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The Chinese Qingyu pig is a typical domestic fatty pig breed and an invaluable indigenous genetic resource in China. Compared with the Landrace pig, the Qingyu pig has unique meat characteristics, including muscle development, intramuscular fat, and other meat quality traits. At present, few studies have explored epigenetic differences due to DNA methylation between the Qingyu pig and the Landrace pig. In this study, 30 Qingyu pigs and 31 Landrace pigs were subjected to reduced representation bisulfite sequencing (RRBS). Genome-wide differential DNA methylation analysis was conducted. Six genomic regions, including regions on Sus scrofa chromosome (SSC) 1: 266.09-274.23 Mb, SSC5: 0.88-10.68 Mb, SSC8: 41.23-48.51 Mb, SSC12: 45.43-54.38 Mb, SSC13: 202.15-207.95 Mb, and SSC14: 126.43-139.85 Mb, were regarded as key regions that may be associated with phenotypic differences between the Qingyu pig and the Landrace pig. Furthermore, according to further analysis, five differentially methylated genes (ADCY1, FUBP3, GRIN2B, KIT, and PIK3R6) were identified as key candidate genes that might be associated with meat characteristics. Our findings provide new insights into the differences in DNA methylation between the Qingyu pig and the Landrace pig. These results enrich the epigenetic research of the Chinese Qingyu pig. Key words: DNA methylation, reduced representation bisulfite sequencing, Qingyu pig, Landrace pig. La race porcine chinoise Qingyu est une race domestique typique a forte teneur en gras et constitue une precieuse ressource genetique indigene en Chine. Compare au porc Landrace, le Qingyu presente des caracteristiques uniques au niveau de sa viande, dont le developpement du muscle, le gras intramusculaire et d'autres aspects de la qualite de la viande. A ce jour, peu d'etudes ont explore les differences epigenetiques due a la methylation de l'ADN entre les races Qingyu et Landrace. Dans ce travail, 30 porcs Qingyu et 31 porcs Landrace ont ete examines au moyen de sequencage au bisulfite d'une representation reduite du genome (RRBS). Une analyse pangenomique de la methylation differentielle a ete realisee. Six regions du genome du Sus scrofa (SSC1 : 266.09-274.23 Mb, SSC5 : 0.88-10.68 Mb, SSC8 : 41.23-48.51 Mb, SSC12 : 45.43-54.38 Mb, SSC13 : 202.15-207.95 Mb et SSC14 : 126.43-139.85 Mb) ont ete trouvees comme etant des regions cles possiblement associees aux differences phenotypiques entre les races Qingyu et Landrace. De plus, sur la base d'analyses plus approfondies, cinq genes affichant une methylation differentielle (ADCY1, FUBP3, GRIN2B, KIT, PIK3R6) sont presentes comme etant des genes cles associes aux caracteristiques de la viande. Ces resultats apportent un nouvel eclairage sur les differences de methylation de l'ADN entre les races Qingyu et Landrace. Ces travaux viennent alimenter la recherche epigenetique sur les porcs chinois Qingyu. [Traduit par la Redaction] Mots-cles : methylation de l'ADN, sequencage bisulfite a representation reduite, porcs Qingyu, porc Landrace., Introduction Pork is an important meat resource. The average intake of meat, especially pork, has continued to increase in China (He et al. 2016). The Qingyu pig is a typical [...]

Streptococcus pneumoniae is an important human pathogen that often carries temperate bacteriophages. As part of a program to characterize the genetic makeup of prophages associated with clinical strains and to assess the potential roles that they play in the biology and pathogenesis in their host, we performed comparative genomic analysis of 10 temperate pneumococcal phages. All of the genomes are organized into five major gene clusters: lysogeny, replication, packaging, morphogenesis, and lysis clusters. All of the phage particles observed showed a Siphoviridae morphology. The only genes that are well conserved in all the genomes studied are those involved in the integration and the lysis of the host in addition to two genes, of unknown function, within the replication module. We observed that a high percentage of the open reading frames contained no similarities to any sequences catalogued in public databases; however, genes that were homologous to known phage virulence genes, including the pblB gene of Streptococcus miffs and the vapE gene of Dicheiobacter nodosus, were also identified. Interestingly, bioinformatic tools showed the presence of a toxin-antitoxin system in the phage [phi]Spn-6, and this represents the first time that an addition system in a pneumophage has been identified. Collectively, the temperate pneumophages contain a diverse set of genes with various levels of similarity among them.

A set of lactobacilli were investigated by polyphasic analysis. Multilocus sequence analysis, DNA typing, microarray analysis, and in silico whole-genome alignments provided a remarkably consistent pattern of similarity within the Lactobacillus acidophilus complex. On microarray analysis, 17 and 5% of the genes from Lactobacillus johnsonii strain NCC533 represented variable and strain-specific genes, respectively, when tested against four independent isolates of L. johnsonii. When projected on the NCC533 genome map, about 10 large clusters of variable genes were identified, and they were enriched around the terminus of replication. A quarter of the variable genes and two-thirds of the strain-specific genes were associated with mobile DNA. Signatures for horizontal gene transfer and modular evolution were found in prophages and in DNA from the exopolysaccharide biosynthesis duster. On microarray hybridizations, Lactobacillus gasseri strains showed a shift to significantly lower fluorescence intensities than the L. johnsonii test strains, and only genes encoding very conserved cellular functions from L. acidophilus hybridized to the L. johnsonii array. In-silico comparative genomics showed extensive protein sequence similarity and genome synteny of L. johnsonii with L. gasseri, L. acidophilus, and Lactobacillus delbrueckii; moderate synteny with Lactobacillus casei; and scattered X-type sharing of protein sequence identity with the other sequenced lactobacilli. The observation of a stepwise decrease in similarity between the members of the L. acidophilus group suggests a strong element of vertical evolution in a natural phylogenetic group. Modern whole-genome-based techniques are thus a useful adjunct to the clarification of taxonomical relationships in problematic bacterial groups.