The complete chloroplast genome sequence of Aspidopterys concava (Wall.) A. Juss. (Malpighiaceae).

Aspidopterys concava is related to a group of important medicinal plants in Malpighiaceae in southeast Asia. Here, we report the first chloroplast genome fully sequenced and annotated for Aspidopterys concava. The genome size was 160,441 bp and contained a large single-copy (LSC) region of 71,434 bp, a small single-copy (SSC) region of 53,544 bp, and a pair of inverted repeats (IRs) regions of 8943 bp. Total GC content was 37.9%. It contained 125 genes in total, comprising 82 protein-coding genes, 37 transfer RNA genes, and six ribosomal RNA genes. Phylogenetic analysis showed that A. concava was the most closely related to A. obcordata from the same genus.

Aspidopterys concava (Wall.) A. Juss. 1840 is a species in family Malpighiaceae distributed across China (Guangxi), the Indo-China Peninsula, Malaysia, Indonesia, and the Philippines (Qin 2010). This woody liana is well adapted to limestone substrates in harsh mountain terrain. According to the survey, residents of the Hechi and Chongzuo areas from Guangxi province (China) eat A. concava as a wild vegetable, underscoring its ecological and economic value. Moreover, a related species A. obcordata is used in Dai traditional medicine (Li et al. 2019; Gong et al. 2020), making A. concava an excellent candidate for bioprospecting for bioactive compounds. Here, we report the first fully assembled and annotated complete chloroplast genome for A. concava.

Fresh young leaves of A. concava were collected from seedlings growing in the Nanning Arboretum, Guangxi, China (108°17′30.46″ E longitude, 22°43′17.42″ N latitude). Tissues were immediately frozen in liquid nitrogen and stored at −80 °C before DNA extraction with a modified CTAB method (Doyle and Doyle 1987). A specimen was deposited at the herbarium of Guangxi Forestry Inventory and Planning Institute (Mr. Qin, gx_qinyonghua@126.com) under the voucher number Qin 200421005. A library was generated using TIANSeq Fast DNA Library Prep Kit NG102 (Illumina, Inc., San Diego, CA) and sequenced on the Illumina HiSeq TM 4000 Platform using paired end runs with 2 × 150 cycles. Briefly, genomic DNA was sonicated to ∼350 bp fragments. Data QC was conducted using Fastp (version 0.21.0) to parse 21.6 Gb clean data. The 144,832,380 reads at 150 bp length were de novo assembled using SPAdes 3.6.1 with K-mer sizes of 55, 87, and 121 (Bankevich et al. 2012). De novo assembled chloroplast contigs were concatenated into larger contigs using Sequencher 5.3.2 (Gene Codes Inc., Ann Arbor, MI). Automatic annotation of the chloroplast genomes was generated by CpGAVAS and a circular representation of both sequences was drawn using the online tool OGDR (https://chlorobox.mpimp-golm.mpg.de/OGDraw.html) (Lohse et al. 2007; Liu et al. 2012).

The chloroplast genome of A. concava is 160,441 bp in length with a typical quadripartite structure. It contains a large single-copy (LSC, 71,434 bp) region, a small single-copy (SSC, 53,544 bp) region, and a pair of inverted repeats (IRs, 8943 bp) regions. The GC-content of the whole cp genomes is 37.9%, and in LSC, SSC, and IR regions are 39.3%, 39.8%, and 38.0%, respectively. The cpDNA contains 125 genes including 82 protein-coding genes (PCGs), 37 transfer RNA genes (tRNAs), and six ribosomal RNA genes (rRNAs).

To determine the phylogenetic location of A. concava, it was aligned with 14 other representative species of Malpighiales using MAFFT v7 (Katoh and Standley 2013). A phylogenetic reconstruction was estimated with a maximum-likelihood (ML) analysis of a whole cp genome dataset using RAxML-HPC BlackBox v.8.1.24 with 1000 bootstrap replicates at the CIPRES Science Gateway (Stamatakis et al. 2008). The results showed that A. concava and the medicinal A. obcordata are strongly supported as sister in a clade containing Banisteriopsis caapi (Figure 1). The plastome of A. concava was similar to that of A. obcordata in length, but the latter had fewer genes including 79 protein-coding genes, 30 transfer RNAs, and four ribosomal RNAs.

Figure 1.

A maximum-likelihood tree reconstructed using 15 complete chloroplast genomes. Bootstrap support values (N = 1000) are shown at each node and the scale bar indicates the number of nucleotide substitutions per site. GenBank accession number used are: Aspidopterys concava (OL471043, in this study), Aspidopterys obcordata (MT590775), Viola websteri (NC_041585), Populus alba (AP008956), Ricinus communis (NC_016736), Manihot esculenta (NC_010433), Averrhoa carambola (KU569488), Hirtella racemosa (KX180069), Chrysobalanus icaco (KJ414480), Byrsonima coccolobifolia (MF359247), Byrsonima crassifolia (MF359248), Bunchosia argentea (NC_041491), Galphimia angustifolia (NC_043795), Banisteriopsis caapi (NC_037945), and Salix purpurea (KP019639).