Abstract
The species of genus Actinidia are economically and nutritionally important fruits with remarkably high vitamin C content. Here, we assembled and characterized the complete chloroplast (cp) genome sequence of Actinidia fulvicoma (A. fulvicoma) using Illumina paired-end sequencing data. The cp genome is 157,339 bp in length, including a large single-copy region (LSC) of 88,741 bp, a small single-copy region (SSC) of 20,512 bp, and a pair of 24,043 bp inverted repeat (IR) regions. A total of 131 genes, consisting of 85 protein-coding genes, 38 tRNA genes, and 8 rRNA genes, were annotated in the A. fulvicoma cp genome. Phylogenetic analysis confirmed the evolutionary position of A. fulvicoma within the genus Actinidia.
Keywords: Actinidia fulvicoma, chloroplast genome, assembly, phylogeny
The classification of the genus Actinidia is difficult and the taxonomy of some taxa is still confusing. The species of Actinidia are highly variable in their vegetative structures, as well as in their flowers and fruits, which is the main reason for the difficulty in the classification of the genus. The species of Actinidia are particularly rich in vitamin C and vitamin K, and have been considered as medicine in traditional Chinese (Huang et al. 2013). Actinidia fulvicoma (A. fulvicoma) is mainly distributed from subtropical to tropical areas of China and Vietnam. Here, we report and characterize the complete cp genome of A. fulvicoma, which will pave the way for the classification of the genus Actinidia and provide important genomic resources for future genetic studies.
The genomic DNA was isolated from fresh leaves of A. fulvicoma collected from South China Botanical Garden (23°11′0.47″N, 113°21′37″E) using the DNeasy plant Mini Kit (Quiagen, Carlsbad, CA). The voucher specimen was deposited at the Herbarium of Nanjing Forestry University (accession number: 20160415AF02). After DNA extraction, an Illumina paired-end library was prepared, and then sequenced using Illumina Hiseq 2000 platform. Using Actinidia delociosa cp genome as a reference genome, we assembled the complete cp genome sequence of A. fulvicoma into a free-of-gap genome using BWA (Li 2013), AbySS (Simpson et al. 2009), CD-Hit (Li and Godzik 2006), and MacVector v17.0.7 from Illumina sequencing data, and annotated it using Plastid Genome Annotator (PGA) (Qu et al. 2019). The annotated cp genome of A. fulvicoma was then submitted to GenBank with accession number MN540960. The circular genome of A. fulvicoma was 157,339 bp in length, with a large single-copy (LSC) region of 88,741 bp, a small single-copy (SSC) region of 20,512 bp, and a pair of inverted repeat (IR) regions of 24,043 bp. The overall GC content of the whole cp genome was 37.17%, while the corresponding GC content of the IR regions was 42.92%, which was higher than that of LSC (35.46%) and SSC (31.1%). A total of 131 genes were annotated in A. setosa cp genome, including 85 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Among the 131 genes, most of them only contain one single copy, while 15 genes contain two copies (ndhB, rps7, ycf2, ycf15, rrn4.5, rrn5, rrn16, rrn23, trnA-UGC, trnfM-CAU, trnH-GUG, trnL-CAA, trnN-GUU, trnR-ACG, and trnV-GAC), and two genes (rps12 and trnI-CAU) were found to contain three and four copies, respectively.
To further clarify the phylogenetic position of A. fulvicoma, a neighbor-joining (NJ) tree was constructed based on 76 conserved protein-coding genes of 23 other plant cp genomes using MEGA 6.0 with 1000 bootstrap replicates (Tamura et al. 2013). As shown in Figure 1, we found that A. fulvicoma was clustered with other two Actinidia species with 100% bootstrap values. Additionally, A. fulvicoma was highly supported to evolutionarily close to Nicotiana tabacum, Capsicum annuum, and Solanum lycopersicum in the family Solanaceae.
Figure 1.
The Neighbor-Joining phylogenetic tree of 24 plant chloroplast genomes based on 76 conserved protein-coding genes. Bootstrap values are listed for each node. GenBank accession numbers are listed right to the scientific names.
Disclosure statement
No potential conflict of interest was reported by the authors.
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