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

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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Genome Sequences of Two Choline-Utilizing Methanogenic Archaea, Methanococcoides spp., Isolated from Marine Sediments

Microbiology Resource Announcements ◽

10.1128/mra.00342-19 ◽

2019 ◽

Vol 8 (18) ◽

Cited By ~ 1

Author(s):

Gordon Webster ◽

Alex J. Mullins ◽

Andrew J. Watkins ◽

Edward Cunningham-Oakes ◽

Andrew J. Weightman ◽

...

Keyword(s):

Marine Sediments ◽

Dna Hybridization ◽

In Silico ◽

Methanogenic Archaea ◽

Nucleotide Identity ◽

Average Nucleotide Identity ◽

Genome Sequences ◽

Content Type

The genomes of two Methanococcoides spp. that were isolated from marine sediments and are capable of carrying out methanogenesis from choline and other methylotrophic substrates were sequenced. The average nucleotide identity and in silico DNA-DNA hybridization analyses demonstrate that they represent species different from those previously described.

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Comparative Genomics of 86 Whole-Genome Sequences in the Six Species of the Elizabethkingia Genus Reveals Intraspecific and Interspecific Divergence

Scientific Reports ◽

10.1038/s41598-019-55795-3 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Chih-Yu Liang ◽

Chih-Hui Yang ◽

Chung-Hsu Lai ◽

Yi-Han Huang ◽

Jiun-Nong Lin

Keyword(s):

Comparative Genomics ◽

Dna Hybridization ◽

In Silico ◽

Whole Genome Sequence ◽

Comparative Genomic ◽

Whole Genome ◽

Genome Sequences ◽

Pan Genome ◽

New Genes ◽

Clusters Of Orthologous Groups

AbstractBacteria of the genus Elizabethkingia are emerging infectious agents that can cause infection in humans. The number of published whole-genome sequences of Elizabethkingia is rapidly increasing. In this study, we used comparative genomics to investigate the genomes of the six species in the Elizabethkingia genus, namely E. meningoseptica, E. anophelis, E. miricola, E. bruuniana, E. ursingii, and E. occulta. In silico DNA–DNA hybridization, whole-genome sequence-based phylogeny, pan genome analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed, and clusters of orthologous groups were evaluated. Of the 86 whole-genome sequences available in GenBank, 21 were complete genome sequences and 65 were shotgun sequences. In silico DNA–DNA hybridization clearly delineated the six Elizabethkingia species. Phylogenetic analysis confirmed that E. bruuniana, E. ursingii, and E. occulta were closer to E. miricola than to E. meningoseptica and E. anophelis. A total of 2,609 clusters of orthologous groups were identified among the six type strains of the Elizabethkingia genus. Metabolism-related clusters of orthologous groups accounted for the majority of gene families in KEGG analysis. New genes were identified that substantially increased the total repertoire of the pan genome after the addition of 86 Elizabethkingia genomes, which suggests that Elizabethkingia has shown adaptive evolution to environmental change. This study presents a comparative genomic analysis of Elizabethkingia, and the results of this study provide knowledge that facilitates a better understanding of this microorganism.

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Draft Genome Sequence of Mediterraneibacter sp. nov. Strain gm002, Isolated from Human Feces

Microbiology Resource Announcements ◽

10.1128/mra.00217-19 ◽

2019 ◽

Vol 8 (31) ◽

Author(s):

Chien-Hsun Huang ◽

Jong-Shian Liou ◽

Chun-Lin Wang ◽

Lina Huang

Keyword(s):

Genome Sequence ◽

Genome Assembly ◽

Dna Hybridization ◽

Novel Species ◽

Draft Genome ◽

Draft Genome Sequence ◽

Nucleotide Identity ◽

Whole Genome ◽

Average Nucleotide Identity ◽

Human Feces

Here, we report a draft genome sequence of Mediterraneibacter sp. strain gm002, isolated from human feces in Taiwan. This strain represents a novel species according to whole-genome-based comparisons using the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) thresholds. The genome assembly comprised 3,568,768 bp, with a 38.7% G+C content.

