Phylogenomic re-assessment of the thermophilic genus Geobacillus

dc.contributor.authorAliyu, Habibu
dc.contributor.authorLebre, Pedro Humberto
dc.contributor.authorBlom, Jochen
dc.contributor.authorCowan, Don A.
dc.contributor.authorDe Maayer, Pieter
dc.contributor.emaildon.cowan@up.ac.zaen_ZA
dc.date.accessioned2016-10-18T09:34:43Z
dc.date.issued2016-12
dc.descriptionSupplementary Figure S1: AAI relationships among sixty-three strains of Geobacillus. The dendrogram was constructed using the distances matrices (derived from ANI and dDDH values) using the web server DendroUPGMA [14].
dc.descriptionSupplementary Table S1: Genome features of sixty-three Geobacillus strains included in this study. The original species and strain designations are indicated, as are the genome size, GenBank Assembly accession numbers or Integrate Microbial Genomics database project ID. The status of the original genome sequence (Complete or Draft), number of contigs for the original and final assembly are shown. The number of genes coded on the genome (as predicted with RAST) and G+C content (%) are indicated.
dc.descriptionSupplementary Table S2: ANI and dDDH relationships among sixty-three strains of Geobacillus species. The lower triangle shows the ANI values with the 96% threshold higlighted using bottom and left borders. The blue, white and red colour code (0-100%) was used to depict the contrast between the ANI values of the two major clades identified in this study. The upper triangle shows the dDDH values with 70% threshold demacated using upper and right borders. The red, yellow and green colour code (0-100%) was used to highlight the contrast between the dDDH values of the two major clades. The strains names were annotated with different colour fills to indicate species recognised in this study. The two major clades identified in this study are demarcated by a thick border line.
dc.descriptionSupplementary Table S3: AAI relationships among sixty-three strains of Geobacillus species. The green, yellow and red colour code (0-100%) was used to highlight the AAI among the Geobacillus species included in this study. The strains names were annotated with different colour fills to indicate species recognised in this study. The species grouping within the clades are highlighted using the different colour fills in the species names. The two major clades identified in this study are demarcated using a thick border line.
dc.description.abstractGeobacillus is a genus of Gram-positive, aerobic, spore-forming obligate thermophiles. The descriptions and subsequent affiliations of the species in the genus have mostly been based on polyphasic taxonomy rules that include traditional sequence-based methods such as DNA–DNA hybridization and comparison of 16S rRNA gene sequences. Currently, there are fifteen validly described species within the genus. The availability of whole genome sequences has provided an opportunity to validate and/or re-assess these conventional estimates of genome relatedness. We have applied whole genome approaches to estimate the phylogenetic relatedness among the sixty-three Geobacillus strains for which genome sequences are currently publicly available, including the type strains of eleven validly described species. The phylogenomic metrics AAI (Average Amino acid Identity), ANI (Average Nucleotide Identity) and dDDH (digital DNA–DNA hybridization) indicated that the current genus Geobacillus is comprised of sixteen distinct genomospecies, including several potentially novel species. Furthermore, a phylogeny constructed on the basis of the core genes identified from the whole genome analyses indicated that the genus clusters into two monophyletic clades that clearly differ in terms of nucleotide base composition. The G + C content ranges for clade I and II were 48.8–53.1% and 42.1–44.4%, respectively. We therefore suggest that the Geobacillus species currently residing within clade II be considered as a new genusen_ZA
dc.description.departmentGeneticsen_ZA
dc.description.departmentMicrobiology and Plant Pathologyen_ZA
dc.description.embargo2017-12-30
dc.description.librarianhb2016en_ZA
dc.description.sponsorshipThe University of Pretoria (Habibu Aliyu—University of Pretoria Postdoctoral Fellowship funding), National Research Foundation (Pieter De Maayer—Research Career Advancement Fellowship, Grant # 91447) and the University of Pretoria Genomic Research Institute.en_ZA
dc.description.urihttp:// www.elsevier.de/syapmen_ZA
dc.identifier.citationAliyu, H, Lebre, P, Blom, J, Cowan, DA & De Maayer, P 2016, 'Phylogenomic re-assessment of the thermophilic genus Geobacillus', Systematic and Applied Microbiology, vol. 39, no. 8, pp. 527-533.en_ZA
dc.identifier.issn0723-2020
dc.identifier.other10.1016/j.syapm.2016.09.004
dc.identifier.urihttp://hdl.handle.net/2263/57344
dc.language.isoenen_ZA
dc.publisherElsevieren_ZA
dc.rights© 2016 Elsevier GmbH. All rights reserved. Notice : this is the author’s version of a work that was accepted for publication in Systematic and Applied Microbiology. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. A definitive version was subsequently published in Systematic and Applied Microbiology, vol. 39, no. 8, pp. 527-533, 2016. doi : 10.1016/j.syapm.2016.09.004.en_ZA
dc.subjectGeobacillusen_ZA
dc.subjectThermophileen_ZA
dc.subjectPhylogenomic metricsen_ZA
dc.subjectAverage Nucleotide Identityen_ZA
dc.subjectDigital DNA–DNA hybridizationen_ZA
dc.titlePhylogenomic re-assessment of the thermophilic genus Geobacillusen_ZA
dc.typePostprint Articleen_ZA

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