Characterization of the chloroplast genome and phylogenetic analysis of Ceratopteris pteridoides (Pteridaceae)

The endangered Ceratopteris pteridoides is an aquatic annual fern possessing several distinct characteristics that makes it an attractive model for the studies of plant biology. The complete chloroplast genome that has been sequenced and annotated revealed a typical quadripartite structure. The genome was 149,426 bp in length and contained 132 genes, including 88 protein-coding, 36 tRNA, and eight rRNA genes. Analyses at the genome level between C. pteridoides and its congeners, C. corunta and C. richardii showed low variability in repeat numbers, sequence alignment, gene content, and genome structure. Based on the analysis of pairwise identity, the newly sequenced chloroplast genome showed identical gene content and structure to a previously published one. However, genome alignment of these two accessions detected three SNPs; while 20 indel sites occurred in eight different events. The topology of the phylogenetic tree based on 88 plastid protein-coding genes was largely concordant with those recent phylogenetic studies, but with generally increased support values. •The understanding of the diversity and dynamic evolution of Pteridaceae is limited.•A gene editing event was detected in the chloroplast genome of Ceratopteris pteridoides.•Low inter- and intraspecific pairwise distance was detected.•The phylogenetic position of C. pteridoides was determined.