Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Photinia serratifolia

Wang, Ying; Chen, Shengjia; Chen, Jiajun; Chen, Chaojie; Lin, Xiaojian; He, Ping; Zhao, Qian; Wang, Xingya

doi:10.1038/s41598-022-24327-x

Cited by 13 publications

(14 citation statements)

References 82 publications

(152 reference statements)

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“…This highlights that the mitogenome structure of A. odorata is not static but rather dynamically varies among these four conformations. The phenomenon of long repeat-mediated recombination is not unique to A. odorata ; it has also been observed in other plant species such as Mimulus guttatus ( Mower et al., 2012 ) , Scutellaria tsinyunensis ( Li et al., 2021 ) , Photinia serratifolia ( Wang et al., 2023a ), and Ginkgo biloba ( Guo et al., 2016 ). Furthermore, extensive research has demonstrated that short dispersed repeats contribute to mitogenome recombination in various plant species, including Nymphaea colorata ( Dong et al., 2018 ) , Silene latifolia ( Sloan et al., 2012 ), and Ginkgo biloba ( Guo et al., 2016 ).…”

Section: Discussionmentioning

confidence: 89%

“…Numerous researchers have delved into the intricate structural variations within plant mitogenomes ( Chevigny et al., 2020 ), leading to the development of various tools for decoding these dynamically evolving genomes ( He et al., 2023 ; Shan et al., 2023 ). Some studies propose that the diversity within mitogenomes may arise from long repeat-mediated recombination ( Wang et al., 2023a ). Within the mitogenome of A. odorata , our analysis unveiled two pairs of lengthy repetitive sequences, measuring 10,113 bp and 6,621 bp, respectively.…”

Section: Discussionmentioning

confidence: 99%

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The complete mitochondrial genome of Aglaia odorata, insights into its genomic structure and RNA editing sites

Hao,

Zhang,

Zhang

et al. 2024

Front. Plant Sci.

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Aglaia odorata, native to Guangdong, Guangxi, and Hainan provinces in China, has long been utilized as an herbal remedy in ancient China. In this study, we assembled and annotated the complete mitochondrial genome (mitogenome) of A. odorata, which spans a total length of 537,321 bp. Conformation of the A. odorata recombination was verified through PCR experiments and Sanger sequencing. We identified and annotated 35 protein-coding genes (PCGs), 22 tRNA genes, and 3 rRNA genes within the mitogenome. Analysis of repeated elements revealed the presence of 192 SSRs, 29 pairs of tandem repeats, and 333 pairs of dispersed repeats in the A. odorata mitogenome. Additionally, we analyzed codon usage and mitochondrial plastid DNAs (MTPTs). Twelve MTPTs between the plastome and mitogenome of A. odorata were identified, with a combined length of 2,501 bp, accounting for 0.47% of the mitogenome. Furthermore, 359 high-confidence C to U RNA editing sites were predicted on PCGs, and four selected RNA editing sites were specially examined to verify the creation of start and/or stop codons. Extensive genomic rearrangement was observed between A. odorata and related mitogenomes. Phylogenetic analysis based on mitochondrial PCGs were conducted to elucidate the evolutionary relationships between A. odorata and other angiosperms.

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Section: Discussionmentioning

confidence: 89%

Section: Discussionmentioning

confidence: 99%

The complete mitochondrial genome of Aglaia odorata, insights into its genomic structure and RNA editing sites

Hao,

Zhang,

Zhang

et al. 2024

Front. Plant Sci.

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“…It is common for plant mitogenomes to undergo recombination facilitated by large repetitive segments dispersed across the mitochondrial DNA. For example, an 16,660 bp long repetitive element were reported in Photinia serratifolia [ 33 ], accounting for 7% of the mitogenome. A repetitive element spanning 21,809 bp was discovered in the mitogenome of Taraxacum mongolicum , and its existence was confirmed through PCR experiments [ 34 ].…”

Section: Discussionmentioning

confidence: 99%

Assembly and comparative analysis of the complete mitochondrial genome of Viburnum chinshanense

