The relationship of the whole genome sequence identity to DNA hybridization varies between genera of prokaryotes

We report the whole-genome sequence of a peste des petits ruminants virus (PPRV) from a lamb exhibiting clinical signs in Turkey in September 2018. The genome of PPRV/Turkey/Central_Anatolia/2018 shows the highest nucleotide sequence identity (97.63%) to PPRV isolated in Turkey in 2000.

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Comparative genome analysis and phylogenomic of Xanthomonas citri pv. viticola lead to new taxonomic insights about species of Xanthomonas

10.21203/rs.2.22059/v1 ◽

2020 ◽

Author(s):

Antonio Roberto Gomes de Farias ◽

Wilson José da Silva Junior ◽

José Bandeira do Nascimento Junior ◽

Valdir de Queiroz Balbino ◽

Ana Maria Benko-Iseppon ◽

...

Keyword(s):

Genome Sequence ◽

Dna Hybridization ◽

In Silico ◽

Whole Genome Sequence ◽

Nucleotide Identity ◽

Whole Genome ◽

Average Nucleotide Identity ◽

Xanthomonas Citri ◽

Genome Sequences ◽

Xanthomonas Species

Abstract Background Xanthomonas citri pv. viticola is one of the most critical grapevine diseases in the Northeast of Brazil, presenting a high risk to Brazilian and worldwide areas of grape production. The X.citri pv. viticola epithet was recently proposed to be changed from X. campestris pv. v iticola based on multilocus sequence analysis and whole-genome sequences. Besides, genomics has revolutionized the field of bacteriology, by associating genome sequencing with comparative analysis such as in silico analysis such as DNA-DNA hybridization, average nucleotide identity, distance between genomes, pan-genomic approach, and phylogenomic, providing valuable insights and knowledge about virulence factors and contributing to increase the understanding and clarifying the taxonomic relationship of Xanthomonas and others prokaryotic species.Results We used the whole-genome sequence of three Brazilian strains and the pathotype to characterize X.citri pv. viticola accessions plus 124 whole-genome sequences of Xanthomonas species available in NCBI, comprising 13 species and 15 pathovars. The whole-genome sequence structure of X. citri pv. viticola was shown presents a high level of conservation concerning other X. citri species. Pan-genomic approaches, average nucleotide identity analysis, and in silico DNA-DNA hybridization were carried out, allowing X.citri pv. viticola characterization and inferences on the phylogenetic relationships within Xanthomonas . The analysis of the sequence of the 128 genomes clustered the Xanthomonas strains in eight main groups according to the recently proposed classification in all approaches used. Also, the analysis revealed that X. hortorum and X. gardneri should be classified as a single species, and the strain 17 of X. campestris and XC01 of X. citri pv. mangiferaeindicae widely described in the literature are misclassified.Conclusions We performed the genomic characterization of three representative Brazilian strains of Xcv . The genomic approaches based in the pan-genome, average nucleotide identity, and in silico DNA-DNA hybridization support the proposed taxonomic position of X.citri pv. viticola and of the recently proposed Xanthomonas species and pathovars. In addition, we detected species delimitation of the misclassified Xanthomonas strains with extensive studies reported in the literature.

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Whole-Genome Sequence of Listeria monocytogenes Serovar 1/2a Strain IZSAM_Lm_15_17439_A144, Representative of a Human Outbreak in 2008

Microbiology Resource Announcements ◽

10.1128/mra.00074-19 ◽

2019 ◽

Vol 8 (36) ◽

Author(s):

Massimiliano Orsini ◽

Alessandra Ordinelli ◽

Alessandra Cornacchia ◽

Vicdalia Acciari ◽

Patrizia Centorame ◽

...

Keyword(s):

Listeria Monocytogenes ◽

Genome Sequence ◽

Whole Genome Sequence ◽

Whole Genome ◽

Content Type ◽

Sequence Identity

Here, we report the genome sequence of Listeria monocytogenes serovar 1/2a strain IZSAM_Lm_15_17439_A144, isolated in Italy from a patient during a Listeria monocytogenes outbreak in 2008. This strain showed 98.9% sequence identity to a strain isolated in Canada in the same year.

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Whole Genome Sequence-Based Identification of Clostridium estertheticum Complex Strains Supports the Need for Taxonomic Reclassification Within the Species Clostridium estertheticum

Frontiers in Microbiology ◽

10.3389/fmicb.2021.727022 ◽

2021 ◽

Vol 12 ◽

Author(s):

Joseph Wambui ◽

Nicole Cernela ◽

Marc J. A. Stevens ◽

Roger Stephan

Keyword(s):

Genome Sequence ◽

Dna Hybridization ◽

Sequence Similarity ◽

Whole Genome Sequence ◽

Whole Genome ◽

Species Identity ◽

16S Rrna Sequence ◽

Meat Juice ◽

Level Identification

Isolates within the Clostridium estertheticum complex (CEC) have routinely been identified through the 16S rRNA sequence, but the high interspecies sequence similarity reduces the resolution necessary for species level identification and often results in ambiguous taxonomic classification. The current study identified CEC isolates from meat juice (MJS) and bovine fecal samples (BFS) and determined the phylogeny of species within the CEC through whole genome sequence (WGS)-based analyses. About 1,054 MJS were screened for CEC using quantitative real-time PCR (qPCR). Strains were isolated from 33 MJS and 34 BFS qPCR-positive samples, respectively. Pan- and core-genome phylogenomics were used to determine the species identity of the isolates. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were used to validate the species identity. The phylogeny of species within the CEC was determined through a combination of these methods. Twenty-eight clostridia strains were isolated from MJS and BFS samples out of which 13 belonged to CEC. At 95% ANI and 70% dDDH thresholds for speciation, six CEC isolates were identified as genomospecies2 (n=3), Clostridium tagluense (n=2) and genomospecies3 (n=1). Lower thresholds of 94% ANI and 58% dDDH were required for the classification of seven CEC isolates into species C. estertheticum and prevent an overlap between species C. estertheticum and Clostridium frigoriphilum. Combination of the two species and abolishment of current subspecies classification within the species C. estertheticum are proposed. These data demonstrate the suitability of phylogenomics to identify CEC isolates and determine the phylogeny within CEC.

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