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1.
Nat Commun ; 10(1): 4625, 2019 10 11.
Artigo em Inglês | MEDLINE | ID: mdl-31604932

RESUMO

Common carp (Cyprinus carpio) is an allotetraploid species derived from recent whole genome duplication and provides a model to study polyploid genome evolution in vertebrates. Here, we generate three chromosome-level reference genomes of C. carpio and compare to related diploid Cyprinid genomes. We identify a Barbinae lineage as potential diploid progenitor of C. carpio and then divide the allotetraploid genome into two subgenomes marked by a distinct genome similarity to the diploid progenitor. We estimate that the two diploid progenitors diverged around 23 Mya and merged around 12.4 Mya based on the divergence rates of homoeologous genes and transposable elements in two subgenomes. No extensive gene losses are observed in either subgenome. Instead, we find gene expression bias across surveyed tissues such that subgenome B is more dominant in homoeologous expression. CG methylation in promoter regions may play an important role in altering gene expression in allotetraploid C. carpio.

2.
Front Genet ; 10: 660, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31354795

RESUMO

The common carp, Cyprinus carpio, is a cyprinid fish species cultured in Europe and Asia. It accounts for >70% of freshwater aquaculture production worldwide. We conducted a population genomics analysis on C. carpio using high-throughput SNP genotyping of 2,198 individuals from 14 populations worldwide to determine the genetic architecture of common carp populations and the genetic bases for environmental adaptation. Structure analyses including phylogeny and principal component analysis were also conducted, showing distinct geographical patterns in European and Asian populations. The linkage disequilibrium block average lengths of the 14 populations ranged from 3.94 kb to 36.67 kb. Genes within selective sweep regions were identified by genome scanning among the different populations, including gdf6a, bmpr1b, and opsin5. Gene Ontology and KEGG enrichment analyses revealed potential trait-related loci and genes associated with body shape, scaling patterns, and skin color. This population genomics analysis may provide valuable clues for future genome-assisted breeding of C. carpio.

3.
Fish Shellfish Immunol ; 92: 590-599, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31252044

RESUMO

HIFs (Hypoxia inducible factors) are the main regulators of the expression change of oxygen-dependent genes, in addition, they also play important roles in immune regulation. HIFs participate in infectious diseases and inflammatory responses, providing us a new therapeutic target for the treatment of diseases. In this study, 16 HIFs were identified in common carp genome database. Comparative genomics analysis showed large expansion of HIF gene family and approved the four round whole genome duplication (WGD) event in common carp. To further understand the function of HIFs, the domain architectures were predicted. All HIF proteins had the conserved HLH-PAS domain, which were essential for them to form dimer and bind to the downstream targets. The differences in domain of HIFα and HIFß might result in their different functions. Phylogenetic analysis revealed that all HIFs were divided into two subfamilies and the HIFs in common carp were clustered with their teleost counterparts indicating they are highly conservative during evolution. In addition, the tissue distribution was examined by RT-PCR showed that most of HIF genes had a wide range of tissue distribution but exhibited tissue-specific expression patterns. The expression divergences were observed between the copy genes, for example, HIF1A-1, HIF2A-1, ARNT-2 had wide tissue distribution while their copies had limited tissue distribution, proving the function divergence of copies post the WGD event. In order to find an effective activation of HIFs and apply to treatment of aquatic diseases, we investigate the dietary supplementation effects of different strains of Lactococcus lactis on the expression of HIFα subfamily members in kidney of common carp infected with A. hydrophila. In addition, all of the HIF genes have a high expression in the early stages of infection, and decreased in the treatment time point of 48 h in common carp. This phenomenon confirms that as a switch, the main function of HIFs is to regulate the production of immune response factors in early infection. So activation of the switch may be an effective method for infectious disease treatment. As expected, the treatment groups improved the expression of HIFs compared with the control group, and the effects of the three strains are different. The strain1 of L. lactis had a stronger induction on HIF genes than strain2 and strain3, and it might be applied as a potential activation of HIF genes for disease treatment. So, adding befitting L. lactis maybe a well method to activate the HIF genes to protect them from mycobacterial infection.


