Phylogenetic Relationships of the Fern Cyrtomium falcatum (Dryopteridaceae) from Dokdo Island Based on Chloroplast Genome Sequencing

Abstract

Cyrtomium falcatum is a popular ornamental fern cultivated worldwide. Native to the Korean Peninsula, Japan, and Dokdo Island in the Sea of Japan, it is the only fern present on Dokdo Island. We isolated and characterized the chloroplast (cp) genome of C. falcatum, and compared it with those of closely related species. The genes trnV-GAC and trnV-GAU were found to be present within the cp genome of C. falcatum, whereas trnP-GGG and rpl21 were lacking. Moreover, cp genomes of Cyrtomium devexiscapulae and Adiantum capillus-veneris lack trnP-GGG and rpl21, suggesting these are not conserved among angiosperm cp genomes. The deletion of trnR-UCG, trnR-CCG, and trnSeC in the cp genomes of C. falcatum and other eupolypod ferns indicates these genes are restricted to tree ferns, non-core leptosporangiates, and basal ferns. The C. falcatum cp genome also encoded ndhF and rps7, with GUG start codons that were only conserved in polypod ferns, and it shares two significant inversions with other ferns, including a minor inversion of the trnD-GUC region and an approximate 3 kb inversion of the trnG-trnT region. Phylogenetic analyses showed that Equisetum was found to be a sister clade to Psilotales-Ophioglossales with a 100% bootstrap (BS) value. The sister relationship between Pteridaceae and eupolypods was also strongly supported by a 100% BS, but Bayesian molecular clock analyses suggested that C. falcatum diversified in the mid-Paleogene period (45.15 ± 4.93 million years ago) and might have moved from Eurasia to Dokdo Island.

Completion of Eight Gynostemma BL. (Cucurbitaceae) Chloroplast Genomes: Characterization, Comparative Analysis, and Phylogenetic Relationships

“…There has been an increasing number of studies using complete cp genome sequences for assessing phylogenetic relationships among angiosperms (Bock et al, 2014 ; Raman et al, 2016 ). Our phylogenetic trees indicated a very clear internal relationship of restricted Cucurbitales plants with high bootstrap values.…”

The Complete Chloroplast Genomes of Echinacanthus Species (Acanthaceae): Phylogenetic Relationships, Adaptive Evolution, and Screening of Molecular Markers

“…It has independent genome (chloroplast DNA, cpDNA) that is characterized by small molecular weight, multiple copies, and simple structure (Olmstead and Palmer, 1994; Wicke et al, 2011). With the development of high-throughput sequencing technologies, cpDNA has been widely utilized for reconstructing phylogenetic relationships, DNA barcoding, and development of molecular markers (Graham and Olmstead, 2000; Dong et al, 2014; Lemieux et al, 2016; Raman et al, 2016;Li Y.G. et al, 2017; Ng et al, 2017; Song et al, 2017; Zhang et al, 2017).…”

Complete Chloroplast Genome of Castanopsis sclerophylla (Lindl.) Schott: Genome Structures, Comparative and Phylogenetic Analysis

“…Phylogenetic evolution and population genomics knowledge are very vital to make effective conservation and management strategies. With the rapid development of next-generation sequencing technology, compared with the Sanger method, the chloroplast genome assembly has become cheaper and easier based on Illumina sequencing technology, comparative analysis of the complete chloroplast genome among closely related species has been proven to be a valid and most effective method for the study of evolutionary history, species conservation, and phylogenetic relationships [12–14].…”