1.3 Characterization of chloroplast genome
The chloroplast genome of Alsophila was used as the reference
genome, and Dual Organellar GenoMe Annotator (DOGMA) (Milne et al.,
2010) was used to predict the protein-coding genes, rRNA genes, and tRNA
genes in other genomes. Geneious Prime (Kearse et al., 2012) was used
for manual correction according to the reference genome. The
Shuffle-Lagan mode in the online software mVISTA (Frazer et al., 2004)
was used for genome-wide comparison. Organellar Genome DRAW (OGDRAW)
(Lohse et al., 2007) was used to draw the physical chloroplast genome
map, and Sequin software was used for the submission of the chloroplast
genome of Alsophila denticulata . Microsatellite repeats were
predicted using the software MISA (Beier et al., 2017). The threshold
repeat number of single-nucleotide units was set to 10, the threshold
repeat number of dinucleotide units was set to six, and the threshold
repeat number of trinucleotides, tetranucleotides, pentanucleotides, and
hexanucleotides was set to three. The minimum distance between two SSRs
was set to 0 bp, that is, there was no statistical compound SSR. The
distribution characteristics of SSRs of different species in the whole
genome and its different regions were compared and analyzed. Among these
characteristics, the relative abundance refers to the number of SSRs in
the unit sequence length (kb), and the relative density refers to the
length of the SSR (bp) in the unit sequence length (kb).