Assuntos
Fatores de Transcrição Hélice-Alça-Hélice Básicos/genética , Carpas/genética , Carpas/imunologia , Doenças dos Peixes/imunologia , Expressão Gênica , Lactococcus lactis/química , Probióticos/metabolismo , Aeromonas hydrophila/fisiologia , Ração Animal/análise , Animais , Fatores de Transcrição Hélice-Alça-Hélice Básicos/metabolismo , Dieta/veterinária , Proteínas de Peixes/genética , Proteínas de Peixes/metabolismo , Infecções por Bactérias Gram-Negativas/imunologia , Infecções por Bactérias Gram-Negativas/veterinária , Família Multigênica , Probióticos/administração & dosagem
4.
Biotechnol Appl Biochem ; 66(4): 591-596, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31050059

RESUMO

Glucose-6-phosphate dehydrogenase (G6PDH) has been used in enzyme multiplied immunoassay technique (EMIT) assays for detecting small molecule metabolites such as cholyglycine (CG). A key parameter for successful EMIT CG assay development is the inhibition rate of the G6PDH-CG conjugate, measured as the decrease in enzyme activity upon CG antibody binding. Several commonly used G6PDH cysteine mutants including A45C and K55C have been labeled with CG-maleimide derivative, but inhibition rates of are unsatisfactory. Herein, we investigated whether other mutation sites can achieve better inhibition rates. We generated eight cysteine mutants (K106C, Y155C, A201C, T258C, D306C, D375C, G426C, and D480C) of G6PDH, measured their inhibition rates, and evaluated the performance of the D306C mutant using EMIT CG assays. One of the eight mutants (D306C) displayed improved inhibition rate, whereas all others exhibited inhibition similar to or lower than that of A45C and K55C. The enhanced inhibition rate of D306C improved the EMIT CG assay calibration curve, using an Abbott c16000 automated biochemical analyzer, resulting in better repeatability, precision, and linearity than with K55C assays and a commercially available EMIT CG kit. The G6PDH mutant D306C has a higher inhibition rate in EMIT CG assays and improves assay performance.


Assuntos
Glucosefosfato Desidrogenase/genética , Glucosefosfato Desidrogenase/metabolismo , Ácido Glicocólico/análise , Imunoensaio , Mutação , Bibliotecas de Moléculas Pequenas/análise , Cisteína/genética , Glucosefosfato Desidrogenase/química , Ácido Glicocólico/metabolismo , Humanos , Bibliotecas de Moléculas Pequenas/metabolismo
5.
Front Genet ; 10: 217, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30930941

RESUMO

Polyunsaturated fatty acids (PUFAs) are a set of important nutrients that mainly include arachidonic acid (ARA4), docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), and α-linolenic acid (ALA). Recently, fish-derived PUFAs have been associated with cardiovascular health, fetal development, and improvement of brain functions. Studies have shown that fish muscular tissues are rich in PUFAs, which are influenced by various factors, including genetic variations, regulatory profiles, and methylation status of desaturase genes during fatty acid desaturation and elongation processes. However, the genetic mechanism and the pathways involved in fatty acid metabolism in fishes remain unclear. The overall aim of this study was to assess differences in gene expression responses among fishes with different fatty acid levels. To achieve this goal, we conducted genome-wide association analysis (GWAS) using a 250K SNP array in a population of 203 samples of common carp (Cyprinus carpio) and identified nine SNPs and 15 genes associated with muscular PUFA content. Then, RNA-Seq and whole genome bisulfite sequencing (WGBS) of different groups with high and low EPA, DHA, ARA4, and ALA contents in muscle, liver and brain tissues were conducted, resulting in 6,750 differentially expressed genes and 5,631 genes with differentially methylated promoters. Gene ontology and KEGG pathway enrichment analyses of RNA-Seq and WGBS results identified enriched pathways for fatty acid metabolism, which included the adipocytokine signaling pathway, ARA4 and linoleic acid metabolism pathway, and insulin signaling pathway. Integrated analysis indicated significant correlations between gene expression and methylation status among groups with high and low PUFA contents in muscular tissues. Taken together, these multi-level results uncovered candidate genes and pathways that are associated with fatty acid metabolism and paved the way for further genomic selection and carp breeding for PUFA traits.

