Comparative analysis of mitochondrial genomes of Broussonetia spp. (Moraceae) reveals heterogeneity in structure, synteny, intercellular gene transfer, and RNA editing

Lai, Chanjuan; Wang, Jie; Kan, Shenglong; Zhang, Shuo; Li, Pan; Reeve, Wayne; Wu, Zhiqiang; Zhang, Yonghua

doi:10.3389/fpls.2022.1052151

Cited by 24 publications

(12 citation statements)

References 63 publications

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“…monoica while a double-ring structure was resolved in B . kaempferi with gene content showing consistency except for a few tRNA genes [ 46 ]. As a whole, homologous regions across the two Gentiana mtDNAs revealed high compositional and low structural conservation.…”

Section: Resultsmentioning

confidence: 99%

Comparative analysis of mitochondrial genomes of two alpine medicinal plants of Gentiana (Gentianaceae)

Gyab

Zhao

et al. 2023

PLoS ONE

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Gentiana crassicaulis and G. straminea are alpine plants of Gentiana with important medicinal value and complex genetic backgrounds. In this study, the mitochondrial genomes (mtDNAs) of these two species were sequenced. The mtDNAs of G. crassicaulis and G. straminea are 368,808 and 410,086 bp long, respectively, 52 and 49 unique genes are annotated in the two species, and the gene arrangement varies widely. Compared to G. crassicaulis, G. straminea loses three effective genes, namely atp6, trnG-GCC and trnV-GAC. As a pseudogene, the atp6 gene of G. straminea is incomplete, which is rare in higher plants. We detected 1696 and 1858 pairs of long repeats and 213 SSRs and 250 SSs in the mtDNAs of G. crassicaulis and G. straminea, respectively. There are 392 SNPs and 18 InDels between the two genomes, and syntenic sequence and structural variation analysis show low collinearity between the two genomes. Chloroplast DNA transferring to mtDNA is observed in both species, and 46,511 and 55,043 bp transferred segments containing three tRNA genes are identified, respectively. Comparative analysis of mtDNAs of G. crassicaulis, G. straminea and four species of Gentianales determined 18 core genes, and there is no specific gene in G. crassicaulis and G. straminea. The phylogenetic tree based on mtDNAs places Gentianaceae in a branch of Gentianales. This study is the first to analyze the mtDNAs of Gentianaceae, which could provide information for analysis of the structure of mtDNAs of higher plants and phylogenetic research of Gentianaceae and Gentianales.

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Section: Resultsmentioning

confidence: 99%

Comparative analysis of mitochondrial genomes of two alpine medicinal plants of Gentiana (Gentianaceae)

Gyab

Zhao

et al. 2023

PLoS ONE

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“…As an important type of intracellular gene transfer (IGT) ( Wang et al., 2018d ) in the mitochondria, the mechanism of transfer events remains challenging because most transferred DNA sequences are located in non-coding regions. Plant mitogenomes maintain massive mitochondrial plastid fragments (MTPTs) ( Lai et al., 2022 ). The proportion of plastid-derived fragments in mitogenomes varies from 0.44% ( P. serratifolia ) to 16.34% ( R. chingii ) in the family Rosaceae ( Sun et al., 2022 ).…”

Section: Discussionmentioning

confidence: 99%

Complete mitochondrial genome of the endangered Prunus pedunculata (Prunoideae, Rosaceae) in China: characterization and phylogenetic analysis

Liu,

Wu,

Tian

et al. 2023

Front. Plant Sci.

