Figure 3 Comparison of microsatellite repeats among the eight Cyatheaceae chloroplast genomes.
(A) The inner circle is the distribution ratio of the four regions (LSC, SSC, and IRs) in the genome, and the outer circle is the distribution ratio of SSRs between the four regions. (B) Distribution ratio of SSRs in different regions (LSC, SSC, and IRs) of chloroplast the genome. (C) Ratio of mono- to pentanucleotide SSRs in different regions (IGS, intron, CDS, and rRNA gene) of the chloroplast genome. Numbers represent the distribution ratio of SSR numbers. LSC: large single-copy region; SSC: small single-copy region; IR: inverted repeat region; IGS: intergenic spacer region; CDS: coding sequence region.
2.3 Analysis of the types and characteristics of SSRs of different nucleotide numbers
The proportions of single-nucleotide, dinucleotide, trinucleotide, tetranucleotide, and pentanucleotide SSRs in each species were 62.5-78.0%, 10.6-15.6%, 0-3.3%, 9.0-18.5%, and 0-1.5%, respectively. No hexanucleotide SSR was detected. Among single-nucleotide repeats, there were more A/T motifs, and the dinucleotide repeats were dominated by AT/TA motifs. The single-nucleotide, dinucleotide, trinucleotide, tetranucleotide, and pentanucleotide SSRs of the chloroplast genomes of the three genera were similar in number, relative abundance, relative density, and GC content at the level of the genome and in the specific regions of the genome (LSC, SSC, and IRs; IGS, intron, CDS, and rRNA gene regions). This was especially true for single-nucleotide and dinucleotide SSRs (Table 3, Supplementary Tables 10 and 11). The number, relative abundance, relative density, and GC content of SSRs of different unit lengths and SSRs in different regions of the genome had genus specificity in the phylogenetic context of dividing the eight species of Cyatheaceae into three genera. In addition, the number, relative abundance, and relative density of SSRs of different base types in the chloroplast genomes of the three genera of plants also had genus specificity. This was especially true for single- and dinucleotide SSRs (Figure 4, Supplementary Table 9).
Table 3 The number, relative abundance, relative density, and GC content of mono- to pentanucleotide SSRs in the eight chloroplast genomes of Cyatheaceae