Feces metagenome breed:Sus scrofa domestica
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PROVIDER: PRJNA547773 | ENA |
REPOSITORIES: ENA
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Project description:For the first time in the domestic pig, meiotic recombination along the 18 porcine autosomes was directly studied by immunolocalization of MLH1 protein. In total, 7,848 synaptonemal complexes from 436 spermatocytes were analyzed, and 13,969 recombination sites were mapped. Individual chromosomes for 113 of the 436 cells (representing 2,034 synaptonemal complexes) were identified by immunostaining and fluorescence in situ hybridization (FISH). The average total length of autosomal synaptonemal complexes per cell was 190.3 µm, with 32.0 recombination sites (crossovers), on average, per cell. The number of crossovers and the lengths of the autosomal synaptonemal complexes showed significant intra- (i.e. between cells) and inter-individual variations. The distributions of recombination sites within each chromosomal category were similar: crossovers in metacentric and submetacentric chromosomes were concentrated in the telomeric regions of the p- and q-arms, whereas two hotspots were located near the centromere and in the telomeric region of acrocentrics. Lack of MLH1 foci was mainly observed in the smaller chromosomes, particularly chromosome 18 (SSC18) and the sex chromosomes. All autosomes displayed positive interference, with a large variability between the chromosomes.
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Project description:To obtain an overview of the transcriptome landscape in developing pig skeletal muscle, 81 high-quality transcriptome libraries that covered 27 developmental stages (3 biological replicates per stage) in pig skeletal muscle were produced by strand-specific rRNA-depleted total RNA sequencing (RNA-seq). We generated 8.59 billion paired-end reads (150 bp × 2) covering 1.24 Tb of sequence for RNA-seq.
2020-09-01 | GSE157044 | GEO
Project description:Immunoglobulin (IG) gene rearrangement and expression are central to disease resistance and health maintenance in animals. The IG kappa (IGK) locus in swine (Sus scrofa domestica) contributes to approximately half of all antibody molecules, in contrast to many other Cetartiodactyla, whose members provide the majority of human dietary protein and in which kappa locus utilization is limited. The porcine IGK variable locus is 27.9 kb upstream of five IG kappa J genes (IGKJ) which are separated from a single constant gene (IGKC) by 2.8 kb. Fourteen variable genes (IGKV) were identified, of which nine are functional and two are open reading frame (ORF). Of the three pseudogenes, IGKV3-1 contains a frameshift and multiple stop codons, IGKV7-2 contains multiple stop codons, and IGKV2-5 is missing exon 2. The nine functional IGKV genes are phylogenetically related to either the human IGKV1 or IGKV2 subgroups. IGKV2 subgroup genes were found to be dominantly expressed. Polymorphisms were identified on overlapping BACs derived from the same individual such that 11 genes contain amino acid differences. The most striking allelic differences are present in IGKV2 genes, which contain as many as 16 amino acid changes between alleles, the majority of which are in complementarity determining region (CDR) 1. In addition, many IGKV2 CDR1 are shared between genes but not between alleles, suggesting extensive diversification of this locus through gene conversion.
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Project description:We have characterized the organization, complexity, and expression of the porcine (Sus scrofa domestica) immunoglobulin lambda (IGL) light chain locus, which accounts for about half of antibody light chain usage in swine, yet is nearly totally unknown. Twenty-two IGL variable (IGLV) genes were identified that belong to seven subgroups. Nine genes appear to be functional. Eight possess stop codons, frameshifts, or both, and one is missing the V-EXON. Two additional genes are missing an essential cysteine residue and are classified as ORF (open reading frame). The IGLV genes are organized in two distinct clusters, a constant (C)-proximal cluster dominated by genes similar to the human IGLV3 subgroup, and a C-distal cluster dominated by genes most similar to the human IGLV8 and IGLV5 subgroups. Phylogenetic analysis reveals that the porcine IGLV8 subgroup genes have recently expanded, suggesting a particularly effective role in immunity to porcine-specific pathogens. Moreover, expression of IGLV genes is nearly exclusively restricted to the IGLV3 and IGLV8 genes. The constant locus comprises three tandem cassettes comprised of a joining (IGLJ) gene and a constant (IGLC) gene, whereas a fourth downstream IGLJ gene has no corresponding associated IGLC gene. Comparison of individual BACs generated from the same individual revealed polymorphisms in IGLC2 and several IGLV genes, indicating that allelic variation in IGLV further expands the porcine antibody light chain repertoire.
