Assembly and comparative analysis of the complete mitochondrial genomes of Pyrus calleryana Decne. and Pyrus betulifolia Bunge
TL;DR
This study provides high-quality mitogenome assemblies for P. calleryana and P. betulifolia, revealing coexisting structural variations and highly conserved sequences, and thereby offers a significant genetic resource for the Rosaceae family that will facilitate further investigations into the molecular diversity and genetic evolution of wild pears.
Abstract
Pyrus calleryana and Pyrus betulifolia are wild pear germplasm resources characterized by robust stress resistance and diverse application potentials, serving as prominent pear rootstocks in China. However, their mitochondrial genomes (mitogenomes) remain poorly characterized. This study presents the sequencing, assembly, and comprehensive analysis of the complete mitogenomes of P. calleryana and P. betulifolia . The mitogenomes of P. betulifolia (432,496 bp) and P. calleryana (422,567 bp) are circular DNA molecules, with sizes within the known range for Pyrus and smaller than those of cultivated pear. Each genome encodes 35 protein-coding genes (PCGs), 3 rRNA genes, and 19–20 tRNA genes, with no core gene loss. The total number of open reading frames (ORFs) is comparable between the two species, each harboring a small set of species-specific ORFs. The mitogenomes of P. betulifolia and P. calleryana contain 139 and 136 simple sequence repeats (SSRs), as well as 520 and 480 dispersed repeats, respectively, with both genomes featuring 20 tandem repeats. Among the PCGs, histidine is the most abundant amino acid and CAU is the most frequently utilized codon (Relative synonymous codon usage = 1.55), while most PCGs in both species are under purifying selection (Ka/Ks< 1). Whole-genome alignment revealed a single nucleotide polymorphism (SNP) in both the core energy metabolism genes nad2 and atp1. Additionally, 54 mitochondrial plastid DNA fragments and 616 predicted C-to-U RNA-editing sites were identified in both mitogenomes. Collinearity analysis revealed extensive genome rearrangements in the two species. Phylogenetic trees constructed using both Pyrus -specific and Rosaceae -wide datasets demonstrate that P. betulifolia and P. calleryana cluster with other Pyrus species, showing the closest relationship to P. ussuriensis × P. communis ‘Zhongai1’, albeit with limited resolution. This study provides high-quality mitogenome assemblies for P. calleryana and P. betulifolia , revealing coexisting structural variations and highly conserved sequences, and thereby offers a significant genetic resource for the Rosaceae family that will facilitate further investigations into the molecular diversity and genetic evolution of wild pears.
