High-Quality Assembly and Comparative Analysis of Actinidia latifolia and A. valvata Mitogenomes

Abstract

Kiwifruit (Actinidia) has been recently domesticated as a horticultural crop with remarkably economic and nutritional value. In this study, by combining sequence datasets from Oxford Nanopore long-reads and Illumina short-reads, we de novo assembled two mitogenomes of Actinidia latifolia and A. valvata, respectively. The results indicated that the A. latifolia mitogenome has a single, circular, 825,163 bp molecule while the A. valvata mitogenome possesses two distinct circular molecules, 781,709 and 301,558 bp, respectively. We characterized the genome structure, repeated sequences, DNA transfers, and dN/dS selections. The phylogenetic analyses showed that A. valvata and A. arguta, or A. latifolia and A. eriantha, were clustered together, respectively. This study provides valuable sequence resources for evolutionary study and molecular breeding in kiwifruit.

A High-Quality Assembly and Comparative Analysis of the Mitogenome of Actinidia macrosperma

“…Meanwhile, evolutionary analysis based on 12 core genes also supports this conclusion in which the relationship of A. macrosperma was closer to A. valvata, A. chinensis, and A. deliciosa, while it was distantly related to A. arguta of Kiwifruit species (Figure 5). Earlier research findings was consistent with the primary conclusions mentioned above, as indicated by evolutionary studies based on the Actinidia mitogenome, showing a closer genetic distance among A. chinensis, A. deliciosa, and A. valvata, while being more distantly related to A. valvata [59].…”

“…Through examination of the correlation between SNPs and gene mutations, comprehensive insights into genome-wide gene mutations can be obtained, enabling the inference of the evolutionary trajectory of the entire species and its underlying causes: positive selection for active adaptation to the environment, negative selection resulting from environmental pressures, or neutral selection to maintain a balance between the two. Consistent with previous research [52,59,70], the majority of mitochondrial genes underwent neutral evolution under the influence of negative selection, displaying a high degree of conservation. However, positive selection may impact genes such as atp4 and ccmB, as indicated by their dN/dS ratio surpassing 1.…”

“…Moreover, a significant abundance of dispersed repeats, comprising primarily forward and palindromic repeats in roughly equal proportions, was identified within the mitogenome. Similar findings have been reported in the mitochondrial genomes of Actinidia [59] and other species, such as Gleditsia sinensi [62].…”

“…Among these, the majority of simple sequence repeats (SSRs) consist of single-nucleotide (A/T) repeats, constituting approximately 55.56% of all SSRs, likely influenced by the low GC content typical of mitochondrial genomes. This trend parallels observations in the mitogenome of A. latifolia [59]. Moreover, a significant abundance of dispersed repeats, comprising primarily forward and palindromic repeats in roughly equal proportions, was identified within the mitogenome.…”

“…Sequence assembly elucidated that the mitogenome of A. macrosperma is represented by a single, circular molecule spanning 752,501 base pairs, displaying a GC content of 46.16% (Figure 1). Notably, the mitogenomes of A. macrosperma and the other six Actinidia species had 39 PCGs each, whether they contained one or two molecules, indicating a high conservation of protein-coding gene numbers in Actinidiaceae family mitogenomes [57][58][59]. In addition, 15 introns were found in the mitogenome of A. macrosperma, compared to the presence of 13-15 introns in the other six Actinidia species (Table S7).…”