The complete chloroplast genome of Antiaris toxicaria, a medicinal and extremely toxic species

Abstract

Antiaris toxicaria (Antiaris, Moraceae) is a medicinal and extremely toxic species. To facilitate species identification and provide genetic information, we determined the complete chloroplast genome of A. toxicaria using the Illumina platform. The genome was 161,412 bp in length, comprising a large single-copy region (LSC) of 89,883 bp, a small single-copy region (SSC) of 20,375 bp, and a pair of inverted repeats (IRs) of 25,577 bp each. The genome contained 130 encoded genes in total, including 85 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the A. toxicaria chloroplast genome is 35.87%. The phylogenetic analysis revealed A. toxicaria was closely related to the genus Ficus within the family Moraceae.

Keywords:

• Complete chloroplast genome
• Antiaris toxicaria
• phylogenetic analysis

Antiaris toxicaria (Antiaris, Moraceae) is a medicinal and extremely toxic species. It is said that the utilization of A. toxicaria began in the 19th century. However, there is still rare genetic information of A. toxicaria. Herein, we reported the chloroplast genome of A. toxicaria. The annotated chloroplast genome has been submitted to GenBank under the accession number of MH606237.

We collected the fresh leaves of an A. toxicaria individual from Jinghong in Yunnan Province, China (100 °54′E, 21 °48′N). Voucher specimen of the species was stored in the Key Laboratory of Bio-resource and Eco-environment of Ministry of Education (Sichuan, China). The total DNA was extracted with the DNAsecure Plant Kit (TIANGEN). The whole-genome sequencing was carried out with the Hiseq4000 Platform (Illumina, USA). Finally, we obtained ∼10G high-quality base pairs of raw data. The software Bwa (Li 2013) and Samtools (Li et al. 2009) were used to map the Illumina reads to the reference Morus indica (DQ226511.1, Ravi et al. 2006) chloroplast genome. The mapped reads were extracted and then used to assemble the genome with the software NOVOPlasty v2.5.9 (Dierckxsens et al. 2017). We aligned the resulting contigs to the reference genome with Bwa and Samtools again and generated a complete genome by Genious v 11.1.14 (Kearse et al. 2012). Finally, we used GapCloser (Luo et al. 2012) to fill the gaps and obtain a chloroplast genome of A. toxicaria with a length of 161,412 bp. The annotation was performed with the software Plann (Huang and Cronk 2015) and Sequin (NCBI website).

The complete chloroplast genome of A. toxicaria contains two inverted repeat (IRA and IRB) regions with the length of 20,577 bp each, separated by a large single-copy (LSC) region of 89,883 bp and a small single-copy (SSC) region of 20,375 bp, respectively. The genome contains 130 genes, including 85 protein-coding genes (PCGs), 37 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes. Most of these genes are single copy genes, while 17 genes (6 PCGs, 7 tRNA genes, and 4 rRNA genes) were duplicated in the IR regions. The overall GC content of A. toxicaria chloroplast genome is 35.87%, and the LSC, SSC, and IR regions occupy 33.46%, 28.97% and 42.86%, respectively.

To infer the phylogenetic position of A. toxicaria and estimate the phylogenetic relationships within the family Moraceae, we reconstructed a phylogenetic tree based on the complete chloroplast genome sequences of 13 species including A. toxicaria. The sequences were aligned with the software MAFFT (Katoh and Standley 2013). And the phylogenetic tree was constructed using the software RaxML (Stamatakis 2014) with 100 bootstrap replicates based on the maximum likelihood (ML) method. The ML tree revealed A. toxicaria was closely related to the genus Ficus (Moraceae) with strongly support (Figure 1). Above all, we provide a valuable genomic information of A. toxicaria, which could help us identify and utilize this medicinal and extremely toxic.

Figure 1. Maximum likelihood (ML) phylogenetic tree based on the complete chloroplast genome sequences of Antiaris toxicaria and other 12 species. Numbers in the nodes are the bootstrap values from 100 replicates. Their accession numbers are as follows: Rosa roxburghii: NC_032038.1, Akebia trifoliata: NC_029427.1, Humulus lupulus: NC_028032.1, Cannabis sativa: NC_026562.1, Artocarpus heterophyllus: MG434693.1, Morus mongolica: NC_025772.2, Morus notabilis: NC_027110.1, Morus indica: DQ226511.1, Broussonetia papyrifera: NC_035569.1, Ficus carica: NC_035237.1, Ficus religiosa: NC_033979.1, Ficus racemosa: NC_028185.1.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was financially supported by Sichuan Provincial Department of Education [Grant 14ZB0268].