Complete Sequence, Multichromosomal Architecture and Transcriptome Analysis of the Solanum tuberosum Mitochondrial Genome
Abstract
:1. Introduction
2. Results and Discussion
2.1. S. tuberosum Mitochondrial Genome Assembly
2.2. Gene Content of the Potato mtDNA
2.3. Transcriptome of the Potato mtDNA
2.4. RNA Editing
2.5. Comparative Analysis of Mitochondrial Genomes among Solanaceae
3. Materials and Methods
3.1. Plant Material
3.2. Isolation of mtDNA
3.3. Genome Sequencing and Assembly
3.4. Genome Annotation
3.5. Transcriptome Sequencing and Analysis
3.6. Detection of Repeats
3.7. Comparative and Evolutionary Analysis
3.8. Data Deposition
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Molecule 1 | ||||
Gene | Start | Stop | Strand | Comments |
nad1e | 3860 | 4118 | + | |
orf119 | 12570 | 12929 | – | |
atp1 | 13197 | 14732 | – | |
Mttb | 31292 | 32122 | – | |
orf265a | 32244 | 33041 | – | N-term atp8 (20 codons), ELF-domain (pfam03317). Co-transcribed with MttB |
26S | 33385 | 36879 | – | |
nad2cde | 50394 | 50581 | – | |
52050 | 52622 | – | ||
55094 | 55254 | – | ||
nad5ab | 61695 | 62910 | – | |
63755 | 63984 | – | ||
nad4 | 64989 | 65077 | – | |
67705 | 68127 | – | ||
71259 | 71773 | – | ||
73185 | 73645 | – | ||
orf125 | 73849 | 74226 | – | |
orf247 | 78169 | 78912 | – | |
rps4 | 90192 | 91013 | + | No evidence of TAG created by editing. Possible non-canonical initiation at GTG codon |
nad6 | 91707 | 92360 | + | Transcript is processed upstream of stop codon |
nad4L | 98027 | 98329 | + | |
atp4 | 98518 | 99114 | + | |
orf438 | 109344 | 110660 | – | RdRp-like |
orf141 | 110784 | 111209 | – | |
5S | 111720 | 111838 | – | |
18S | 112001 | 113946 | – | |
orf304 | 117275 | 118189 | + | N-term pfam12725. C-term has 59% identity to hypothetical protein RirG_027070 |
nad1d | 118391 | 118449 | + | |
matR | 119111 | 121087 | + | |
nad5de | 125647 | 125793 | – | |
126889 | 127283 | – | ||
orf152 | 127397 | 127855 | – | |
orf105 | 128459 | 128776 | – | |
orf159 | 128839 | 129318 | – | RdRp-like |
orf137 | 139197 | 139610 | – | CMS-associated protein |
nad1a | 148955 | 149339 | + | |
rps19 | 159585 | 159869 | + | |
rps3 | 159883 | 159956 | + | |
161026 | 162643 | + | ||
rpl16 | 162534 | 163049 | + | Editing site 162570 (96%) creates internal stop codon. Editing is conserved in Arabidopsis. It implies that there is no re-initiation of translation inside rps3. Possible initiation at GTG codon. |
cox2 | 163299 | 163680 | + | |
165066 | 165466 | + | ||
ccmC | 172753 | 173583 | + | ORF overlaps with tRNA and transcript is processd at the tRNA 5’, without stop codon. |
rps19 | 208754 | 209038 | + | |
rps3 | 209052 | 209125 | + | |
210195 | 211812 | + | ||
rpl16 | 211703 | 212218 | + | |
cox2 | 212468 | 212849 | + | |
214235 | 214635 | + | ||
orf77 | 233142 | 233375 | + | |
