scholarly journals The Ever-Expanding Pseudomonas Genus: Description of 43 New Species and Partition of the Pseudomonas Putida Group

2021 ◽  
Author(s):  
Léa Girard ◽  
Cédric Lood ◽  
Monica Höfte ◽  
Peter Vandamme ◽  
Hassan Rokni-Zadeh ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Whole Genome ◽  
Genome Sequences ◽  
Taxonomic Assignment ◽  
Metabolic Potential ◽  
Rpod Gene ◽  
Integrative Studies ◽  
Pseudomonas Species ◽  
Type Strains ◽  
Selection Of

The genus Pseudomonas hosts an extensive genetic diversity and is one of the largest genera among Gram-negative bacteria. Type strains of Pseudomonas are well-known to represent only a small fraction of this diversity and the number of available Pseudomonas genome sequences is increasing rapidly. Consequently, new Pseudomonas species are regularly reported and the number of species within the genus is in constant evolution. In this study, whole genome se-quencing enabled us to define 43 new Pseudomonas species and to provide an update of the Pseu-domonas evolutionary and taxonomic relationships. Phylogenies based on the rpoD gene and whole genome sequences, including 316 and 313 type strains of Pseudomonas, respectively, re-vealed sixteen groups of Pseudomonas and justified the partitioning of the P. putida group into fifteen subgroups. Pairwise average nucleotide identities were calculated between type strains and a selection of 60 genomes of non-type strains of Pseudomonas. Forty-one strains were incor-rectly assigned at the species level and among those, 19 strains were shown to represent an addi-tional 13 new Pseudomonas species that remain to be formally classified. This work pinpoints the importance of correct taxonomic assignment and phylogenetic classification in order to perform integrative studies linking genetic diversity, lifestyle and metabolic potential of Pseudomonas spp.

scholarly journals The Ever-Expanding Pseudomonas Genus: Description of 43 New Species and Partition of the Pseudomonas putida Group

2021 ◽  
Vol 9 (8) ◽  
pp. 1766
Author(s):  
Léa Girard ◽  
Cédric Lood ◽  
Monica Höfte ◽  
Peter Vandamme ◽  
Hassan Rokni-Zadeh ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Clusters ◽  
Whole Genome ◽  
Genome Sequences ◽  
Taxonomic Assignment ◽  
Metabolic Potential ◽  
Cyclic Lipopeptide ◽  
Rpod Gene ◽  
Pseudomonas Species ◽  
Type Strains

The genus Pseudomonas hosts an extensive genetic diversity and is one of the largest genera among Gram-negative bacteria. Type strains of Pseudomonas are well known to represent only a small fraction of this diversity and the number of available Pseudomonas genome sequences is increasing rapidly. Consequently, new Pseudomonas species are regularly reported and the number of species within the genus is constantly evolving. In this study, whole genome sequencing enabled us to define 43 new Pseudomonas species and provide an update of the Pseudomonas evolutionary and taxonomic relationships. Phylogenies based on the rpoD gene and whole genome sequences, including, respectively, 316 and 313 type strains of Pseudomonas, revealed sixteen groups of Pseudomonas and, together with the distribution of cyclic lipopeptide biosynthesis gene clusters, enabled the partitioning of the P. putida group into fifteen subgroups. Pairwise average nucleotide identities were calculated between type strains and a selection of 60 genomes of non-type strains of Pseudomonas. Forty-one strains were incorrectly assigned at the species level and among these, 19 strains were shown to represent an additional 13 new Pseudomonas species that remain to be formally classified. This work pinpoints the importance of correct taxonomic assignment and phylogenetic classification in order to perform integrative studies linking genetic diversity, lifestyle, and metabolic potential of Pseudomonas spp.

scholarly journals Design and performance of a bovine 200 k SNP chip developed for endangered German Black Pied cattle (DSN)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Guilherme B. Neumann ◽  
Paula Korkuć ◽  
Danny Arends ◽  
Manuel J. Wolf ◽  
Katharina May ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Association Studies ◽  
Bos Indicus ◽  
Diversity Management ◽  
Whole Genome Sequencing Data ◽  
General Interest ◽  
Whole Genome ◽  
Sequencing Data ◽  
Snp Chip ◽  
Selection Of

