The Mitochondrial Genome Assembly of Fennel (Foeniculum vulgare) Reveals Two Different atp6 Gene Sequences in Cytoplasmic Male Sterile Accessions
Abstract
:1. Introduction
2. Results
2.1. Mitochondrial Genome Sequence and Annotation
2.2. SNP and InDel Detection
2.3. Selection of Candidate Gene Controlling Cytoplasmic Male Sterility
2.4. Expression Analyses of atp6+, atp6−, atp1, and atp9
3. Discussion
4. Materials and Methods
4.1. Assembly of Mitochondrial DNA
4.2. Variant Calling and Sanger DNA Sequencing Validation
4.3. RNA Isolation and Quantitative Real-Time PCR
Supplementary Materials
Author Contributions
Acknowledgments
Conflicts of Interest
References
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CMS mtDNA Position | Type | Ref | Alt | ID | CMS mtDNA Position | Type | Ref | Alt | ID |
---|---|---|---|---|---|---|---|---|---|
4407^4408 | Ins | - | T | 210132 | SNV | A | G | atp6 | |
4413^4414 | Ins | - | T | 210134..210137 | MNV | ACCC | GGAA | atp6 | |
9932 | Del | A | - | 210140..210141 | MNV | CC | TT | atp6 | |
9937 | Del | A | - | 210143 | SNV | A | G | atp6 | |
17054 | SNV | T | A | 210145 | SNV | C | T | atp6 | |
17779 | SNV | A | C | 210148..210150 | MNV | CGA | TAG | atp6 | |
19036 | Del | T | - | 210152..210153 | MNV | TA | GG | atp6 | |
23779..23780 | Del | GG | - | nad4 (intron) | 210155 | SNV | T | G | atp6 |
26757^26758 | Ins | - | G | nad4 (intron) | 210157..210158 | MNV | CT | AG | atp6 |
29433 | Del | G | - | nad4 (intron) | 210160..210163 | MNV | ATAT | CCCC | atp6 |
38972^38973 | Ins | - | A | 210168..210171 | MNV | GCTT | ATCC | atp6 | |
85033 | Del | A | - | 210176 | SNV | T | C | atp6 | |
97184 | Del | A | - | 210179 | SNV | T | A | atp6 | |
97194 | Del | C | - | 210193..210194 | MNV | AA | CC | atp6 | |
103048 | Del | T | - | 210218 | SNV | G | T | atp6 | |
106177^106178 | Ins | - | T | 210225 | SNV | G | C | atp6 | |
109983 | Del | G | - | 210276 | SNV | G | A | atp6 | |
110419 | SNV | T | G | 210291 | SNV | T | C | atp6 | |
175249 | SNV | T | C | rps3 | 210293 | SNV | G | A | atp6 |
175458 | SNV | C | G | rps3 | 210296 | SNV | T | G | atp6 |
176686 | SNV | G | A | rps3 | 210374 | SNV | C | T | atp6 |
181657 | Del | T | - | cox2 (intron) | 212667 | Del | T | - | |
210097..210102 | Del | CCGCTC | - | atp6 | 213187 | SNV | A | G | |
210103..210105 | MNV | CCA | TTT | atp6 | 213216 | SNV | A | C | |
210111 | SNV | C | T | atp6 | 238616^238617 | Ins | - | C | |
210113 | SNV | G | A | atp6 | 238643^238644 | Ins | - | G | |
210117 | SNV | A | G | atp6 | 240379^240380 | Ins | - | TTTATTAT | orf43 |
210117^210118 | Ins | - | AG | atp6 | 247260 | Del | C | - | |
210122 | SNV | A | G | atp6 | 248437 | Del | A | - | |
210124..210126 | MNV | TAA | GTG | atp6 | 293347 | Del | T | - | nad2 (intron) |
210129^210130 | Ins | - | CTT | atp6 | 295317 | Del | T | - | nad2 (intron) |
210130 | SNV | A | T | atp6 |
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Palumbo, F.; Vitulo, N.; Vannozzi, A.; Magon, G.; Barcaccia, G. The Mitochondrial Genome Assembly of Fennel (Foeniculum vulgare) Reveals Two Different atp6 Gene Sequences in Cytoplasmic Male Sterile Accessions. Int. J. Mol. Sci. 2020, 21, 4664. https://doi.org/10.3390/ijms21134664
Palumbo F, Vitulo N, Vannozzi A, Magon G, Barcaccia G. The Mitochondrial Genome Assembly of Fennel (Foeniculum vulgare) Reveals Two Different atp6 Gene Sequences in Cytoplasmic Male Sterile Accessions. International Journal of Molecular Sciences. 2020; 21(13):4664. https://doi.org/10.3390/ijms21134664
Chicago/Turabian StylePalumbo, Fabio, Nicola Vitulo, Alessandro Vannozzi, Gabriele Magon, and Gianni Barcaccia. 2020. "The Mitochondrial Genome Assembly of Fennel (Foeniculum vulgare) Reveals Two Different atp6 Gene Sequences in Cytoplasmic Male Sterile Accessions" International Journal of Molecular Sciences 21, no. 13: 4664. https://doi.org/10.3390/ijms21134664