Complete Plastid and Mitochondrial Genomes of Aeginetia indica Reveal Intracellular Gene Transfer (IGT), Horizontal Gene Transfer (HGT), and Cytoplasmic Male Sterility (CMS)

Choi, Kyoung Su; Park, SeonJoo

doi:10.3390/ijms22116143

Cited by 46 publications

(49 citation statements)

References 60 publications

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“…Plastomes in green autotrophic plants are very conserved, while those in parasitic plants always show reduced size, loss of photosynthesis genes, different IR boundaries, and ascending substitution rates [38], as reported for Cuscuta [10,11,18]. For mitogenomes, many obligate parasitic plants exhibited extensive HGTs from hosts, even including the replacements of the native genes, such as in Cynomorium (Cynomoriaceae [39,40];), Lophophytum mirabile (Balanophoraceae [41,42];, Viscum album (Santalaceae [43];), and Aeginetia indica (Orobanchaceae [44];). Therefore, it might not be surprising that Cu.…”

Section: Divergent Evolution Of the Mitogenomes In Doddersmentioning

confidence: 87%

Unprecedented organelle genomic variations in morning glories reveal independent evolutionary scenarios of parasitic plants and the diversification of plant mitochondrial complexes

et al. 2022

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Background The morning glories (Convolvulaceae) are distributed worldwide and produce economically important crops, medicinal herbs, and ornamentals. Members of this family are diverse in morphological characteristics and trophic modes, including the leafless parasitic Cuscuta (dodders). Organelle genomes were generally used for studying plant phylogeny and genomic variations. Notably, plastomes in parasitic plants always show non-canonical features, such as reduced size and accelerated rates. However, few organelle genomes of this group have been sequenced, hindering our understanding of their evolution, and dodder mitogenome in particular. Results We assembled 22 new mitogenomes and 12 new plastomes in Convolvulaceae. Alongside previously known ones, we totally analyzed organelle genomes of 23 species in the family. Our sampling includes 16 leafy autotrophic species and 7 leafless parasitic dodders, covering 8 of the 12 tribes. Both the plastid and mitochondrial genomes of these plants have encountered variations that were rarely observed in other angiosperms. All of the plastomes possessed atypical IR boundaries. Besides the gene and IR losses in dodders, some leafy species also showed gene and intron losses, duplications, structural variations, and insertions of foreign DNAs. The phylogeny reconstructed by plastid protein coding sequences confirmed the previous relationship of the tribes. However, the monophyly of ‘Merremieae’ and the sister group of Cuscuta remained uncertain. The mitogenome was significantly inflated in Cuscuta japonica, which has exceeded over 800 kb and integrated massive DNAs from other species. In other dodders, mitogenomes were maintained in small size, revealing divergent evolutionary strategies. Mutations unique to plants were detected in the mitochondrial gene ccmFc, which has broken into three fragments through gene fission and splicing shift. The unusual changes likely initially happened to the common ancestor of the family and were caused by a foreign insertion from rosids followed by double-strand breaks and imprecise DNA repairs. The coding regions of ccmFc expanded at both sides after the fission, which may have altered the protein structure. Conclusions Our family-scale analyses uncovered unusual scenarios for both organelle genomes in Convolvulaceae, especially in parasitic plants. The data provided valuable genetic resources for studying the evolution of Convolvulaceae and plant parasitism.

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Section: Divergent Evolution Of the Mitogenomes In Doddersmentioning

confidence: 87%

Unprecedented organelle genomic variations in morning glories reveal independent evolutionary scenarios of parasitic plants and the diversification of plant mitochondrial complexes

et al. 2022

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“…Here, we found three complete genes in the mitogenomes that migrated from the cpDNA of okra, including psaA , rps7 and psbJ , as well as several plastid-derived gene fragments. However, as previously reported, these genes transferred from plastids might not function in mitochondria, and they might undergo pseudogenization as the mitochondrial genome evolves [ 33 , 35 ]. In our study, a typical example was the psbJ gene, which has a total length of 123 bp, but the two genes we annotated in plastids and mitochondria had 12 mismatches, accounting for nearly 10% of the total length (Table S 4 ).…”

Section: Discussionmentioning

confidence: 98%

“…For example, the plastid-derived rpl32 gene has been transferred into the nucleus of the subfamily Thalictroideae [ 32 ]. The atpI gene in the Aeginetia indica mitogenome was acquired from another angiosperm’s chloroplast genome [ 33 ], and IGT events of multiple ribosomal proteins were also found in Geranium [ 34 ]. Here, we found three complete genes in the mitogenomes that migrated from the cpDNA of okra, including psaA , rps7 and psbJ , as well as several plastid-derived gene fragments.…”

