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