nad1e | 233431 | 233689 | + | |
atp6 | 233940 | 235106 | + | Editing site 235065 creates stop codon making orf 13 aa shorter, with the same C-term as Arabidopsis atp6. |
atp9 | 243146 | 243379 | + | Editing site 243368 creates stop codon making protein 3 aa shorter. With editing it is the same C-term as Arabidopsis atp9. |
nad5c | 246225 | 246246 | + | |
orf161 | 246314 | 246799 | + | |
nad7 | 271765 | 272026 | – | |
273770 | 274477 | – | ||
275936 | 276004 | – | ||
276920 | 277062 | – | ||
orf103 | 278419 | 278730 | – | |
nad1bc | 292250 | 292441 | – | |
293925 | 294007 | – | ||
rps13 | 294547 | 294897 | – | |
nad1d | 295623 | 295681 | – | |
orf304 | 295883 | 296797 | – | hypothetical protein RirG (Rhizophagus irregularis) |
18S | 300126 | 302071 | + | |
5S | 302234 | 302352 | + | |
orf141 | 302863 | 303288 | + | Similarities to region 3’ UTR of orf247 |
orf438 | 303412 | 304728 | + | RdRp-like |
orf320 | 310786 | 311748 | – | Chimeric orf: 5’ of atp1, 3’ region upstream nad5c. Promoter of atp1 that is present in repeat R5 |
Molecule 2 | ||||
Gene | Start | Stop | Strand | Comments |
ccmFC | 6136 | 6685 | – | |
7635 | 8401 | – | ||
Cob | 33524 | 34705 | – | |
sdh4 | 51176 | 51589 | – | Overlaps cox3. Real ATG might be at codon 24. The transcript is processed about 8 codons before stop codon. Internal stop codon created by partial editing (26%) at codon 93. |
cox3 | 51517 | 52314 | – | |
atp8 | 52947 | 53417 | – | |
orf118 | 54391 | 54747 | – | Chimeric orf: C-term is from atp6 |
rps1 | 54964 | 55635 | – | |
ccmFN | 71926 | 73737 | – | |
cox1 | 76329 | 77825 | – | Initiation codon created by editing |
rps10 | 78075 | 78187 | – | Stop codon created by editing (78107) |
78963 | 79212 | – | Initiation codon created by editing (79211). | |
rps14 * | 81682 | 82051 | – | Pseudo-gene |
rpl5 | 82053 | 82613 | – | |
rps12 | 99496 | 99867 | – | |
nad3 | 99916 | 100272 | – | |
orf265b | 100423 | 101220 | – | N-term atp8, ELF-domain (pfam03317) |
Molecule 3 | ||||
Gene | Start | Stop | Strand | Comments |
ccmB | 9945 | 10565 | + | Editing site 10238 creates stop codon in about 50% of the transcripts, in the middle of the ORF. |
rpl10 | 16440 | 16919 | – | |
rpl2 | 17204 | 17320 | – | |
19230 | 20114 | – | ||
orf210 | 20294 | 20926 | – | |
sdh3 | 35400 | 35726 | + | |
nad2ab | 36302 | 36453 | + | |
37470 | 37862 | + | ||
nad9 | 41589 | 42161 | – |
tRNA Gene | Start | Stop | Strand | Editing NGS | Expression |
---|---|---|---|---|---|
Molecule 1 | |||||
trnP(UGG) | 17220 | 17294 | - | + | |
trnF(GAA) | 17545 | 17618 | - | + | + |
trnS(GCU) | 17981 | 18068 | - | + | |
trnMf(CAU) | 37458 | 37531 | - | + | |
trnY(GUA) | 55772 | 55854 | - | + | |
trnN(GUU) * | 56390 | 56461 | - | + | |
trnC(GCA) | 58606 | 58676 | - | + | + |
trnC(GCA) * | 171005 | 171076 | + | - | |
trnI(CAU) * | 173488 | 173561 | + | nd | |
