Characterizing complete mitochondrial genome of Aquilegia amurensis and its evolutionary implications

Abstract

Background: Aquilegia is a model system for studying the evolution of adaptive radiation. However, very few studies have been conducted on the Aquilegia mitochondrial genome. Since mitochondria play a key role in plant adaptation to abiotic stress, analyzing the mitochondrial genome may provide a new perspective for understanding adaptive evolution.

Results: The Aquilegia amurensis mitochondrial genome was characterized by a circular chromosome and two linear chromosomes, with a total length of 538,736 bp; the genes included 33 protein-coding genes, 24 transfer RNA (tRNA) genes and 3 ribosomal RNA (rRNA) genes. We subsequently conducted a phylogenetic analysis based on single nucleotide polymorphisms (SNPs) in the mitochondrial genomes of 18 Aquilegia species, which were roughly divided into two clades: the European-Asian clade and the North American clade. Moreover, the genes mttB and rpl5 were shown to be positively selected in European-Asian species, and they may help European and Asian species adapt to environmental changes.

Conclusions: In this study, we assembled and annotated the first mitochondrial genome of the adaptive evolution model plant Aquilegia. The subsequent analysis provided us with a basis for further molecular studies on Aquilegia mitochondrial genomes and valuable information on adaptive evolution in Aquilegia.

Keywords: Aquilegia; Mitochondrial genome; Phylogenetic analysis; Selection pressure analysis.

Fig. 1

Schematic of the mitochondrial genome of A. amurensis. Genes belonging to different functional groups are color-coded

Fig. 2

Relative synonymous codon usage (a), SSRs (b) and other repeats (c) in the mitochondrial genome of A. amurensis

Fig. 3

Comparison of phylogenetic relationship in Aquilegia. Comparison of phylogenetic tree between mitochondrial and chloroplast genome (a); comparison of phylogenetic relationship between mitochondrial and nuclear genome (b). The phylogenetic trees of mitochondrial genome, chloroplast genome and nuclear genome were constructed based on 1533, 599 and 363,842 SNPs, respectively. The blue, orange, and green dots represent species from Asia, Europe, and North America, respectively. The gray dots represent outgroup species. The ML ultrafastbootstrap (ufbs) and BI posterior probability (PP) values are indicated above the branches. “*” are ufbs or PP of 100

Fig. 4

d_N/d_S ratios of protein-coding genes in the mitochondrial genome of Aquilegia. The upper and lower limits and circles in the thick lines represent the upper quartile, lower quartile, and median of the pairwise d_N/d_S ratios of each gene, respectively