Table 4.
Classification of repeat family origin in S. nodorum SN15.
| Repeat family | Predicted origin [19,20] | Predicted origin after deRIP | comparison type | informative hits | Majority Consensus e-value | deRIP consensus e-value | deRIP improvement factor (maximum) |
|---|---|---|---|---|---|---|---|
| X26 | Sub-telomeric, transposon remnant | Telomere-associated RecQ helicase | blastx vs NR |
EAL89306.1 telomere-associated RecQ helicase, putative Aspergillus fumigatus Af293 |
1.00E-07 | 2.00E-12 | 1.25 |
| R25 | Transposon remnant | Histone H3 | blastx vs NR |
EDU47581.1 histone H3 Pyrenophora tritici-repentis Pt-1C-BFP |
0.032 | 2.00E-04 | 1.16 |
| tblastx vs Repbase | TDD4 DNA transposon Dictyostelium_discoideum |
6.00E-04 | |||||
| R10 | Unknown | Uncharacterized endogenous gene region and DNA transposon | blastx vs NR |
EAT76576.1 hypothetical protein SNOG_15997 Phaeosphaeria nodorum SN15 |
2.2 | 2.00E-13 | 2.13 |
| blastx vs NR |
EAT81769.1 hypothetical protein SNOG_11270 Phaeosphaeria nodorum SN15 |
5.00E-11 | |||||
| blastx vs NR |
EAT76052.1 hypothetical protein SNOG_16585 Phaeosphaeria nodorum SN15 |
0.006 | 2.00E-08 | 1.40 | |||
| tblastx vs Repbase | CR1-3_HM CR1 Hydra magnipapillata |
9.00E-06 | |||||
| R31 | Unknown | DNA Transposon | blastx vs NR |
CAP79587.1 Pc23g00930 Penicillium chrysogenum Wisconsin 54-1255 |
0.013 | 1.00E-06 | 1.28 |
| tblastx vs Repbase | hAT-1_AN hAT DNA transposon Emericella nidulans |
1.00E-05 | 1.00E-06 | 1.07 | |||
| R39 | Unknown | Mariner/Tc1-like DNA transposon | blastx vs NR |
EAT91063.1 hypothetical protein SNOG_01414 Phaeosphaeria nodorum SN15 |
2.00E-62 | 3.00E-73 | 1.15 |
| blastx vs NR |
EED11513.1 pogo transposable element, putative Talaromyces stipitatus ATCC 10500 |
2.00E-28 | 1.00E-36 | 1.20 | |||
| tblastx vs Repbase | Mariner-9_AN Mariner/Tc1 Emericella_nidulans |
8.00E-37 | 1.00E-25 | 1.01 | |||
| R51 | Unknown | Mariner/Tc1-like DNA transposon | tblastx vs Repbase | P-29_HM P Hydra magnipapillata |
1.00E-05 | ||
| tblastx vs Repbase | Mariner-31_HM Mariner/Tc1 Hydra magnipapillata |
3.00E-05 | |||||
| X23 | Unknown | LTR Retrotransposon | tblastx vs Repbase | ATCOPIA80_I Copia Arabidopsis thaliana |
1.00E-04 | ||
| tblastx vs Repbase | CR1-3_HM CR1 Hydra magnipapillata |
9.00E-05 | 3.00E-04 | 0.82 | |||
| X36 | Unknown | Retrotransposon | blastx vs NR |
EAS29858.1 hypothetical protein CIMG_08604 Coccidioides immitis RS |
4.9 | 2.00E-04 | 1.43 |
| blastx vs NR | gag-pol polyprotein Podospora anserina |
4.00E-03 | |||||
| X3X3R8 | X3: Helicase | Endogenous gene cluster containing tandem duplicated Rad5/SNF2-like helicase, Rad6/ubiquitin conjugating enzyme and uncharacterised ORFs | blastx vs NR |
EAT83378.1 hypothetical protein SNOG_09186 EAT91019.1 hypothetical protein SNOG_01370 Phaeosphaeria nodorum SN15 |
1.00E-165 | 0 | 1.48 |
| blastx vs NR |
EAT90556.1 hypothetical protein SNOG_02344 Phaeosphaeria nodorum SN15 |
6.00E-75 | 1.00E-122 | 1.54 | |||
| blastx vs NR |
EAT83381.1 hypothetical protein SNOG_09189 EAT91023.1 hypothetical protein SNOG_01374 Phaeosphaeria nodorum SN15 |
8.00E-93 | 1.00E-117 | 1.51 | |||
| blastx vs NR |
EAT90553.1 hypothetical protein SNOG_02341 Phaeosphaeria nodorum SN15 |
7.00E-61 | 1.00E-100 | 1.51 | |||
| blastx vs NR |
EAT92620.1 hypothetical protein SNOG_16597 Phaeosphaeria nodorum SN15 |
9.00E-39 | 2.00E-49 | 1.43 | |||
