The complete chloroplast genome of Choerospondias axillaris (Roxb.) B. L. Burtt et A. W. Hill, an ancient and versatile plant

Abstract

Choerospondias axillaris, an ancient and versatile plant of Anacardiaceae, which is widespread in eastern Asia. The complete chloroplast (cp) genome of C. axillaris was generated and determined in this work. The genome of cp was 159,131 bp in length with a total GC content of 37.6%. The circular molecular genome presented a quadripartite structure, comprising a 91,305 bp large single-copy region (LSC), a 19,092 bp small single-copy region (SSC), and a pair of inverted repeat regions with 24,367 bp. The complete genome encoded 128 genes, including 83 protein coding, 37 tRNA and eight rRNA genes. Phylogenetic analysis indicated that C. axillaris was most related to Sclerocarya birrea.

Keywords:

• Choerospondias axillaris
• Anacardiaceae
• chloroplast genome
• Illumina sequencing

Choerospondias axillaris (Roxb.) B. L. Burtt et A. W. Hill is a deciduous broad-leaved tree species of Anacardiaceae, which is a monospecific species of genus Choerospondias in eastern Asia and mainly distributed in Japan and South China. C. axillaris has a long cultivation and utilization history, whose fruit fossil with 15-million-year-old was first discovered in Fujian, China (Wang et al. 2020). For its characteristics of fast growth and strong adaptability, C. axillaris is suitable for artificial afforestation. So that C. axillaris has a growing popularity and important economic effects, it is noted for timber, edible, and medicinal values. Previous researches on C. axillaris have mainly focused on pharmacological action (Sun et al. 2015; Mann et al. 2020), phytochemical investigation (Li et al. 2018), photosynthetic physiology (Li and Xu 2020), and morphological diversity (Wang et al. 2019). However, there is no report on the chloroplast (cp) genome of C. axillaris. The complete cp genome has been progressively analyzed in diverse species to provide insight into species identification and population dynamics (Shaw et al. 2014). In this study, we established and characterized the complete C. axillaris cp genome and performed phylogenetic analysis with the cp genomes of other species of Anacardiaceae.

The leaves of C. axillaris were sampled from Chenshan Botanical Garden, Shanghai, China (31°08′N, 121°18′E). And the voucher specimen (Accession number: CSSH202104) was stored in Shanxi Datong University (http://www.sxdtdx.edu.cn/, Kun Zhang, [email protected]). Genomic DNA extraction of C. axillaris was processed according to the modified CTAB method (Murray and Thompson 1980). After DNA purification, the libraries with an average length of 350 bp were constructed using the NexteraXT DNA Library Preparation Kit (Illumina, San Diego, CA), and high-throughput sequencing was carried out on Illumina Novaseq 6000 platform. In total, 3.7 Gb clean reads were generated by editing raw sequence reads with NGS QC Tool kit (Patel and Jain 2012). The cp genome was de novo assembled by SPAdes version 3.11.0 software (Bankevich et al. 2012), and cp genes of C. axillaris were annotated by using PGA (Qu et al. 2019) through aligning to genome of Sclerocarya birrea (A. Rich.) Hochst cp (Accession number: NC043919). The annotated sequence was submitted to GenBank and data were openly available at (https://www.ncbi.nlm.nih.gov/nuccore/MZ042936.1/) under the accession MZ042936. The associated SRA number is SRR14328382.

The cp genome of C. axillaris was a circular molecular genome presented a quadripartite structure. The genome was 159,131 bp in length, and consisted of a 91,305 bp large single-copy (LSC) region, a 19,092 bp small single-copy (SSC) region, and a pair of inverted repeat (IRa and IRb) regions with 24,367 bp. The overall GC content detected in the C. axillaris cp genome was 37.6%. The assembled genome encoded 128 genes, including 83 protein coding, 37 tRNA and eight rRNA genes. The majority of these genes did not contain intron, while 15 genes (atpF, ndhA, ndhB, petB, petD, rpl2, rpl16, rpoC1, rps16, trnA-UGC, trnG-UCC, trnI-GAU, trnK-UUU, trnL-UAA, and trnV-UAC) contained one intron and two genes (clpP and ycf3) contained double introns. All genes occurred as a single copy, except that 10 genes (ycf1, rrn4.5, rrn5, rrn16, rrn23, tRNA-Ile, tRNA-Ala, tRNA-Arg, tRNA-Asn, and ORF302) were duplicated in IR regions.

To further determine the phylogenetic position of C. axillaris, 20 complete cp genomes of different species within Anacardiaceae family and other three species as outgroup were selected to construct a phylogenetic tree. The sequences were downloaded from NCBI GenBank database and aligned by using MAFFT (Katoh and Standley 2013). Subsequently, a maximum-likelihood phylogenetic tree was established by IQTREE version 1.6 (Jana et al. 2016) with 1000 bootstrap replicates. The main genera displayed on the phylogenetic tree were Rhus, Mangifera, Toxicodendron, Pistacia, and Spondias. Phylogenetic analysis revealed that C. axillaris exhibited the closest relationship with Sclerocarya birrea (Figure 1). The information derived from this work provides a basis for future genetic and evolutionary studies in C. axillaris, which may help facilitate the utilization and protection of this ancient and versatile plant.

Figure 1. Maximum-likelihood phylogenetic tree for C. axillaris based on 21 complete cp genome in Anacardiaceae, with Litchi chinensis Sonn., Punica granatum L., and Ficus carica L. as outgroup. The bootstrap values are located on each node and the Genbank accession numbers are shown beside the Latin name of the species.

Disclosure statement

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the article.

Data availability statement

The assembled complete cp genome sequence of C. axillaris has been submitted to GenBank of NCBI and is openly available under the accession number: MZ042936 (https://www.ncbi.nlm.nih.gov/nuccore/MZ042936.1/). The associated BioProject, SRA, and Bio-Sample numbers are PRJNA725317, SRR14328382, and SAMN18875962, respectively.

Additional information

Funding

This work was supported by Science and Technology Innovation Project of Higher Education in Shanxi Province [Grant No. 2019L0770] and Datong Science and Technology Bureau Applied Basic Research Project [Grant No. 2020137].