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.

Hane and Oliver BMC Genomics 2010 11:655   doi:10.1186/1471-2164-11-655

Open Data