6.
Data Brief ; 22: 812-814, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-30705926

RESUMO

Bighead carp (Aristichthys nobilis) and silver carp (Hypophthalmichthys molitrix) are closely related species in the subfamily Xenocypridinae within Cyprinidae, and they are also two of the four most important pond-cultured fish species in China. The ability to resist some diseases often differs significantly in silver carp and bighead carp during fishery production. However, the evolutionary divergence of the immune defense functions in these two species is still not understood at the molecular level. The data presented in this article are related to the research article entitled "Comparative analysis of spleen transcriptome detects differences in evolutionary adaptation of immune defense functions in bighead carp and silver carp" (Li et al., 2018). Please refer to this data article for interpretation of the data. Data provided in this submission comprise the Ka/Ks ratios of orthologs as well as adaptive evolution genes, expression levels of orthologs, and TPM value of genes expressed only in spleen of bighead carp or silver carp. These data provide a better understanding of the differences in evolutionary adaptation of immune defense functions in bighead carp and silver carp.

7.
Fish Shellfish Immunol ; 84: 148-157, 2019 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-30287346

RESUMO

The evolutionary divergence of the immune defense functions in bighead carp (A. nobilis) and silver carp (H. molitrix) is still not understood at the molecular level. Here, we obtained 48,821,754 and 55,054,480 clean reads from spleen tissue libraries prepared for bighead carp and silver carp using Illumina paired-end sequencing technology, respectively, and identified 4976 orthologous genes from the transcriptome data sets by comparative analysis. Adaptive evolutionary analysis showed that 212 orthologous genes and 255 Gene Ontology (GO) terms were subjected to positive selection(Ka/Ks values > 1) only in bighead carp, and 195 orthologous genes and 309 GO terms only in silver carp. Among immune defense functions with significant evolutionary divergence, the positively selected biological processes in bighead carp mainly included B cell-mediated immunity, chemokine-mediated signaling pathway, and immunoglobulin mediated immune response, whereas those in silver carp mainly included the antigen processing and presentation, defense response to fungus, and detection of bacteria. Moreover, we found 2974 genes expressed only in spleen of bighead carp and 3494 genes expressed only in spleen of silver carp, where these genes were mostly enriched in the same biological processes or pathways. These results provide a better understanding of the differences in resistance to some diseases by bighead carp and silver carp, and also facilitate the identification of candidate genes related to disease resistance.


Assuntos
Carpas/fisiologia , Baço/fisiologia , Transcriptoma , Adaptação Fisiológica , Animais , Evolução Molecular , Sistema Imunitário , Análise de Sequência de DNA
8.
Front Genet ; 9: 448, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30356829

RESUMO

Head size is important economic trait for many aquaculture fish which is directly linked to their carcass yield. The genetic basis of head size trait remains unclear in many widely cultured fish species. Common carp (Cyprinus carpio) is one of the most widely studied fish due to its importance on both economic and environmental aspects. In this study, we performed genome-wide association study using 433 Yellow River carp individuals from multiple families to identify loci and genes potentially associated with head size related traits including head length (HL), head length/body length ratio (HBR), eye diameter (ED), and eye cross (EC). QTL mapping was utilized to filter the effects of population stratification and improve power for the candidates identification in the largest surveyed family with a published genetic linkage map. Twelve SNPs showed significant for head size traits in GWAS and 18 QTLs were identified in QTL mapping. Our study combining both GWAS and QTL mapping could compensate the deficiency from each other and advance our understanding of head size traits in common carp. To acquire a better understanding of the correlation between head size and body growth, we also performed comparisons between QTLs of head size traits and growth-related traits. Candidate genes underlying head size traits were identified surrounding the significant SNPs, including parvalbumin, srpk2, fsrp5, igf1, igf3, grb10, igf1r, notch2, sfrp2. Many of these genes have been identified with potential functions on bone formation and growth. Igf1 was a putative gene associated with both head size and body growth in Yellow River carp. The teleost-specific igf3 was a candidate head size related gene, related to both HL and HBR. Our study also indicated the importance of Igf signaling pathway for both growth and head size determination in common carp, which could be potentially used in future selective breeding in common carp as well as other species.

