2.2 Analysis of the characteristics of SSRs
The number, relative abundance, relative density, and GC content of SSRs in the chloroplast genomes of all eight species of Cyatheaceae were systematically compared (Table 2). The number (121–122), relative abundance (0.77–0.78/bp), relative density (9.81–9.82 bp/kb), and GC content (0.18–0.20) of SSRs in the chloroplast genomes ofAlsophila spinulosa and Alsophila costularis ; the number (102), relative abundance (0.63–0.65/bp), relative density (6.70–8.18 bp/kb), and GC content (0.08–0.10) of SSRs in the chloroplast genomes of Sphaeropteris brunoniana and Sphaeropteris lepifera ; and the number (61–67), relative abundance (0.40/bp), relative density (4.11–5.06 bp/kb), and GC content (0.22–0.29) of SSRs ofAlsophila denticulata , Alsophila podophylla ,Alsophila metteniana , and Alsophila gigantea had similar values, which were not proportional to the size of the genome. The proportions of GC bases in the chloroplast genomes of the eight species of Cyatheaceae were much lower than the proportions of AT. SSRs accounted for 75.5–86.2%, 13.7–20.6%, 2.0–3.9%, and 2.0% of the IGS, Intron, CDS, and rRNA gene regions (pseudogenes were treated as IGS). Among them, SSR was only detected in the CDS of the chloroplast genomes of Sphaeropteris brunoniana , Sphaeropteris lepifera , Alsophila spinulosa , and Alsophila costularis , and SSRs were detected in the rRNA genes of the chloroplast genomes ofSphaeropteris brunoniana and Sphaeropteris lepifera . WhenGymnosphaera was considered as an independent classification unit at the genus level, the eight species of Cyatheaceae were divided into three genera. That is, Alsophila denticulata , Alsophila podophylla , Alsophila metteniana , and Alsophila giganteabelonged to the genus Gymnosphaera ; Alsophila spinulosaand Alsophila costularis belonged to the genus Alsophila ; and Sphaeropteris brunoniana and Sphaeropteris lepiferabelonged to the genus Sphaeropteris . The number, relative abundance, relative density, and GC content of SSRs in the chloroplast genomes of the three genera of Cyatheaceae also had similar values in different regions of the genome (LSC, SSC, and IR; IGS, intron, CDS, and rRNA gene regions), indicating that in the phylogenetic background of the three genera, the characteristics of SSRs are genus specific at the level of the genome and its different regions (Figure 3, Tables 2 and 3, and Supplementary Tables 9 and 10). The distribution of SSRs of different motif types in the three Cyatheaceae genera also had genus specificity (Figure 2). These results showed that on the phylogenetic background of dividing the eight species of Cyatheaceae into three genera, different taxa had different patterns of SSR characteristics in the chloroplast genome, namely, the SSR characteristics of the chloroplast genomes of the eight species of Cyatheaceae were consistent with their phylogenetic relationship.
Table 2 Overview of the eight Cyatheaceae chloroplast genomes and characteristics of their SSRs