The complete chloroplast genome sequence of Viola japonica (Violaceae)

Abstract

We determined the complete chloroplast genome sequence of Viola japonica using Illumina pair-end sequencing data. The whole chloroplast genome was 156,504 bp in length, consisting of a pair of inverted repeats (IR) of 26,427 bp, a large single-copy (LSC) region of 85,647 bp, and a small single-copy (SSC) region of 18,003 bp. The gene contents and order were exactly the same as published five Violaceae plastomes. A total of 111 unique genes were annotated, including 77 protein-coding genes, 30 tRNAs, and 4 rRNAs. Among the annotated genes, 16 genes contained one or two introns. The ML tree showed that V. japonica formed a clade with Viola seoulensis.

Keywords:

• Violaceae
• Viola
• chloroplast genome
• phylogeny

Violaceae Batch. consists of approximately 22 genera and 1000–1100 species of herbs, shrubs, lianas, and trees (Wahlert et al. 2014; Marcussen et al. 2015; Cheon et al. 2019). Viola L., the largest genus in the Violaceae, comprises 583–620 species and is distributed mainly in temperate and tropical regions (Clausen 1967; Yoo and Jang 2010; Wahlert et al. 2014, Cheon et al. 2019). This genus is known as one of the more difficult groups to classify and although many phylogenetic studies carried out, the phylogenetic relationships are still unclear among the section and species (Clausen 1967; Ballard et al. 1998; Yockteng et al. 2003; Yoo et al. 2005; Liang and Xing 2010; Yoo and Jang 2010).

In this study, we report the whole cp genome sequence of V. japonica to gain information for further studies on the phylogenomics. The sampled V. japonica was collected from Minoreum (33°28′32.9′′N, 126°30′29.8′′E), Jeju-si in Korea. The specimen (voucher number KWNU93664) was deposited the Kangwon National University Herbarium (KWNU). Total DNA was extracted using a DNeasy Plant Mini Kit (Qiagen Inc., Valencia, CA). Genomic DNA was used for sequencing with the Illumina Miseq (Illumina Inc., San Diego, CA) platform. Viola japonica was sequenced to produce 5,862,188 raw reads and 301 bp were obtained from them. Using these sequence data, we assembled the complete chloroplast genome with Geneious 7.1 (Biomatters Ltd, Auckland, New Zealand). Annotation of the chloroplast genome was based on an online available program, DOGMA (Wyman et al. 2004), coupled with manual corrections for start and stop codons. We also compared each gene to the published complete chloroplast genome sequences of Campanulaceae for correct gene annotation. The tRNAs were confirmed using tRNAscan-SE (Schattner et al. 2005). A circular plastid genome map was drawn using the OGDRAW program (Greiner et al. 2019).

The plastid genome of V. japonica (GenBank accession no. MT012304) is a circular DNA molecule 156,504 bp in length with 36.3% G + C content, consisting of a pair of inverted repeats (IR) of 26,427 bp, a large single-copy (LSC) region of 85,647 bp, and a small single-copy (SSC) region of 18,003 bp. The cp genome contains a total of 111 unique genes constituting 77 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. The gene contents and order were exactly the same with published five Violaceae plastomes (Viola mirabilis, Viola phalacrocarpa, Viola raddeana, Viola seoulensis, and Viola websteri). Among the annotated genes, 16 genes contain one or two introns (trnA-UGC, trnG-UCC, trnI-GAU, trnK-UUU, trnL-UAA, trnV-UAC, petB, petD, atpF, ndhA, ndhB, clpP, rpl2, rpl16, rps12, rpoC1, and ycf3).

To investigate the phylogenetic relationships among the Malphigiales, we conducted a phylogenetic analysis. A total of 76 protein-coding genes from 28 Malphigiales species and one outgroup (Averrhoa carambola) were aligned using MAFFT (Katoh et al. 2002). We then conducted maximum-likelihood (ML) analysis using RAxML v.7.4.2 with 1000 bootstrap replicates and the GTR + I model (Stamatakis 2006). The phylogenetic tree (Figure 1) is clearly divided into five clades at the family level. The Violaceae was monophyletic with a high support value (BS = 100) and was divided into two clades. Also, V. japonica was closely related to V. seoulensis.

Figure 1. The ML tree based on 76 protein-coding genes from 28 Malphigiales and one outgroup.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This work was supported by grants from Scientific Research [KNA1-1-13, 14-1] of Korea National Arboretum.