Characterization and Comparative Analysis of the Actinidia rufa Mitochondrial Genome.
- 1College of Food and Bioengineering, Bengbu University, Bengbu 233000, China.
Abstract
Background/objectives
Actinidia rufa provides a wild kiwifruit resource for examining mitochondrial sequence conservation and structural variation. We examined the hypothesis that coding-sequence (CDS) coordinates retain higher interspecific alignment coverage than non-CDS coordinates despite differences in block organization. We also assessed reference support, repeat-associated junctions, and mitochondrial gene-tree concordance.Methods
NC_086781.1 was evaluated using PacBio HiFi reads (CRR3429456), uniform repeat-junction screening, six interspecific one-to-one comparisons, repeat and mitochondrial plastid DNA (MTPT) masking, and single-gene trees.Results
The 1,022,459 bp reference contains 39 protein-coding loci. Across six comparisons, CDS coverage was 99.90-100%, versus 68.94-87.79% for non-CDS sequence; adjusted circular-shift p values were 0.001674-0.008745. Homologous sequence occurred in 32-61 merged blocks per comparison, and separate repeat and MTPT masks retained 94.39-98.29% and 93.60-99.39% of baseline aligned reference sequence, respectively. Stringent competitive mapping gave a mean depth of 40.35× and breadth of 73.9% at ≥1×. Of 192 repeat pairs ≥50 bp, 41 were evaluable and none met the reciprocal-alternative-support rule; R43 and R47 each had one-sided single-read support. Eight of 16 informative gene trees contained the A. rufa-A. chinensis split, but phylogenetic information was limited.Conclusions
The comparisons support higher CDS than non-CDS coordinate coverage within a reference set with variable block organization. Repeat-junction support and single-gene resolution remain limited; the data do not establish ongoing recombination, an exclusive circular physical architecture, or a mitochondrial contribution to waterlogging tolerance.
Related
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BibTeX
@article{ling2026characterization,
title = {{Characterization and Comparative Analysis of the Actinidia rufa Mitochondrial Genome.}},
author = {Chengcheng Ling and Zirou Xie and Hang Yuan and Jun Yang},
journal = {Genes},
year = {2026},
month = sep,
doi = {10.3390/genes17101209},
url = {https://europepmc.org/article/MED/42938325},
note = {CC BY},
}
RIS
TY - JOUR
TI - Characterization and Comparative Analysis of the Actinidia rufa Mitochondrial Genome.
AU - Chengcheng Ling
AU - Zirou Xie
AU - Hang Yuan
AU - Jun Yang
PY - 2026
DA - 2026/09/29
JO - Genes
DO - 10.3390/genes17101209
UR - https://europepmc.org/article/MED/42938325
AB - Background/objectives Actinidia rufa provides a wild kiwifruit resource for examining mitochondrial sequence conservation and structural variation. We examined the hypothesis that coding-sequence (CDS) coordinates retain higher interspecific alignment coverage than non-CDS coordinates despite differences in block organization. We also assessed reference support, repeat-associated junctions, and mitochondrial gene-tree concordance.Methods NC_086781.1 was evaluated using PacBio HiFi reads (CRR3429456), uniform repeat-junction screening, six interspecific one-to-one comparisons, repeat and mitochondrial plastid DNA (MTPT) masking, and single-gene trees.Results The 1,022,459 bp reference contains 39 protein-coding loci. Across six comparisons, CDS coverage was 99.90-100%, versus 68.94-87.79% for non-CDS sequence; adjusted circular-shift p values were 0.001674-0.008745. Homologous sequence occurred in 32-61 merged blocks per comparison, and separate repeat and MTPT masks retained 94.39-98.29% and 93.60-99.39% of baseline aligned reference sequence, respectively. Stringent competitive mapping gave a mean depth of 40.35× and breadth of 73.9% at ≥1×. Of 192 repeat pairs ≥50 bp, 41 were evaluable and none met the reciprocal-alternative-support rule; R43 and R47 each had one-sided single-read support. Eight of 16 informative gene trees contained the A. rufa-A. chinensis split, but phylogenetic information was limited.Conclusions The comparisons support higher CDS than non-CDS coordinate coverage within a reference set with variable block organization. Repeat-junction support and single-gene resolution remain limited; the data do not establish ongoing recombination, an exclusive circular physical architecture, or a mitochondrial contribution to waterlogging tolerance.
SN - 2073-4425
ER -