Zhu,

Shan,

et al. 2023

BMC Plant Biol

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Background Viburnum chinshanense is an endemic species found exclusively in the North-Central and South-Central regions of China. This species is a lush garden ornamental tree and is extensively utilized for vegetation restoration in rocky desertification areas. Results In this study, we obtained 13.96 Gb of Oxford Nanopore data for the whole genome, and subsequently, by combining Illumina short-reads, we successfully assembled the complete mitochondrial genome (mitogenome) of the V. chinshanense using a hybrid assembly strategy. The assembled genome can be described as a circular genome. The total length of the V. chinshanense mitogenome measures 643,971 bp, with a GC content of 46.18%. Our annotation efforts have revealed a total of 39 protein-coding genes (PCGs), 28 tRNA genes, and 3 rRNA genes within the V. chinshanense mitogenome. The analysis of repeated elements has identified 212 SSRs, 19 long tandem repeat elements, and 325 pairs of dispersed repeats in the V. chinshanense mitogenome. Additionally, we have investigated mitochondrial plastid DNAs (MTPTs) and identified 21 MTPTs within the mitogenome and plastidial genome. These MTPTs collectively span a length of 9,902 bp, accounting for 1.54% of the mitogenome. Moreover, employing Deepred-mt, we have confidently predicted 623 C to U RNA editing sites across the 39 protein-coding genes. Furthermore, extensive genomic rearrangements have been observed between V. chinshanense and the mitogenomes of related species. Interestingly, we have also identified a bacterial-derived tRNA gene (trnC-GCA) in the V. chinshanense mitogenome. Lastly, we have inferred the phylogenetic relationships of V. chinshanense with other angiosperms based on mitochondrial PCGs. Conclusions This study marks the first report of a mitogenome from the Viburnum genus, offering a valuable genomic resource for exploring the evolution of mitogenomes within the Dipsacales order.

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“…Mitochondrial DNA differs from chloroplast DNA and nuclear DNA, with a generally lower substitution rate in plant mitochondria compared to chloroplast and nuclear DNA (Fan et al 2022). Mitochondrial DNA is commonly used to study evolutionary relationships, hybridization events, and nuclear interactions among species (Zhang et al 2019, , (Wang et al 2023).…”

Section: Introductionmentioning

confidence: 99%

The complete mitochondrial genome assembly of Capsicum pubescens reveals key evolutionary characteristics of mitochondrial genes of two Capsicum subspecies

Liu

et al. 2023

Preprint

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Pepper (Capsicum pubescens), one of the five domesticated pepper species, boasts unique characteristics such as numerous hairs on the epidermis of its leaves and stems, black seeds, and vibrant purple flowers. Previously, no studies have reported on the complete assembly of the mitochondrial genome (mitogenome) of C. pubescens. Understanding the mitogenome is crucial for further research on C. pubescens. In our study, we successfully assembled the first mitogenome of C. pubescens, which has been assigned the GenBank accession number OP957066. This mitogenome has a length of 454,165 bp and exhibits the typical circular structure observed in most mitogenomes. We have annotated a total of 70 genes, including 35 protein-coding genes (PCGs), 30 tRNA genes, 3 rRNA genes, and 2 pseudogenes. Compared to the other three pepper mitogenomes (KJ865409, KJ865410, and MN196478), C. pubescens OP957066 exhibits 4 unique PCGs (atp4, atp8, mttB, and rps1), while 2 PCGs (rpl10 and rps3) are absent. It's worth mentioning that each of the three pepper mitogenomes (KJ865409, KJ865410, and MN196478) experienced the loss of 4 PCGs (atp4, atp8, mttB, and rps1). To further explore the evolutionary relationships, we reconstructed a phylogenetic tree using the mitogenomes of C. pubescens and fourteen other species. The structural comparison and synteny analysis of the above four pepper mitogenomes showed that C. pubescens has a higher sequence similarity with KJ865409, and C. pubescens experienced rearrangements with the other three pepper mitogenomes. Interestingly, we observed 72 homologous sequences between the mitochondrial and chloroplast genomes, which accounted for 12.60% of the mitogenome, with a total length of 57,207 bp. These sequences encompassed 12 tRNA genes and the rRNA gene (rrn18). Remarkably, selective pressure analysis suggests that the nad5 gene underwent obvious positive selection. Furthermore, the single base mutation in three genes (nad1, nad2, and nad4) resulted in amino acid change. This study has provided a high-quality mitogenome of pepper, offering valuable molecular data for future investigations into the genetic information exchange between organelle genomes in pepper.

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Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Photinia serratifolia

Cited by 13 publications

References 82 publications

The complete mitochondrial genome of Aglaia odorata, insights into its genomic structure and RNA editing sites

The complete mitochondrial genome of Aglaia odorata, insights into its genomic structure and RNA editing sites

Assembly and comparative analysis of the complete mitochondrial genome of Viburnum chinshanense

The complete mitochondrial genome assembly of Capsicum pubescens reveals key evolutionary characteristics of mitochondrial genes of two Capsicum subspecies

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