Identification and profiling of growth-related microRNAs in Chinese perch (Siniperca chuatsi)

Abstract Background MicroRNAs (miRNAs) are endogenous small non-coding RNAs that play important roles in the regulation of diverse biological processes in eukaryotes. Chinese perch (Siniperca chuatsi) is one of the most economically important fish species widely cultured in China. Growth is an extremely important characteristic in fish. Individual differences in body size are common in Siniperca chuatsi, which significantly influence the aquaculture production of Siniperca chuatsi. However, the underline growth-related regulatory factors, such as miRNAs, are still unknown. Results To investigate the growth-related miRNAs in Siniperca chuatsi, two RNA libraries from four growth-related tissues (brain, pituitary, liver, and muscle) of Siniperca chuatsi at 6-month stage with relatively high or low growth rates (big-size group or small-size group) were obtained and sequenced using Solexa sequencing. A total of 252 known miRNAs and 12 novel miRNAs were identified. The expression patterns of these miRNAs in big-size group and small-size group were compared, and the results showed that 31 known and 5 novel miRNAs were differently expressed (DE). Furthermore, to verify the Solexa sequencing, five DE miRNAs were randomly selected and quantified by quantitative reverse transcription polymerase chain reaction (qRT-PCR). The results showed that their expression patterns were consistent with those of Solexa sequencing. In addition, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of target genes of DE miRNAs was performed. It showed that the target genes were involved in multiple biological processes including metabolic process, suggesting that metabolic process played an important role in growth of fish. Conclusions Siniperca chuatsi is a popular and economically important species in aquaculture. In this study, miRNAs in Siniperca chuatsi with different growth rates were identified, and their expression profiles were compared. The data provides the first large-scale miRNA profiles related to growth of Siniperca chuatsi, which is expected to contribute to a better understanding of the role of miRNAs in regulating the biological processes of growth and possibly useful for Siniperca chuatsi breeding

Comparative Mitogenomics of the Genus Odontobutis (Perciformes: Gobioidei: Odontobutidae) Revealed Conserved Gene Rearrangement and High Sequence Variations

To understand the molecular evolution of mitochondrial genomes (mitogenomes) in the genus Odontobutis, the mitogenome of Odontobutis yaluensis was sequenced and compared with those of another four Odontobutis species. Our results displayed similar mitogenome features among species in genome organization, base composition, codon usage, and gene rearrangement. The identical gene rearrangement of trnS-trnL-trnH tRNA cluster observed in mitogenomes of these five closely related freshwater sleepers suggests that this unique gene order is conserved within Odontobutis. Additionally, the present gene order and the positions of associated intergenic spacers of these Odontobutis mitogenomes indicate that this unusual gene rearrangement results from tandem duplication and random loss of large-scale gene regions. Moreover, these mitogenomes exhibit a high level of sequence variation, mainly due to the differences of corresponding intergenic sequences in gene rearrangement regions and the heterogeneity of tandem repeats in the control regions. Phylogenetic analyses support Odontobutis species with shared gene rearrangement forming a monophyletic group, and the interspecific phylogenetic relationships are associated with structural differences among their mitogenomes. The present study contributes to understanding the evolutionary patterns of Odontobutidae species

Additional file 1: of Identification and profiling of growth-related microRNAs in Chinese perch (Siniperca chuatsi)

Target gene prediction and analysis of miRNAs. (XLS 1498 kb

Effect of dissolved oxygen levels on growth performance, energy budget and antioxidant responses of yellow catfish, Pelteobagrus fulvidraco (Richardson)