trnMe(CAU) * | 189363 | 189435 | - | + | |
trnG(GCC) | 201326 | 201397 | + | + | |
trnQ(UUG) | 204702 | 204773 | + | + | |
trnI(CAU) | 260636 | 260709 | + | + | |
Molecule 2 | |||||
trnN(GUU) * | 28511 | 28582 | + | + | |
trnS(UGA) | 35798 | 35884 | - | + | |
trnD(GUC) * | 43141 | 43214 | + | + | |
trnS(GGA) * | 43901 | 43987 | + | + | |
trnV(GAC) * | 64733 | 64804 | - | - | |
Molecule 3 | |||||
trnK(UUU) | 7326 | 7398 | - | + | |
trnE(UUC) | 23306 | 23377 | - | + | |
trnW(CCA) * | 40411 | 40484 | - | + | |
trnP(UGG) | 40642 | 40715 | - | + | |
trnH(GUG) * | 45897 | 45971 | - | + |
Arabidopsis thaliana | ||||
Gene | mRNA End | Kind of Secondary Structure | Putative Nuclease | Conservation in Potato |
ccmFC | 5’ | trnG | RNAseZ | No |
rps3 | 5’ | trnK | RNAseZ | No |
rps4 | 5’ | t-element | RNAseZ | No |
ccmFN1 | 5’ | t-element | RNAseZ | No |
cox1 | 5’ | t-element | RNAseZ | No |
rpl5 | 5’ | Acceptor stem-like stem–loop | RNAseZ | No |
rpl5 | 5’ | Acceptor stem-like stem–loop | RNAseZ | No |
atp6-2 | 5’ | Acceptor stem-like stem–loop | RNAseZ | No |
nad7 | 5’ | Acceptor stem-like stem–loop | RNAseP | No |
atp6-1 | 3’ | trnS | RNAseP | No |
atp6-2 | 3’ | trnS | RNAseP | No |
atp9 | 3’ | Double stem-loop | RNAseZ | No |
nad1e | 3’ | Double stem-loop | RNAseZ | No |
cox2 | 3’ | Stem-loop | RNAseZ | No |
ccmC | 3’ | t-element | RNAseP | trnI |
nad6 | 3’ | t-element | RNAseP | Yes |
Solanum tuberosum | ||||
rrrn26S | 5’ precursor | trnfM | RNAseZ | |
nad2cde | 5’ | trnY | RNAseZ | |
non-coding RNA | 5’ | trnC | RNAseZ | |
Cob | 5’ | trnS | RNAseZ | |
ccmC | 5’ | trnC | RNAseZ | |
ccmC | 3’ | trnI | RNaseP | |
atp1 | 3’ | Double stem-loop | RNAseZ | 12397–12441 |
mttB | 3’ | Stem-loop | RNAseZ | 31111–31148 |
nad5ab | 3’ | Double stem-loop | RNAseZ | 60956–60986 |
orf247 | 3’ | Double stem-loop | RNAseZ | 76895–76938 |
nad6 | 3’ | t-element | RNAseZ | 92309–92353 |
atp4 | 3’ | Stem-loop | RNAseZ | 99142–99166 |
nad1a | 3’ | Stem-loop | RNAseZ | 150600–150637 |
orf438 | 3’ | Stem-loop | RNAseZ | 305247–305291 |
Gene | S. tuberosum | S. commersonii | S. lycopersicum | S. pennellii | C. annuum | N. tabacum | N. sylvestris | H. niger |
---|---|---|---|---|---|---|---|---|
atp1 | ● | ● | ● | ● | ● | ● | ● | ● |
atp4 | ● | ● | ● | ● | ● | ● | ● | ● |
atp6 | ● | ● a | ● | ● | ● | ● | ● | ● |
atp8 | ● | ● | ● | ● | ● | ● | ● | ● |
atp9 | ● | ● | ● | ● | ● | ● | ● | ● |
ccmB | ● | ● | ● | ● | ● | ● | ● | ● |
ccmC | ● | ● | ● | ● | ● | ● | ● | ● |
ccmFc | ● | ● | ● | ● | ● | ● | ● | ● |
ccmFN | ● | ● | ● | ● | ● | ● | ● | ● |
cob | ● | ● | ● | ● | ● | ● | ● | ● |
cox1 | ● | ● | ● | ● | ● | ● | ● | ● |
cox2 | ● | ● | ● | ● | ● | ● | ● | ● |
cox3 | ● | ● | ● | ● | ● | ● | ● | ● |
matR | ● | ● | ● | ● | ● | ● | ● | ● |
mttB | ● | ● | ● | ● | ● | ● | ● | ● |
