The complete chloroplast genome sequence of Acer takesimense (Sapindaceae), an endemic to Ullenung Island of Korea

Abstract

The complete chloroplast (cp) genome sequence of Acer takesimense, a member of maple tree and an endemic species to Ulleung Island of Korea, was firstly analyzed in this study. It was formed a typical circular structure of 157,023 bp in length and composed of a large single copy region (85,371 bp) and a small single copy region (18,160 bp) which were separated by two inverted repeat regions (26,746 bp). Interestingly, rps2 gene was pseudogene due to two deletions of 5 bp. In the phylogenetic tree using chloroplast genome sequence, it was clear that the genus Acer, a monophyletic group, was sister to Dipteronia in the subfamily Hippocastanoideae and A. takesimense was a sister group of A. palmatum.

Keywords:

• Acer takesimense
• endemic species
• Sapindaceae
• chloroplast genome

The genus Acer L., well-known as maple trees and the largest tree genus in the Northern Hemisphere besides oak tree (Quercus), is widely distributed from Europe to North America with the center of species diversity in the central and eastern Asia. It was classified to the family Aceraceae with Dipteronia but now it is recognized as a member of the family Sapindaceae in APG IV (2016) system. It includes over 120 species and has been suggested different infra-generic classification systems composed of 12-25 sections which are still unclear the relationships among them (Suh et al. 2000; Grimm et al. 2006; Li et al. 2006). Acer takesimense is an endemic to Ulleng Island, where located at the eastern sea of Korea and is famous place of its high endemism. For understanding the genomic feature of this plant, we analyzed the complete chloroplast genome sequence.

We collected the plant material from Bongrae-dong of Ulleung Island and the voucher was deposited at the Herbarium of Kyungpook National University (KNU). Complete chloroplast genome of Acer takesimense (MK329223) was sequenced by HiSeq4000 of Illumina. Totally 51,682,020 paired-end reads (2x151bp) were obtained and 226,486 reads were assembled to the reference chloroplast genomes after reads end trimming with an error probability limit of 0.01. And then assembled reads were de novo assembled using the Geneious assembler. Using the assembled contigs, we conducted to align and repeat the procedure up to make a single contig. Complete chloroplast genome was annotated using Geneious 10.2.6 (Kearse et al. 2012) with manual correction and tRNAScan-SE (Lowe and Eddy 1997) for tRNA gene. The average coverage of this chloroplast genome was 210.2. The phylogenetic tree was constructed with related Asteraceae members based on the concatenated 78 coding genes using RAxML (Stamatakis 2014)

It was typical circular form with 157,023 bp in length and comprised a large single copy region (LSC, 85,371 bp), a small single copy region (SSC, 18,160 bp), and two inverted repeat regions (IR, 26,746 bp). It was composed of 134 genes and they were identified 86 coding genes, eight rRNA genes, 37 tRNA genes, and three pseudogenes. rps2 gene was pseudogene as well as ycf1 and trnH, which were positioned in the boundary area of IR because of two deletions of 5 bp. In the phylogenetic tree conducted using the protein coding genes, the monophyly of the genus was strongly supported and A. takesimense was a sister group of A. palmatum (KY457568). And also, it was clear the sister relationship with the genus Dipteronia in the subfamily Hippocastanoideae (Figure 1). Comparing to A. palmatum chloroplast genome, it was 344bp shorter in length, especially in the inter genic spacer regions of LSC. From the result, it is expected to provide useful information for understanding the diversification and developing the molecular marker in the genus Acer.

Figure 1. Phylogenetic tree of Acer takesimense and related taxa using the complete chloroplast genome sequences.

Disclosure statement

The authors have no conflicts of interest about this study.

Additional information

Funding

This research was supported by the research grant of the Chungbuk National University in 2017 and the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education [2016R1A6A1A050511910].