9.
Oxid Med Cell Longev ; 2018: 7163057, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30224945

RESUMO

Myocardial dysfunction is a major manifestation of sepsis and closely associated with the increased mortality. MicroRNA-146 is one of the most important microRNAs identified as a potent negative regulator in innate immune and inflammatory responses induced by lipopolysaccharide (LPS). We aimed to identify the role and potential regulatory mechanism of miR-146a in sepsis-induced cardiac dysfunction with the induction of ErbB4 signaling. H9C2 cells were treated with LPS to induce sepsis, and miR-146a overexpression significantly increased the cell viability, reduced the apoptosis and ROS level, and attenuated the release of proinflammatory cytokines including TNF-α and IL-1ß. Levels of ErbB4, p-NF-κB, NF-κB, TRAF6, IRAK1, caspase 3, Bcl-2, and Bax were measured by Western blot. The overexpression of miR-146a significantly increased the ErbB4 expression, decreased the expression of TRAF6, IRAK1, caspase 3, and the phosphorylation level of NF-κB, and also increased the Bcl-2/Bax ratio, suggesting the inhibition of inflammation and apoptosis. The protective effects were all abolished by the use of siErbB4. In conclusion, our results demonstrated that the overexpression of miR-146a mitigates myocardial injury by negatively regulating NF-κB activation and inflammatory cytokine production via targeting ErbB4 in LPS-induced sepsis.


Assuntos
Cardiomiopatias/genética , Quinases Associadas a Receptores de Interleucina-1/genética , MicroRNAs/metabolismo , Receptor ErbB-4/genética , Sepse/genética , Fator 6 Associado a Receptor de TNF/genética , Cardiomiopatias/metabolismo , Cardiomiopatias/patologia , Células Cultivadas , Humanos , Quinases Associadas a Receptores de Interleucina-1/metabolismo , Receptor ErbB-4/metabolismo , Sepse/metabolismo , Transdução de Sinais , Fator 6 Associado a Receptor de TNF/metabolismo
10.
Mar Biotechnol (NY) ; 20(5): 573-583, 2018 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-29882019

RESUMO

Common carp (Cyprinus carpio) is one of the most widely studied fish species due to its great economic value and strong environmental adaptability. Scattered scale, a typical phenotype of the mirror carp that is derived from Europe, has never been observed in the Yellow River carp previously. We recently identified approximately one fourth of the F1 progenies displaying scattered scale in a full-sib Yellow River carp family in our breeding program, despite both parents that showed wild type with normal scale patterns. This family provides us unique materials to investigate the genetic basis underlying the abnormal scale mutant in Yellow River carp population. Genome-wide association study (GWAS) and association mapping were performed based on genome-wide single nucleotide polymorphisms (SNP) genotyped with common carp 250 K SNP genotyping array in 82 samples of the Yellow River carp family. We identified a 1.4 Mb genome region that was significantly associated with abnormal scattered scale patterns. We further identified a deletion mutation in fibroblast growth factor receptor 1 a1 (fgfr1a1) gene within this genome region. Amplification and sequencing analysis of this gene revealed a 311-bp deletion in intron 10 and exon 11, which proved that fgfr1a1 could be the causal gene responsible for abnormal scattered scale in the Yellow River carp family. Since similar fragment mutation with 306-bp and 310-bp deletions had been previously reported as causal mutation of scattered scale patterns in the mirror carp, we speculate that either the deletion mutation was introduced from Europe-derived mirror carp or the deletion independently occurred in the mutation hotspot in fgfr1a1 gene. The results provided insights into the genetic basis of scale pattern mutant in Yellow River carp population, which would help us to eliminate the recessive allele of the abnormal scale patterns in Yellow River carp population by molecular marker-assisted breeding.