Abstract Background German Black Pied cattle (DSN) are an endangered dual-purpose breed which was largely replaced by Holstein cattle due to their lower milk yield. DSN cattle are kept as a genetic reserve with a current herd size of around 2500 animals. The ability to track sequence variants specific to DSN could help to support the conservation of DSN’s genetic diversity and to provide avenues for genetic improvement. Results Whole-genome sequencing data of 304 DSN cattle were used to design a customized DSN200k SNP chip harboring 182,154 variants (173,569 SNPs and 8585 indels) based on ten selection categories. We included variants of interest to DSN such as DSN unique variants and variants from previous association studies in DSN, but also variants of general interest such as variants with predicted consequences of high, moderate, or low impact on the transcripts and SNPs from the Illumina BovineSNP50 BeadChip. Further, the selection of variants based on haplotype blocks ensured that the whole-genome was uniformly covered with an average variant distance of 14.4 kb on autosomes. Using 300 DSN and 162 animals from other cattle breeds including Holstein, endangered local cattle populations, and also a Bos indicus breed, performance of the SNP chip was evaluated. Altogether, 171,978 (94.31%) of the variants were successfully called in at least one of the analyzed breeds. In DSN, the number of successfully called variants was 166,563 (91.44%) while 156,684 (86.02%) were segregating at a minor allele frequency > 1%. The concordance rate between technical replicates was 99.83 ± 0.19%. Conclusion The DSN200k SNP chip was proved useful for DSN and other Bos taurus as well as one Bos indicus breed. It is suitable for genetic diversity management and marker-assisted selection of DSN animals. Moreover, variants that were segregating in other breeds can be used for the design of breed-specific customized SNP chips. This will be of great value in the application of conservation programs for endangered local populations in the future.

scholarly journals Evolution and genetic diversity of SARSCoV-2 in Africa using whole genome sequences

2020 ◽  
Author(s):  
Babatunde Olarenwaju Motayo ◽  
Olukunle Oluwapamilerin Oluwasemowo ◽  
Babatunde Adebiyi Olusola ◽  
Paul Akiniyi Akinduti ◽  
Olamide T Arege ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Whole Genome ◽  
Genome Sequences

scholarly journals Draft Genome Sequences of 64 Type Strains of 50 Species and 25 Subspecies of the Genus Staphylococcus Rosenbach 1884

2019 ◽  
Vol 8 (17) ◽  
Author(s):  
Kevin Cole ◽  
Dona Foster ◽  
Julie E. Russell ◽  
Tanya Golubchik ◽  
Martin Llewelyn ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Draft Genome ◽  
Whole Genome ◽  
Genome Sequences ◽  
Accurate Identification ◽  
Access To Data ◽  
Type Strains

Members of the genus Staphylococcus have been isolated from humans, animals, and the environment. Accurate identification with whole-genome sequencing requires access to data derived from type strains.

scholarly journals Whole-Genome Characterization and Genotyping of Global WU Polyomavirus Strains

2010 ◽  
Vol 84 (12) ◽  
pp. 6229-6234 ◽  
Author(s):  
Seweryn Bialasiewicz ◽  
Rebecca Rockett ◽  
David W. Whiley ◽  
Yacine Abed ◽  
Tobias Allander ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Discriminatory Power ◽  
Whole Genome ◽  
Nucleotide Variation ◽  
Genome Sequences ◽  
Typing Method ◽  
Genome Characterization ◽  
Wu Polyomavirus

ABSTRACT Exploration of the genetic diversity of WU polyomavirus (WUV) has been limited in terms of the specimen numbers and particularly the sizes of the genomic fragments analyzed. Using whole-genome sequencing of 48 WUV strains collected in four continents over a 5-year period and 16 publicly available whole-genome sequences, we identified three main WUV clades and five subtypes, provisionally termed Ia, Ib, Ic, II, IIIa, and IIIb. Overall nucleotide variation was low (0 to 1.2%). The discriminatory power of the previous VP2 fragment typing method was found to be limited, and a new, larger genotyping region within the VP2/1 interface was proposed.

scholarly journals Draft Whole-Genome Sequences of 18 Flavobacterium spp

2017 ◽  
Vol 5 (46) ◽  
Author(s):  
Cynthia B. Stine ◽  
Cong Li ◽  
Tina C. Crosby ◽  
Nicholas R. Hasbrouck ◽  
Claudia Lam ◽  
...  
Keyword(s):  
Whole Genome ◽  
Genome Sequences ◽  
Fish Gill ◽  
Species Type ◽  
Gill Disease ◽  
Type Strains

ABSTRACT We report here the draft whole-genome sequences for 18 Flavobacterium species type strains that have historically been associated with fish gill disease.

scholarly journals Within-Host Variations of Human Papillomavirus Reveal APOBEC Signature Mutagenesis in the Viral Genome

2018 ◽  
Vol 92 (12) ◽  
pp. e00017-18 ◽  
Author(s):  
Yusuke Hirose ◽  
Mamiko Onuki ◽  
Yuri Tenjimbayashi ◽  
Seiichiro Mori ◽  
Yoshiyuki Ishii ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cervical Cancer ◽  
Deep Sequencing ◽  
Viral Genome ◽  
Reference Sequence ◽  
Characteristic Change ◽  
Whole Genome ◽  
Cervical Carcinogenesis ◽  
Genome Sequences ◽  
Host Genetic

