scholarly journals Updated reference genome sequence and annotation ofMycobacterium bovisAF2122/97

2016 ◽  
Author(s):  
Kerri M. Malone ◽  
Damien Farrell ◽  
Tod P. Stuber ◽  
Olga T. Schubert ◽  
Reudi Aebersold ◽  
...  
Keyword(s):  
Mycobacterium Bovis ◽  
Genome Sequence ◽  
Bovine Tuberculosis ◽  
Reference Genome ◽  
Reference Genome Sequence

AbstractWe report an update to the reference genome of the bovine tuberculosis bacillusMycobacterium bovisAF2122/97 generated using an integrative multi-‘omics approach. Updates include 42 new CDS, 14 modified annotations, 26 SNP corrections, and disclosure that the RD900 locus, previously described as absent from the genome, is in fact present.

scholarly journals Updated Reference Genome Sequence and Annotation of Mycobacterium bovis AF2122/97

2017 ◽  
Vol 5 (14) ◽  
Author(s):  
Kerri M. Malone ◽  
Damien Farrell ◽  
Tod P. Stuber ◽  
Olga T. Schubert ◽  
Ruedi Aebersold ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Mycobacterium Bovis ◽  
Genome Sequence ◽  
Bovine Tuberculosis ◽  
Reference Genome ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Coding Sequences ◽  
Content Type ◽  
Reference Genome Sequence

ABSTRACT We report here an update to the reference genome sequence of the bovine tuberculosis bacillus Mycobacterium bovis AF2122/97, generated using an integrative multiomics approach. The update includes 42 new coding sequences (CDSs), 14 modified annotations, 26 single-nucleotide polymorphism (SNP) corrections, and disclosure that the RD900 locus, previously described as absent from the genome, is in fact present.

scholarly journals Exploiting the reference genome sequence of hexaploid wheat: a proteomic study of flour proteins from the cultivar Chinese Spring

2019 ◽  
Vol 20 (1) ◽  
pp. 1-16 ◽  
Author(s):  
Susan B. Altenbach ◽  
Han-Chang Chang ◽  
Annamaria Simon-Buss ◽  
Toni Mohr ◽  
Naxin Huo ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Hexaploid Wheat ◽  
Chinese Spring ◽  
Reference Genome ◽  
Reference Genome Sequence ◽  
Proteomic Study

scholarly journals A novel genome-wide microsatellite resource for species ofEucalyptuswith linkage-to-physical correspondence on the reference genome sequence

2014 ◽  
Vol 15 (2) ◽  
pp. 437-448 ◽  
Author(s):  
Dario Grattapaglia ◽  
Eva M. C. Mamani ◽  
Orzenil B. Silva-Junior ◽  
Danielle A. Faria
Keyword(s):  
Genome Sequence ◽  
Reference Genome ◽  
Reference Genome Sequence ◽  
Genome Wide

scholarly journals Development of a Genome-Wide Oligonucleotide Microarray Platform for Detection of DNA Copy Number Aberrations in Feline Cancers

2020 ◽  
Vol 7 (3) ◽  
pp. 88
Author(s):  
Rachael Thomas ◽  
Joan U Pontius ◽  
Luke B Borst ◽  
Matthew Breen
Keyword(s):  
Genome Sequence ◽  
Copy Number ◽  
Reference Genome ◽  
Microarray Platform ◽  
Domestic Cat ◽  
Dna Copy Number ◽  
Reference Genome Sequence ◽  
Copy Number Aberrations ◽  
Genome Sequence Assembly ◽  
Dna Copy Number Aberrations

The utility of the domestic cat as a model system for biomedical studies was constrained for many years by the absence of a comprehensive feline reference genome sequence assembly. While such a resource now exists, the cat continues to lag behind the domestic dog in terms of integration into the ‘One Health’ era of molecular medicine. Stimulated by the advances being made within the evolving field of comparative cancer genomics, we developed a microarray platform that allows rapid and sensitive detection of DNA copy number aberrations in feline tumors using comparative genomic hybridization analysis. The microarray comprises 110,456 unique oligonucleotide probes anchored at mean intervals of 22.6 kb throughout the feline reference genome sequence assembly, providing ~350-fold higher resolution than was previously possible using this technique. We demonstrate the utility of this resource through genomic profiling of a feline injection-site sarcoma case, revealing a highly disrupted profile of DNA copy number imbalance involving several key cancer-associated genes including KIT, TP53, PTEN, FAS and RB1. These findings were supported by targeted fluorescence in-situ hybridization analysis, which identified major alterations in chromosome structure, including complex intrachromosomal reorganization events typical of those seen in aggressive soft-tissue sarcomas of other species. We then characterized a second mass that was identified at a nearby site in the same patient almost 12 months later. This mass demonstrated a remarkably conserved genomic profile consistent with a recurrence of the original tumor; however the detection of subtle differences reflected evolution of the tumor over time. These findings exemplify the diverse potential of this microarray platform to incorporate domestic cat cancers into comparative and translational research efforts in molecular oncology.

scholarly journals Chromosome Painting Facilitates Anchoring Reference Genome Sequence to Chromosomes In Situ and Integrated Karyotyping in Banana (Musa Spp.)

2019 ◽  
Vol 10 ◽  
Author(s):  
Denisa Šimoníková ◽  
Alžbeěta Němečková ◽  
Miroslava Karafiátová ◽  
Brigitte Uwimana ◽  
Rony Swennen ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Chromosome Painting ◽  
Reference Genome ◽  
Reference Genome Sequence ◽  
Musa Spp

scholarly journals Draft Genome Sequence of Mycobacterium bovis Strain D-10-02315 Isolated from Wild Boar

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Maxime Branger ◽  
Amandine Hauer ◽  
Lorraine Michelet ◽  
Claudine Karoui ◽  
Thierry Cochard ◽  
...  
Keyword(s):  
Infectious Disease ◽  
Wild Boar ◽  
Mycobacterium Bovis ◽  
Genome Sequence ◽  
Bovine Tuberculosis ◽  
Draft Genome ◽  
Etiologic Agent ◽  
Draft Genome Sequence ◽  
Wild Animals

Mycobacterium bovis is the etiologic agent of bovine tuberculosis, a chronic infectious disease, affecting livestock, wild animals, and sometimes humans. We report the draft genome sequence of a Mycobacterium bovis strain isolated from wild boar of spoligotype SB0120 (or BCG-like) also present in wildlife-livestock multi-host systems.

scholarly journals Updated functional annotation of the Mycobacterium bovis AF2122/97 reference genome

2019 ◽  
Author(s):  
Damien Farrell ◽  
Joseph Crispell ◽  
Stephen V. Gordon
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Mycobacterium Bovis ◽  
Bovine Tuberculosis ◽  
Genome Annotation ◽  
Functional Annotation ◽  
Reference Strain ◽  
Reference Genome ◽  
Coding Sequences ◽  
New Gene ◽  
New Protein

AbstractMycobacterium bovis AF2122/97 is the reference strain for the bovine tuberculosis bacillus. We here report an update to the M. bovis AF2122/97 genome annotation to reflect 616 new protein identifications which replace many of the old hypothetical coding sequences and proteins of unknown function in the genome. These changes integrate information from functional assignments of orthologous coding sequences in the Mycobacterium tuberculosis H37Rv genome. We have also added 69 additional new gene names.

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