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