Evolution and Diversification of Kiwifruit Mitogenomes through Extensive Whole-Genome Rearrangement and Mosaic Loss of Intergenic Sequences in a Highly Variable Region

Abstract

Angiosperm mitochondrial genomes (mitogenomes) are notable for their extreme diversity in both size and structure. However, our current understanding of this diversity is limited, and the underlying mechanism contributing to this diversity remains unclear. Here, we completely assembled and compared the mitogenomes of three kiwifruit (Actinidia) species, which represent an early divergent lineage in asterids. We found conserved gene content and fewer genomic repeats, particularly large repeats (>1 kb), in the three mitogenomes. However, sequence transfers such as intracellular events are variable and dynamic, in which both ancestral shared and recently species-specific events as well as complicated transfers of two plastid-derived sequences into the nucleus through the mitogenomic bridge were detected. We identified extensive whole-genome rearrangements among kiwifruit mitogenomes and found a highly variable V region in which fragmentation and frequent mosaic loss of intergenic sequences occurred, resulting in greatly interspecific variations. One example is the fragmentation of the V region into two regions, V1 and V2, giving rise to the two mitochondrial chromosomes of Actinidia chinensis. Finally, we compared the kiwifruit mitogenomes with those of other asterids to characterize their overall mitogenomic diversity, which identified frequent gain/loss of genes/introns across lineages. In addition to repeat-mediated recombination and import-driven hypothesis of genome size expansion reported in previous studies, our results highlight a pattern of dynamic structural variation in plant mitogenomes through global genomic rearrangements and species-specific fragmentation and mosaic loss of intergenic sequences in highly variable regions on the basis of a relatively large ancestral mitogenome.

Keywords: Actinidia; asterids; genomic rearrangement; intracellular gene transfer; mitochondrial evolution; structural variation.

Fig. 1.

—Circular diagram showing the information on kiwifruit mitogenomes. The Actinidia chinensis (red), Actinidia eriantha (purple) and Actinidia arguta (green) mitogenomes are circular but are shown here as linear starting from the atp1 gene (from the atp6 gene in the small chromosome of Actinidia chinensis). (a) Gene blocks shown on the outside and inside the circle were transcribed clockwise and counter clockwise, respectively. Genes from the same complex are similarly colored. (b) RNA-Seq depth ratio* supporting the annotated protein-coding genes. (c) Plastid-derived fragments characterized by the black blocks inlaid in the karyotypes. (d) DNA-Seq depth ratio* supporting the assemblies and identified plastid-derived regions. (e) The GC content in 1,000-bp windows. (f) The colored bands in the center show links between syntenic blocks among the three mitogenomes. The inner repeats in each mitogenome (>300 bp) are represented by black lines. *The depth ratio = average depth in 100-bp windows/average total depth.

Fig. 2.

—Gene transfer events in kiwifruit mitogenomes. (a) IGT events in kiwifruit mitogenomes. The mtDNA of Actinidia chinensis (red), Actinidia eriantha (purple), and Actinidia arguta (green). The cpDNA of A. chinensis (Ac-cpDNA; blue) and related nuclear fragments (mt-lg23, mt-lg14; light blue) are depicted with a circular diagram. (b) The mtpt11 event revealed a complex intracellular gene transfer event between the A. chinensis mitogenome and cpDNA. (c) The phylogenetic tree of the Actinidia rps2 gene and homologous genes from 14 species. (d) The top six BLAST results using the Actinidia rps2 gene and its upstream/downstream 1,000-bp flanking sequences against the NCBI nr database.

Fig. 3.

—The structural comparison of kiwifruit mitogenomes. (a) Genome alignment of the three mitogenomes. Conserved LCBs among the three species are shown in green. Regions conserved only among subsets of the three mitogenomes are color coded. Specifically, the LCBs conserved between Actinidia arguta and Actinidia chinensis are orange; the LCBs conserved between Actinidia eriantha and Actinidia chinensis are purple; and the LCBs conserved between Actinidia arguta and Actinidia eriantha are red. (b) The details show the evolution of four chimeric LCBs. The markers inlaid in the LCBs indicate homologous fragments between two of the three kiwifruit species. (c–e) Synteny analysis of pairs of the three mitogenomes.

Fig. 4.

—The comparative analysis of asterid mitogenomes. (a) The phylogenetic distribution of genes and introns and genomic features of asterid mitogenomes. The phylogenetic tree of asterids was constructed based on the concatenated coding regions of 24 core protein-coding genes (PCGs) with Vitis vinifera and Nelumbo nucifera as outgroups. Genes and introns are presented in red and blue, respectively. The arrow represents the loss or gain of a gene or intron from the corresponding clade. The framed introns are those in which their absence accompanied the loss of the corresponding gene. (b–d) The linear regression analysis between GC content and length of plastid-derived fragment, between mitogenome size and length of repeats, and between GC content and mitogenome size, respectively.

Fig. 5.

—Putative dynamic evolution and diversification of three kiwifruit mitogenomes.