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

Rui Gao,Guangming Zhao,Hongli Ren,Ruifeng Fan,Wenzhong Wang,Xu Wang,Shuang Bian,Ying Chang,Qingyang Huang,Peng Feng

doi:10.1038/s41598-018-35061-8

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.

Highlights

The chloroplast is a plant-specific and vital organelle that serves as the site of photosynthesis by converting light energy into chemical energy
The long repeat structures were extremely abundant compared with other species, and most were located in the intergenic spacer (IGS) region, which exhibited high GC content repeat structures and which may enhance cp genome stability
Because the inverted repeats (IRs) region had double the coverage compared with the remaining scaffold, it was used twice in the complete cpDNA sequence

Summary

Introduction

The chloroplast (cp) is a plant-specific and vital organelle that serves as the site of photosynthesis by converting light energy into chemical energy. This fern possesses special mechanisms to help it live in its severe environment Previous studies of this species have mostly focused on its secondary metabolites and related genes[14,15,16,17,18,19,20,21,22,23,24,25,26]. The thermal denaturation experiment showed that the D. fragrans cp genome exhibited strong thermal stability These data would provide useful information and contribute to a better understanding of how this special fern lives in harsh environments. It will be helpful in the study of secondary metabolism, genetic engineering, physiology and evolution within ferns and other species in the future

Methods

Results

Conclusion