Complete mitochondrial genome of the endangered Prunus pedunculata (Prunoideae, Rosaceae) in China: characterization and phylogenetic analysis

Qian Liu; Zinian Wu; Chunyu Tian; Yanting Yang; Lemeng Liu; Yumei Feng; Zhiyong Li

doi:10.3389/fpls.2023.1266797

Complete mitochondrial genome of the endangered Prunus pedunculata (Prunoideae, Rosaceae) in China: characterization and phylogenetic analysis

Front Plant Sci. 2023 Dec 8:14:1266797. doi: 10.3389/fpls.2023.1266797. eCollection 2023.

Authors

Qian Liu¹, Zinian Wu^{1

2}, Chunyu Tian¹, Yanting Yang¹, Lemeng Liu¹, Yumei Feng¹, Zhiyong Li^{1

2}

Affiliations

¹ Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China.
² Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot, China.

Abstract

Introduction: Prunus pedunculata (Prunoideae: Rosaceae), a relic shrub with strong resistance and multiple application values, is endangered in China. Extensive research had been devoted to gene expression, molecular markers, plastid genome analysis, and genetic background investigations of P. pedunculata. However, the mitochondrial genome of this species has not been systematically described, owing to the complexity of the plant mitogenome.

Methods: In the present research, the complete mitochondrial genome of P. pedunculata was assembled, annotated, and characterized. The genomic features, gene content and repetitive sequences were analyzed. The genomic variation and phylogenetic analysis have been extensively enumerated.

Results and discussion: The P. pedunculata mitogenome is a circular molecule with a total length of 405,855 bp and a GC content of 45.63%, which are the smallest size and highest GC content among the known Prunus mitochondrial genomes. The mitogenome of P. pedunculata encodes 62 genes, including 34 unique protein-coding genes (PCGs, excluding three possible pseudogenes), three ribosomal RNA genes, and 19 transfer RNA genes. The mitogenome is rich in repetitive sequences, counting 112 simple sequence repeats, 15 tandem repeats, and 50 interspersed repetitive sequences, with a total repeat length of 11,793 bp, accounting for 2.91% of the complete genome. Leucine (Leu) was a predominant amino acid in PCGs, with a frequency of 10.67%, whereas cysteine (Cys) and tryptophan (Trp) were the least adopted. The most frequently used codon was UUU (Phe), with a relative synonymous codon usage (RSCU) value of 1.12. Selective pressure was calculated based on 20 shared PCGs in the mitogenomes of the 32 species, most of which were subjected to purifying selection (Ka/Ks < 1), whereas ccmC and ccmFn underwent positive selection. A total of 262 potential RNA editing sites in 26 PCGs were identified. Furthermore, 56 chloroplast-derived fragments were ascertained in the mitogenome, ranging from 30 to 858 bp, and were mainly located across IGS (intergenic spacer) regions or rRNA genes. These findings verify the occurrence of intracellular gene transfer events from the chloroplast to the mitochondria. Furthermore, the phylogenetic relationship of P. pedunculata was supported by the mitogenome data of 30 other taxa of the Rosaceae family. Understanding the mitochondrial genome characteristics of P. pedunculata is of great importance to promote comprehension of its genetic background and this study provides a basis for the genetic breeding of Prunus.

Keywords: Prunus pedunculata; RNA editing; endangered plants; gene transfer; mitochondrial genome; phylogenetic analysis.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. The research was funded by the Central Public-interest Scientific Institution Basal Research Fund (No. Y2023PT02), Inner Mongolia Science and Technology Plan (2021CG0019, 2020GG0127 and 2022YFHH0140), Hohhot Science and Technology Plan (2022-she-zhong-1-2), High-level talents for scientific research funds for Inner Mongolia Autonomous Region (2202000010131440006).