Mitochondrial plastid DNA can cause DNA barcoding paradox in plants

Park, Hyun Seung; Jayakodi, Murukarthick; Lee, Sae Hyun; Jeon, Jae Hyeon; Lee, Hyun Oh; Park, Jee Young; Moon, Byeong Cheol; Kim, Chang Kug; Wing, Rod A.; Newmaster, Steven G.; Kim, Ji Yeon; Yang, Tae Jin

doi:10.1038/s41598-020-63233-y

Cited by 36 publications

(33 citation statements)

References 52 publications

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“…The rich mitochondrial genome diversity may be caused by its paternal inheritance pattern in cucumber. Many plastid-derived DNA fragments have been identified in plant mitochondrial genomes 45,46 .…”

Section: Discussionmentioning

confidence: 99%

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Inheritance of chloroplast and mitochondrial genomes in cucumber revealed by four reciprocal F1 hybrid combinations

Park

Lee

et al. 2021

Sci Rep

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Both genomes in chloroplasts and mitochondria of plant cell are usually inherited from maternal parent, with rare exceptions. To characterize the inheritance patterns of the organelle genomes in cucumber (Cucumis sativus var. sativus), two inbred lines and their reciprocal F1 hybrids were analyzed using an next generation whole genome sequencing data. Their complete chloroplast genome sequences were de novo assembled, and a single SNP was identified between the parental lines. Two reciprocal F1 hybrids have the same chloroplast genomes with their maternal parents. Meanwhile, 292 polymorphic sites were identified between mitochondrial genomes of the two parental lines, which showed the same genotypes with their paternal parents in the two reciprocal F1 hybrids, without any recombination. The inheritance patterns of the chloroplast and mitochondria genomes were also confirmed in four additional cucumber accessions and their six reciprocal F1 hybrids using molecular markers derived from the identified polymorphic sites. Taken together, our results indicate that the cucumber chloroplast genome is maternally inherited, as is typically observed in other plant species, whereas the large cucumber mitochondrial genome is paternally inherited. The combination of DNA markers derived from the chloroplast and mitochondrial genomes will provide a convenient system for purity test of F1 hybrid seeds in cucumber breeding.

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Section: Discussionmentioning

confidence: 99%

“…The total length of this mitochondrial plastid DNA (MTPT) in cucumber is 69 kb, which is the highest amount of MTPT among the mitochondrial genome sequences reported to date 46 (Supplementary Fig. 3).…”

Section: Discussionmentioning

confidence: 99%

Inheritance of chloroplast and mitochondrial genomes in cucumber revealed by four reciprocal F1 hybrid combinations

Park

Lee

et al. 2021

Sci Rep

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“…In NGS sequencing, MIPTs can be bioinformatically sorted out from actual plastid sequences based on their read coverage and sequence divergence [20,59]. However, PCR-based DNA barcoding can coamplify both inter-compartmental paralogous copies and produce mixed signals in Sanger sequencing [60]. Thus, special attention should be paid to future studies involving analysis on the plastid sequence in the Damnacanthus to avoid the inclusion of MIPTs.…”

Section: Discussionmentioning

confidence: 99%

Comparative Mitogenomic Analysis Reveals Gene and Intron Dynamics in Rubiaceae and Intra-Specific Diversification in Damnacanthus indicus

Han

Cho

Tamaki

et al. 2021

IJMS

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The dynamic evolution of mitochondrial gene and intron content has been reported across the angiosperms. However, a reference mitochondrial genome (mitogenome) is not available in Rubiaceae. The phylogenetic utility of mitogenome data at a species level is rarely assessed. Here, we assembled mitogenomes of six Damnacanthus indicus (Rubiaceae, Rubioideae) representing two varieties (var. indicus and var. microphyllus). The gene and intron content of D. indicus was compared with mitogenomes from representative angiosperm species and mitochondrial contigs from the other Rubiaceae species. Mitogenome structural rearrangement and sequence divergence in D. indicus were analyzed in six individuals. The size of the mitogenome in D. indicus varied from 417,661 to 419,435 bp. Comparing the number of intact mitochondrial protein-coding genes in other Gentianales taxa (38), D. indicus included 32 genes representing several losses. The intron analysis revealed a shift from cis to trans splicing of a nad1 intron (nad1i728) in D. indicus and it is a shared character with the other four Rubioideae taxa. Two distinct mitogenome structures (type A and B) were identified. Two-step direct repeat-mediated recombination was proposed to explain structural changes between type A and B mitogenomes. The five individuals from two varieties in D. indicus diverged well in the whole mitogenome-level comparison with one exception. Collectively, our study elucidated the mitogenome evolution in Rubiaceae along with D. indicus and showed the reliable phylogenetic utility of the whole mitogenome data at a species-level evolution.

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“…Mitochondrial plastid DNA (MTPT) has been reported in various plants, such as Amborella trichopoda, Zea mays (maize), and Cynanchum wilfordii. [30][31][32] . The degree of MTPT was examined by sequence comparison with the S. tuberosum plastome sequence (GenBank accession No.…”

Section: Mitogenome Homologs In Plastome and Nuclear Genomementioning

confidence: 99%

Mitochondrial Genome Recombination in Somatic Hybrids of Solanum Commersonii and S. Tuberosum

Cho

Lee

et al. 2021

Preprint

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Interspecific somatic hybridization has been performed in potato breeding experiments to increase plant resistance against biotic and abiotic stress conditions. We analyzed the mitochondrial and plastid genomes and 45S nuclear ribosomal DNA (45S rDNA) for the cultivated potato (S. tuberosum, St), wild potato (S. commersonii, Sc), and their somatic hybrid (StSc). Complex genome components and structure, such as the hybrid form of 45S rDNA in StSc, unique plastome in Sc, and recombinant mitogenome were identified. However, the mitogenome exhibited dynamic multipartite structures in both species as well as in the somatic hybrid. In St, the mitogenome is 756,058 bp and is composed of five subgenomes ranging from 297,014 to 49,171 bp in St. In Sc, it is 552,103 bp long and is composed of two sub-genomes of 338,427 and 213,676 bp length. StSc has 447,645 bp long mitogenome with two subgenomes of length 398,439 and 49,206 bp. The mitogenome structure exhibited dynamic recombination mediated by tandem repeats; however, it contained highly conserved genes in the three species. Among the 35 protein-coding genes of the StSc mitogenome, 21 were identical for all the three species, and 12 and 2 were unique in Sc and St, respectively. The recombinant mitogenome might be derived from homologous recombination between both species during somatic hybrid development.

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Mitochondrial plastid DNA can cause DNA barcoding paradox in plants

Cited by 36 publications

References 52 publications

Inheritance of chloroplast and mitochondrial genomes in cucumber revealed by four reciprocal F1 hybrid combinations

Inheritance of chloroplast and mitochondrial genomes in cucumber revealed by four reciprocal F1 hybrid combinations

Comparative Mitogenomic Analysis Reveals Gene and Intron Dynamics in Rubiaceae and Intra-Specific Diversification in Damnacanthus indicus

Mitochondrial Genome Recombination in Somatic Hybrids of Solanum Commersonii and S. Tuberosum

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