Assembly and comparative analysis of the first complete mitochondrial genome of Acer truncatum Bunge: a woody oil-tree species producing nervonic acid

Abstract

Background: Acer truncatum (purpleblow maple) is a woody tree species that produces seeds with high levels of valuable fatty acids (especially nervonic acid). The species is admired as a landscape plant with high developmental prospects and scientific research value. The A. truncatum chloroplast genome has recently been reported; however, the mitochondrial genome (mitogenome) is still unexplored.

Results: We characterized the A. truncatum mitogenome, which was assembled using reads from PacBio and Illumina sequencing platforms, performed a comparative analysis against different species of Acer. The circular mitogenome of A. truncatum has a length of 791,052 bp, with a base composition of 27.11% A, 27.21% T, 22.79% G, and 22.89% C. The A. truncatum mitogenome contains 62 genes, including 35 protein-coding genes, 23 tRNA genes and 4 rRNA genes. We also examined codon usage, sequence repeats, RNA editing and selective pressure in the A. truncatum mitogenome. To determine the evolutionary and taxonomic status of A. truncatum, we conducted a phylogenetic analysis based on the mitogenomes of A. truncatum and 25 other taxa. In addition, the gene migration from chloroplast and nuclear genomes to the mitogenome were analyzed. Finally, we developed a novel NAD1 intron indel marker for distinguishing several Acer species.

Conclusions: In this study, we assembled and annotated the mitogenome of A. truncatum, a woody oil-tree species producing nervonic acid. The results of our analyses provide comprehensive information on the A. truncatum mitogenome, which would facilitate evolutionary research and molecular barcoding in Acer.

Keywords: Acer truncatum; Mitochondrial genome; Phylogenetic analysis; Repeats.

Fig. 1

Circular map of the A. truncatum mitogenome. Genes shown on the outside and inside of the circle are transcribed clockwise and counterclockwise, respectively. The dark gray region in the inner circle depicts GC content. Asterisks besides genes denote intron-containing genes

Fig. 2

Codon usage pattern of the A. truncatum mitogenome compared with A. yangbiense, A. thaliana, and C. sinensis. The relative percentage of each amino acid residue in all mitochondrial proteins is shown on the y-axis

Fig. 3

Relative synonymous codon usage (RSCU) in the A. truncatum mitogenome. Codon families are shown on the x-axis. RSCU values are the number of times a particular codon is observed relative to the number of times that codon would be expected for a uniform synonymous codon usage

Fig. 4

Ka/Ks ratios of 26 protein-coding genes in A. truncatum, A. yangbiense, A. thaliana, and C. sinensis

Fig. 5

The distribution of RNA editing sites in mitogenome protein-coding genes of four angiosperms

Fig. 6

Detected repeats in the A. truncatum mitogenome. A Type and proportion of detected repeats. B Frequency distribution of repeat lengths

Fig. 7

Maximum-likelihood phylogenetic tree based on 25 single-copy orthologous genes shared among 26 species. Numbers at nodes are bootstrap support values. The position of A. truncatum is indicated in bold. Triticum aestivum, Sorghum bicolor, Ginkgo biloba, and Zea mays served as outgroups

Fig. 8

Characteristics of nuclear–mitochondrial sequences in A. truncatum. A Distributions of percent identities between shared nuclear–mitochondrial matches. The number of matches is shown by blue boxes and is plotted on the left ordinate. The orange lines, which represent the coverage of matches on nuclear and mitochondrial genomes, are plotted on the right ordinate. B Distributions of lengths between shared nuclear–mitochondrial matches

Fig. 9

Schematic diagram of the development of an NAD1 intron marker in seven Acer species. A Electrophoretic gel visualization of the amplified fragments. Lanes are as follows: 1, A. tonkinense; 2, A. ginnala; 3, A. pubipalmatum; 4, A. palmatum; 5, A. truncatum; 6, A. buergerianum; 7, A. yangbiense; M, 2000-bp ladder. B Alignment of the NAD1 intron marker sequence in MEGA 6.0. The arrow indicates the 33-bp insertion in A. yangbiense