*3.1. Distribution of the SSRs in the Capsicum Frutescens Genome*

The search results of the genome sequences of *C. frutescens* resulted in a total number of 278,425 SSR loci being identified. (AT)n(TTG)n(AAAT)n(AAATA)n(TATAGA)n is the most common repeat motifs corresponding to the dinucleotide to hexanucleotide repeat, respectively. The SSR repeat types were found to be different. For example, the dominant amongst the 1638 SSR repeats were the trinucleotides and dinucleotides, which accounted for 57.1% (158,967) and 34.1% (94,916), respectively. The remaining was occupied by tetranucleotide, pentanucleotide, and hexanucleotide repeat motifs, accounting for 5.9% (16,351), 1.6% (4531), and 1.3% (3660), respectively. Taken together, it was found that the majority of the SSR repeat motifs along the entirety of genome sequences were trinucleotide repeats, and the hexanucleotide repeats were the fewest, as illustrated in Figure 1A. The frequencies of each of SSR motif types along the entire *C. frutescens* genome were also detected. Among the dinucleotide motifs, AT/TA was observed to be the most common (69.91%; 66,356). This was followed by AC/GT (9.14%; 8671) and TC/GA (7.88%; 7476). Meanwhile, the CG/GC motif repeats were rarely observed (0.05%). The trinucleotide repeat motif consisted of 30 different types. The predominant motifs were TTG/CAA and AAT/ATT, which accounted for 12.41 and 10.02%, respectively (Figure 1B). In addition, AAAT/ATTT (13.85%) were the predominantly found tetranucleotide repeats (Figure 1C).

The statistical data showed that the SSR loci were widely distributed on all 12 chromosomes of the *C. frutescens* genome. These were mainly found in Chr3 (25,014), followed by Chr1 (23,644), Chr12 (23,240), Chr9 (22,761), Chr11 (22,617), Chr7 (22,066), Chr5 (21,976), Chr6 (21,448), Chr8 (21,286), Chr4 (20,939), Chr10 (20,333), and Chr2 (16,579), respectively. In addition, 16,522 SSR loci were unable to allocate in the chromosomes. It was found that, while analyzing the distribution frequency of the SSR loci/Mb, the results revealed that the number of SSR loci/Mb on each chromosome ranged from 91.27 to 104.13. However, the number of SSR loci on Chr3 was the highest. The density of the SSR loci on Chr3 was found to be the third highest, with an average of 97.45 SSR loci/Mb. Moreover, although the number of SSR loci on Chr2 was found to the fewest, the density of the SSR loci was the highest overall (104.13 SSR loci/Mb), as shown in Figure 1D.
