kcs genes  (Medicago)

Journal: bioRxiv

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

doi: 10.1101/2025.07.10.664019

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. Solid boxes are genes (same position across genomes), and patterned boxes are copy number variants (different positions across genomes), and checkered boxes are truncated genes. 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 we did not find differences in S. musiva (Septoria) severity, but did find decreased severity of Melampsora 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 lacks the first exon.

Techniques: Comparison, Sequencing

Journal: bioRxiv

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

doi: 10.1101/2025.07.10.664019

Figure Lengend Snippet: A) Helitrons have a unique peel-and-paste method of transposition in which a rolling circle is generated and inserted between an AT target nucleotide pair, with no duplications at the end, and the empty single strand from which it was derived is restored, retaining the original gene. Nearly all helitrons harbor an ‘A’ upstream from the ‘CTAG’ site, and a ‘TCT’ just downstream from its KCS paired gene (Table S6, S7), as would be expected if they were inserted as helitrons. Several alkene-deficient genotypes have mutations in the stem-loop structure that may affect helitron efficiency. B) Hypothetical evolutionary model of copy number generation via helitrons. Given the shared helitron between Potri.010G79500 and Potri.010G079700 in BESC-377_H2 and the presence of that helitron in all Potri.010G79700 sequences, we propose that Potri.010G079500 represents the origin of KCS copies. Once the transposase machinery and the DRT111 gene were inserted proximal to the helitron in Potri.010G79500 it was able to replicate itself and generate Potri.010G79700. This additional gene copy provided an advantage and rapidly spread throughout the population.

Article Snippet: Note though that among the 39 genotypes several KCS genes, including those in Nisqually-1, have an indel that lacks the first exon.

Techniques: Generated, Derivative Assay