Complete chloroplast genome sequence of Dryopteris fragrans (L.) Schott and the repeat structures against the thermal environment

Abstract

Dryopteris fragrans (L.) Schott is a fern growing on the surface of hot rocks and lava. It is exposed to sunlight directly and bears local hot environment. We sequenced the complete nucleotide sequence of its chloroplast (cp) genome. The cp genome was 151,978 bp in length, consisting of a large single-copy region (85,332 bp), a small single-copy region (31,947 bp) and a pair of inverted repeats (17,314 bp). The cp genome contained 112 genes and 345 RNA editing sites in protein-coding genes. Simple sequence repeats (SSRs) and long repeat structure pairs (30–55 bp) were identified. The number and percent of repeat structures are extremely high in ferns. Thermal denaturation experiments showed its cp genome to have numerous, dispersed and high GC percent repeat structures, which conferred the strongest thermal stability. This repeat-heavy genome may provide the molecular basis of how D. fragrans cp survives its hot environment.

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

“…Most editing events in these four chloroplast genomes were C-to-U events in this study, which is consistent with D. fragrans [26]. It has been reported that the excess of C-to-U RNA editing developed in early stages of vascular plant evolution [46].…”

“…goeringiana and P. tripteron for the first time, ranging from 148,539 bp to 151,341 bp in length. The whole chloroplast genomes size of more than 20 ferns were compared in the study of Gao et al [26] and RuizRuano et al [1], which revealed that the length of ferns ranging between 131,760 bp (Equisetum hyemale) and 181,684 bp (C. devexiscapulae) based on the current researches, and the four ferns detected in our study is within this range. The genomes of these four ferns chloroplast exhibit a typical quadripartite structure, including LSC, SSC and two IRs, as reported in other spore plants [27,28].…”

“…Additionally, the gene number and order were largely similar with other ferns, but there were still some differences among species, which should let the length variation in the IR and SSC regions take the responsibility [29]. We compared the chloroplast genomes of D. crassirhizoma, D. goeringiana and D. fragrans [26], and found a genomes loss of 4033 bp in D. fragrans, which caused a longest SSC and shorter IRs. Therefore, the D. fragrans was found has dispersed gene distribution and longer sequence length, because of more intergenic sequences.…”

“…Therefore, the D. fragrans was found has dispersed gene distribution and longer sequence length, because of more intergenic sequences. As demonstrated by Gao et al [26] and Lu et al [16], they revealed that fern chloroplast genome extends the intergenic sequences but reduces the overlapping genes, thus, sequence utilization is more specific and genes are more independent.…”

“…fragrans, which have high GC content than AT in SSRs. Taken the living environment into consideration, the author speculated that high GC content of repeat structures may allow D. fragrans coping with heat and large temperature differences [26]. The kind and amount of SSRs in D. fragrans, D. crassirhizoma and D. goeringiana exist great differences though they all belonging to the Dryopteridaceae family.…”