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.

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 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 , 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 0 E, 34 79 0 N) and the specimens were deposited in the Herbarium of Henan Agricultural University (http://bbg.henau. edu.cn/, Liu Yiping and E-mail: Lyp_163@163.com) 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).
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.

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

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.