Assembly of the complete mitochondrial genome of an endemic plant, Scutellaria tsinyunensis, revealed the existence of two conformations generated by a repeat-mediated recombination

Xu, Yicen; Shan, Yuanyu; Pei, Xiaoying; Yong, Shunyuan; Liu, Chang; Li, Jingling

doi:10.1007/s00425-021-03684-3

Cited by 69 publications

(50 citation statements)

References 72 publications

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“…The long repeats we found in the okra mitochondrial genome also have a high frequency of recombination. For short repeats, they all had low recombination frequency, which is consistent with those previously reported [ 28 , 30 ].…”

Section: Discussionsupporting

confidence: 92%

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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Section: Discussionsupporting

confidence: 92%

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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“…For large repeats, such as the typical inverted repeats observed in chloroplast DNA (cp DNA), it was previously thought that equal proportions mediate SSC region recombination [ 57 ]. Here, all of the repeats identified in the mitogenome of plum are short repeats, and they all have low recombination frequency, which are findings that are consistent with those previously reported [ 49 , 50 ]. However, organelles tend to have high copy numbers.…”

Section: Discussionsupporting

confidence: 92%

“…However, 182 long reads supported the master circle conformation, suggesting a lower frequency of recombination. As for the remaining repeats, they recombined the mitogenome at a lower frequency, similar to the results previously observed in Scutellaria tsinyunensis and Nymphaea colorata [ 49 , 50 ], namely that the configuration of the master circle was overwhelmingly dominant in the mitochondrion. Our results also support previous studies that showed that the frequency of recombination mediated by short repeats tends to be lower than that mediated by long repeats, with the isomers mediated by this being closer to equal proportions.…”

Section: Resultssupporting

confidence: 81%

Assembly of the Complete Mitochondrial Genome of Chinese Plum (Prunus salicina): Characterization of Genome Recombination and RNA Editing Sites

Fang

Zhao

Liang

et al. 2021

Genes

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Despite the significant progress that has been made in the genome sequencing of Prunus, this area of research has been lacking a systematic description of the mitochondrial genome of this genus for a long time. In this study, we assembled the mitochondrial genome of the Chinese plum (Prunus salicina) using Illumina and Oxford Nanopore sequencing data. The mitochondrial genome size of P. salicina was found to be 508,035 base pair (bp), which is the largest reported in the Rosaceae family to date, and P. salicina was shown to be 63,453 bp longer than sweet cherry (P. avium). The P. salicina mitochondrial genome contained 37 protein-coding genes (PCGs), 3 ribosomal RNA (rRNA) genes, and 16 transfer RNA (tRNA) genes. Two plastid-derived tRNA were identified. We also found two short repeats that captured the nad3 and nad6 genes and resulted in two copies. In addition, nine pairs of repeat sequences were identified as being involved in the mediation of genome recombination. This is crucial for the formation of subgenomic configurations. To characterize RNA editing sites, transcriptome data were used, and we identified 480 RNA editing sites in protein-coding sequences. Among them, the initiation codon of the nad1 gene confirmed that an RNA editing event occurred, and the genomic encoded ACG was edited as AUG in the transcript. Combined with previous reports on the chloroplast genome, our data complemented our understanding of the last part of the organelle genome of plum, which will facilitate our understanding of the evolution of organelle genomes.

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“…It has been reported that the size of the repeats is closely related to the frequency of recombination [ 63 ]; namely, the frequency of recombination mediated by short repeats tends to be lower than that mediated by long repeats. For example, in Nymphaea colorata Peter [ 64 ], Scutellaria tsinyunensis C. Y. Wu et S. Chow [ 65 ] and Abelmoschus esculentus (L.) Moench [ 66 ], the long repeats had high recombination frequencies, and the short repeats had lower recombination frequencies; all of the repeats identified in the Prunus salicina Lindl. [ 67 ] mitogenome were short repeats, and they all had low recombination frequency.…”

Section: Discussionmentioning

confidence: 99%

Complex Physical Structure of Complete Mitochondrial Genome of Quercus acutissima (Fagaceae): A Significant Energy Plant

Liú

Guo²,

Zhu

et al. 2022

Genes

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Quercus acutissima Carruth. is a Chinese important energy plant with high ecological and economic values. While the species chloroplast genome has been reported, its mitochondrial genome (mitogenome) is still unexplored. Here, we assembled and annotated the Q. acutissima mitogenome, and we compared its characteristic differences with several closely related species. The Q. acutissima mitogenome’s main structure is branched with three distinguished contigs (linear molecule 1, circular molecule 2, and circular molecule 3) with 448,982 bp total length and 45.72% GC content. The mitogenome contained 51 genes, including 32 protein-coding, 16 tRNA and 3 rRNA genes. We examined codon usage, repeated sequences, genome recombination, chloroplast to mitochondrion DNA transformation, RNA editing, and synteny in the Q. acutissima mitogenome. Phylogenetic trees based on 29 species mitogenomes clarified the species classification. Our results provided comprehensive information of Q. acutissima mitogenome, and they are expected to provide valuable information for Fagaceae evolutionary biology and to promote the species germplasm utilization.

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Assembly of the complete mitochondrial genome of an endemic plant, Scutellaria tsinyunensis, revealed the existence of two conformations generated by a repeat-mediated recombination

Abstract: Main conclusionWe assembled the complete mitochondrial genome of Scutellaria tsinyunensis in this study. Repeatmediated recombination resulted in the formation of two conformations of the mitochondrial genome in S. tsinyunensis.

Cited by 69 publications

References 72 publications

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

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

Assembly of the Complete Mitochondrial Genome of Chinese Plum (Prunus salicina): Characterization of Genome Recombination and RNA Editing Sites

Complex Physical Structure of Complete Mitochondrial Genome of Quercus acutissima (Fagaceae): A Significant Energy Plant

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