Exploring SSR patterns and properties in Ilex cornuta transcriptome

Based on the transcriptome data of Ilex cornuta, the SSR loci were identified and profiled for I. cornuta unigenes by using MicroSAtellite (MISA) software. A total of 31335 SSR loci were detected on 24964 Unigene sequences in 124003 Unigenes with a length greater than 500 bp. The frequency of SSR loci was 20.13 %, the frequency of occurrence was 25.27 %, and the average distribution distance was 2.62 kb in I. cornuta. A total of 77 repeat motif types were present in the transcriptome of this species. The major repeat types were single nucleotide (52.91%) and dinucleotide (39.47%), while the dominant repeat motifs were (A/T)n and (AG/CT)n, accounting for 50.11% and 28.11% of the total number of SSR loci, respectively. The lengths of the SSR motifs of I. cornuta were distributed between 10 and 92 bp with an average length of 13.81 bp, among which the number of SSRs with a length of 10 bp was the largest, with 5847, accounting for 18.66% of the total number of SSR loci. The study provides a theoretical foundation for SSR-based genetic diversity analysis and characterization of genetic resources in I. cornuta, while supporting future conservation efforts and molecular-assisted breeding programs.