De Novo Assembly and Comparative Analysis of the Complete Mitochondrial Genome of Chaenomeles speciosa (Sweet) Nakai Revealed the Existence of Two Structural Isomers
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials, DNA Extraction, and Sequencing
2.2. Assembly and Annotation of the Mitochondrial Genome and Chloroplast Genome
2.3. Analysis of Repeated Sequences and Genome Recombination
2.4. DNA Transfer and Phylogenetic Tree Construction
2.5. RNA Editing Site Identification and Synteny Analysis
2.6. dN/dS Analysis
3. Results
3.1. General Features of the C. speciosa Mitochondrial Genome
3.2. Repeats and Homologous Recombination
3.3. Gene Transfers between Chloroplast and Mitochondrial Genomes
3.4. Phylogenetic Analysis
3.5. RNA Editing Sites Prediction
3.6. Synteny Analysis
3.7. Evolutionary Selection Pressure Analysis
4. Discussion
4.1. Features of the C. speciosa Mitochondrial Genome and IGT Events
4.2. The Conformations of C. speciosa Mitochondrial Genome Mediated by Repeated Sequences
4.3. Evolutionary Analysis and dN/dS Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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NCBI Accession Number | Contigs | Type | Length | GC Content |
---|---|---|---|---|
OL450370-OL450371 | Chromosome 1-2 | Branched | 436,464 bp | 45.20% |
OL450370 | Chromosome 1 | Circular | 307,720 bp | 45.15% |
OL450371 | Chromosome 2 | Circular | 128,744 bp | 45.33% |
Group of Genes | Name of Genes |
---|---|
ATP synthase | atp1, atp4, atp6, atp8, atp9 |
NADH dehydrogenase | nad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad7, nad9 |
Cytochrome c biogenesis | cob |
Ubiquinol cytochrome c reductase | ccmB, ccmC, ccmFC, ccmFN |
Cytochrome c oxidase | cox1, cox2, cox3 |
Maturases | matR |
Transport membrane protein | mttB |
Large subunit of ribosome | rpl5, rpl10, rpl16 |
Small subunit of ribosome | rps1, rps3, rps4, rps12, rps13 |
Succinate dehydrogenase | sdh4 |
Ribosome RNA | rrn5, rrn18, rrn26 |
Transfer RNA | trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA (×3), trnG-GCC, trnH-GUG, trnK-UUU, trnL-CAA, trnM-CAU (×3), trnN-GUU, trnP-UGG, trnQ-UUG, trnS-GGA, trnS-UGA, trnT-GUA, trnV-GAC, trnW-CCA, trnY-GUA |
ID | Length (bp) | Identity (%) | Position | Number of Supported Reads | Percentage (%) | ||||
---|---|---|---|---|---|---|---|---|---|
Major 1 | Major 2 | Alternative 1 | Alternative 2 | Major Conformation | Alternative ConformatioN | ||||
R1 | 7887 | 100 | chr1: 299834-307720; chr1: 107714-115600 | 16 | 18 | 21 | 20 | 0.4533 | 0.5467 |
R2 | 1235 | 100 | chr1: 63771-65005; chr2: 1-1235 | 168 | 100 | 3 | 0 | 0.9889 | 0.0111 |
R4 | 331 | 100 | chr1: 48854-48524; chr1: 116771-117101 | 161 | 188 | 1 | 0 | 0.9971 | 0.0029 |
R5 | 244 | 100 | chr1: 12185-12428; chr1: 33887-34130 | 244 | 206 | 0 | 1 | 0.9978 | 0.0022 |
R7 | 163 | 100 | chr1: 107876-107714; chr2: 121991-122153 | 242 | 237 | 2 | 0 | 0.9958 | 0.0042 |
R14 | 163 | 100 | chr1: 299996-299834; chr2: 121991-122153 | 17 | 26 | 1 | 0 | 0.9773 | 0.0227 |
R15 | 89 | 96.629 | chr1: 169238-169150; chr1: 207012-207100 | 228 | 146 | 1 | 0 | 0.9973 | 0.0027 |
Chromosome | Order in Contigs |
---|---|
Contig 1 | 3-R12-1-R12-12-R10-10-R11-8-R4-6 |
Contig 2 | 27-R13-31-R7/R1-R7-26-R8-25-R11-24-R9-23-R6-30-R3-29-R6-28 |
Contig 3 | 22-R3-21-R5-20-R5-19-R9-18-R4-17-R8-16-R13-15 |
Contig 4 | 14-R10-13-R7 |
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Cao, P.; Huang, Y.; Zong, M.; Xu, Z. De Novo Assembly and Comparative Analysis of the Complete Mitochondrial Genome of Chaenomeles speciosa (Sweet) Nakai Revealed the Existence of Two Structural Isomers. Genes 2023, 14, 526. https://doi.org/10.3390/genes14020526
Cao P, Huang Y, Zong M, Xu Z. De Novo Assembly and Comparative Analysis of the Complete Mitochondrial Genome of Chaenomeles speciosa (Sweet) Nakai Revealed the Existence of Two Structural Isomers. Genes. 2023; 14(2):526. https://doi.org/10.3390/genes14020526
Chicago/Turabian StyleCao, Pei, Yuan Huang, Mei Zong, and Zilong Xu. 2023. "De Novo Assembly and Comparative Analysis of the Complete Mitochondrial Genome of Chaenomeles speciosa (Sweet) Nakai Revealed the Existence of Two Structural Isomers" Genes 14, no. 2: 526. https://doi.org/10.3390/genes14020526