Pan-Genomic Approaches in Lactobacillus reuteri as a Porcine Probiotic: Investigation of Host Adaptation and Antipathogenic Activity
Sign Up to like & getrecommendations! Published in 2017 at "Microbial Ecology"
DOI: 10.1007/s00248-017-0977-z
Abstract: After the introduction of a ban on the use of antibiotic growth promoters (AGPs) for livestock, reuterin-producing Lactobacillus reuteri is getting attention as an alternative to AGPs. In this study, we investigated genetic features of… read more here.
Keywords: lactobacillus reuteri; group; genomic approaches; host ... See more keywords
Pan-Genomic Illumination of Tomato Identifies Novel Gene-Trait Interactions.
Sign Up to like & getrecommendations! Published in 2019 at "Trends in plant science"
DOI: 10.1016/j.tplants.2019.08.001
Abstract: A recent study by Gao et al., (Nat. Genet., 2019) presents a tomato pan-genome that was constructed using genome sequences of 725 phylogenetically and geographically representative accessions. The study revealed 4873 genes that are absent… read more here.
Keywords: identifies novel; genomic illumination; tomato identifies; novel gene ... See more keywords
Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors
Sign Up to like & getrecommendations! Published in 2020 at "Nature Communications"
DOI: 10.1038/s41467-020-17302-5
Abstract: Our understanding of polyploid genome evolution is constrained because we cannot know the exact founders of a particular polyploid. To differentiate between founder effects and post polyploidization evolution, we use a pan-genomic approach to study… read more here.
Keywords: evolution; diploid progenitors; genome evolution; brachypodium hybridum ... See more keywords
A comparative pan-genomic analysis of 53 C. pseudotuberculosis strains based on functional domains
Sign Up to like & getrecommendations! Published in 2020 at "Journal of Biomolecular Structure and Dynamics"
DOI: 10.1080/07391102.2020.1805017
Abstract: Abstract Corynebacterium pseudotuberculosis is a pathogenic bacterium with great veterinary and economic importance. It is classified into two biovars: ovis, nitrate-negative, that causes lymphadenitis in small ruminants and equi, nitrate-positive, causing ulcerative lymphangitis in equines.… read more here.
Keywords: analysis; pseudotuberculosis strains; pseudotuberculosis; functional domains ... See more keywords
PRAWNS: compact pan-genomic features for whole-genome population genomics
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac844
Abstract: Abstract Motivation Scientists seeking to understand the genomic basis of bacterial phenotypes, such as antibiotic resistance, today have access to an unprecedented number of complete and nearly complete genomes. Making sense of these data requires… read more here.
Keywords: pan genomic; genomic features; whole genome; prawns compact ... See more keywords
Exploring Frequented Regions in Pan-Genomic Graphs
Sign Up to like & getrecommendations! Published in 2019 at "IEEE/ACM Transactions on Computational Biology and Bioinformatics"
DOI: 10.1109/tcbb.2018.2864564
Abstract: We consider the problem of identifying regions within a pan-genome De Bruijn graph that are traversed by many sequence paths. We define such regions and the subpaths that traverse them as frequented regions (FRs). In… read more here.
Keywords: exploring frequented; biology; frequented regions; regions pan ... See more keywords
Comparative pan-genomic analysis of 51 Renibacterium salmoninarum indicates heterogeneity in the principal virulence factor, the 57 kDa protein.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of fish diseases"
DOI: 10.1111/jfd.13653
Abstract: Renibacterium salmoninarum, a Gram-positive intracellular pathogen, is the causative agent of bacterial kidney disease (BKD), the impacts of which are high mortalities and economic losses for the salmon industry. This study provides novel analyses for… read more here.
Keywords: salmoninarum; pan genomic; analysis; virulence ... See more keywords
Pan-genomic open reading frames: A potential supplement of single nucleotide polymorphisms in estimation of heritability and genomic prediction
Sign Up to like & getrecommendations! Published in 2020 at "PLoS Genetics"
DOI: 10.1371/journal.pgen.1008995
Abstract: Pan-genomic open reading frames (ORFs) potentially carry protein-coding gene or coding variant information in a population. In this study, we suggest that pan-genomic ORFs are promising to be utilized in estimation of heritability and genomic… read more here.
Keywords: genomic prediction; heritability genomic; prediction; pan genomic ... See more keywords
An in silico pan-genomic probe for the molecular traits behind Lactobacillus ruminis gut autochthony
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DOI: 10.1371/journal.pone.0175541
Abstract: As an ecological niche, the mammalian intestine provides the ideal habitat for a variety of bacterial microorganisms. Purportedly, some commensal genera and species offer a beneficial mix of metabolic, protective, and structural processes that help… read more here.
Keywords: traits behind; lactobacillus ruminis; genomic probe; gut autochthony ... See more keywords
A Complete Genome of Nocardia terpenica NC_YFY_NT001 and Pan-Genomic Analysis Based on Different Sources of Nocardia spp. Isolates Reveal Possibly Host-Related Virulence Factors
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DOI: 10.2147/idr.s384673
Abstract: Objective We aimed to identify the possible virulence genes associated with Nocardia NC_YFY_NT001 isolated by ourselves and other Nocardia spp. Methods The genome of Nocardia terpenica NC_YFY_NT001 was completed by using PacBio and Illumina platforms.… read more here.
Keywords: yfy nt001; nocardia terpenica; pan genomic; genomic analysis ... See more keywords
Pan-Genomic and Transcriptomic Analyses of Marine Pseudoalteromonas agarivorans Hao 2018 Revealed Its Genomic and Metabolic Features
Sign Up to like & getrecommendations! Published in 2022 at "Marine Drugs"
DOI: 10.3390/md20040248
Abstract: The genomic and carbohydrate metabolic features of Pseudoalteromonas agarivorans Hao 2018 (P. agarivorans Hao 2018) were investigated through pan-genomic and transcriptomic analyses, and key enzyme genes that may encode the process involved in its extracellular… read more here.
Keywords: metabolic features; pan genomic; transcriptomic analyses; hao 2018 ... See more keywords