The complete chloroplast genome sequence of the Korean maple tree (Acer pseudosieboldianum (Pax) Kom.)

Abstract

The complete chloroplast genome sequence of Acer pseudosieboldianum (Sapindaceae) was determined. The chloroplast genome of A. pseudosieboldianum is 157,053 bp in length with two inverted repeats (26,747 bp) between a large single-copy (85,391 bp) and a small single-copy (18,168 bp). The GC content was 37.8% and it was composed of 86 coding genes, eight rRNA genes, 37 tRNA genes, and two pseudogenes, rps2, and ycf1. Molecular phylogenetic analysis based on the plastid genome sequences strongly supported the hypothesis that A. pseudosieboldianum was embedded in the series Palmata of section Palmata. However, the phylogenetic positions of A. ukurunduense and A. buergerianum, which are a members of the series Penninervia of sections Palmata and Pentaphylla, respectively, were incongruent with the recent sectional classification system.

Keywords:

• Acer pseudosieboldianum
• chloroplast genome
• section Palmata

Introduction

The genus Acer L. is a large plant group that includes over 120 species and is one of the most diverse and ecologically important tree genera in the northern temperate forest (Areces-Berazain et al. 2020; Yu et al. 2021). Although different infra-generic classification systems composed of 12–25 sections have been suggested, the relationships and circumscription in this group remain unclear (Suh et al. 2000; Grimm et al. 2006; Li et al. 2006). To resolve this problem, a phylogenomic study was recently conducted based on the complete chloroplast genome sequences (Areces-Berazain et al. 2020; Yu et al. 2021), using both genomic data and biogeographical information (Li et al. 2019) in the major lineages. Acer pseudosieboldianum (Pax) Kom. 1904, also known as a Korean maple or purplebloom maple, is taxonomically classified as a member of the largest section Palmata in the genus. In the present study, we confirmed the complete chloroplast genome sequence of A. pseudosieboldianum and evaluated its phylogenetic position within the genus.

Materials and methods

To obtain the complete chloroplast genome sequence of A. pseudosieboldianum, we collected plant material (Figure 1) from Jeongok-valley, Mt. Juwang-san, Korea (36° 36′ 92.57″ N, 129° 18′ 32.43″ E, alt. 338 m) and conducted the molecular phylogenetic analysis of the genus Acer using previously published genome data together. The voucher specimen of the plant material was deposited at the Herbarium of Kyungpook National University (KNU) under accession number Back-2016 ([email protected]). Total genomic DNA was extracted from a dehydrated leaf using silica gel by following the manufacturer’s protocol using the DNeasy Plant Mini Kit (Qiagen, Hilden, Germany). Then, the sample was sequenced using Illumina HiSeq4000 (Illumina, San Diego, CA) and totally 46,089,072 paired end reads (151 bp in length) were obtained. For trimming the raw data, we used trimmomatic 0.39 (Bolger et al. 2014) with the option LEADING:10, TRAILING:10, SLIDINGWINDOW:4:20, and MINLEN:50. After trimming, 622,944 reads were assembled into the reference plastome of A. palmatum (NC 034932) following Kim and Chase’s protocol (Kim and Chase 2017). The final circular cp genome sequence was constructed, and the coverage depth of the genome was 555.6 (Figure S1). Based on existing genes in other maple tree chloroplast genomes, all of the genes were annotated using Geneious 10.2.6 (Kearse et al. 2012) with manual correction and tRNAScan-SE (Lowe and Eddy 1997), especially for the tRNA gene. The cp genome map was drawn by CPGView program (Liu et al. 2023; http://www.1kmpg.cn/cpgview/). To understand the phylogenetic relationship of A. pseudosieboldianum and its related taxa, the phylogenetic tree was constructed based on the concatenated 78 coding genes of the released Sapindaceae chloroplast genome data using RAxML (Stamatakis 2014). The cp genome of Aesculus wangii (NC 035955) was included as an outgroup, and those of 32 related taxa, 30 released data from the genus Acer (Zhou et al. 2016; Xu et al. 2017; Dong et al. 2019; Kim et al. 2019; Ling & Zhang 2019; Shi et al. 2020; Liu et al. 2022; Wang et al. 2022), and both Dipteronia dyeriana (NC 031899) and D. sinensis (MK 193760) were also analyzed together (Supplementary table 1).

