Integrated analysis of four new sequenced fern Chloroplast Genomes: Genome structure and Comparative Analysis

Abstract Background: Dryopteris goeringiana (Kunze) Koidz, Arthyrium brevifrons Nakai ex Kitagawa, Dryopteris crassirhizoma Nakai, and Polystichum tripteron (Kunze) Presl are fern species with their chloroplast genomes uncovered, except D. crassirhizoma . In this study, high throughput sequences were performed to get better understand of their chloroplast genomes and comparison analysis with other fern species. Methods: Fresh fern leaves were used for sequencing. Simple Sequence Repeat (SSR) analysis, high-variety regions comparison, IR border comparison, nucleotide diversity, RNA editing, and phylogenetic analysis were performed. Results: They have different genome structure characteristics in terms of genome and its area size, gene types and location. The quantity and type of SSRs in D. crassirhizoma is very similar to D. goeringiana , with (ATAA)2, (ATCT)1 and (TTTA)1 only present in D. crassirhizoma . SSRs contain more AT bases than GC. There were divergent genes existed in fern species. Ten genes have a Pi value >0.20. C-to-U RNA editing was most common. Phylogenetic analyses showed that species in the same genus clustered together. Conclusion: The genomic structure and genetic resources of D. goeringiana , A. brevifrons , D. crassirhizoma , and P. tripteron contribute to further studies on phylogenetics, population genetics, and conservation biology of ferns.