Complete sequence and comparative analysis of the mitochondrial genome of the rare and endangered Clematis acerifolia, the first clematis mitogenome to provide new insights into the phylogenetic evolutionary status of the genus

Dan Liu; Kai Qu; Yangchen Yuan; Zhiheng Zhao; Ying Chen; Biao Han; Wei Li; Yousry A El-Kassaby; Yangyang Yin; Xiaoman Xie; Boqiang Tong; Hongshan Liu

doi:10.3389/fgene.2022.1050040

Complete sequence and comparative analysis of the mitochondrial genome of the rare and endangered Clematis acerifolia, the first clematis mitogenome to provide new insights into the phylogenetic evolutionary status of the genus

Front Genet. 2023 Jan 4:13:1050040. doi: 10.3389/fgene.2022.1050040. eCollection 2022.

Authors

Dan Liu^{1

2}, Kai Qu², Yangchen Yuan^{3

4}, Zhiheng Zhao⁵, Ying Chen⁶, Biao Han¹, Wei Li², Yousry A El-Kassaby⁷, Yangyang Yin⁸, Xiaoman Xie¹, Boqiang Tong¹, Hongshan Liu⁴

Affiliations

¹ Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, China.
² State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
³ College of Landscape Architecture and Tourism, Hebei Agricultural University, Baoding, China.
⁴ Hebei Hongya Mountain State-Owned Forest Farm, Baoding, China.
⁵ Guangxi Forestry Research Institute, Guangxi Key Laboratory of Special Non-wood Forest Cultivation &; Utilization, Nanning, China.
⁶ Forestry Protection and Development Service Center of Shandong Province, Jinan, China.
⁷ Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada.
⁸ Wuhan Benagen Technology Co., Ltd, Wuhan, China.

Abstract

Clematis is one of the large worldwide genera of the Ranunculaceae Juss. Family, with high ornamental and medicinal value. China is the modern distribution centre of Clematis with abundant natural populations. Due to the complexity and high morphological diversity of Clematis, the genus is difficult to classify systematically, and in particular, the phylogenetic position of the endangered Clematis acerifolia is highly controversial. The use of the mitochondrial complete genome is a powerful molecular method that is frequently used for inferring plants phylogenies. However, studies on Clematis mitogenome are rare, thus limiting our full understanding of its phylogeny and genome evolution. Here, we sequenced and annotated the C. acerifolia mt genome using Illumina short- and Nanopore long-reads, characterized the species first complete mitogenome, and performed a comparative phylogenetic analysis with its close relatives. The total length of the C. acerifolia mitogenome is 698,247 bp and the main structure is multi-branched (linear molecule 1 and circular molecule 2). We annotated 55 genes, including 35 protein-coding, 17 tRNA, and 3 rRNA genes. The C. acerifolia mitogenome has extremely unconserved structurally, with extensive sequence transfer between the chloroplast and mitochondrial organelles, sequence repeats, and RNA editing. The phylogenetic position of C. acerifolia was determined by constructing the species mitogenome with 24 angiosperms. Further, our C. acerifolia mitogenome characteristics investigation included GC contents, codon usage, repeats and synteny analysis. Overall, our results are expected to provide fundamental information for C. acerifolia mitogenome evolution and confirm the validity of mitochondrial analysis in determining the phylogenetic positioning of Clematis plants.

Keywords: Clematis acerifolia; clematis; mitochondrial genome; organelle genome; phylogenetic relationship; repeats.

Associated data

figshare/10.6084/m9.figshare.21299757.v1

Grants and funding

This research was supported by the National Forest Germplasm Resources Sharing Service Platform Construction and Operation Project (2005 - DKA21003), and the State Forestry and Grassland Administration Rare and Endangered Species Investigation and Supervision and Industry Regulation Project (2,020,070,316).