Delineating bacterial subspecies Additional file 3 to : “ Complete genome sequence of DSM 30083 T , the type strain ( U 5 / 41 T ) of Escherichia coli , and a proposal for delineating subspecies in…
- Jan P. Meier-Kolthoff, R. Hahnke, H. Klenk
- Biology
- 2014
We here describe our approach to finding clustering parameters suitable for delineating subspecific bacterial lineages using the same intergenomic distances that can be used to estimate digital…
Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy
- Jan P. Meier-Kolthoff, R. Hahnke, H. Klenk
- BiologyStandards in Genomic Sciences
- 8 December 2014
Analyses of the genome sequences of a large number of E. coli strains and of strains from > 100 other bacterial genera indicate a value of 79-80% dDDH as the most promising threshold for delineating subspecies, which in turn suggests the presence of five subspecies withinE.
Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21T)
- Yun-juan Chang, M. Land, A. Lapidus
- BiologyStandards in Genomic Sciences
- 1 October 2011
The Ktedonobacter racemifer corrig genome is the largest prokaryotic genome reported so far and comprises a large number of over-represented COGs, particularly genes associated with transposons, causing the genetic redundancy within the genome being considerably larger than expected by chance.
opm: an R package for analysing OmniLog® phenotype microarray data
- L. Vaas, J. Sikorski, M. Göker
- BiologyBioinform.
- 15 July 2013
SUMMARY
opm is an R package designed to analyse multidimensional OmniLog® phenotype microarray (PM) data. opm provides management, visualization and statistical analysis of PM data, including…
Multiple wheat genomes reveal global variation in modern breeding
- S. Walkowiak, Liangliang Gao, C. Pozniak
- Medicine, BiologyNature
- 25 November 2020
Comparative analysis of multiple genome assemblies from wheat reveals extensive diversity that results from the complex breeding history of wheat and provides a basis for further potential improvements to this important food crop.
The barley pan-genome reveals the hidden legacy of mutation breeding
- Murukarthick Jayakodi, S. Padmarasu, N. Stein
- Biology, MedicineNature
- 25 November 2020
Chromosome-scale sequence assemblies of 20 diverse varieties of barley are used to construct a first-generation pan-genome, revealing previously hidden genetic variation that can be used by studies aimed at crop improvement.
Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov.
- S. Breider, Carmen Scheuner, M. Göker
- BiologyFrontiers in Microbiology
- 11 August 2014
P phylogenetic reconstruction from genome-scale data, MALDI-TOF mass-spectrometry analysis and a re-assessment of the phenotypic data from the literature are used to settle the matter, aiming at a reclassification of the two genera Phaeobacter and Leisingera.
Genomics and Physiology of a Marine Flavobacterium Encoding a Proteorhodopsin and a Xanthorhodopsin-Like Protein
- T. Riedel, L. Gómez-Consarnau, I. Wagner-Döbler
- BiologyPLoS ONE
- 4 March 2013
Although PRO95 contains and expresses two rhodopsin genes, light did not stimulate its growth as determined by cell numbers in a nutrient poor seawater medium that mimics its natural environment, confirming previous experiments at intermediate carbon concentrations.
Complete genome sequence of the rapeseed plant-growth promoting Serratia plymuthica strain AS9
- S. Neupane, N. Högberg, R. Finlay
- BiologyStandards in Genomic Sciences
- 5 March 2012
The genome of S. plymuthica AS9 is of special interest for its ability to inhibit fungal pathogens of rapeseed and to promote plant growth.
Complete genome sequence of the marine methyl-halide oxidizing Leisingera methylohalidivorans type strain (DSM 14336T), a representative of the Roseobacter clade
- Nora Buddruhs, O. Chertkov, H. Klenk
- BiologyStandards in Genomic Sciences
- 4 October 2013
The complete genome sequence and annotation of this bacterium is described together with previously unreported aspects of its phenotype, including methylohalidivorans strain MB2T, of special interest due to its methylotrophy.
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