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Whole genome characterization of strains belonging to the Ralstonia solanacearum species complex and in silico analysis of TaqMan assays for detection in this heterogenous species complex

European Journal of Plant Pathology ◽

10.1007/s10658-020-02190-8 ◽

2021 ◽

Author(s):

Viola Kurm ◽

Ilse Houwers ◽

Claudia E. Coipan ◽

Peter Bonants ◽

Cees Waalwijk ◽

...

Keyword(s):

Ralstonia Solanacearum ◽

In Silico ◽

Species Complex ◽

Sequence Data ◽

In Silico Analysis ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequences ◽

Pcr Assays

AbstractIdentification and classification of members of the Ralstonia solanacearum species complex (RSSC) is challenging due to the heterogeneity of this complex. Whole genome sequence data of 225 strains were used to classify strains based on average nucleotide identity (ANI) and multilocus sequence analysis (MLSA). Based on the ANI score (>95%), 191 out of 192(99.5%) RSSC strains could be grouped into the three species R. solanacearum, R. pseudosolanacearum, and R. syzygii, and into the four phylotypes within the RSSC (I,II, III, and IV). R. solanacearum phylotype II could be split in two groups (IIA and IIB), from which IIB clustered in three subgroups (IIBa, IIBb and IIBc). This division by ANI was in accordance with MLSA. The IIB subgroups found by ANI and MLSA also differed in the number of SNPs in the primer and probe sites of various assays. An in-silico analysis of eight TaqMan and 11 conventional PCR assays was performed using the whole genome sequences. Based on this analysis several cases of potential false positives or false negatives can be expected upon the use of these assays for their intended target organisms. Two TaqMan assays and two PCR assays targeting the 16S rDNA sequence should be able to detect all phylotypes of the RSSC. We conclude that the increasing availability of whole genome sequences is not only useful for classification of strains, but also shows potential for selection and evaluation of clade specific nucleic acid-based amplification methods within the RSSC.

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Whole-proteome tree of life suggests a deep burst of organism diversity

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1915766117 ◽

2020 ◽

Vol 117 (7) ◽

pp. 3678-3686 ◽

Cited By ~ 5

Author(s):

JaeJin Choi ◽

Sung-Hou Kim

Keyword(s):

Information Theory ◽

Genome Sequence ◽

Tree Of Life ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequences ◽

Alignment Free ◽

Whole Transcriptome ◽

Evolutionary Progression ◽

Feature Frequency

An organism tree of life (organism ToL) is a conceptual and metaphorical tree to capture a simplified narrative of the evolutionary course and kinship among the extant organisms. Such a tree cannot be experimentally validated but may be reconstructed based on characteristics associated with the organisms. Since the whole-genome sequence of an organism is, at present, the most comprehensive descriptor of the organism, a whole-genome sequence-based ToL can be an empirically derivable surrogate for the organism ToL. However, experimentally determining the whole-genome sequences of many diverse organisms was practically impossible until recently. We have constructed three types of ToLs for diversely sampled organisms using the sequences of whole genome, of whole transcriptome, and of whole proteome. Of the three, whole-proteome sequence-based ToL (whole-proteome ToL), constructed by applying information theory-based feature frequency profile method, an “alignment-free” method, gave the most topologically stable ToL. Here, we describe the main features of a whole-proteome ToL for 4,023 species with known complete or almost complete genome sequences on grouping and kinship among the groups at deep evolutionary levels. The ToL reveals 1) all extant organisms of this study can be grouped into 2 “Supergroups,” 6 “Major Groups,” or 35+ “Groups”; 2) the order of emergence of the “founders” of all of the groups may be assigned on an evolutionary progression scale; 3) all of the founders of the groups have emerged in a “deep burst” at the very beginning period near the root of the ToL—an explosive birth of life’s diversity.

