Insight into the Fecal Microbiota Signature Associated with Growth Specificity in Korean Jindo Dogs Using 16S rRNA Sequencing.

Gut microbiomes are well recognized to serve a variety of roles in health and disease, even though their functions are not yet completely understood. Previous studies have demonstrated that the microbiomes of juvenile and adult dogs have significantly different compositions and characteristics. However, there is still a scarcity of basic microbiome research in dogs. In this study, we aimed to advance our understanding by confirming the difference in fecal microbiome between young and adult dogs by analyzing the feces of 4-month and 16-month-old Jindo dogs, a domestic Korean breed. Microbiome data were generated and examined for the two age groups using 16S rRNA analysis. Comparison results revealed that the 16-month-old group presented a relatively high distribution of Bacteroides, whereas the 4-month-old group presented a comparatively high distribution of the Lactobacillus genus. Microbial function prediction analyses confirmed the relative abundance of lipid metabolism in 4-month-old dogs. In 16-month-old dogs, glucose metabolism was determined using microbial function prediction analyses. This implies that the functional microbiome changes similarly to the latter in adults compared with childhood. Overall, we discovered compositional and functional variations between genes of the gut microbial population in juveniles and adults. These microbial community profiles can be used as references for future research on the microbiome associated with health and development in the canine population.

A Gene-Set Enrichment and Protein-Protein Interaction Network-Based GWAS with Regulatory SNPs Identifies Candidate Genes and Pathways Associated with Carcass Traits in Hanwoo Cattle.

Non-synonymous SNPs and protein coding SNPs within the promoter region of genes (regulatory SNPs) might have a significant effect on carcass traits. Imputed sequence level data of 10,215 Hanwoo bulls, annotated and filtered to include only regulatory SNPs (450,062 SNPs), were used in a genome-wide association study (GWAS) to identify loci associated with backfat thickness (BFT), carcass weight (CWT), eye muscle area (EMA), and marbling score (MS). A total of 15, 176, and 1 SNPs were found to be significantly associated (p < 1.11 × 10-7) with BFT, CWT, and EMA, respectively. The significant loci were BTA4 (CWT), BTA6 (CWT), BTA14 (CWT and EMA), and BTA19 (BFT). BayesR estimated that 1.1%~1.9% of the SNPs contributed to more than 0.01% of the phenotypic variance. So, the GWAS was complemented by a gene-set enrichment (GSEA) and protein-protein interaction network (PPIN) analysis in identifying the pathways affecting carcass traits. At p < 0.005 (~2,261 SNPs), 25 GO and 18 KEGG categories, including calcium signaling, cell proliferation, and folate biosynthesis, were found to be enriched through GSEA. The PPIN analysis showed enrichment for 81 candidate genes involved in various pathways, including the PI3K-AKT, calcium, and FoxO signaling pathways. Our finding provides insight into the effects of regulatory SNPs on carcass traits.

Cetaceans evolution: insights from the genome sequences of common minke whales.

BACKGROUND: Whales have captivated the human imagination for millennia. These incredible cetaceans are the only mammals that have adapted to life in the open oceans and have been a source of human food, fuel and tools around the globe. The transition from land to water has led to various aquatic specializations related to hairless skin and ability to regulate their body temperature in cold water. RESULTS: We present four common minke whale (Balaenoptera acutorostrata) genomes with depth of ×13 ~ ×17 coverage and perform resequencing technology without a reference sequence. Our results indicated the time to the most recent common ancestors of common minke whales to be about 2.3574 (95% HPD, 1.1521 - 3.9212) million years ago. Further, we found that genes associated with epilation and tooth-development showed signatures of positive selection, supporting the morphological uniqueness of whales. CONCLUSIONS: This whole-genome sequencing offers a chance to better understand the evolutionary journey of one of the largest mammals on earth.

Comparative transcriptomic analysis to identify differentially expressed genes in fat tissue of adult Berkshire and Jeju Native Pig using RNA-seq.

Pork is a major source of animal protein for humans. The subcutaneous, intermuscular and the intramuscular fat are the factors responsible for meat quality. RNA-seq is rapidly adopted for the profiling of the transcriptomes in the studies related to gene regulation. The discovery of differentially expressed genes (DEGs) between adult animals of Jeju Native Pig (JNP) and Berkshire breeds are of particular interest for the current study. RNA-seq was used to investigate the transcriptome profiling in the fat tissue. Sequence reads were obtained from Ilumina HiSeq2000 and mapped to the pig genome using Tophat2. Total 153 DEGs were identified and 71 among the annotated genes, have BLAST matches in the non- redundant database. Metabolic, immune response and protein binding are enriched pathways in the fat tissue. In our study, biological adhesion, cellular, developmental and multicellular organismal processes in fat were up-regulated in JNP as compare to Berkshire. Multicellular organismal process, developmental process, embryonic morphogenesis and skeletal system development were the most significantly enriched terms in fat of JNP and Berkshire breeds (p = 1.17E-04, 0.044, 3.47E-04 and 4.48E-04 respectively). COL10A1, COL11A2, PDK4 and PNPLA3 genes responsible for skeletal system morphogenesis and body growth were down regulated in JNP. This study is the first statistical analysis for the detection of DEGs from RNA-seq data generated from fat tissue sample. This analysis can be used as stepping stone to understand the difference in the genetic mechanisms that might influence the identification of novel transcripts, sequence polymorphisms, isoforms and noncoding RNAs.