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).