This study was conducted to determine the effect of dissolved oxygen (DO) levels on growth performance, energy budget and antioxidant responses of yellow catfish Pelteobagrus fulvidraco. Yellow catfish was exposed to four levels of DO, consisting of hypoxia (2.28mgL(-1)), moderate hypoxia (4.04mgL(-1)), saturation (6.51mgL(-1)) and super-saturation groups (9.11mgL(-1)), respectively, for 8weeks. Specific growth rate and feed efficiency in dry matter were lowest in hypoxia and highest in the saturation and super-saturation groups. Apparent digestibility coefficients of dry matter and energy increased with increasing DO levels. Gross energy and growth energy were lowest for hypoxia, followed by moderate hypoxia and the highest for other two groups. Faecal energy was highest in hypoxia and lowest in saturation and super-saturation group. DO levels also significantly influenced activities of antioxidant enzymes and malondialdehyde level in liver and serum. Based on the observation described previously, saturated DO level helps to improve growth performance, feed utilization and antioxidant responses in yellow catfish. Super-saturation did not increase fish performance. To our knowledge, this is the first study involved in the effect of DO levels on energy budget of fish and provides new insight into aeration regime for yellow catfish culture

Molecular Basis of Gene-Gene Interaction: Cyclic Cross-Regulation of Gene Expression and Post-GWAS Gene-Gene Interaction Involved in Atrial Fibrillation.

Atrial fibrillation (AF) is the most common cardiac arrhythmia at the clinic. Recent GWAS identified several variants associated with AF, but they account for <10% of heritability. Gene-gene interaction is assumed to account for a significant portion of missing heritability. Among GWAS loci for AF, only three were replicated in the Chinese Han population, including SNP rs2106261 (G/A substitution) in ZFHX3, rs2200733 (C/T substitution) near PITX2c, and rs3807989 (A/G substitution) in CAV1. Thus, we analyzed the interaction among these three AF loci. We demonstrated significant interaction between rs2106261 and rs2200733 in three independent populations and combined population with 2,020 cases/5,315 controls. Compared to non-risk genotype GGCC, two-locus risk genotype AATT showed the highest odds ratio in three independent populations and the combined population (OR=5.36 (95% CI 3.87-7.43), P=8.00×10-24). The OR of 5.36 for AATT was significantly higher than the combined OR of 3.31 for both GGTT and AACC, suggesting a synergistic interaction between rs2106261 and rs2200733. Relative excess risk due to interaction (RERI) analysis also revealed significant interaction between rs2106261 and rs2200733 when exposed two copies of risk alleles (RERI=2.87, P<1.00×10-4) or exposed to one additional copy of risk allele (RERI=1.29, P<1.00×10-4). The INTERSNP program identified significant genotypic interaction between rs2106261 and rs2200733 under an additive by additive model (OR=0.85, 95% CI: 0.74-0.97, P=0.02). Mechanistically, PITX2c negatively regulates expression of miR-1, which negatively regulates expression of ZFHX3, resulting in a positive regulation of ZFHX3 by PITX2c; ZFHX3 positively regulates expression of PITX2C, resulting in a cyclic loop of cross-regulation between ZFHX3 and PITX2c. Both ZFHX3 and PITX2c regulate expression of NPPA, TBX5 and NKX2.5. These results suggest that cyclic cross-regulation of gene expression is a molecular basis for gene-gene interactions involved in genetics of complex disease traits

<i>PITX2c</i> and <i>ZFHX3</i> regulate expression of <i>NKX2</i>.<i>5</i>, <i>TBX5</i>, <i>KCNQ1</i> and <i>SCN1B</i>.

<p>HCT116 cells were transfected with siRNA specific for <i>PITX2c</i> or <i>ZFHX3</i> and used for isolation of total RNA samples and real-time RT-PCR analysis. Transfection of siRNA for <i>PITX2c</i> increased expression of <i>NKX2</i>.<i>5</i>, <i>TBX5</i>, <i>KCNQ1</i> and <i>SCN1B</i>. Transfection of siRNA for <i>ZFHX3</i> increased expression of <i>NKX2</i>.<i>5</i> and <i>TBX5</i>,but decreased expression of <i>SCN1B</i>. <i>ZFHX3</i> did not affect on the expression of <i>KCNQ1</i>. Transfection of siRNAs for both <i>PITX2c</i> and <i>ZFHX3</i> increased expression of <i>NKX2</i>.<i>5</i> and <i>TBX5</i>.</p