Journal: Forestry Research

Article Title: Telomere-to-telomere assemblies of chromosome 10 reveal complex adaptive variation of 3-ketoacyl-CoA-synthases in Populus trichocarpa likely driven by Helitrons

doi: 10.48130/forres-0026-0019

Figure Lengend Snippet: KCS gene copy counts for each genotype and their alkene levels colored by mean Z-9-heptadecosene amount. The first six genotypes are alkene minus (AM) accessions. The gray heatmap indicates copy numbers for genes listed as columns. A more detailed breakdown by differing amino acids is also provided in the Supplementary Table S2a.

Article Snippet: Note, though, that among the 39 genotypes, several KCS genes, including those in Nisqually-1, have an indel that causes the loss of the first exon and therefore a non-functional protein.

Techniques:

Journal: Forestry Research

Article Title: Telomere-to-telomere assemblies of chromosome 10 reveal complex adaptive variation of 3-ketoacyl-CoA-synthases in Populus trichocarpa likely driven by Helitrons

doi: 10.48130/forres-0026-0019

Figure Lengend Snippet: Comparison of our results to published reports of the KCS locus. (a) KCS genes in the Nisqually-1 reference and the new 78 haploid assemblies. Boxes with solid edges are genes (same position across genomes), boxes with broken edges are copy number variants (different positions across genomes), and short boxes represent shorter-length KCS variants with intact open reading frames. Nomenclature corresponds to Nisqually-1 reference. Yellow arrows indicate Helitrons with archetypal CTAG palindrome. Note, each gene is paired with a Helitron. (b) Gene model for Potri.010G079500 in alkene-minus (AM) and alkene plus (AP) haplotypes. In AM individuals, the 5' end of Potri.010G079500 was inverted and placed on the reverse strand, deleting portions of the coding sequence, confirming the prediction of Gonzales-Vigil et al. (c) Differences in disease severity in AM and AP phenotypes. Contrary to Gonzales-Vigil et al. we did not find differences in S. musiva (Septoria) severity but did find decreased severity of Melampsora in 2014 ( p < 0.012) but not in 2012.

Article Snippet: Note, though, that among the 39 genotypes, several KCS genes, including those in Nisqually-1, have an indel that causes the loss of the first exon and therefore a non-functional protein.

Techniques: Comparison, Sequencing