Development of 30 Novel Polymorphic Expressed Sequence Tags (EST)-Derived Microsatellite Markers for the Miiuy Croaker, Miichthys miiuy

Expressed sequence tags (ESTs) can be used to identify microsatellite markers. We developed 30 polymorphic microsatellite markers from 5053 ESTs of the Miichthys miiuy. Out of 123 EST derived microsatellites for which PCR primers were designed, 30 loci were polymorphic in 30 individuals from a single natural population with 2–13 alleles per locus. The observed and expected heterozygosities were from 0.1024 to 0.7917 and from 0.2732 to 0.8845, respectively. Nine loci deviated from the Hardy-Weinberg equilibrium, and linkage disequilibrium was significant between 22 pairs of loci. These polymorphic microsatellite loci will be useful for genetic diversity analysis and molecule-assisted breeding for M. miiuy

Characterization of the Major Histocompatibility Complex Class II Genes in Miiuy Croaker

Major histocompatibility complex (MHC) has a central role in the adaptive immune system by presenting foreign peptide to the T-cell receptor. In order to study the molecular function and genomic characteristic of class II genes in teleost, the full lengths of MHC class IIA and IIB cDNA and genomic sequence were cloned from miiuy croaker (Miichthys miiuy). As in other teleost, four exons and three introns were identified in miiuy croaker class IIA gene; but the difference is that six exons and five introns were identified in the miiuy croaker class IIB gene. The deduced amino acid sequence of class IIA and class IIB had 26.3–85.7% and 11.0–88.8% identity with those of mammal and teleost, respectively. Real-time quantitative RT-PCR demonstrated that the MHC class IIA and IIB were ubiquitously expressed in ten normal tissues; expression levels of MHC genes were found first upregulated and then downregulated, and finally by a recovery to normal level throughout the pathogenic bacteria infection process. In addition, we report on the underlying mechanism that maintains sequences diversity among many fish species. A series of site-model tests implemented in the CODEML program revealed that positive Darwinian selection is likely the cause of the molecular evolution in the fish MHC class II genes

Miiuy Croaker Hepcidin Gene and Comparative Analyses Reveal Evidence for Positive Selection

Hepcidin antimicrobial peptide (HAMP) is a small cysteine-rich peptide and a key molecule of the innate immune system against bacterial infections. Molecular cloning and genomic characterization of HAMP gene in the miiuy croaker (Miichthys miiuy) were reported in this study. The miiuy croaker HAMP was predicted to encode a prepropeptide of 99 amino acids, a tentative RX(K/R)R cleavage motif and eight characteristic cysteine residues were also identified. The gene organization is also similar to corresponding genes in mammals and fish consisting of three exons and two introns. Sequence polymorphism analysis showed that only two different sequences were identified and encoded two proteins in six individuals. As reported for most other species, the expression level was highest in liver and an up-regulation of transcription was seen in spleen, intestine and kidney examined at 24 h after injection of pathogenic bacteria, Vibrio anguillarum, the expression pattern implied that miiuy croaker HAMP is an important component of the first line defense against invading pathogens. In addition, we report on the underlying mechanism that maintains sequences diversity among fish and mammalian species, respectively. A series of site-model tests implemented in the CODEML program revealed that moderate positive Darwinian selection is likely to cause the molecular evolution in the fish HAMP2 genes and it also showed that the fish HAMP1 genes and HAMP2 genes under different selection pressures

Analysis of C3 Suggests Three Periods of Positive Selection Events and Different Evolutionary Patterns between Fish and Mammals

BACKGROUND: The third complement component (C3) is a central protein of the complement system conserved from fish to mammals. It also showed distinct characteristics in different animal groups. Striking features of the fish complement system were unveiled, including prominent levels of extrahepatic expression and isotypic diversity of the complement components. The evidences of the involvement of complement system in the enhancement of B and T cell responses found in mammals indicated that the complement system also serves as a bridge between the innate and adaptive responses. For the reasons mentioned above, it is interesting to explore the evolutionary process of C3 genes and to investigate whether the huge differences between aquatic and terrestrial environments affected the C3 evolution between fish and mammals. METHODOLOGY/PRINCIPAL FINDINGS: Analysis revealed that these two groups of animals had experienced different evolution patterns. The mammalian C3 genes were under purifying selection pressure while the positive selection pressure was detected in fish C3 genes. Three periods of positive selection events of C3 genes were also detected. Two happened on the ancestral lineages to all vertebrates and mammals, respectively, one happened on early period of fish evolutionary history. CONCLUSIONS/SIGNIFICANCE: Three periods of positive selection events had happened on C3 genes during history and the fish and mammals C3 genes experience different evolutionary patterns for their distinct living environments

Particular gene order and complete mitochondrial genome of Parupeneus chrysopleuron (Perciformes, Mullidae)

Parupeneus chrysopleuron were under threat of climate change and unregulated fishing. For protecting the fish, complete mitochondrial genome (mitogenome) of P. chrysopleuron was firstly determined. The mitogenome is 17,397 nucleotides, including 38 genes. The gene arrangement of the P. chrysopleuron mitogenome is different from most of bony fishes. Investigating the mitochondrial gene arrangement pattern found that the tRNAIle and tRNAGln, followed by tRNAMe. Observing four notable non-coding regions, a non-coding region of 814 bp was identified as control region based on its location and central conserved sequence blocks (CSB-1 and CSB-2) were recognized

