Abstract
Diversity in structure and organization is one of the main features of angiosperm mitochondrial genomes (mitogenomes). The ultra-long reads of Oxford Nanopore Technology (ONT) provide an opportunity to obtain a complete mitogenome and investigate the structural variation in unprecedented detail. In this study, we compared mitogenome assembly methods using Illumina and/or ONT sequencing data and obtained the complete mitogenome (208 kb) of Chrysanthemum nankingense based on the hybrid assembly method. The mitogenome encoded 19 transfer RNA genes, three ribosomal RNA genes, and 34 protein-coding genes with 21 group II introns disrupting eight intron-contained genes. A total of seven medium repeats were related to homologous recombination at different frequencies as supported by the long ONT reads. Subsequently, we investigated the variations in gene content and constitution of 28 near-complete mitogenomes from Asteraceae. A total of six protein-coding genes were missing in all Asteraceae mitogenomes, while four other genes were not detected in some lineages. The core fragments (~88 kb) of the Asteraceae mitogenomes had a higher GC content (~46.7%) than the variable and specific fragments. The phylogenetic topology based on the core fragments of the Asteraceae mitogenomes was highly consistent with the topologies obtained from the corresponding plastid datasets. Our results highlighted the advantages of the complete assembly of the C. nankingense mitogenome and the investigation of its structural variation based on ONT sequencing data. Moreover, the method based on local collinear blocks of the mitogenomes could achieve the alignment of highly rearrangeable and variable plant mitogenomes as well as construct a robust phylogenetic topology.
Highlights
IntroductionIt has long been recognized that the structure of mitochondrial genomes (mitogenomes) is extremely variable among angiosperms, representing an important component of the whole genome’sGenes 2018, 9, 547; doi:10.3390/genes9110547 www.mdpi.com/journal/genesGenes 2018, 9, 547 diversity [1]
It has long been recognized that the structure of mitochondrial genomes is extremely variable among angiosperms, representing an important component of the whole genome’sGenes 2018, 9, 547; doi:10.3390/genes9110547 www.mdpi.com/journal/genesGenes 2018, 9, 547 diversity [1]
We aimed to explore the effectiveness of complete mitogenome recovery in C. nankingense and investigate repeat-mediated homologous recombination based on the Oxford Nanopore Technology (ONT) long sequencing reads
Summary
It has long been recognized that the structure of mitochondrial genomes (mitogenomes) is extremely variable among angiosperms, representing an important component of the whole genome’sGenes 2018, 9, 547; doi:10.3390/genes9110547 www.mdpi.com/journal/genesGenes 2018, 9, 547 diversity [1]. It has long been recognized that the structure of mitochondrial genomes (mitogenomes) is extremely variable among angiosperms, representing an important component of the whole genome’s. With the development of Generation Sequencing (NGS) technology, more than 150 mitogenomes of angiosperm species have been completely sequenced and assembled, but this is far less than the sequenced plastid genomes The genomic information from the mitogenomes of higher plants has been extensively used for the investigation of genomic evolution related to the gain/loss of genetic materials [2], phylogenetic relationships [3], nucleo-cytoplasmic interactions (e.g., cytoplasmic male sterility) [4], RNA editing [5], and genomic recombination and structural rearrangements [6]. The information of the diversity and evolution of mitogenomes within large angiosperm lineages remains limited
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