Genomic Neighborhoods of Sunflower RLK/Pelle Kinases Reveal Distinct Associations with Transposable Elements

The plant RLK/Pelle family is one of the largest kinase groups and includes key regulators of development, environmental signaling, and stress responses. Transposable elements (TEs) also shape plant genome structure and can contribute to regulatory variation, yet their landscape around RLK/Pelle loci remains poorly explored in large, repeat-rich crop genomes. Here, we identified 2196 protein kinases in the sunflower (Helianthus annuus) XRQ reference genome and 702 in non-reference contigs assembled from reads unmapped to XRQ. Within this total kinome, 2289 kinases were assigned to RLK/Pelle subfamilies, of which 763 also fulfilled the architecture-based criteria for structurally supported RLKs. The broader RLK/Pelle set was used for TE-association analyses. Genome-wide analyses showed that RLK/Pelle loci occupy non-random TE environments that depend on TE superfamily and relative position. TIR, LTR/Copia, TRIM, and Mutator elements were enriched among TEs overlapping RLK/Pelle genes, whereas downstream regions showed enrichment of LTR/Copia elements and underrepresentation of LTR/Gypsy elements. TE associations also differed among RLK/Pelle duplication classes, with the strongest signal involving TRIM elements and tandemly duplicated genes. Integration of public RNA-seq datasets revealed a more restricted transcriptional component: ten flanking TE–RLK/Pelle pairs showed significant positive expression correlations in drought or Sclerotinia sclerotiorum stress datasets. Motif enrichment analyses further identified NAC- and TCP-associated sequence features in selected TE subsets. Together, these findings reveal position- and context-dependent TE associations around sunflower RLK/Pelle loci and identify candidate TE–RLK/Pelle relationships for future functional validation.