Complete mitochondrial genome of Semicossyphus reticulatus: genome characterization and phylogenetic analysis

The Semicossyphus reticulatus is a marine fish species belongs to the family Labridae. To understand the phylogenetic relationship of S. reticulatus in teleost, we firstly determined the complete mitochondrial genome of S. reticulatus. The entire mitochondrial genome (mtDNA) of S. reticulatus is 16610 bp in length, including 13 protein-coding genes and 2 ribosomal RNA genes, 22 tRNAs and 2 main non-coding regions. The gene arrangement, base composition, and tRNA structures of the mtDNA of S. reticulatus is consistent with those of other teleost. The S. reticulatus mtDNA was used to construct phylogenetic tree, which shows that S. reticulatus is clustered with the fishes of the order Perciformes. We expect that the availability of mtDNA of S. reticulatus will facilitate the further investigations of the taxonomic resolution, biogeography and molecular systematic

Complete sequence of the mitochondrial genome of Uranoscopus tosae: genome characterization and phylogenetic analysis

Uranoscopus tosae is a marine fish which some wild populations are in danger, and need urgent conservation. In this study, the complete mitochondrial genome of the U. tosae which is 17,286 base pairs in length, and contained 13 protein-coding genes and 2 ribosomal RNA genes, 22 tRNA genes and 2 main non-coding regions was firstly determined. Most of the genes of U. tosae were encoded on the H-strand, while the ND6 and eight tRNA (Gln, Ala, Asn, Cys, Tyr, Ser (UCN), Glu and Pro) genes were encoded on the L-strand. In addition, the complete mitochondrial genome of U. tosae was used to construct phylogenetic tree, which shows that U. tosae clustered with the species of Howellidae. The mitochondrial genome of U. tosae provides important data for studying on population genetic diversity and genetic conservation

The complete mitochondrial genome of the small yellow croaker and partitioned Bayesian analysis of Sciaenidae fish phylogeny

To understand the phylogenetic position of Larimichthys polyactis within the family Sciaenidae and the phylogeny of this family, the organization of the mitochondrial genome of small yellow croaker was determined herein. The complete, 16,470 bp long, mitochondrial genome contains 37 mitochondrial genes (13 protein-coding, 2 ribosomal RNA and 22 transfer RNA genes), as well as a control region (CR), as in other bony fishes. Comparative analysis of initiation/termination codon usage in mitochondrial protein-coding genes of Percoidei species, indicated that COI in Sciaenidae entails an ATG/AGA codon usage different from other Percoidei fishes, where absence of a typical conserved domain or motif in the control regions is common. Partitioned Bayesian analysis of 618 bp of COI sequences data were used to infer the phylogenetic relationships within the family Sciaenidae. An improvement in harmonic mean -lnL was observed when specific models and parameter estimates were assumed for partitions of the total data. The phylogenetic analyses did not support the monophyly of Otolithes, Argyrosomus, and Argyrosominae. L. polyactis was found to be most closely related to Collichthys niveatus, whereby, according to molecular systematics studies, the relationships within the subfamily Pseudosciaenidae should be reconsidered

Long Noncoding RNA MIR122HG Inhibits MAVS-Mediated Antiviral Immune Response by Deriving miR-122 in Miiuy Croaker (<i>Miichthys miiuy</i>)

Long noncoding RNAs (lncRNAs) function as micro regulators to impact gene expression after multiple pathogen infections, which have been largely studied in the last few years. Although lncRNA studies on lower vertebrates have received less attention than those on mammals, current studies suggest that lncRNA plays an important role in the immune response of fish to pathogen infections. Here, we studied the effect of MIR122HG as the host gene of miR-122 and indirectly negatively regulate MAVS-mediated antiviral immune responses in miiuy croaker (Miichthysmiiuy). We found that poly(I:C) significantly increases the host MIR122HG expression. The increased MIR122HG expression inhibited the production of the antiviral immune-related genes IFN-1, ISG15 and Viperin upon SCRV treatment. In addition, MIR122HG can act as a pivotally negative regulator involved in the MAVS-mediated NF-κB and IRF3 signaling pathways, which can effectively avoid an excessive immune response. Additionally, we found that MIR122HG can promote the replication of SCRV. Our study provides evidence about the involvement of lncRNAs in the antiviral immune response of fish and broadens the understanding of the function of lncRNAs as a precursor miRNA in teleost fish

Effectiveness of Group Parent-Child Interaction Therapy on Problem Behaviors in Chinese Kindergartners

Problem behaviors in early childhood may put young children at risk for negative behavioral and psychosocial problems. This study examined the effectiveness of group PCIT on Chinese young children’s externalizing and internalizing problems. The participants were 58 mothers with their children aged 2–3 years (M = 2.95 years, SD = 0.22), assigned to an immediate treatment (n = 26) group or to a waitlist (n = 32) control group. The program involved comprehensive group intervention and featured weekly 60–90-min sessions, totaling ten sessions over three months. Results indicate that group PCIT not only significantly improved teacher-reported problem behaviors in children, but also improved observed maternal parenting behavior. These findings support the use of group PCIT in Chinese children and provide mothers with an evidence-based tool to address problem behaviors in a non-clinical population