Assuntos
Escamas de Animais/metabolismo , Sequência de Bases , Carpas/genética , Proteínas de Peixes/genética , Genoma , Receptor Tipo 1 de Fator de Crescimento de Fibroblastos/genética , Deleção de Sequência , Escamas de Animais/anormalidades , Animais , Cruzamento , China , Mapeamento Cromossômico , Europa (Continente) , Éxons , Feminino , Expressão Gênica , Estudo de Associação Genômica Ampla , Genótipo , Íntrons , Masculino , Análise de Sequência com Séries de Oligonucleotídeos , Fenótipo , Polimorfismo de Nucleotídeo Único , Rios
11.
Gene ; 666: 32-43, 2018 Aug 05.
Artigo em Inglês | MEDLINE | ID: mdl-29684491

RESUMO

The Japanese ornamental carp (Cyprinus carpio var. Koi) is famous for multifarious colors and patterns, making it commonly culture and trade across the world. Although functional genes and inheritance of color traits have been commonly studied, seldom attentions were focused on the genetic regulation during the developmental process of pigmentation. To better understand the mechanism of skin color development, we observed the morphogenesis of pigment cells during the post-embryonic stages and analysed the temporal expression pattern of mRNAs/miRNAs profiles in four distinct developmental stages. 59 and 103 differentially expressed genes/miRNAs (DEGs/DEMs) associated with pigmentation and skin were identified, including pax7, mitf, tyr, tyrp1, etc., and the highest DEGs were detected at 11 days post hatching (dph). In addition, the functional characteristics of mRNAs/miRNAs associated with pteridine and carotenoid pathway were also examined. Furthermore, 65 miRNA-mRNA interaction pairs related to pigmentation, pteridines and carotenoids metabolism were detected between different stages. Interestingly, the largest pairs appeared in the transition from 11 dph to 48 dph, which had the similar trend with DEGs further manifesting the importance of 11 dph. This study produced a comprehensive programme of DEGs/DEMs during color development, which will provide resources to understand the regulation mechanism in color formation. The understanding of genetic basis in color formation might promote the production and breeding of the Koi carp.


Assuntos
Carpas/genética , MicroRNAs/genética , RNA Mensageiro/genética , Pigmentação da Pele , Transcriptoma , Animais , Carpas/crescimento & desenvolvimento , Carpas/metabolismo , Proteínas de Peixes/genética , Proteínas de Peixes/metabolismo , Regulação da Expressão Gênica no Desenvolvimento , MicroRNAs/metabolismo , Interferência de RNA , RNA Mensageiro/metabolismo , Pele/crescimento & desenvolvimento , Pele/metabolismo
12.
J Med Chem ; 60(14): 6166-6190, 2017 07 27.
Artigo em Inglês | MEDLINE | ID: mdl-28635286

RESUMO

Agonism of the 5-HT2C receptor represents one of the most well-studied and clinically proven mechanisms for pharmacological weight reduction. Selectivity over the closely related 5-HT2A and 5-HT2B receptors is critical as their activation has been shown to lead to undesirable side effects and major safety concerns. In this communication, we report the development of a new screening paradigm that utilizes an active site mutant D134A (D3.32) 5-HT2C receptor to identify atypical agonist structures. We additionally report the discovery and optimization of a novel class of nonbasic heterocyclic amide agonists of 5-HT2C. SAR investigations around the screening hits provided a diverse set of potent agonists at 5-HT2C with high selectivity over the related 5-HT2A and 5-HT2B receptor subtypes. Further optimization through replacement of the amide with a variety of five- and six-membered heterocycles led to the identification of 6-(1-ethyl-3-(quinolin-8-yl)-1H-pyrazol-5-yl)pyridazin-3-amine (69). Oral administration of 69 to rats reduced food intake in an ad libitum feeding model, which could be completely reversed by a selective 5-HT2C antagonist.


