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For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe(More)
BACKGROUND The recent completion of the swine genome sequencing project and development of a high density porcine SNP array has made genome-wide association (GWA) studies feasible in pigs. METHODOLOGY/PRINCIPAL FINDINGS Using Illumina's PorcineSNP60 BeadChip, we performed a pilot GWA study in 820 commercial female pigs phenotyped for backfat, loin muscle(More)
The chicken (Gallus gallus) is an important model organism that bridges the evolutionary gap between mammals and other vertebrates. Copy number variations (CNVs) are a form of genomic structural variation widely distributed in the genome. CNV analysis has recently gained greater attention and momentum, as the identification of CNVs can contribute to a(More)
Through posttranscriptional gene regulation, microRNA (miRNA) is linked to a wide variety of biological processes, including adipogenesis and lipid metabolism. Although miRNAs in mammalian adipogenesis have been worked on extensively, their study in chicken adipogenesis is still very limited. To find miRNAs potentially important for chicken preadipocyte(More)
Scrotal hernia in pigs is a complex trait likely affected by genetic and environmental factors. A large-scale association analysis of positional and functional candidate genes was conducted in four previously identified genomic regions linked to hernia susceptibility on Sus scrofa chromosomes 2 and 12, as well as the fifth region around 67 cM on chromosome(More)
Peroxinectin (PX) with cell adhesion and peroxidase activities is important in invertebrate immune responses. We identified a novel PX homolog from Scylla paramamosain (designated as Sp-PX) through transcriptome sequencing. The full-length of cDNA sequence was 3,165 bp. And there was a peroxidase domain in the deduced protein sequence. A cell-adhesive(More)
Most studies on the origin and evolution of microRNA in the human genome have been focused on its relationship with repetitive elements and segmental duplications. However, duplication events at a smaller scale (<1 kb) could also contribute to microRNA expansion, as demonstrated in this study. Using comparative genome analysis and bioinformatics methods, we(More)
Ordinal regression is to predict categories of ordinal scale and it has wide applications in many domains where the human evaluation plays a major role. So far several algorithms have been proposed to tackle ordinal regression problems from a machine learning perspective. However, most of these algorithms only seek one direction where the projected samples(More)
Meiotic maturation of mammalian oocytes is a precisely orchestrated and complex process. Dimethyl sulfoxide (DMSO), a widely used solvent, drug, and cryoprotectant, is capable of disturbing asymmetric cytokinesis of oocyte meiosis in mice. However, in pigs, DMSO's effect on oocyte meiosis still remains unknown. We aimed to evaluate if DMSO treatment will(More)
Crayfish has become one of the most important farmed aquatic species in China due to its excellent disease resistance against bacteria and viruses. However, the antiviral mechanism of crayfish is still not very clear. In the present study, many high-quality sequence reads from crayfish intestine were obtained using Illumina-based transcriptome sequencing.(More)