| blastx vs NR | EAT91018.1 hypothetical protein SNOG_01369 Phaeosphaeria nodorum SN15 | 3.00E-30 | 1.00E-48 | 1.44 | |||
| blastx vs NR |
EAT90555.1 hypothetical protein SNOG_02343 Phaeosphaeria nodorum SN15 |
7.00E-36 | 5.00E-33 | 1.31 | |||
| blastx vs NR |
EAT90554.1 hypothetical protein SNOG_02342 Phaeosphaeria nodorum SN15 |
1.00E-36 | 2.00E-26 | 1.34 | |||
| blastx vs NR |
EAT83379.1 hypothetical protein SNOG_09187 Phaeosphaeria nodorum SN15 |
3.00E-14 | 1.00E-21 | 1.28 | |||
| blastx vs NR |
EAT91020.2 hypothetical protein SNOG_01371 Phaeosphaeria nodorum SN15 |
3.00E-15 | 2.00E-20 | 1.19 | |||
| blastx vs NR |
EAT83294.1 hypothetical protein SNOG_09102 Phaeosphaeria nodorum SN15 |
2.00E-13 | 4.00E-20 | 1.25 | |||
| blastx vs NR |
EAT83377.2 hypothetical protein SNOG_09185 Phaeosphaeria nodorum SN15 |
1.00E-13 | 8.00E-20 | 1.23 | |||
| blastx vs NR | EAT92618.1 hypothetical protein SNOG_16595 Phaeosphaeria nodorum SN15 | 3.00E-07 | 4.00E-19 | 1.60 | |||
| blastx vs NR |
EAT83380.1 hypothetical protein SNOG_09188 EAT91022.1 hypothetical protein SNOG_01373 EAT92619.1 hypothetical protein SNOG_16596 Phaeosphaeria nodorum SN15 |
4.00E-05 | 7.00E-15 | 1.57 | |||
| blastx vs NR |
EAT91021.1 hypothetical protein SNOG_01372 Phaeosphaeria nodorum SN15 |
2.00E-06 | 8.00E-14 | 1.40 | |||
| blastx vs NR |
EDU40406.1 ubiquitin-conjugating enzyme E2-21 kDa Pyrenophora tritici-repentis Pt-1C-BFP |
2.00E-10 | 2.00E-16 | 1.27 | |||
| blastx vs NR |
EAW17873.1 ubiquitin conjugating enzyme (UbcC), putative Neosartorya fischeri NRRL 181 |
1.00E-07 | 2.00E-13 | 1.29 | |||
| R8: Ubiquitin conjugating enzyme | blastx vs NR |
EAT91013.2 hypothetical protein SNOG_01364 Phaeosphaeria nodorum SN15 |
0 | 0 | 0.91 | ||
| blastx vs NR |
EAT92627.2 hypothetical protein SNOG_16589 Phaeosphaeria nodorum SN15 |
0 | 0 | 0.91 | |||
| blastx vs NR |
EAT83373.2 hypothetical protein SNOG_09181 Phaeosphaeria nodorum SN15 |
1.00E-177 | 0 | 0.95 | |||
| blastx vs NR |
EAT90557.2 hypothetical protein SNOG_02345 Phaeosphaeria nodorum SN15 |
2.00E-65 | 1.00E-106 | 2.80 | |||
| blastx vs NR |
EAT90559.2 hypothetical protein SNOG_02347 Phaeosphaeria nodorum SN15 |
1.00E-62 | 5.00E-91 | 1.38 | |||
| blastx vs NR |
EAT91015.1 hypothetical protein SNOG_01366 Phaeosphaeria nodorum SN15 |
3.00E-40 | 3.00E-62 | 1.35 | |||
| blastx vs NR |
EAT85951.1 hypothetical protein SNOG_06120 Phaeosphaeria nodorum SN15 |
2.00E-18 | 3.00E-24 | 1.19 | |||
| blastx vs NR |
EAT91016.1 hypothetical protein SNOG_01367 Phaeosphaeria nodorum SN15 |
1.00E-15 | 2.00E-23 | 1.28 | |||
| blastx vs NR |
EAT83374.2 hypothetical protein SNOG_09182 Phaeosphaeria nodorum SN15 |
5.00E-05 | 4.00E-08 | 1.23 | |||
| blastx vs NR |
EAT91014.2 hypothetical protein SNOG_01365 Phaeosphaeria nodorum SN15 |
1.00E-04 | 2.00E-04 | 1.15 | |||
After deRIP analysis the predicted origin of 8 repeat families has been altered from that described in Hane & Oliver (2008) [20]. Details of the blast hits which were most informative in re-classifying a repeat family are listed below. E-values are shown for matches to both the majority and deRIP consensus sequences. DeRIP improvement is a measure of how much better the deRIP consensus matched the hit compared to the majority consensus. DeRIP improvement > 1 indicates that the repeat family was derived from the hit or a related homolog, but was subsequently mutated by RIP.