Pangenome graphs
Low-cost whole-genome assembly has enabled the collection of haplotype-resolved
pangenomes for numerous organisms. In turn, this technological change is encouraging the …
pangenomes for numerous organisms. In turn, this technological change is encouraging the …
Producing polished prokaryotic pangenomes with the Panaroo pipeline
Population-level comparisons of prokaryotic genomes must take into account the substantial
differences in gene content resulting from horizontal gene transfer, gene duplication and …
differences in gene content resulting from horizontal gene transfer, gene duplication and …
Population genomics confirms acquisition of drug-resistant Aspergillus fumigatus infection by humans from the environment
Infections caused by the fungal pathogen Aspergillus fumigatus are increasingly resistant to
first-line azole antifungal drugs. However, despite its clinical importance, little is known …
first-line azole antifungal drugs. However, despite its clinical importance, little is known …
Current status of pan-genome analysis for pathogenic bacteria
Highlights•Wealth of genome data are making pan-genome analysis increasingly
possible.•Pan-genome analysis is an effective approach to understand pathogenic …
possible.•Pan-genome analysis is an effective approach to understand pathogenic …
Genomic features of bacterial adaptation to plants
Plants intimately associate with diverse bacteria. Plant-associated bacteria have ostensibly
evolved genes that enable them to adapt to plant environments. However, the identities of …
evolved genes that enable them to adapt to plant environments. However, the identities of …
A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments
Metagenomic binning is the step in building metagenome-assembled genomes (MAGs)
when sequences predicted to originate from the same genome are automatically grouped …
when sequences predicted to originate from the same genome are automatically grouped …
Resistance gene cloning from a wild crop relative by sequence capture and association genetics
Disease resistance (R) genes from wild relatives could be used to engineer broad-spectrum
resistance in domesticated crops. We combined association genetics with R gene …
resistance in domesticated crops. We combined association genetics with R gene …
Fecal IgA levels are determined by strain-level differences in Bacteroides ovatus and are modifiable by gut microbiota manipulation
Fecal IgA production depends on colonization by a gut microbiota. However, the bacterial
strains that drive gut IgA production remain largely unknown. Here, we assessed the IgA …
strains that drive gut IgA production remain largely unknown. Here, we assessed the IgA …
Phylogenetic background and habitat drive the genetic diversification of Escherichia coli
Escherichia coli is mostly a commensal of birds and mammals, including humans, where it
can act as an opportunistic pathogen. It is also found in water and sediments. We …
can act as an opportunistic pathogen. It is also found in water and sediments. We …
Hypervirulent Listeria monocytogenes clones' adaption to mammalian gut accounts for their association with dairy products
MM Maury, H Bracq-Dieye, L Huang, G Vales… - Nature …, 2019 - nature.com
Listeria monocytogenes (Lm) is a major human and animal foodborne pathogen. Here we
show that hypervirulent Lm clones, particularly CC1, are strongly associated with dairy …
show that hypervirulent Lm clones, particularly CC1, are strongly associated with dairy …