Identification and Classification of Prokaryotes using whole-genome sequences.

2021 ◽  
pp. 217-230
Author(s):  
Luis M. Rodriguez-R ◽  
Ramon Rosselló-Móra ◽  
Konstantinos T. Konstantinidis
Keyword(s):  
Species Identification ◽  
Special Focus ◽  
Whole Genome ◽  
Genome Sequences ◽  
Future Directions ◽  
The Past ◽  
Major Genome ◽  
Taxonomic Studies

Abstract This book chapter attempts to summarize the major findings from genome-based taxonomic studies in the past two decades, and briefly describe the major genome-based approaches currently available for species identification and classification with special focus on the 'uncultivated majority' and associated limitations, as well as outlines future directions towards a truly genome-based taxonomy for prokaryotes that will equally encompass cultured and uncultivated taxa. Importantly, the need for a system to catalogue uncultivated taxa is very urgent, because the genomes and ecological/functional data that are becoming available are already overwhelming, and alphanumeric identifiers and synonyms are creating confusion of Babylonian dimensions.

scholarly journals 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

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.

The Strength of Chemotaxonomy.

2021 ◽  
pp. 141-167
Author(s):  
Nisha B. Patel ◽  
Paul A. Lawson
Keyword(s):  
In Silico ◽  
Future Directions ◽  
Classification Schemes ◽  
Minimum Standards ◽  
The Past ◽  
The Family ◽  
Primary Literature ◽  
Extensive Reference ◽  
In Silico Methods

Abstract This book chapter discusses the history and development of chemotaxonomic methods, with examples of the application to different taxa, and with extensive reference to primary literature and reviews. The application of in silico methods utilizing information from the genome and future directions will also be discussed. The delineation of higher taxa at the family level and above may especially be aided by chemotaxonomic criteria, as demonstrated in published minimum standards. Although chemotaxonomic methods have been enormously important in the past with identification and classification schemes, it remains to be seen in what form they will be utilized in the genomic era, and in the suite of methods available in the era of omics.

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

2015 ◽  
Vol 3 (6) ◽  
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.

scholarly journals Whole-Genome Sequences and Classification of Streptococcus agalactiae Strains Isolated from Laboratory-Reared Long-Evans Rats (Rattus norvegicus)

2017 ◽  
Vol 5 (1) ◽  
Author(s):  
C. Bodi Winn ◽  
J. Dzink-Fox ◽  
Y. Feng ◽  
Z. Shen ◽  
V. Bakthavatchalu ◽  
...  
Keyword(s):  
Streptococcus Agalactiae ◽  
Genomic Analysis ◽  
Opportunistic Pathogen ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Genome Sequences ◽  
Content Type ◽  
Long Evans ◽  
Fatal Septicemia

ABSTRACT In collaboration with the CDC’s Streptococcus Laboratory, we report here the whole-genome sequences of seven Streptococcus agalactiae bacteria isolated from laboratory-reared Long-Evans rats. Four of the S. agalactiae isolates were associated with morbidity accompanied by endocarditis, metritis, and fatal septicemia, providing an opportunity for comparative genomic analysis of this opportunistic pathogen.

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

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2742-2751 ◽  
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.

scholarly journals Phylogenetic classification of the whole-genome sequences of SARS-CoV-2 from India & evolutionary trends

2021 ◽  
Vol 153 (1) ◽  
pp. 166
Author(s):  
Sarah Cherian ◽  
Varsha Potdar ◽  
Veena Vipat ◽  
Ashwini Ramdasi ◽  
Santosh Jadhav ◽  
...  
Keyword(s):  
Whole Genome ◽  
Evolutionary Trends ◽  
Genome Sequences ◽  
Phylogenetic Classification

scholarly journals Re-identification of strains deposited as Pseudomonas aeruginosa, Pseudomonas fluorescens and Pseudomonas putida in GenBank based on whole genome sequences

2020 ◽  
Vol 70 (11) ◽  
pp. 5958-5963
Author(s):  
Yuh Morimoto ◽  
Mari Tohya ◽  
Zulipiya Aibibula ◽  
Tadashi Baba ◽  
Hiroyuki Daida ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Genome Sequencing ◽  
Dna Hybridization ◽  
Type Species ◽  
Whole Genome ◽  
Average Nucleotide Identity ◽  
Genome Sequences ◽  
Content Type ◽  
Link Type

The taxonomic classification of Pseudomonas species has been revised and updated several times. This study utilized average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) cutoff values of 95 and 70 %, respectively, to re-identify the species of strains deposited in GenBank as P. aeruginosa , P. fluorescens and P. putida . Of the 264 deposited P. aeruginosa strains, 259 were correctly identified as P. aeruginosa , but the remaining five were not. All 28 deposited P. fluorescens strains had been incorrectly identified as P. fluorescens . Four of these strains were re-identified, including two as P. kilonensis and one each as P. aeruginosa and P. brassicacearum , but the remaining 24 could not be re-identified. Similarly, all 35 deposited P. putida strains had been incorrectly identified as P. putida . Nineteen of these strains were re-identified, including 12 as P. alloputida , four as P. asiatica and one each as P. juntendi , P. monteilii and P. mosselii . These results strongly suggest that Pseudomonas bacteria should be identified using ANI and dDDH analyses based on whole genome sequencing when Pseudomonas species are initially deposited in GenBank/DDBJ/EMBL databases.

Looking into the past - the reaction of three grouse species to climate change over the last million years using whole genome sequences

2016 ◽  
Vol 25 (2) ◽  
pp. 570-580 ◽  
Author(s):  
Radoslav Kozma ◽  
Páll Melsted ◽  
Kristinn P. Magnússon ◽  
Jacob Höglund
Keyword(s):  
Climate Change ◽  
Whole Genome ◽  
Genome Sequences ◽  
The Past
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