Journal: BMC Genomics

Article Title: A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency

doi: 10.1186/s12864-017-3791-6

Figure Lengend Snippet: The tobacco genome. Circos plot showing the 24 pseudomolecules (Nt1–Nt24) generated by the tobacco genome assembly. With tracks for ( a ) gene density, ( b ) N. sylvestris sequence coverage, ( c ) N. tomentosiformis coverage, ( d ) regions of T- ( red bars ; inner track ) or S- ( blue bars ; outer track ) putative genome origin and ( e ) Physical super-scaffolds generated by hybrid assembly of NGS and optical map data anchored to the genetic map. Note that track e is split over two levels due to the density of the super-scaffolds visible at the displayed scale. Synteny between pseudomolecules is represented by coloured linkers across the centre of the plot. Tracks a , b and c represent density over 50 kb bins

Article Snippet: Fig. 4 Map-based cloning of the yb mutant genes NtEGY1 and NtEGY2 . a picture showing yellow, chlorotic phenotype of yb1 yb2 genotype NIL ( left ) versus wild type YB1 YB2 parent ( right ) in one of the lines used in mapping of yb loci (Cultivar SC58). b , High density genetic map for tobacco ( N. tabacum 30 k Infinium HD consensus map 2015; https://solgenomics.net/cview/map.pl?map_version_id=178 ) showing location of SNP markers linked to yb1 ( blue box ) on Nt24 and yb2 ( red box ) on Nt5 .

Techniques: Generated, Sequencing

Journal: BMC Genomics

Article Title: A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency

doi: 10.1186/s12864-017-3791-6

Figure Lengend Snippet: Map-based cloning of the yb mutant genes NtEGY1 and NtEGY2 . a picture showing yellow, chlorotic phenotype of yb1 yb2 genotype NIL ( left ) versus wild type YB1 YB2 parent ( right ) in one of the lines used in mapping of yb loci (Cultivar SC58). b , High density genetic map for tobacco ( N. tabacum 30 k Infinium HD consensus map 2015; https://solgenomics.net/cview/map.pl?map_version_id=178 ) showing location of SNP markers linked to yb1 ( blue box ) on Nt24 and yb2 ( red box ) on Nt5 . Mapping of yb1 ( c ) and yb2 ( d ) loci showing position of SNP markers linked to the loci on (i) genetic and (ii) physical maps. Physical map shows position of super-scaffolds ( alternating light and dark green bars ) and underlying sequence scaffolds/contigs ( blue bars ), as well as genes ( green triangles ). Position of NtEGY1 and NtEGY2 in physical map shown (iii) with schematic representation of exons ( wide dark blue boxes ), introns ( narrow light blue bar ) and 5’ and 3’ UTRs ( intermediate blue boxes ), with direction of gene indicated by white arrow-head at 3’end. Sequence polymorphisms between wild type and mutant alleles indicated, showing single base insertion in exon 9 of NtEGY2 ( c ) and 8 bp deletion in exon 2 of NtEGY1 ( d ). e , protein alignment based on predicted sequence translated from cDNA of NtEGY1 and NtEGY2 from YB1 YB2 genotype K326 and yb1 yb2 genotype TN90 cultivars, showing truncated proteins produced from the TN90 alleles of the genes. Coloured regions of alignment indicate sequence identity between the four proteins ( dark blue 100%, green 60–80%, and grey <60%)

Article Snippet: Fig. 4 Map-based cloning of the yb mutant genes NtEGY1 and NtEGY2 . a picture showing yellow, chlorotic phenotype of yb1 yb2 genotype NIL ( left ) versus wild type YB1 YB2 parent ( right ) in one of the lines used in mapping of yb loci (Cultivar SC58). b , High density genetic map for tobacco ( N. tabacum 30 k Infinium HD consensus map 2015; https://solgenomics.net/cview/map.pl?map_version_id=178 ) showing location of SNP markers linked to yb1 ( blue box ) on Nt24 and yb2 ( red box ) on Nt5 .