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Draft Genome Sequences of Thiorhodococcus mannitoliphagus and Thiorhodococcus minor, Purple Sulfur Photosynthetic Bacteria in the Gammaproteobacterial Family Chromatiaceae

Microbiology Resource Announcements ◽

10.1128/mra.00193-20 ◽

2020 ◽

Vol 9 (14) ◽

Author(s):

Fabiola A. Aviles ◽

Terry E. Meyer ◽

John A. Kyndt

Keyword(s):

Photosynthetic Bacteria ◽

Draft Genome ◽

Nucleotide Identity ◽

Whole Genome ◽

Average Nucleotide Identity ◽

Genome Sequences ◽

Content Type

We have determined the draft genome sequences of Thiorhodococcus mannitoliphagus and Thiorhodococcus minor for comparison with those of T. drewsii and Imhoffiella purpurea. According to average nucleotide identity (ANI) and whole-genome phylogenetic comparisons, these two species are clearly distinct from the Imhoffiella species and T. drewsii.

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Whole-Genome Sequence and Classification of 11 Endophytic Bacteria from Poison Ivy ( Toxicodendron radicans ): TABLE 1.

Genome Announcements ◽

10.1128/genomea.01319-15 ◽

2015 ◽

Vol 3 (6) ◽

Cited By ~ 5

Author(s):

Phuong N. Tran ◽

Nicholas E. H. Tan ◽

Yin Peng Lee ◽

Han Ming Gan ◽

Steven J. Polter ◽

...

Keyword(s):

Genome Sequence ◽

Endophytic Bacteria ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequences ◽

Poison Ivy

Here, we report the whole-genome sequences and annotation of 11 endophytic bacteria from poison ivy ( Toxicodendron radicans ) vine tissue. Five bacteria belong to the genus Pseudomonas , and six single members from other genera were found present in interior vine tissue of poison ivy.

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Taxonomic revision of Harveyi clade bacteria (family Vibrionaceae) based on analysis of whole genome sequences

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.051110-0 ◽

2013 ◽

Vol 63 (Pt_7) ◽

pp. 2742-2751 ◽

Cited By ~ 38

Author(s):

Henryk Urbanczyk ◽

Yoshitoshi Ogura ◽

Tetsuya Hayashi

Keyword(s):

Genome Sequence ◽

Sequence Data ◽

Draft Genome ◽

Taxonomic Revision ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequences ◽

Genome Sequence Data ◽

The Family

Use of inadequate methods for classification of bacteria in the so-called Harveyi clade (family Vibrionaceae, Gammaproteobacteria) has led to incorrect assignment of strains and proliferation of synonymous species. In order to resolve taxonomic ambiguities within the Harveyi clade and to test usefulness of whole genome sequence data for classification of Vibrionaceae, draft genome sequences of 12 strains were determined and analysed. The sequencing included type strains of seven species: Vibrio sagamiensis NBRC 104589T, Vibrio azureus NBRC 104587T, Vibrio harveyi NBRC 15634T, Vibrio rotiferianus LMG 21460T, Vibrio campbellii NBRC 15631T, Vibrio jasicida LMG 25398T, and Vibrio owensii LMG 25443T. Draft genome sequences of strain LMG 25430, previously designated the type strain of [Vibrio communis], and two strains (MWB 21 and 090810c) from the ‘beijerinckii’ lineage were also determined. Whole genomes of two additional strains (ATCC 25919 and 200612B) that previously could not be assigned to any Harveyi clade species were also sequenced. Analysis of the genome sequence data revealed a clear case of synonymy between V. owensii and [V. communis], confirming an earlier proposal to synonymize both species. Both strains from the ‘beijerinckii’ lineage were classified as V. jasicida, while the strains ATCC 25919 and 200612B were classified as V. owensii and V. campbellii, respectively. We also found that two strains, AND4 and Ex25, are closely related to Harveyi clade bacteria, but could not be assigned to any species of the family Vibrionaceae. The use of whole genome sequence data for the taxonomic classification of the Harveyi clade bacteria and other members of the family Vibrionaceae is also discussed.

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