Assuntos
Arginina/análogos & derivados , Flavonas/química , Receptor 5-HT2C de Serotonina/metabolismo , Agonistas do Receptor 5-HT2 de Serotonina/química , Membro 1 da Subfamília B de Cassetes de Ligação de ATP/genética , Membro 2 da Subfamília G de Transportadores de Cassetes de Ligação de ATP/genética , Animais , Arginina/síntese química , Arginina/química , Arginina/farmacologia , Encéfalo/metabolismo , Células CACO-2 , Permeabilidade da Membrana Celular , Comportamento Alimentar/efeitos dos fármacos , Flavonas/síntese química , Flavonas/farmacologia , Células HEK293 , Humanos , Masculino , Membranas Artificiais , Camundongos Knockout , Microssomos Hepáticos/metabolismo , Mutação , Ratos Sprague-Dawley , Receptor 5-HT2A de Serotonina/metabolismo , Receptor 5-HT2B de Serotonina/metabolismo , Receptor 5-HT2C de Serotonina/genética , Agonistas do Receptor 5-HT2 de Serotonina/síntese química , Agonistas do Receptor 5-HT2 de Serotonina/farmacocinética , Agonistas do Receptor 5-HT2 de Serotonina/farmacologia , Relação Estrutura-Atividade
13.
Data Brief ; 10: 598-600, 2017 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-28116337

RESUMO

The data presented in this paper are related to the research article entitled "Transcriptome profiling of developing spleen tissue and discovery of immune-related genes in grass carp (Ctenopharyngodon idella)" (Li et al. 2016) [1]. Please refer to this article for interpretation of the data. Data provided in this submission are comprised of the expression levels of unigenes, significantly differentially expressed genes(DEGs), significant enrichment GO term and KEGG pathway of DEGs, and information of the transcripts assigned to six immune pathways.

14.
Fish Shellfish Immunol ; 60: 400-410, 2017 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-27965162

RESUMO

Grass carp Ctenopharyngodon idella is an important freshwater aquaculture species. However, studies regarding transcriptomic profiling of developing spleen tissue in the grass carp are lacking. Here, the transcriptome sequencing from the spleen tissue of one-year-old (cis1) and three-year-old (cis3) grass carp was performed using Illumina paired-end sequencing technology. The de novo assemblies yielded 48,970 unigenes with average lengths of 1264.51 bp from the two libraries. The assembled unigenes were evaluated and functionally annotated by comparing with sequences in major public databases including Nr, COG, Swiss-Prot, KEGG, Pfam and GO. Comparative analysis of expression levels revealed that a total of 38,254 unigenes were expressed in both the cis1 and cis3 libraries, while 4356 unigenes were expressed only in the cis1 library, and 3312 unigenes were expressed only in the cis3 library. Meanwhile, 1782 unigenes (including 903 down-regulated and 879 up-regulated unigenes) were differentially expressed between the two developmental stages of the grass carp spleen. Based on GO and KEGG enrichment analysis, these differentially expressed genes widely participated in the regulation of immunity and response in the grass carp. Moreover, the main components of six immune-related pathways were identified, including complement and coagulation cascades, Toll-like receptor signaling, B-cell receptor signaling, T-cell receptor signaling, antigen processing and presentation, and chemokine signaling. Finally, two identified transcripts including TLR 8 and complement component C8 were validated for reliability by RT-PCR. Collectively, the results obtained in this study will provide a basis for the study of molecular mechanisms in grass carp spleen development.


Assuntos
Carpas/genética , Carpas/imunologia , Proteínas de Peixes/genética , Transcriptoma , Animais , Carpas/crescimento & desenvolvimento , Carpas/metabolismo , Proteínas de Peixes/metabolismo , Perfilação da Expressão Gênica/veterinária , Biblioteca Gênica , Imunidade Inata/genética , Reação em Cadeia da Polimerase em Tempo Real/veterinária , Análise de Sequência de DNA/veterinária , Transdução de Sinais , Baço/crescimento & desenvolvimento , Baço/imunologia , Baço/metabolismo
15.
Fish Shellfish Immunol ; 57: 41-48, 2016 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-27521591

RESUMO

The common carp is an important aquaculture species that is worldwide distributed. Nowadays, intensive rearing in aquaculture increases the susceptibility of fish to various pathogens such as Aeromonas hydrophila, which has caused severe damage to carp production. However, systematic analysis on the host response of common carp against A. hydrophila is less studied. In order to better understand the common carp immune response process against bacteria at the global gene expression level, we examined transcriptional profiles of the common carp spleen at three timepoints following experimental infection with A. hydrophila. A total of 545 million 125-bp paired end reads were generated, and all trimmed clean reads were mapped onto the common carp whole genome sequence. Comparison of the transcriptomes between the treatment and control group fish revealed 2900 unigenes with significantly differential expression, including 732, 936, 928 genes up-regulated, and 248, 475, 700 genes down-regulated at 4 h, 12 h, 24 h post infection respectively. The captured significantly differentially expressed genes are mainly involved in the pathways including junction/adhesion, pathogen recognition, cell surface receptor signaling, and immune system process/defense response. Our study will provide fundamental information on molecular mechanism underlying the immune response of teleost against bacterial infection and might suggest strategies for selection of resistant strains of common carp in aquaculture.


Assuntos
Aeromonas hydrophila/fisiologia , Carpas , Doenças dos Peixes/imunologia , Infecções por Bactérias Gram-Negativas/imunologia , Imunidade Inata , Baço/imunologia , Transcriptoma , Animais , Doenças dos Peixes/genética , Doenças dos Peixes/microbiologia , Proteínas de Peixes/genética , Proteínas de Peixes/metabolismo , Infecções por Bactérias Gram-Negativas/genética , Infecções por Bactérias Gram-Negativas/microbiologia , Infecções por Bactérias Gram-Negativas/virologia , Baço/microbiologia
17.
Sci Rep ; 6: 26693, 2016 05 26.
Artigo em Inglês | MEDLINE | ID: mdl-27225429

RESUMO

High density genetic linkage maps are essential for QTL fine mapping, comparative genomics and high quality genome sequence assembly. In this study, we constructed a high-density and high-resolution genetic linkage map with 28,194 SNP markers on 14,146 distinct loci for common carp based on high-throughput genotyping with the carp 250 K single nucleotide polymorphism (SNP) array in a mapping family. The genetic length of the consensus map was 10,595.94 cM with an average locus interval of 0.75 cM and an average marker interval of 0.38 cM. Comparative genomic analysis revealed high level of conserved syntenies between common carp and the closely related model species zebrafish and medaka. The genome scaffolds were anchored to the high-density linkage map, spanning 1,357 Mb of common carp reference genome. QTL mapping and association analysis identified 22 QTLs for growth-related traits and 7 QTLs for sex dimorphism. Candidate genes underlying growth-related traits were identified, including important regulators such as KISS2, IGF1, SMTLB, NPFFR1 and CPE. Candidate genes associated with sex dimorphism were also identified including 3KSR and DMRT2b. The high-density and high-resolution genetic linkage map provides an important tool for QTL fine mapping and positional cloning of economically important traits, and improving common carp genome assembly.