Figure 1. Photographs of Acer pseudosieboldianum taken by Mr. S. H. Park at the same place of sample collection site: (A) plant and (B) leaves with nine lobes. It is generally small tree up to 8 m tall and has deciduous palmate leaves with 9–11 lobes. The number of lobes are one of key characters for distinguishing the species from the related taxa in Korea. The leaves are densely pubescent when young and leaf blade is abaxially light green but adaxially dark green.

Results and discussion

The complete chloroplast genome of A. pseudosieboldianum (NC 046487, Figure 2, Figure S2) is a typical circular form composed of 157,053 bp in length with two inverted repeats (IRs) (26,747 bp) between a large single-copy (LSC) (85,391 bp) and a small single-copy (SSC) (18,168 bp) with 37.8% GC contents. It was composed of 134 genes and they identified 86 coding genes, eight rRNA genes, 37 tRNA genes, and two pseudogenes of rps2 with a 15-bp deletion in LSC and ycf1 in the boundary area of IR.

Figure 2. Complete chloroplast genome map of Acer pseudosieboldianum, containing six tracks. From the center, the first track shows the dispersed repeats which consist of direct (red) and palindromic (green) repeats. The second and third tracks show the long and short tandem repeats, respectively. The regional composition of the genome, LSC, SSC, and IRs, is identified on the fourth track. In the fifth track, the GC content along the genome is plotted. The genes are shown on the outer sixth track.

The monophyly of the genus was strongly supported in the phylogenetic tree conducted with the plastid genome sequences of 30 released data from the genus Acer and two genomes of close related genera Dipteronia, and the sister relationship between the genus Acer and Dipteronia was also cleared (Figure 3). Within the genus, A. pseudosieboldianum was embedded in the series Palmata of section Palmata with its related species, though the section Palmata was paraphyletic because the series Penninervia formed a clade with section Spicata. Section Lithocarpa was sister to the sections Palmata + Spicata. In addition, A. buergerianum, a member of section Pentaphylla, was included in the section Palmata clade (Figure 3). These results indicate that the infra-sectional classification within section Palmata needs to be reconsidered due to the paraphyletic relationship of A. ukurunduense (series Penninervia).

Figure 3. Phylogenetic tree of Acer pseudosieboldianum and related taxa inferred from maximum likelihood based on the 78 coding genes sequences. The outgroup was Aesculus wangii (NC 035955). The bootstrap supporting values are described on the branches, with black spots indicating 100% BP values. The position of A. pseudosieboldianum is indicated in red and the sectional classification of A. pseudosieboldianum and its related taxa are shown in different colors. The details of cp genome sequences of 30 Acer and two Dipteronia for the present molecular phylogenetic analysis are provided in Supplementary Table 1.

Conclusions

The complete chloroplast genome of the Korean maple tree Acer pseudosieboldianum is presented for the first time in this study. It has a typical circular form, composed of 157,053 bp and 134 genes. Based on the molecular phylogenetic analysis using cp genome sequence data, the phylogenetic position of A. pseudosieboldianum was confirmed within the series Palmata of section Palmata in the genus. However, the sectional classification of the genus needs to be reconsidered due to the paraphyly of section Palmata.

Author contributions

Conceiving and designing, JSK and HTK; performing and analyzing data, HTK; writing – original draft preparation, JSK and HTK; writing – review and editing, JSK; supervision, JSK; all authors have read and agreed to the published version of the manuscript.

Ethical approval

Acer pseudosieboldianum is not an endangered or protected species; therefore, specific permission was not required to collect this species. Research on this species, including the collection of plant material, was conducted following the guidelines provided by Kyungpook National University.

Disclosure statement

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

Data availability statement

The genome sequence data that support the findings of this study are available in GenBank of NCBI under the accession no. NC 046487 (https://www.ncbi.nlm.nih.gov/nucleotide/NC_046487.1). The associated BioProject, SRA, and Bio-Sample numbers are PRJNA914786, SRR22857887, and SAMN32358162, respectively.

Additional information

Funding

This work was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education [2018R1D1A3B07048213 and 2020R1I1A2053517].