ABSTRACTPersistent infection with oncogenic human papillomaviruses (HPVs) causes cervical cancer, accompanied by the accumulation of somatic mutations into the host genome. There are concomitant genetic changes in the HPV genome during viral infection; however, their relevance to cervical carcinogenesis is poorly understood. Here, we explored within-host genetic diversity of HPV by performing deep-sequencing analyses of viral whole-genome sequences in clinical specimens. The whole genomes of HPV types 16, 52, and 58 were amplified by type-specific PCR from total cellular DNA of cervical exfoliated cells collected from patients with cervical intraepithelial neoplasia (CIN) and invasive cervical cancer (ICC) and were deep sequenced. After constructing a reference viral genome sequence for each specimen, nucleotide positions showing changes with >0.5% frequencies compared to the reference sequence were determined for individual samples. In total, 1,052 positions of nucleotide variations were detected in HPV genomes from 151 samples (CIN1,n= 56; CIN2/3,n= 68; ICC,n= 27), with various numbers per sample. Overall, C-to-T and C-to-A substitutions were the dominant changes observed across all histological grades. While C-to-T transitions were predominantly detected in CIN1, their prevalence was decreased in CIN2/3 and fell below that of C-to-A transversions in ICC. Analysis of the trinucleotide context encompassing substituted bases revealed that TpCpN, a preferred target sequence for cellular APOBEC cytosine deaminases, was a primary site for C-to-T substitutions in the HPV genome. These results strongly imply that the APOBEC proteins are drivers of HPV genome mutation, particularly in CIN1 lesions.IMPORTANCEHPVs exhibit surprisingly high levels of genetic diversity, including a large repertoire of minor genomic variants in each viral genotype. Here, by conducting deep-sequencing analyses, we show for the first time a comprehensive snapshot of the within-host genetic diversity of high-risk HPVs during cervical carcinogenesis. Quasispecies harboring minor nucleotide variations in viral whole-genome sequences were extensively observed across different grades of CIN and cervical cancer. Among the within-host variations, C-to-T transitions, a characteristic change mediated by cellular APOBEC cytosine deaminases, were predominantly detected throughout the whole viral genome, most strikingly in low-grade CIN lesions. The results strongly suggest that within-host variations of the HPV genome are primarily generated through the interaction with host cell DNA-editing enzymes and that such within-host variability is an evolutionary source of the genetic diversity of HPVs.

scholarly journals Evolution and Genetic Diversity of SARSCoV-2 in Africa Using Whole Genome Sequences

2020 ◽  
Author(s):  
Babatunde Olarenwaju Motayo ◽  
Olukunle Oluwapamilerin Oluwasemowo ◽  
Paul Akiniyi Akinduti ◽  
Babatunde Adebiyi Olusola ◽  
Olumide T Aerege ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Amino Acid ◽  
Spike Protein ◽  
Recent Common Ancestor ◽  
Whole Genome ◽  
Genome Sequences ◽  
Protein Amino Acid ◽  
Protein Variant ◽  
Health Crisis ◽  
Most Recent Common Ancestor

ABSTRACTThe ongoing SARSCoV-2 pandemic was introduced into Africa on 14th February 2020 and has rapidly spread across the continent causing severe public health crisis and mortality. We investigated the genetic diversity and evolution of this virus during the early outbreak months using whole genome sequences. We performed; recombination analysis against closely related CoV, Bayesian time scaled phylogeny and investigated spike protein amino acid mutations. Results from our analysis showed recombination signals between the AfrSARSCoV-2 sequences and reference sequences within the N and S genes. The evolutionary rate of the AfrSARSCoV-2 was 4.133 × 10−4 high posterior density HPD (4.132 × 10−4 to 4.134 × 10−4) substitutions/site/year. The time to most recent common ancestor TMRCA of the African strains was December 7th 2019. The AfrSARCoV-2 sequences diversified into two lineages A and B with B being more diverse with multiple sub-lineages confirmed by both maximum clade credibility MCC tree and PANGOLIN software. There was a high prevalence of the D614-G spike protein amino acid mutation (82.61%) among the African strains. Our study has revealed a rapidly diversifying viral population with the G614 spike protein variant dominating, we advocate for up scaling NGS sequencing platforms across Africa to enhance surveillance and aid control effort of SARSCoV-2 in Africa.

scholarly journals Whole-Genome Assemblies for Three Yersinia pestis Strains Isolated in Erenhot, China

2020 ◽  
Vol 9 (45) ◽  
Author(s):  
Jing Wang ◽  
Xifeng Yang ◽  
Hongyuan Zheng ◽  
Li Tian ◽  
Qi Shi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Yersinia Pestis ◽  
Draft Genome ◽  
Meriones Unguiculatus ◽  
Whole Genome ◽  
Genome Sequences ◽  
Content Type ◽  
Genome Assemblies

ABSTRACT To explore the genetic diversity of Yersinia pestis strains in Erenhot, China, and their relationship with Mongolian strains, we collected and sequenced three Y. pestis strains from Erenhot, China, in 2018. Here, we report the draft genome sequences of three Y. pestis bv. Medievalis strains belonging to the 2.MED phylogroup that were circulating in Meriones unguiculatus populations.

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