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IntroductionPrunus pedunculata (Prunoideae: Rosaceae), a relic shrub with strong resistance and multiple application values, is endangered in China. Extensive research had been devoted to gene expression, molecular markers, plastid genome analysis, and genetic background investigations of P. pedunculata. However, the mitochondrial genome of this species has not been systematically described, owing to the complexity of the plant mitogenome.MethodsIn the present research, the complete mitochondrial genome of P. pedunculata was assembled, annotated, and characterized. The genomic features, gene content and repetitive sequences were analyzed. The genomic variation and phylogenetic analysis have been extensively enumerated.Results and discussionThe P. pedunculata mitogenome is a circular molecule with a total length of 405,855 bp and a GC content of 45.63%, which are the smallest size and highest GC content among the known Prunus mitochondrial genomes. The mitogenome of P. pedunculata encodes 62 genes, including 34 unique protein-coding genes (PCGs, excluding three possible pseudogenes), three ribosomal RNA genes, and 19 transfer RNA genes. The mitogenome is rich in repetitive sequences, counting 112 simple sequence repeats, 15 tandem repeats, and 50 interspersed repetitive sequences, with a total repeat length of 11,793 bp, accounting for 2.91% of the complete genome. Leucine (Leu) was a predominant amino acid in PCGs, with a frequency of 10.67%, whereas cysteine (Cys) and tryptophan (Trp) were the least adopted. The most frequently used codon was UUU (Phe), with a relative synonymous codon usage (RSCU) value of 1.12. Selective pressure was calculated based on 20 shared PCGs in the mitogenomes of the 32 species, most of which were subjected to purifying selection (Ka/Ks < 1), whereas ccmC and ccmFn underwent positive selection. A total of 262 potential RNA editing sites in 26 PCGs were identified. Furthermore, 56 chloroplast-derived fragments were ascertained in the mitogenome, ranging from 30 to 858 bp, and were mainly located across IGS (intergenic spacer) regions or rRNA genes. These findings verify the occurrence of intracellular gene transfer events from the chloroplast to the mitochondria. Furthermore, the phylogenetic relationship of P. pedunculata was supported by the mitogenome data of 30 other taxa of the Rosaceae family. Understanding the mitochondrial genome characteristics of P. pedunculata is of great importance to promote comprehension of its genetic background and this study provides a basis for the genetic breeding of Prunus.

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“…Secondly, the graph representations of the plant mitochondrial genomes are mostly generated from bioinformatics analysis ( Kang et al., 2020 ). Although the repeat sequences involved could be validated by PCR amplification and Sanger sequencing ( Lai et al., 2022 ), the complete graphic structures of the plant mitochondrial genomes are difficult to validate. Lastly, there is a lack of comparative tools to compare genomes represented as graph.…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity of Coffea arabica L. mitochondrial genomes caused by repeat- mediated recombination and RNA editing

Ni,

Zhang,

et al. 2023

Front. Plant Sci.

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BackgroundCoffea arabica L. is one of the most important crops widely cultivated in 70 countries across Asia, Africa, and Latin America. Mitochondria are essential organelles that play critical roles in cellular respiration, metabolism, and differentiation. C. arabica’s nuclear and chloroplast genomes have been reported. However, its mitochondrial genome remained unreported. Here, we intended to sequence and characterize its mitochondrial genome to maximize the potential of its genomes for evolutionary studies, molecular breeding, and molecular marker developments.ResultsWe sequenced the total DNA of C. arabica using Illumina and Nanopore platforms. We then assembled the mitochondrial genome with a hybrid strategy using Unicycler software. We found that the mitochondrial genome comprised two circular chromosomes with lengths of 867,678 bp and 153,529 bp, encoding 40 protein-coding genes, 26 tRNA genes, and three rRNA genes. We also detected 270 Simple Sequence Repeats and 34 tandem repeats in the mitochondrial genome. We found 515 high-scoring sequence pairs (HSPs) for a self-to-self similarity comparison using BLASTn. Three HSPs were found to mediate recombination by the mapping of long reads. Furthermore, we predicted 472 using deep-mt with the convolutional neural network model. Then we randomly validated 90 RNA editing events by PCR amplification and Sanger sequencing, with the majority being non-synonymous substitutions and only three being synonymous substitutions. These findings provide valuable insights into the genetic characteristics of the C. arabica mitochondrial genome, which can be helpful for future study on coffee breeding and mitochondrial genome evolution.ConclusionOur study sheds new light on the evolution of C. arabica organelle genomes and their potential use in genetic breeding, providing valuable data for developing molecular markers that can improve crop productivity and quality. Furthermore, the discovery of RNA editing events in the mitochondrial genome of C. arabica offers insights into the regulation of gene expression in this species, contributing to a better understanding of coffee genetics and evolution.

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Comparative analysis of mitochondrial genomes of Broussonetia spp. (Moraceae) reveals heterogeneity in structure, synteny, intercellular gene transfer, and RNA editing

Cited by 24 publications

References 63 publications

Comparative analysis of mitochondrial genomes of two alpine medicinal plants of Gentiana (Gentianaceae)

Comparative analysis of mitochondrial genomes of two alpine medicinal plants of Gentiana (Gentianaceae)

Complete mitochondrial genome of the endangered Prunus pedunculata (Prunoideae, Rosaceae) in China: characterization and phylogenetic analysis

Genetic diversity of Coffea arabica L. mitochondrial genomes caused by repeat- mediated recombination and RNA editing

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