Dataset Information

Draft Genome Sequence of the Bacteriocinogenic Strain Enterococcus faecalis DBH18, Isolated from Mallard Ducks (Anas platyrhynchos).

ABSTRACT: Here, we report the draft genome sequence of Enterococcus faecalis DBH18, a bacteriocinogenic lactic acid bacterium (LAB) isolated from mallard ducks (Anas platyrhynchos). The assembly contains 2,836,724 bp, with a G+C content of 37.6%. The genome is predicted to contain 2,654 coding DNA sequences (CDSs) and 50 RNAs.

SUBMITTER: Arbulu S

PROVIDER: S-EPMC4945798 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature

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Draft Genome Sequence of the Bacteriocinogenic Strain Enterococcus faecalis DBH18, Isolated from Mallard Ducks (Anas platyrhynchos).

Arbulu Sara S Jimenez Juan J JJ Borrero Juan J Sánchez Jorge J Frantzen Cyril C Herranz Carmen C Nes Ingolf F IF Cintas Luis M LM Diep Dzung B DB Hernández Pablo E PE

Genome announcements 20160714 4

Here, we report the draft genome sequence of Enterococcus faecalis DBH18, a bacteriocinogenic lactic acid bacterium (LAB) isolated from mallard ducks (Anas platyrhynchos). The assembly contains 2,836,724 bp, with a G+C content of 37.6%. The genome is predicted to contain 2,654 coding DNA sequences (CDSs) and 50 RNAs. ...[more]

PMID: 27417838

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Project description:ObjectiveCage rearing has critical implications for the laying duck industry because it is convenient for feeding and management. However, caging stress is a type of chronic stress that induces maladaptation. Environmental stress responses have been extensively studied, but no detailed information is available about the comprehensive changes in plasma metabolites at different stages of caging stress in ducks. We designed this experiment to analyze the effects of caging stress on performance parameters and oxidative stress indexes in ducks.MethodsLiquid chromatography tandem mass spectrometry (LC/MS-MS) was used to determine the changes in metabolites in duck plasma at 5 (CR5), 10 (CR10), and 15 (CR15) days after cage rearing and traditional breeding (TB). The associated pathways of differentially altered metabolites were analyzed using Kyoto encyclopedia of genes and genomes (KEGG) database.ResultsThe results of this study indicate that caging stress decreased performance parameters, and the plasma total superoxide dismutase levels were increased in the CR10 group compared with the other groups. In addition, 1,431 metabolites were detected. Compared with the TB group, 134, 381, and 190 differentially produced metabolites were identified in the CR5, CR10, and CR15 groups, respectively. The results of principal component analysis (PCA) show that the selected components sufficiently distinguish the TB group and CR10 group. KEGG analysis results revealed that the differentially altered metabolites in duck plasma from the CR5 and TB groups were mainly associated with ovarian steroidogenesis, biosynthesis of unsaturated fatty acids, and phenylalanine metabolism.ConclusionIn this study, the production performance, blood indexes, number of metabolites and PCA were compared to determine effect of the caging stress stage on ducks. We inferred from the experimental results that caging-stressed ducks were in the sensitive phase in the first 5 days after caging, caging for approximately 10 days was an important transition phase, and then the duck continually adapted.

Project description:BackgroundNext generation sequencing technologies allow to obtain at low cost the genomic sequence information that currently lacks for most economically and ecologically important organisms. For the mallard duck genomic data is limited. The mallard is, besides a species of large agricultural and societal importance, also the focal species when it comes to long distance dispersal of Avian Influenza. For large scale identification of SNPs we performed Illumina sequencing of wild mallard DNA and compared our data with ongoing genome and EST sequencing of domesticated conspecifics. This is the first study of its kind for waterfowl.ResultsMore than one billion base pairs of sequence information were generated resulting in a 16× coverage of a reduced representation library of the mallard genome. Sequence reads were aligned to a draft domesticated duck reference genome and allowed for the detection of over 122,000 SNPs within our mallard sequence dataset. In addition, almost 62,000 nucleotide positions on the domesticated duck reference showed a different nucleotide compared to wild mallard. Approximately 20,000 SNPs identified within our data were shared with SNPs identified in the sequenced domestic duck or in EST sequencing projects. The shared SNPs were considered to be highly reliable and were used to benchmark non-shared SNPs for quality. Genotyping of a representative sample of 364 SNPs resulted in a SNP conversion rate of 99.7%. The correlation of the minor allele count and observed minor allele frequency in the SNP discovery pool was 0.72.ConclusionWe identified almost 150,000 SNPs in wild mallards that will likely yield good results in genotyping. Of these, ~101,000 SNPs were detected within our wild mallard sequences and ~49,000 were detected between wild and domesticated duck data. In the ~101,000 SNPs we found a subset of ~20,000 SNPs shared between wild mallards and the sequenced domesticated duck suggesting a low genetic divergence. Comparison of quality metrics between the total SNP set (122,000 + 62,000 = 184,000 SNPs) and the validated subset shows similar characteristics for both sets. This indicates that we have detected a large amount (~150,000) of accurately inferred mallard SNPs, which will benefit bird evolutionary studies, ecological studies (e.g. disentangling migratory connectivity) and industrial breeding programs.

Dataset Information

Draft Genome Sequence of the Bacteriocinogenic Strain Enterococcus faecalis DBH18, Isolated from Mallard Ducks (Anas platyrhynchos).

Publications

Draft Genome Sequence of the Bacteriocinogenic Strain Enterococcus faecalis DBH18, Isolated from Mallard Ducks (Anas platyrhynchos).

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