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 25 publications

(17 citation statements)

References 82 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The rps19 gene was missing in all Papilionoideae species used in our study ( Table 1 ). Similarly, Wang et al (2023) reported that most rps genes ( rps2 , rps7 , rps10 , rps11 , and rps19 ) were absent in the mitogenome of Photinia serratifolia , as well as in some Rosacea species. The loss of ribosomal protein genes ( rps genes) and the occurrence of putative mutations in the first start codon (RNA editing) can potentially be compensated for by nuclear genes ( Newton et al, 2004 ).…”

Section: Resultsmentioning

confidence: 82%

Comparative analysis of the complete mitogenome of Geoffroea decorticans: a native tree surviving in the Atacama Desert

2023

View full text Add to dashboard Cite

Chañar (Geoffroea decorticans (Gill., ex Hook. & Arn.) Burkart) has been highly significant for indigenous people in the Atacama Desert for over 3,000 years. Through evolutionary processes, the G. decorticans mitogenome likely underwent changes facilitating its adaptation to the extreme conditions of the Atacama Desert. Here, we compare the mitochondrial genome of G. decorticans with those of other Papilionoideae family species. The complete mitogenome of G. decorticans was sequenced and assembled, making it the first in the genus Geoffroea. The mitogenome contained 383,963 base pairs, consisting of 33 protein coding genes, 21 transfer RNA genes, and 3 ribosomal RNA genes. The Chañar mitogenome is relatively compact, and has two intact genes (sdh4 and nad1) which were not observed in most other species. Additionally, Chañar possessed the highest amount of mitochondrial DNA of plastid origin among angiosperm species. The phylogenetic analysis of the mitogenomes of Chañar and 12 other taxa displayed a high level of consistency in taxonomic classification, when compared to those of the plastid genome. Atp8 was subjected to positive selection, while the ccmFc and rps1 were subjected to neutral selection. This study provides valuable information regarding its ability to survive the extreme environmental conditions of the Atacama Desert.

show abstract

Section: Resultsmentioning

confidence: 82%

Comparative analysis of the complete mitogenome of Geoffroea decorticans: a native tree surviving in the Atacama Desert

2023

View full text Add to dashboard Cite

show abstract

“…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%

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.

View full text Add to dashboard Cite

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.

show abstract

“…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

View full text Add to dashboard Cite

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.

show abstract

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

Cited by 25 publications

References 82 publications

Comparative analysis of the complete mitogenome of Geoffroea decorticans: a native tree surviving in the Atacama Desert

Comparative analysis of the complete mitogenome of Geoffroea decorticans: a native tree surviving in the Atacama Desert

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

Contact Info

Product

Resources

About