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Assembly of a Complete Mitogenome of Chrysanthemum nankingense Using Oxford Nanopore Long Reads and the Diversity and Evolution of Asteraceae Mitogenomes

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Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou 510650, China
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Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou 510650, China
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University of Chinese Academy of Sciences, Beijing 100049, China
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College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China
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Amway (China) Botanical R&D Center, Wuxi 214115, China
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Wuhan Benagen Tech Solutions Company Limited, Wuhan 430070, China
*
Author to whom correspondence should be addressed.
Genes 2018, 9(11), 547; https://doi.org/10.3390/genes9110547
Received: 21 October 2018 / Revised: 3 November 2018 / Accepted: 7 November 2018 / Published: 12 November 2018
(This article belongs to the Section Plant Genetics and Genomics)
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. View Full-Text
Keywords: mitochondrial genome; Chrysanthemum nankingense; Asteraceae; Oxford Nanopore Technology; recombination; genome evolution mitochondrial genome; Chrysanthemum nankingense; Asteraceae; Oxford Nanopore Technology; recombination; genome evolution
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Wang, S.; Song, Q.; Li, S.; Hu, Z.; Dong, G.; Song, C.; Huang, H.; Liu, Y. Assembly of a Complete Mitogenome of Chrysanthemum nankingense Using Oxford Nanopore Long Reads and the Diversity and Evolution of Asteraceae Mitogenomes. Genes 2018, 9, 547.

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