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

Qiuyue Ma,Zhu Chen,Qianzhong Li,Shushun Li,Jing Wen,Jie Ren,Shuxian Li,Yuxiao Wang,Kunyuan Yan,Lu Zhu,Yiming Du,Changwei Bi

doi:10.1186/s12870-021-03416-5

Abstract

BackgroundAcer 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.ResultsWe 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.ConclusionsIn 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.

Highlights

Acer truncatum is a woody tree species that produces seeds with high levels of valuable fatty acids
In A. truncatum mitogenome, we found that five pair of large repeats (> 1 kb) by rearrangements could produce two subgenomic circles, which comprising of 457,840 bp and 333,212 bp, mediated by the pairwise large repeats R3a and R3b (Table S2 and Fig.S1)
In this study, we assembled and annotated the mitogenome of A. truncatum and performed extensive analyses based on Deoxyribonucleic acid (DNA) and amino acid sequences of annotated genes

Summary

Introduction

Acer truncatum (purpleblow maple) is a woody tree species that produces seeds with high levels of valuable fatty acids (especially nervonic acid). Acer truncatum Bunge (Sapindaceae) is a versatile, oilproducing woody tree widely distributed mainly in northern China, Japan and Korea [1, 2]. Previous studies have indicated that nervonic acid is potentially useful for treatment of schizophrenia, psychosis, and attention deficit disorder [5, 6] It has been detected in several plant species [2, 7, 8], but issues related to their nervonic acid content and growth adaptability have limited the utility of these species. 6026 complete land plant organelle genomes, including 5735 chloroplast and 291 plant mitogenomes have been assembled and deposited in GenBank Organelle Genome Resources (https://www.ncbi.nlm.nih.gov/genome/browse/), as the mitochondrial genome is more complex and harder to assemble than that of other organelles [9, 14]

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