TABLE 4.
Chimeric ORFs (≥70 codons) present in the five maize mitochondrial genomes
| Genome
|
|||||
|---|---|---|---|---|---|
| NB | NA | CMS-C | CMS-S | CMS-T | Gene fragments present |
| orf73 | — | — | — | — | 28 bp atp9 |
| orf75 | orf75 | — | orf75 | orf75 | 29 bp atp9 |
| orf70 | orf70 | orf70 | orf70 | orf70 | 42 bp nad7 exon 4 |
| — | — | — | orf72 | — | 153 bp nad2 pseudo-exon 1 |
| orf73-a | — | — | — | — | 219 bp nad2 pseudo-exon 4 |
| orf73-b | — | — | — | — | 51 bp nad2 pseudo-exon 4 |
| orf86 | orf86 | orf86 | orf86 | — | 67 bp atp6 |
| orf90 | — | orf90 | orf90 | orf90 | 31 bp rps3 exon 1 |
| orf89 | orf89 | orf89 | orf89 | orf89 | 28 bp plastid rrn23 |
| orf197 | — | — | orf221 | — | 573 bp nad2 pseudo-exon 4 |
| orf191a | — | orf191a | orf191a | orf191a | 30 bp rps3 exon 1 |
| — | orf130-bb | — | — | — | 30 bp rps3 exon 1 |
| orf159-a | orf159-a | orf163-b | orf163-b | orf159-a | 264 bp rps3 (exon 1 + 190 bp of intron 1); 209 bp rps12 |
| orf101-c | orf101-c | orf101-c | orf101-c | — | 26 bp rps3 exon 2 |
| orf186 | orf186 | orf186 | orf186 | — | 80 bp cox2 exon 1; 28 bp rps2B |
| — | orf179-b | — | — | orf179-b | 21, 43 bp cox2 exon 1 |
| orf248 | orf248 | orf246 | — | orf248 | 26, 24, 23, 29 bp atp6-CMS-C; 21 bp rps3 exon 2 |
| orf248b | orf248b | orf246b | orf189 | orf248b | 26, 24 bp atp6-CMS-C |
| orf396 | orf364 | orf410 | orf462 | — | 112 bp atp6-NBc |
| – | orf105-h | — | — | orf105-h | 47 bp atp9 |
| orf147-b | orf147-b | orf147-b | orf147-b | orf190 | 24 bp atp4; 39 bp atp9; 19 bp cox1 |
| orf149-a | orf149-a | orf149-a | orf134-b | orf149-a | 35 bp cp trnR |
| — | — | — | — | orf118-b | 31 bp cp trnRd |
| 8 | 4 | 4 | 6 | 4 | Chimeric ORFs 70–99 codons |
| 9 | 10 | 8 | 9 | 8 | Chimeric ORFs ≥100 codons |
| 296 | 360 | 388 | 279 | 280 | Total ORFs 70–99 codons |
| 105 | 116 | 103 | 107 | 95 | Total ORFs ≥100 codons |
| 2.7% | 1.1% | 1.0% | 2.2% | 1.4% | Chimeric ORFs 70–99 codons as percentage of all ORFs 70–99 codons |
| 8.6% | 8.6% | 7.8% | 8.4% | 8.4% | Chimeric ORFs ≥100 codons as percentage of all ORFs ≥100 codons |
ORFs of 70–99 codons are in the top portion of the list, and ORFs of ≥100 codons are in the bottom portion of the list. Identified CMS-related ORFs (T-urf13, orf355, orf77) and ORFs within sequences of plastid origin (see materials and methods) are not included. ORF totals are for genome complexity. ORFs must have at least one gene fragment ≥26 bp, but additional fragments of 16–25 bp are shown if present.
The orf130-b sequence lies within the orf191 sequence and contains the same gene fragment, but is in the opposite orientation.
Contains the fragments listed plus additional fragments listed in the line above. See Figure 2 for a graphic representation of some of the chimeric ORFs or supplemental Table 1 at http://www.genetics.org/supplemental/ for all of them.
This atp6 version is also the version in NA, CMS-S, and CMS-T. This 112-bp segment is also found 7 bp upstream of the cox2 ATG in all the genomes except CMS-C.
Part of the fragment on the line above it.