the strains, 2) 12 genes exist that are differentially expressed across the inbred strains (termed core genes), and 3) there are >2,600 significantly differentially expressed genes (DEGs) among the strains (termed non-core genes). We found that DBA/2J uniquely has a substantial majority (89%) of DEGs that are more highly expressed in females than males; 129/SvImJ is the most strongly male-biased with a majority (69%) of DEGs that are more highly expressed in males. To gain insight into the sex-biased DEGs, we examined gene ontology, pathway and phenotype enrichment and found significant enrichment in phenotypes related to abnormal nervous system morphology and physiology, among others. In addition, several pathways are enriched significantly, including Alzheimer’s disease (AD), with 32 genes implicated in AD, 8 of which are male-biased. Three of the male-biased genes have been implicated in a neuroprotective role in AD. Our transcriptomic data provide new insight into understanding the possible genetic bases for sex-specific susceptibility and severity of brain disorders. Hippocampal mRNA from adult males and females of six inbred strains of mice were analyzed by RNA sequencing of 3 biological replicates using an Illumina HiSeq 2500
Project description:Eucommia ulmoides is a model representative of the dioecious plants with sex differentiation at initiation. Nevertheless, the genetic mechanisms of sexual dimorphism and sex determination in E. ulmoides remain poorly understood. In this study de novo transcriptome sequencing on Illumina platform generated >45 billion high-quality bases from fresh leaves of six male and female individuals of E. ulmoides. A total of 148,595 unigenes with an average length of 801 base-pairs (bp) were assembled. Through comparative transcriptome analyses, 116 differentially expressed genes (DEGs) between the males and the females were detected, including 73 male-biased genes and 43 female-biased genes. Of these DEGs, three female-biased genes were annotated to be related with the sexually dimorphic gutta content in E. ulmoides. One male-biased DEG was identified as putative MADS box gene APETALA3, a B class floral organ identity gene in the flowering plants. SNPs calling analyses further confirmed that the APETALA3-like gene was probably involved in the sex determination in E. ulmoides. Four other male-biased DEGs were potential sex-associated genes as well with segregated SNPs in accord with sex type. In addition, the SNPs density was 1.02 per kilobase (kb) in the expressed genes of E. ulmoides, implying a relatively high genetic diversity.
Project description:RNA-sequencing was used to identify sex-biased gene expression in brains of rare minnow (Gobiocypris rarus) by comparing transcriptomic profiles between females and males. Furthermore, transcriptomic responses to 10?ng/L tributyltin (TBT) in both male and female brains were also investigated to understand whether TBT affects the identified sex-biased genes. Differentially expressed genes (DEGs) were identified using the IDEG6 web tool. In this article, we presented male- and female-biased DEGs, and up-regulated and down-regulated DEGs after TBT exposure. The raw reads data supporting the present analyses has been deposited in NCBI Sequence Read Archive (SRA, http://www.ncbi.nlm.nih.gov/Traces/sra) with accession number PRJNA376634. The data presented in this article are related to the research article entitled "Transcriptomic analyses of sexual dimorphism of rare minnow (G. rarus) brains and effects of tributyltin exposure" (doi: 10.1016/j.ecoenv.2018.02.049).