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Project description:Previously, the benefits of early-life socialisation on later-life social development have been reported in pigs. Here we investigated the effect of pre-weaning socialisation on the later-life cognitive ability of pigs using a range of techniques. Pre-weaning, 101 piglets had access to a neighbouring pen from ~ 15 days of age and interacted with non-littermates (socialised). An additional 89 piglets remained isolated within their home pen (controls). After weaning, 100 individuals were selected for a range of cognitive tests including a food reward T-maze test, reversal learning T-maze test, a social preference T-maze test, and a puzzle box test. Performance during the food reward test was not influenced by treatment. Treatment effected improvement over the course of the reversal learning test, with controls showing a significant decrease in trial duration after the first two trials. During the social preference test, socialised pigs spent significantly more time in the presence of larger stimulus pigs than controls and were quicker to leave the middle of the maze, suggesting improved social skills. Neither sex nor treatment was observed to influence pig's ability to solve the puzzle box. Thus, overall, evidence from the social preference test suggests an effect of pre-weaning socialisation on aspects of social cognitive development.
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Project description:The aim of this study was to investigate whether the well-known positive effects of immunocastration on the behavior and welfare of pigs persist under varying environments. One hundred forty-four male pigs were studied with regard to their sex category (EM: entire males, IC: immunocastrates, BA: barrows) and housing environment (ENR: enriched, STD: standard, MIX: repeated social mixing). The vaccination of immunocastrates included two injections at the age of 12 and 22 weeks. Regardless of the housing conditions, frequencies of sexual and fighting behavior expressed by immunocastrates shifted from boar-like to barrow-like behavior after the second immunocastration vaccination (Mixed model analysis, p < 0.05). Penis biting decreased in IC after the second vaccination (Wilcoxon signed-rank tests, p = 0.036) and penile injuries were lower in IC animals compared to EM (Mixed model analysis, p < 0.001). Housing-dependent effects on behavior could also be observed in the animals at a relatively young age. Enriched housing showed a beneficial effect on play behavior (Chi-square test, p < 0.001) and the social mixing environment reduced the number of social nosing events (Mixed model analysis, p < 0.05). The positive effects of immunocastration thus are robust to all housing conditions assessed in this study.
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Project description:Porcine reproductive and respiratory syndrome virus (PRRSV) infection was diagnosed in 6 Göttingen minipigs (Sus scrofa domestica) with severe interstitial pneumonia. The virus was defined as a North American (NA) subtype virus, which is common in the commercial pig population and might be derived from a widely used attenuated live-virus vaccine in Europe. The ORF5 sequence of the isolated PRRSV was 98% identical to the vaccine virus. The affected pigs were part of a lung transplantation model and received tacrolimus and steroids as well as irradiation or CD8 antibody for immunosuppression. The likely source of the infection was pigs that were shedding the identified PRRSV, which were housed in a separate room of the same building. This case report provides evidence that a virus closely related to an attenuated live vaccine might cause severe pneumonia and death in PRRSVseronegative pigs receiving immunosuppressive treatment. We recommend strict barrier housing for immunocompromised pigs.
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Project description:Sus scrofa scrofa breed:Duroc Raw sequence reads
| PRJNA642005 | ENA
Project description:Sus scrofa scrofa breed:Pampa Raw sequence reads
| PRJNA481305 | ENA