key: cord-0884256-29ake6j4
authors: Wang, Qi; Xu, Wenting; Zhou, Lirong; Mai, Biwei; Zhu, Naiyun; Zhao, Xiaoli; Lei, Zhixian
title: The complete chloroplast genome of Dryopteris crassirhizoma Nakai
date: 2021-05-27
journal: Mitochondrial DNA. Part B, Resources
DOI: 10.1080/23802359.2021.1933634
sha: 744ffbaf627dbaa40433b4f419ef497b9ff0716e
doc_id: 884256
cord_uid: 29ake6j4

Dryopteris crassirhizoma Nakai is a fern plant with important evolutionary and medicinal values. Herein, we assembled the complete chloroplast genome of D. crassirhizoma by next-generation sequencing technology. The complete chloroplast genome of D. crassirhizoma was 153,355 bp in length, and the GC content was 42.86%; the genome consisted of a pair of inverted repeats (IRs, 23,470 bp), a small single copy region (SSC, 21,570 bp) and a large single copy region (LSC, 84,854 bp). The genome contained 111 genes, namely, 73 protein-coding genes, 34 tRNA genes and four rRNA genes. The phylogenetic analysis suggested that both D. crassirhizoma and D. decipiens from Dryopteridaceae were most closely related to Lepisorus clathratus from Polypodiaceae.

Dryopteris crassirhizoma Nakai is a fern plant classified into the Dryopteridaceae family (Sessa et al. 2012) . The dry rhizomes and petiole residues of this plant is a traditional Chinese herbal medicine used for the treatment of diseases such as fever, cancer, ancylostomiasis and other parasitosis. In particular, this herb was used to cure severe acute respiratory syndrome (SARS) and bird flu (Zhao et al. 2007; Wang et al. 2017) . Previous studies have demonstrated that special active ingredients from its dried rhizome show potential pharmacological activities (Wang et al. 2017; Chen et al. 2020 ), but limited genomic and genetic resources have impeded the precise identification of D. crassirhizoma until now. Herein, we generated the whole chloroplast genome of D. crassirhizoma, which will provide useful informative data for further research on molecular identification of D. crassirhizoma and evolution of fern plants.

DNA was isolated via the modified CTAB method from the fresh leaves of an individual D. crassirhizoma plant in the greenhouse at Chengxi District (110 19.245 0 E, 19 59.757 0 N), Haikou, China (Ding et al. 2020) , and a specimen was deposited at the herbarium of Hainan Maternal and Children's Medical Center (http://www.hnwcmc.com/, Qi Wang, wqi1220@163.com) under voucher number 11_1. The DNA library was constructed with the NEBNext Ultra TM DNA library Prep Kit (New England Biolabs, Ipswich, MA) and then sequenced on the Illumina NovaSeq platform (Illumina, CA, USA). The raw data were filtered using SOAPnuke v1.3.0 with default settings (Chen et al. 2018) , and the paired-end reads of the cleaned data were assembled into circular contigs using SPAdes v3.13.0 with the parameter -k 127 (Bankevich et al. 2012) . The final draft cp genome was corrected using GapCloser v 1.12 (Xu et al. 2020) . The annotation was performed using PGA (Qu et al. 2019 ) and then submitted to GenBank (accession no. MW557379).

This complete chloroplast genome of D. crassirhizoma was 153,355 bp in length and consisted of a small single copy region (SSC) of 21,570 bp, a large single copy (LSC) region of 84,854 bp and a pair of inverted repeat (IR) regions of 23,470 bp. This cp genome showed an overall GC content of 42.86%, whereas the corresponding GC contents in the SSC, LSC and IR regions were 41.83%, 40.25% and 45.37%, respectively. Genome annotation indicated the presence of 111 full-length genes, including 73 protein-coding genes with an average length of 597.08 bp, 34 transfer RNA genes with an average length of 75.31 bp and four ribosomal RNA genes with an average length of 1123.5 bp. Seven genes (atpF, matK, ndhA, petA, rpoC1, rps12, rps16) contained a single intron, and two genes (clpP, ycf3) contained two introns, whereas eight genes (rps12, rrn5, rrn4, rrn23, rrn16, trnA-UGC, trnG-UCC, trnL-UAA) had two copies in this cp genome.

Phylogenetic analysis was performed with the neighbor-joining (NJ) method in MEGA X based on 14 complete cp genomes of ferns, including D. crassirhizoma (Kumar et al. 2018) . The results revealed that D. crassirhizoma was classified into the genus of Dryopeteris from Dryopteridaceae with high bootstrap support values, indicating that the genus of Dryopteris has a closer evolutionary relationship with the genus of Lepisorus than with the genera of Athyrium, Diplazium, Rhachidosorus and Cystopteris (Figure 1 ). This finding is consistent with a previous study of phylogenetic trees in Dryopteridaceae and Polypodiaceae (Wang et al. 2019) . 

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing

SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data

Acylphloroglucinols-based meroterpenoid enantiomers with antiviral activities from Dryopteris crassirhizoma

Genome sequence of agarwood tree Aquilaria sinensis (Lour.) Spreng: the first chromosome-level draft genome in the Thymelaeceae family

Mega x: molecular evolutionary genetics analysis across computing platforms

PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes

Unraveling reticulate evolution in North American Dryopteris (Dryopteridaceae)

Anti-influenza virus (H5N1) activity screening on the phloroglucinols from rhizomes of Dryopteris crassirhizoma

The complete chloroplast genome sequence of a typical alpine fern Lepisorus waltonii (Ching) SL Yu in Polypodiaceae

TGS-GapCloser: a fast and accurate gap closer for large genomes with low coverage of error-prone long reads

Identification of Dryopteris crassirhizoma and the adulterant species based on cpDNA rbcL and translated amino acid sequences

No potential conflict of interest was reported by the author(s).

This research was supported by the Natural Science Foundation of Hainan Province [819QN396].

The data that support the findings of this study are openly available in the US National Center for Biotechnology Information (NCBI database) at https://www.ncbi.nlm.nih.gov/, reference number: MW557379. The associated BioProject, BioSample and SRA numbers are PRJNA692559, SAMN17348916, SRR13447701 and SSR13447702.