nad1 | ● | ● | ● | ● | ● | ● | ● | ● |
nad2 | ● | ● | ● | ● | ● | ● | ● | ● |
nad3 | ● | ● | ● | ● | ● | ● | ● | ● |
nad4 | ● | ● | ● | ● | ● | ● | ● | ● |
nad4L | ● | ● | ● | ● | ● | ● | ● | ● |
nad5 | ● | ● | ● | ● | ● | ● | ● | ● |
nad6 | ● | ● | ● | ● | ● | ● | ● | ● |
nad7 | ● | ● | ● | ● | ● | ● | ● | ● |
nad9 | ● | ● | ● | ● | ● | ● | ● | ● |
rpl2 | ● | ● | ● | ● | ● | ● | ● | ● |
rpl5 | ● | ● | ● | ● | ● | ● | ● | ● |
rpl10 | ● | ● | ● | ● | ● | ● | ● | ● |
rpl16 | ● | ● | ● | ● | ● | ● | ● | ● |
rps1 | ● | ● | ● | ● | ● | ● | ● | ● |
rps3 | ● | ● | ● | ● | ● | ● | ● | ● |
rps4 | ● | ● | ● | ● | ● | ● | ● | ● |
rps10 | ● | ● | ● | ● | ● | ● | ● | ● |
rps12 | ● | ● | ● | ● | ● | ● | ● | ● |
rps13 | ● | ● | ● | ● | ● | ● | ● | ● |
rps14 | ψ | ψ | ψ | ψ | ψ | ψ | ψ | ψ |
rps19 | ● | ● | ● | ● | ● | ● | ● | ● |
sdh3 | ● | ● | ● | ● | ● | ● | ● | ● |
sdh4 | ● | ● | ● | ● | ● | ● | ● | ● |
orf77 | ● | ● | ● | ● | ● | ● | ● | - |
orf103 | ● | ● | ● | ● | ● | ● | ● | ● |
orf105 | ● | ● | ● | ● | ● | ● | ● | - |
orf118 | ● | ● | ψ | ψ | - | - | - | - |
orf119 | ● | ● | ● | ● | ● | ● | ● | ● |
orf125 | ● | - | - | - | - | - | - | - |
orf137 | ● | - | - | - | - | - | - | - |
orf141 | ● | ● | ● | ● | - | - | - | - |
orf152 | ● | ● | ● | ● | ● | ● | ● | - |
orf159 | ● | ● | ● | ● | ψ | - | - | - |
orf161 | ● | ● | ● | ● | ● | ● | ● | ψ |
orf210 | ● | ● | ● | ● | - | - | - | - |
orf247 | ● | ● | ● | ● | - | - | - | - |
orf265a | ● | ● | ● | ● | ● | ● | ● | ψ |
orf265b | ● | ● | ● | ● | ● | ● | ● | ψ |
orf304 | ● | ● | ● | ● | ψ | - | - | - |
orf320 | ● | ● | ● | ● | ● | ● | ● | ● |
orf438 | ● | ● | ● | ● | - | - | - | - |
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Varré, J.-S.; D’Agostino, N.; Touzet, P.; Gallina, S.; Tamburino, R.; Cantarella, C.; Ubrig, E.; Cardi, T.; Drouard, L.; Gualberto, J.M.; et al. Complete Sequence, Multichromosomal Architecture and Transcriptome Analysis of the Solanum tuberosum Mitochondrial Genome. Int. J. Mol. Sci. 2019, 20, 4788. https://doi.org/10.3390/ijms20194788
Varré J-S, D’Agostino N, Touzet P, Gallina S, Tamburino R, Cantarella C, Ubrig E, Cardi T, Drouard L, Gualberto JM, et al. Complete Sequence, Multichromosomal Architecture and Transcriptome Analysis of the Solanum tuberosum Mitochondrial Genome. International Journal of Molecular Sciences. 2019; 20(19):4788. https://doi.org/10.3390/ijms20194788
Chicago/Turabian StyleVarré, Jean-Stéphane, Nunzio D’Agostino, Pascal Touzet, Sophie Gallina, Rachele Tamburino, Concita Cantarella, Elodie Ubrig, Teodoro Cardi, Laurence Drouard, José Manuel Gualberto, and et al. 2019. "Complete Sequence, Multichromosomal Architecture and Transcriptome Analysis of the Solanum tuberosum Mitochondrial Genome" International Journal of Molecular Sciences 20, no. 19: 4788. https://doi.org/10.3390/ijms20194788