The complete chloroplast genome sequence of Polypodiodes amoena (Polypodiaceae), an important medical fern

Abstract

Polypodiodes amoena is an important medical fern of Polypodiaceae. Its complete chloroplast genome is obtained through Illumina sequencing, which is 152,067 bp in length with a large single copy (LSC) region (81,187 bp), a small single copy (SSC) region (21,590 bp), and two inverted repeats (IRa and IRb) regions (24,645 bp). The genome encodes 130 genes, including 88 protein-coding genes, 33 tRNA genes, eight rRNA genes, and one pseudogene. ML phylogenetic analysis reveals that P. amoena is clustered with polypodiaceous ferns.

Keywords:

• Polypodiodes amoena
• chloroplast genome
• phylogenetic analysis

Polypodiodes amoena (Wallich ex Mettenius) Ching is an important medical fern of Polypodiaceae known as ‘Gusuibu’ for relieving rigidity of muscles and activating collaterals, and clearing heat and detoxication (National Pharmacopoeia Committee 2010). As a medicinal part, its rhizome is 5–7 mm in diameter, densely covered with dark-brown scales. The plant is epiphytic growing on rocks or on tree trunks with a wide distribution in south China such as Guangdong, Guangxi, and Guizhou, etc. (Zhang et al. 2013). In addition, Polypodiodes is a core group for investigating the controversial phylogenetic relationship among Polypodiastrum, Schellolepis, and Goniophlebium (Schneider et al. 2004; Lu and Li 2006). Therefore, the sequencing of the whole chloroplast genome of P. amoena lays a solid foundation for further exploring phylogeny of the family Polypodiaceae.

The fern was provided by South China Botanical Garden, Chinese Academy of Sciences (23°11′3.56″N, 113°21′43.28″E). The specimen is held by Herbarium of Sun Yat-sen University (SYS; voucher: SS Liu 20161021). The total genomic DNA was isolated from fresh leaves using Tiangen Plant Genomic DNA kit (Tiangen Biotech Co., Beijing, China). We constructed a paired-end genome library with an insert size of 300 bp, which was further sequenced on Illumina Hiseq 2500 platform (Illumina Inc., San Diego, CA). Approximately 2.24 Gb of sequence data were generated. After trimming and filtering through Trimmomatic v0.32 (Bolger et al. 2014), 2.03G clean data were de novo assembled into the chloroplast genome by Velvet v1.2.07 (Zerbino and Birney 2008). Annotation was conducted by tRNAscan-SE (Schattner et al. 2005) and DOGMA (Wyman et al. 2004) with default settings to identify protein-coding genes, rRNAs, and tRNAs.

The circular genome is 152,067 bp in size (Genbank accession number: MN017598) and comprises a large single copy (LSC) region (81,187 bp), a small single copy (SSC) region (21,590 bp), and two inverted repeats (IRa and IRb) regions (24,645 bp). The total GC content is 41.33%, while the corresponding values are 44.89%, 37.58%, and 40.15% in IRs, SSC, and LSC, respectively. The genome encodes 130 genes, including 88 protein-coding genes, 33 tRNA genes, eight rRNA genes, and one pseudogene. Among them, 13 genes are duplicated, including four protein-coding genes (rps12, rps7, psbA, and ycf2), five tRNA genes (trnH-GUG, trnI-GAU, trnA-UGC, trnT-UGU, and trnR-ACG) and four rRNA genes (rrn4.5, rrn5, rrn16, and rrn23). Moreover, 18 genes contain introns with 15 having one intron (ndhB, rps16, atpF, rpoC1, petB, petD, ndhA, rpl16, rpl2, trnG-UCC, trnV-UAC, trnA-UGC, trnI-GAU, trnL-UAA, and trnT-UGU), while three have three introns (ycf3, clpP, and rps12).

In order to assess the phylogenetic relationship among P. amoena and the other ferns, we selected 13 related complete chloroplast genomes with Alsophila spinulosa as outgroup. Their alignment was created by MAFFT (Katoh and Standley 2013) and further used to constructed Maximum Likelihood (ML) phylogenetic tree through RAxML with 1000 replicates (Stamatakis 2014). The result reveals that P. amoena is clustered with polypodiaceous fern with high bootstrap values (Figure 1). This study provides new genomic resources to resolve taxonomic disputes of Polypodiaceae.

Disclosure statement

The authors declare no conflict of interests. The authors alone are responsible for the content and writing of the paper.

Figure 1. Maximum-likelihood (ML) analysis of P. amoena and other related ferns based on the complete chloroplast genome sequence with Alsophila spinulosa as outgroup. Numbers in the nodes exhibit bootstrap support values.

Additional information

Funding

This work was supported by the National Natural Science Foundation of China [31370364, 31570652, 31670200, 31770587, and 31872670], the Natural Science Foundation of Guangdong Province, China [2016A030313320 and 2017A030313122], Science and Technology Planning Project of Guangdong Province, China [2017A030303007], Project of Department of Science and Technology of Shenzhen City, Guangdong, China [JCYJ20160425165447211, JCYJ20170413155402977, and JCYJ20170818155249053], and Science and Technology Planning Project of Guangzhou City, China [201804010389].