Journal: iScience

Article Title: An integrated systems biology approach reveals differences in formate metabolism in the genus Methanothermobacter

doi: 10.1016/j.isci.2023.108016

Figure Lengend Snippet:

Article Snippet: GEM modeling related files M. thermautotrophicus Z-245 , This manuscript , Biomodels: MODEL2211290002.

Techniques: Virus, Recombinant, Staining, Sequencing, RNA Sequencing, Software, Combined Bisulfite Restriction Analysis Assay, Mass Spectrometry

Journal: Scientific Reports

Article Title: Genome-wide estimation of recombination, mutation and positive selection enlightens diversification drivers of Mycobacterium bovis

doi: 10.1038/s41598-021-98226-y

Figure Lengend Snippet: Detailed information concerning the recombination events identified by Gubbins and RDP4 in the entire dataset.

Article Snippet: The FASTQ files from the newly sequenced M. bovis obtained from Illumina sequencing were aligned with M. bovis AF2122/97 reference genome (LT708304.1) with the help of vSNP pipeline ( https://github.com/USDA-VS/vSNP ).

Techniques: Membrane

Journal: Scientific Reports

Article Title: Genome-wide estimation of recombination, mutation and positive selection enlightens diversification drivers of Mycobacterium bovis

doi: 10.1038/s41598-021-98226-y

Figure Lengend Snippet: Detailed visualization of alignment in the recombination region of M. bovis dataset affecting the narX gene encoding a probable nitrate reductase. No gaps or undefined nucleotides were identified in the recombination region of internal nodes. This specific event was registered across Eu1 genomes. The quality of sequencing of narX gene was evaluated by read mapping against M. bovis AF2122/97. The SNP positions suggested in the recombination region were confirmed by applying the criteria referred to in the methods section (at least 20 reads and 0.9 frequency of alteration). The polymorphisms at narX gene were fully confirmed in genomes Mb1792361 and Mb7240415 (2.3%).

Article Snippet: The FASTQ files from the newly sequenced M. bovis obtained from Illumina sequencing were aligned with M. bovis AF2122/97 reference genome (LT708304.1) with the help of vSNP pipeline ( https://github.com/USDA-VS/vSNP ).

Techniques: Sequencing

Journal: Scientific Reports

Article Title: Genome-wide estimation of recombination, mutation and positive selection enlightens diversification drivers of Mycobacterium bovis

doi: 10.1038/s41598-021-98226-y

Figure Lengend Snippet: Detailed visualization of alignment in the recombination region of M. bovis dataset affecting the pks12 gene. No gaps or undefined nucleotides were identified in the recombination region of internal nodes. With respect to this event affecting the pks12 gene that encodes a probable polyketide synthase, it encompasses exclusively Eu2 genomes. The quality of sequencing of pks12 was evaluated by read mapping against M. bovis AF2122/97. The SNP positions suggested in the recombination region were confirmed by applying the criteria referred to in the methods section (at least 20 reads and 0.9 frequency of alteration). The polymorphisms were fully confirmed for genomes Mb0891, Mb1711, Mb1789, Mb1870, Mb1758, Mb2043, Mb1960.

Article Snippet: The FASTQ files from the newly sequenced M. bovis obtained from Illumina sequencing were aligned with M. bovis AF2122/97 reference genome (LT708304.1) with the help of vSNP pipeline ( https://github.com/USDA-VS/vSNP ).

Techniques: Sequencing

Journal: Scientific Reports

Article Title: Genome-wide estimation of recombination, mutation and positive selection enlightens diversification drivers of Mycobacterium bovis

doi: 10.1038/s41598-021-98226-y

Figure Lengend Snippet: Characteristics of Mycobacterium bovis genomes used in this work.

Article Snippet: The FASTQ files from the newly sequenced M. bovis obtained from Illumina sequencing were aligned with M. bovis AF2122/97 reference genome (LT708304.1) with the help of vSNP pipeline ( https://github.com/USDA-VS/vSNP ).

Techniques: Sequencing