Assuntos
Carpas/genética , Mapeamento Cromossômico , Ligação Genética , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , Animais , Peixe-Zebra/genética
18.
PLoS One ; 11(4): e0153246, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27058731

RESUMO

The ATP-binding cassette (ABC) gene family is considered to be one of the largest gene families in all forms of prokaryotic and eukaryotic life. Although the ABC transporter genes have been annotated in some species, detailed information about the ABC superfamily and the evolutionary characterization of ABC genes in common carp (Cyprinus carpio) are still unclear. In this research, we identified 61 ABC transporter genes in the common carp genome. Phylogenetic analysis revealed that they could be classified into seven subfamilies, namely 11 ABCAs, six ABCBs, 19 ABCCs, eight ABCDs, two ABCEs, four ABCFs, and 11 ABCGs. Comparative analysis of the ABC genes in seven vertebrate species including common carp, showed that at least 10 common carp genes were retained from the third round of whole genome duplication, while 12 duplicated ABC genes may have come from the fourth round of whole genome duplication. Gene losses were also observed for 14 ABC genes. Expression profiles of the 61 ABC genes in six common carp tissues (brain, heart, spleen, kidney, intestine, and gill) revealed extensive functional divergence among the ABC genes. Different copies of some genes had tissue-specific expression patterns, which may indicate some gene function specialization. This study provides essential genomic resources for future studies in common carp.


Assuntos
Transportadores de Cassetes de Ligação de ATP/genética , Carpas/genética , Proteínas de Peixes/genética , Transportadores de Cassetes de Ligação de ATP/classificação , Animais , Evolução Molecular , Proteínas de Peixes/classificação , Deleção de Genes , Duplicação Gênica , Perfilação da Expressão Gênica , Variação Genética , Estudo de Associação Genômica Ampla , Família Multigênica , Filogenia , Sintenia , Distribuição Tecidual
19.
Mitochondrial DNA A DNA Mapp Seq Anal ; 27(4): 2531-2, 2016 07.
Artigo em Inglês | MEDLINE | ID: mdl-26061340

RESUMO

The complete mitochondrial genomes of two ornamental fishes, black molly (Poecilia sphenops) and blue gourami (Trichogaster trichopterus), were obtained by the traditional polymerase chain reaction (PCR)-based sequencing approach. The mitogenomes of P. sphenops and T. trichopterus are determined as 16,533 bp and 16,456 bp in length, respectively. Both the genomes include 22 transfer RNA genes, 13 protein-coding genes and 2 ribosomal RNA genes. Phylogenetic tree was constructed based on the complete mitogenomes of these two species and closely related 20 teleost species to assess their phylogenic relationship and evolution.


Assuntos
Peixes/genética , Genoma Mitocondrial/genética , Animais , DNA Mitocondrial/genética , Peixes/classificação , Filogenia , Reação em Cadeia da Polimerase , RNA Ribossômico/genética , RNA de Transferência/genética
20.
Mitochondrial DNA A DNA Mapp Seq Anal ; 27(5): 3536-7, 2016 09.
Artigo em Inglês | MEDLINE | ID: mdl-26260174

RESUMO

The complete mitochondrial genome of the first individual Rhinogobio typus collected from the Yellow River were sequenced and compared with the previously reported complete mitochondrial sequence of Rhinogobio typus from the Yangtze River. The length of their circular mitochondrial genome was determined to be 16 599 and 16 608 bp respectively. The comparison of two mitochondrial genomes revealed 237 base pair substitutions and 17 insertions or deletions (indels), including 182 base pair substitutions and 2 indels in protein-coding region. Phylogenetic tree was constructed based on complete mitogenomes of the two populations and closely related 13 teleost species to assess their phylogenic relationship and evolution.


Assuntos
Cyprinidae/classificação , Genoma Mitocondrial , Mitocôndrias/genética , Análise de Sequência de DNA/métodos , Animais , Composição de Bases , China , Cyprinidae/genética , Evolução Molecular , Genes de RNAr , Variação Genética , Tamanho do Genoma , Filogenia , RNA de Transferência/genética
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