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