Complex Physical Structure of Complete Mitochondrial Genome of Quercus acutissima (Fagaceae): A Significant Energy Plant

Abstract

Quercus acutissima Carruth. is a Chinese important energy plant with high ecological and economic values. While the species chloroplast genome has been reported, its mitochondrial genome (mitogenome) is still unexplored. Here, we assembled and annotated the Q. acutissima mitogenome, and we compared its characteristic differences with several closely related species. The Q. acutissima mitogenome’s main structure is branched with three distinguished contigs (linear molecule 1, circular molecule 2, and circular molecule 3) with 448,982 bp total length and 45.72% GC content. The mitogenome contained 51 genes, including 32 protein-coding, 16 tRNA and 3 rRNA genes. We examined codon usage, repeated sequences, genome recombination, chloroplast to mitochondrion DNA transformation, RNA editing, and synteny in the Q. acutissima mitogenome. Phylogenetic trees based on 29 species mitogenomes clarified the species classification. Our results provided comprehensive information of Q. acutissima mitogenome, and they are expected to provide valuable information for Fagaceae evolutionary biology and to promote the species germplasm utilization.

Complete sequence and comparative analysis of the mitochondrial genome of the rare and endangered Clematis acerifolia, the first clematis mitogenome to provide new insights into the phylogenetic evolutionary status of the genus

“…GC content is also one of the important indicators for species evaluation, and C. acerifolia mitogenome GC content was 46.91%, which is similar to the GC content of the mitogenomes of most angiosperms ( Q. acutissima , 45.72%; Dalbergia odorifera , 45.1%, Cucumis hystrix , 44.59%; Elymus sibiricus ; 44.47%) and higher than that of the clematis chloroplast genome (37.87–38.19%) ( Hong et al, 2021 ; Liu et al, 2022 ; Xia et al, 2022 ). The C. acerifolia mitogenome exhibits a multi-branched structure (linear molecule 1 and circular molecule 2), and the vast majority of published plant mitogenomes are presented as circular DNA molecules, and there are also conformational forms such as Y- and H-type linear, but mitochondrial DNA in its real state is often a mixture of different conformational forms ( Backert and Börner, 2000 ; Kitazaki and Kubo, 2010 ; Bonen, 2014 ; Christensen, 2019 ).…”

“…Although plant mitogenomes are very large, they do not contain many coding genes, typically 50-60 (Kitazaki and Kubo, 2010). With 55 genes (35 PCGs) annotated in the C. acerifolia mitogenome, which is close to the number of genes annotated in Actinidia chinensis (Wang et al, 2019), Quercus acutissima (Liu et al, 2022), and Populus simonii (Bi et al, 2022). The sequences of the coding regions of angiosperms account for only 7-17% of the total genome, and the rest is occupied by intergenic regions (Kubo and Newton, 2008).…”

Complete mitochondrial genome of Thuja sutchuenensis and its implications on evolutionary analysis of complex mitogenome architecture in Cupressaceae

“…However, we also identified that four genes, atp8 , ccmB , mttB and sdh4 , may have undergone positive selection in the evolution of gymnosperms in most species. These four genes are involved in the biosynthesis of ATP synthase, ubiquinol cytochrome c reductase, transport membrane protein and succinate dehydrogenase, respectively [ 5 , 7 ]. Based on previous studies, it is speculated that these four genes may have undergone positive selection under environmental stress to generate new functions to adapt to the new environment.…”

Deciphering the mitochondrial genome ofJuglans mandshurica(Juglandaceae)

“… 2019 ; Liu et al. 2022 ). Although plant mitogenomes are often assembled and displayed as circular maps, they mostly exist as complex and dynamic collections of linear DNA interspersed with smaller circular and branched configurations (Oldenburg and Bendich et al.…”

“…For example, the Quercus acutissima mt genome is a branched structure comprising one linear and two circular formations (Liu et al. 2022 ), the Abelmoschus esculentus mt genome is composed of one linear and one circular structure (Li et al. 2022 ), and the Ipomoea batatas mt genome is arranged as four circular sections (Yang et al.…”