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. 2022 Oct 9;13(10):1827.
doi: 10.3390/genes13101827.

A Comparative Genomics Approach for Analysis of Complete Mitogenomes of Five Actinidiaceae Plants

Jun Yang  1 , Chengcheng Ling  1 , Huamin Zhang  1 , Quaid Hussain  2 , Shiheng Lyu  2 , Guohua Zheng  3 , Yongsheng Liu  1
Affiliations

A Comparative Genomics Approach for Analysis of Complete Mitogenomes of Five Actinidiaceae Plants

Jun Yang et al. Genes (Basel). .

Abstract

Actinidiaceae, an economically important plant family, includes the Actinidia, Clematoclethra and Saurauia genus. Kiwifruit, with remarkably high vitamin C content, is an endemic species widely distributed in China with high economic value. Although many Actinidiaceae chloroplast genomes have been reported, few complete mitogenomes of Actinidiaceae have been studied. Here, complete circular mitogenomes of the four kiwifruit species and Saurauia tristyla were assembled. Codon usage, sequence repeats, RNA editing, gene transfers, selective pressure, and phylogenetic relationships in the four kiwifruit species and S. tristyla were comparatively analyzed. This research will contribute to the study of phylogenetic relationships within Actiniaceae and molecular barcoding in kiwifruit.

Keywords: Actinidiaceae; comparative analysis; mitogenome; phylogenetic analysis.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
(A–D) Gene map of four kiwifruit species (A. chinensis (2×–6×), A. eriantha) and S. tristyla, representing the mitogenome structure. Genes drawn outside the circle are transcribed clockwise, and those inside are counterclockwise. Genes that belong to different functional groups are color coded. The darker grey in the inner circle indicates the GC content of the mitogenome.
Figure 2
Figure 2
The tandem and SSR repeats in five Actiniaceae mitogenomes. (A) The number of tandem repeats. (B) The number of SSRs. (C) Pie chart for SSR distribution. The colors represent different types of SSRs.
Figure 3
Figure 3
(A–E) Shared genome regions of each species between chloroplasts and mitochondria of A. chinensis (2×), A. chinensis (4×), A. chinensis var deliciosa (6×), A. eriantha and S. tristyla, respectively. The green circular segment represents the mitogenome, and the purple circular segment represents the chloroplast genome. (F) Shared sequence length of each species between chloroplasts and mitochondria genomes.
Figure 4
Figure 4
The distribution of RNA editing sites in mitogenome protein-coding genes.
Figure 5
Figure 5
Relative synonymous codon usage (RSCU) in mitochondrial protein-coding genes of five Actinidiaceae mitogenomes. The y-axis represents the value for RSCU. (A) The RSCU value of A. chinensis (2×). (B) The RSCU value of A. chinensis (4×). (C) The RSCU value of A. chinensis var deliciosa (6×). (D) The RSCU value of A. eriantha. (E) The RSCU value of S. tristyla.
Figure 6
Figure 6
The pairwise Ka/Ks ratios among each mitochondrial gene in the six Actinidiaceae family species.
Figure 7
Figure 7
Maximum likelihood phylogenetic tree analysis of Actinidiaceae mitogenomes based on 20 PCGs of 23 plant mitogenomes with V. vinifera and N. nucifera as outgroups.
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