Section: Discussionmentioning

confidence: 99%

The complete mitochondrial genome of okra (Abelmoschus esculentus): using nanopore long reads to investigate gene transfer from chloroplast genomes and rearrangements of mitochondrial DNA molecules

et al. 2022

BMC Genomics

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Background Okra (Abelmoschus esculentus L. Moench) is an economically important crop and is known for its slimy juice, which has significant scientific research value. The A. esculentus chloroplast genome has been reported; however, the sequence of its mitochondrial genome is still lacking. Results We sequenced the plastid and mitochondrial genomes of okra based on Illumina short reads and Nanopore long reads and conducted a comparative study between the two organelle genomes. The plastid genome of okra is highly structurally conserved, but the mitochondrial genome of okra has been confirmed to have abundant subgenomic configurations. The assembly results showed that okra’s mitochondrial genome existed mainly in the form of two independent molecules, which could be divided into four independent molecules through two pairs of long repeats. In addition, we found that four pairs of short repeats could mediate the integration of the two independent molecules into one complete molecule at a low frequency. Subsequently, we also found extensive sequence transfer between the two organelles of okra, where three plastid-derived genes (psaA, rps7 and psbJ) remained intact in the mitochondrial genome. Furthermore, psbJ, psbF, psbE and psbL were integrated into the mitochondrial genome as a conserved gene cluster and underwent pseudogenization as nonfunctional genes. Only psbJ retained a relatively complete sequence, but its expression was not detected in the transcriptome data, and we speculate that it is still nonfunctional. Finally, we characterized the RNA editing events of protein-coding genes located in the organelle genomes of okra. Conclusions In the current study, our results not only provide high-quality organelle genomes for okra but also advance our understanding of the gene dialogue between organelle genomes and provide information to breed okra cultivars efficiently.

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“…2 and Supplementary Table S3 ). These protein-coding genes could be lost during evolution and might be transferred to the nuclear genome as observed in other angiosperm mitogenomes 9 , 29 – 31 such as S. latifolia 32 , S. noctiflora 33 , P. dactylifera , and A. indica 27 , 30 . For instance, rps12 was not found in Mesta mitogenome as well as Oenothera and Zostera marina 34 , 35 .…”

Section: Discussionmentioning

confidence: 99%

Mitochondrial genome of Garcinia mangostana L. variety Mesta

Wee

Muhammad

Subbiah

et al. 2022

Sci Rep

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Fruits of Garcinia mangostana L. (mangosteen) are rich in nutrients with xanthones found in the pericarp having great pharmaceutical potential. Mangosteen variety Mesta is only found in Malaysia, which tastes sweeter than the common Manggis variety in Southeast Asia. In this study, we report the complete mitogenome of G. mangostana L. variety Mesta with a total sequence length of 371,235 bp of which 1.7% could be of plastid origin. The overall GC content of the mitogenome is 43.8%, comprising 29 protein-coding genes, 3 rRNA genes, and 21 tRNA genes. Repeat and tandem repeat sequences accounted for 5.8% and 0.15% of the Mesta mitogenome, respectively. There are 333 predicted RNA-editing sites in Mesta mitogenome. These include the RNA-editing events that generated the start codon of nad1 gene and the stop codon of ccmFC gene. Phylogenomic analysis using both maximum likelihood and Bayesian analysis methods showed that the mitogenome of mangosteen variety Mesta was grouped under Malpighiales order. This is the first complete mitogenome from the Garcinia genus for future evolutionary studies.

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Complete Plastid and Mitochondrial Genomes of Aeginetia indica Reveal Intracellular Gene Transfer (IGT), Horizontal Gene Transfer (HGT), and Cytoplasmic Male Sterility (CMS)

Cited by 46 publications

References 60 publications

Unprecedented organelle genomic variations in morning glories reveal independent evolutionary scenarios of parasitic plants and the diversification of plant mitochondrial complexes

Unprecedented organelle genomic variations in morning glories reveal independent evolutionary scenarios of parasitic plants and the diversification of plant mitochondrial complexes

The complete mitochondrial genome of okra (Abelmoschus esculentus): using nanopore long reads to investigate gene transfer from chloroplast genomes and rearrangements of mitochondrial DNA molecules

Mitochondrial genome of Garcinia mangostana L. variety Mesta

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