Complete chloroplast genome and evolutionary analysis of Acer paihengii (Sapindales:Aceraceae)

Abstract

In this study, the complete chloroplast genome of Acer paihengii, a tree species native to China, was sequenced and assembled through second-generation sequencing. The complete chloroplast genome of A. paihengii is 155,967 bp in length with a typical quadripartite structure, encompassing 130 genes including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis of 22 related species indicated that A. paihengii was more closely related to Acer coriaceifolium and Acer sino-oblongum.

Keywords:

• Acer paihengii
• chloroplast genome
• phylogenetic analysis

Acer paihengii is a unique deciduous tree species with high ornamental value in China. It is mainly distributed in Yunnan Province, China, where it is a provincial key protected wild plant species (Zhou 2010; Qin et al. 2017). Most studies on Aceraceae plants in China mainly focus on genetic breeding, introduction and domestication, cultivation techniques, economic uses, and landscape ecological applications, among other aspects. However, few studies have focused on A. paihengii. The research involved in this species mainly focused on resource investigation and biodiversity.

The chloroplast (cp) genome is highly conserved among plants due to its semi-autonomous and maternal inheritance characteristics, and can thus provide important molecular data onto the characterization of plant systematic evolution and biogeography research (Gao et al. 2020; Yang et al. 2020). Here, the complete chloroplast genome of A. paihengii was assembled, annotated, and phylogenetically analyzed, thus providing crucial insights into the evolutionary relationship between A. paihengii and other members of the Acer genus such as Acer miaotaiense (Zhang et al. 2016), Acer buergerianum (Xu et al. 2017), Acer saccharum (Deng et al. 2019), Acer truncatum (Chen et al. 2019), and Acer tataricum subsp. ginnala (Yang et al. 2020).

Acer paihengii Fang was first mentioned in Act. Phytotax. Sin. 11: 169. 1966. Leaf samples of A. paihengii were collected from Henan Agricultural University (Henan, China, 113°67′E, 34°79′N) and the specimens were deposited in the Herbarium of Henan Agricultural University (http://bbg.henau.edu.cn/, Liu Yiping and E-mail: [email protected]) under the voucher number YJ20210325. Total genomic DNA was extracted using the OMEGA kit, after which an Illumina opposite-end library was constructed by Shanghai Yuanshen Biomedical Technology Co., Ltd. (Origingene, Shanghai, China) on an Illumina HiSeq TM sequencer (Illumina, San Diego, CA, USA). The raw data was approximately 5.26 G and low-quality sequences were filtered out to obtain clean and high-quality data. The chloroplast genome was assembled using the NOVOPlasty4.2 software (Nicolas et al. 2017). Gene annotation was performed using the PGA annotation software (https://github.com/quxiaojian/PGA) (Qu et al. 2019).

The whole length of the A. paihengii chloroplast genome (GenBank accession: MZ934750) is 155,967 bp, including a pair of 26,063 bp inverted repeat regions (IRa and IRb), a large single-copy (LSC) 85,798 bp region, and a small single-copy (SSC) 18,043 bp region. Furthermore, the total GC content of this circular DNA molecule was 35.62%. A total of 130 functional genes were annotated, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. These three types of genes accounted for 65.39, 28.46, and 6.15% of all annotated functional genes, respectively. Among them, a total of 15 genes (trnK-UUU, trnG, trnL-UAA, trnV-UAC, trnl-GUA, trnA-UGC, rps16, ropC1, atpF, petB, petD, rpl16, rpl2, ndhA, and ndhB) contained one intron. In contrast, clpP and rps12 possess two introns. Among which trnI-GUA, trnA-UGC, rpl2, ndhB, and rps12 exist as double copies.

To study the phylogenetic position of A. paihengii, 22 complete chloroplast genome sequences were downloaded from the NCBI GenBank. Sequence alignment was performed using MAFFT v7.158b (Katoh and Standley 2013). A phylogenetic tree was then generated via maximum likelihood analysis in RaxML (Stamatakis 2014). The development analysis results indicated that most nodes in the phylogenetic tree were strongly supported and all 23 Acer plants were clustered in an evolutionary branch. A. paihengii, A. coriaceifolium, and A. sino-oblongum clustered together, indicating a close evolutionary relationship (Figure 1). In summary, the complete chloroplast genome of A. paihengii obtained in this study provides a robust basis for future phylogenetic studies of the Acer genus.

Figure 1. Phylogenetic tree of 23 complete chloroplast genome sequences of members of the order Sapindales. The numbers next to the nodes represent the bootstrap support values.

The following sequences were used: Acer truncatum NC_037211.1(Chen et al. 2019), Acer miaotaiense NC_030343.1 (Zhang et al. 2016), Acer amplum subsp. catalpifolium NC_041080.1 (Wang et al. 2019), Acer tataricum subsp. ginnala MN790641.1 (Yang et al. 2020), Acer wilsonii NC_040988.1, Acer tutcheri NC_051542.1 (Shi et al. 2020), Acer buergerianum NC_034744.1 (Xu et al. 2017), Acer palmatum NC_034932.1, Acer laevigatum NC_042443.1, Acer tsinglingense MN393475.1 (Dong et al. 2019), Acer yangbiense MN652924.1 (Ling and Zhang 2020), Acer macrophyllum NC_056217.1, Acer saccharum NC_051960.1 (Deng et al. 2019), Acer sutchuenense NC_049166.1 (Zhang et al. 2020), Acer paihengii MZ934750.1, Acer sino-oblongum NC_040106.1, Acer cinnamomifolium MN414240.1 (Chen et al. 2019), Acer nikoense NC_049165.1 (Fu et al. 2020), Acer griseum NC_034346.1 (Wang et al. 2017), Acer davidii NC_030331.1 (Jia et al. 2016), Acer morrisonense NC_029371.1 (Li et al. 2017), Acer tegmentosum MK942342.1 (Kim et al. 2019), Aesculus wangii NC_035955.1 (Zheng et al. 2018).

Ethical approval

We ensure that all experiments comply with ethical requirements. The research permission is provided by Henan Agricultural University.

Author contributions

Yiping Liu: Conceptualization; Project administration; Resources; Supervision; Review and editing. Yunru Zhai: Resources; Data curation; Software; Formal analysis; Original draft; Review and editing; Visualization. Dan He: Methodology; Conceptualization. Hongli Liu: Conceptualization; Review and editing. Man Zhang: Methodology; Conceptualization. Dezheng Kong: Supervision; Project administration; Funding acquisition.

Disclosure statement

No potential conflict of interest was reported by the author(s). We guarantee that this article has not been submitted to other journals at the same time, and that all content has not been published. All authors agree to the publication of the article and have no conflict of interest, financial or otherwise.

Data availability statement

The genome sequence data supporting the findings of this study are openly available in the NCBI GenBank database at https://www.ncbi.nlm.nih.gov/ under the accession no. MZ934750. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA767933, SRR16970252, and SAMN22253490, respectively.

Additional information

Funding

This work was supported by the National Natural Science Foundation of China [No. 31600568], the Major Research Project of Henan University [21A220003], and the Scientific and Technological Innovation Foundation of Henan Agricultural University [KJCX2017C01].