Techniques: Cloning, Mutagenesis, Sequencing, Produced

Journal: Scientific Reports

Article Title: Temporal and spatial Mycobacterium bovis prevalence patterns as evidenced in the All Wales Badgers Found Dead (AWBFD) survey of infection 2014–2016

doi: 10.1038/s41598-020-72297-9

Figure Lengend Snippet: Maps depicting prevalence (% of all submissions that were infected with M. bovis ) by Spatial Unit in Wales Found Dead badgers (Wales RTA) 2005–2006 and the All Wales Badger Found Dead Survey (AWBFD) 2014–2016. Submissions positive for M. bovis /total submissions are given for each Spatial Unit. The colour scale representing prevalence is applied for Spatial Units with at least 10 badger submissions. Mapping software Esri ArcGIS 10.2.2 ( https://www.esri.com/en-us/arcgis ).

Article Snippet: The information is overlaid with M. bovis genotype ‘home ranges’ derived from M. bovis isolates obtained from cattle in 2015 (APHA Annual Surveillance Data) Mapping software Esri ArcGIS 10.2.2 ( https://www.esri.com/en-us/arcgis ).

Techniques: Infection, Software

Journal: Scientific Reports

Article Title: Temporal and spatial Mycobacterium bovis prevalence patterns as evidenced in the All Wales Badgers Found Dead (AWBFD) survey of infection 2014–2016

doi: 10.1038/s41598-020-72297-9

Figure Lengend Snippet: Location and M. bovis status of found dead badgers post-mortem examined in Wales in 2005–2006 as part of the RTA survey 2005–2006 and in 2014–2016 as part of the AWBFD. This data is overlaid with Wales TB regionalisation and 2015 herd density data. Herd density info taken from APHA Annual Surveillance Data; mapping software Esri ArcGIS 10.2.2 ( https://www.esri.com/en-us/arcgis ).

Article Snippet: The information is overlaid with M. bovis genotype ‘home ranges’ derived from M. bovis isolates obtained from cattle in 2015 (APHA Annual Surveillance Data) Mapping software Esri ArcGIS 10.2.2 ( https://www.esri.com/en-us/arcgis ).

Techniques: Software

Journal: Scientific Reports

Article Title: Temporal and spatial Mycobacterium bovis prevalence patterns as evidenced in the All Wales Badgers Found Dead (AWBFD) survey of infection 2014–2016

doi: 10.1038/s41598-020-72297-9

Figure Lengend Snippet: Geographical distribution of genotypes of M. bovis isolates from the 2014 to 2016 All Wales Found Dead Badger Survey. Locations and genotypes of M. bovis isolates from individual badgers are presented as coloured symbols as per key. The information is overlaid with M. bovis genotype ‘home ranges’ derived from M. bovis isolates obtained from cattle in 2015 (APHA Annual Surveillance Data) Mapping software Esri ArcGIS 10.2.2 ( https://www.esri.com/en-us/arcgis ).

Article Snippet: The information is overlaid with M. bovis genotype ‘home ranges’ derived from M. bovis isolates obtained from cattle in 2015 (APHA Annual Surveillance Data) Mapping software Esri ArcGIS 10.2.2 ( https://www.esri.com/en-us/arcgis ).

Techniques: Derivative Assay, Software

Journal: Scientific Reports

Article Title: Temporal and spatial Mycobacterium bovis prevalence patterns as evidenced in the All Wales Badgers Found Dead (AWBFD) survey of infection 2014–2016

doi: 10.1038/s41598-020-72297-9

Figure Lengend Snippet: 2014–2016 map of annual cattle prevalence (number of herds under bTB restriction at any point of year/registered live herds in region) by Spatial Unit (SU), after direct standardisation to account for variation in herd size. APHA Annual Surveillance Data; mapping software Esri ArcGIS 10.2.2 ( https://www.esri.com/en-us/arcgis ).

Article Snippet: The information is overlaid with M. bovis genotype ‘home ranges’ derived from M. bovis isolates obtained from cattle in 2015 (APHA Annual Surveillance Data) Mapping software Esri ArcGIS 10.2.2 ( https://www.esri.com/en-us/arcgis ).

Techniques: Software

Journal: Frontiers in Endocrinology

Article Title: Perspective of the GEMSTONE Consortium on Current and Future Approaches to Functional Validation for Skeletal Genetic Disease Using Cellular, Molecular and Animal-Modeling Techniques

doi: 10.3389/fendo.2021.731217

Figure Lengend Snippet: Scheme of proposed “roadmap” and integration of GEMSTONE Working Groups.

Article Snippet: The mapping was expanded in 2015 by the Roadmap Epigenomics Consortium ( ).

Techniques: