Refined Systematics of the Genus Rhodococcus Based on Whole Genome Analyses

Comparative whole-genome analyses have demonstrated that horizontal gene transfer (HGT) provides a significant contribution to prokaryotic genome innovation. The evolution of specific prokaryotes is therefore tightly linked to the environment in which they live and the communal pool of genes available within that environment. Here we use the term supergenome to describe the set of all genes that a prokaryotic ‘individual’ can draw on within a particular environmental setting. Conjugative plasmids can be considered particularly successful entities within the communal pool, which have enabled HGT over large taxonomic distances. These plasmids are collections of discrete regions of genes that function as ‘backbone modules’ to undertake different aspects of overall plasmid maintenance and propagation. Conjugative plasmids often carry suites of ‘accessory elements’ that contribute adaptive traits to the hosts and, potentially, other resident prokaryotes within specific environmental niches. Insight into the evolution of plasmid modules therefore contributes to our knowledge of gene dissemination and evolution within prokaryotic communities. This communal pool provides the prokaryotes with an important mechanistic framework for obtaining adaptability and functional diversity that alleviates the need for large genomes of specialized ‘private genes’.

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Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI)

Science ◽

10.1126/science.aak9787 ◽

2017 ◽

Vol 356 (6334) ◽

pp. 189-194 ◽

Cited By ~ 138

Author(s):

Chongyi Chen ◽

Dong Xing ◽

Longzhi Tan ◽

Heng Li ◽

Guangyu Zhou ◽

...

Keyword(s):

Single Cell ◽

Whole Genome ◽

Linear Amplification ◽

Transposon Insertion ◽

Genome Analyses

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Whole genome sequence and comparative genome analyses of multi-resistant Staphylococcus warneri GD01 isolated from a diseased pig in China

PLoS ONE ◽

10.1371/journal.pone.0233363 ◽

2020 ◽

Vol 15 (5) ◽

pp. e0233363

Author(s):

Canying Liu ◽

Xianjie Zhao ◽

Honglin Xie ◽

Xi Zhang ◽

Kangjian Li ◽

...

Keyword(s):

Genome Sequence ◽

Whole Genome Sequence ◽

Whole Genome ◽

Comparative Genome ◽

Staphylococcus Warneri ◽

Genome Analyses

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6 Translating genomics for clinical benefit

Postgraduate Medical Journal ◽

10.1136/postgradmedj-2019-fpm.6 ◽

2019 ◽

Vol 95 (1130) ◽

pp. 686.3-686

Author(s):

Mark Caulfield

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genomic Medicine ◽

Health Gain ◽

Annual Review ◽

Whole Genome ◽

Department Of Health ◽

Data Points ◽

Genome Analyses ◽

The Uk

The UK 100,000 Genomes Project has focussed on transforming genomic medicine in the National Health Service using whole genome sequencing in rare disease, cancer and infection. Genomics England partnering with the NHS established 13 Genomic Medicine Centres, the NHS whole genome sequencing centre and the Genomics England Clinical Interpretation Partnership (3337 researchers from 24 countries). We sequenced the 100,000th genome on the 5th December 2019 and completed an initial analysis for participants in July 2019. Alongside these genomes we have assembled a longitudinal life course dataset for research and diagnosis including 2.6 billion clinical data points for the 3000 plus researchers to work on to drive up the value of the genomes for direct healthcare. In parallel we have partnered the NHS to establish one of the world’s most advanced Genomic Medicine Service where we re-evaluated 300,000 genomic tests and upgraded 25% of tests to newer technologies with an annual review. The Department of Health have announced the ambition to undertake 5 million genome analyses over the next 5 years focused on new areas tractable to health gain.

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Whole genome analyses reveal no pathogenetic single nucleotide or structural differences between monozygotic twins discordant for amyotrophic lateral sclerosis

Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration ◽

10.3109/21678421.2015.1040029 ◽

2015 ◽

Vol 16 (5-6) ◽

pp. 385-392 ◽

Cited By ~ 18

Author(s):

Karyn Meltz Steinberg ◽

Thomas J. Nicholas ◽

Daniel C. Koboldt ◽

Bing Yu ◽

Elaine Mardis ◽

...

Keyword(s):

Amyotrophic Lateral Sclerosis ◽

Monozygotic Twins ◽

Whole Genome ◽

Single Nucleotide ◽

Structural Differences ◽

Genome Analyses ◽

Lateral Sclerosis

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Genomics in Bacterial Taxonomy: Impact on the Genus Pseudomonas

Genes ◽

10.3390/genes11020139 ◽

2020 ◽

Vol 11 (2) ◽

pp. 139 ◽

Cited By ~ 12

Author(s):

Jorge Lalucat ◽

Magdalena Mulet ◽

Margarita Gomila ◽

Elena García-Valdés

Keyword(s):

New Technologies ◽

Genome Comparison ◽

Whole Genome ◽

Bacterial Taxonomy ◽

Phylogenetic Groups ◽

Genomic Species ◽

Subspecies Level ◽

Taxonomic Approach ◽

Phylogenomic Analyses ◽

Genome Analyses

The introduction of genomics is profoundly changing current bacterial taxonomy. Phylogenomics provides accurate methods for delineating species and allows us to infer the phylogeny of higher taxonomic ranks as well as those at the subspecies level. We present as a model the currently accepted taxonomy of the genus Pseudomonas and how it can be modified when new taxonomic methodologies are applied. A phylogeny of the species in the genus deduced from analyses of gene sequences or by whole genome comparison with different algorithms allows three main conclusions: (i) several named species are synonymous and have to be reorganized in a single genomic species; (ii) many strains assigned to known species have to be proposed as new genomic species within the genus; and (iii) the main phylogenetic groups defined by 4-, 100- and 120-gene multilocus sequence analyses are concordant with the groupings in the whole genome analyses. Moreover, the boundaries of the genus Pseudomonas are also discussed based on phylogenomic analyses in relation to other genera in the family Pseudomonadaceae. The new technologies will result in a substantial increase in the number of species and probably split the current genus into several genera or subgenera, although these classifications have to be supported by a polyphasic taxonomic approach.

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First Complete Coding Sequence of a Venezuelan Equine Encephalitis Virus Strain Isolated from an Equine Encephalitis Case in Costa Rica

Microbiology Resource Announcements ◽

10.1128/mra.00672-19 ◽

2019 ◽

Vol 8 (36) ◽

Author(s):

Bernal León ◽

Carlos Jiménez ◽

Rocío González ◽

Lisbeth Ramirez-Carvajal

Keyword(s):

Costa Rica ◽

Venezuelan Equine Encephalitis Virus ◽

Costa Rican ◽

Encephalitis Virus ◽

Whole Genome ◽

Venezuelan Equine Encephalitis ◽

Coding Sequence ◽

Equine Encephalitis Virus ◽

The Pacific ◽

Genome Analyses

The first complete coding sequence of the Venezuelan equine encephalitis virus IE, isolated from a Costa Rican mare with severe encephalitis, was confirmed by histological and viral whole-genome analyses. The isolated virus grouped in the Pacific cluster.

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