Supplementary Table 2: Database homologies for sequences flanking PDR1 insertions
RBIP/Flank HOMOLOGY
Sequences 5’ to PDR1
399L1Non-LTR retrotransposon reverse transcriptase
399L10-
399L13-
399L23-
399L24-
399L29-
399L36-
399L37-
399L41-
399L45-
399L55-
399L79-
399L81putative TNP2-like transposon protein?
399L89-
399L98-
LTR_aa_1+Tomato cDNA BT013571
LTR_ac_22--
LTR_ac_25--
LTR_ac_26+Chicory RGC2-like protein coding region AY193694
LTR_ac_27+-
LTR_ac_28+ *-
LTR_ag_30+ *-
LTR_ag_31+-
LTR_ag_32+-
LTR_ag_33- *Ogre Ty3-gypsy group retrotransposon
LTR_ag_34+Ty1-copia group retrotransposon
LTR_at_41+-
LTR_ta_54+homology with region upstream of pea Lox1:Ps:3 gene
LTR_ta_55--
LTR_ta_56--
LTR_ta_57+-
LTR_tc_60--
LTR_tg_70+-
LTR_tg_71+Protein coding region homologous to tomato RNA BT014596
LTR_tg_75a-Adjacent insertion of PDR1 Ty1-copia group retrotransposon, starts at base 38
LTR_tg_76+-
LTR_tg_77+Ty3-gypsy group retrotransposon very similar to Ogre
LTR_tt_80--
LTR_tt_81--
LTR_tt_83--
LTR_tt_83-_2Coding region homologous to Zea mays multidrug resistance associated protein AY186245 posn ~2565
LTR_tt_84+-
LTR_tt_86+ *-
LTR_tt_87- *-
LTR_ca_95--
LTR_ca_96-Ty1-copia group retrotransposon
LTR_ca_97+ *Repetitious sequence
LTR_ca_98-
LTR_cg_102- * -
LTR_cg_104+ * Chloroplast DNA
LTR_ct_110+Ty3-gypsy group retrotransposon
LTR_ct_111+Ty3-gypsy group retrotransposon
LTR_ct_112--
LTR_ga_124--
LTR_ga_125+-
LTR_ga_127+-
LTR_gc_131--
LTR_gc_132+ *Ty3-gypsy group retrotransposon
LTR_gc_134+Repeated sequence
LTR_gc_135-Glycine-rich RNA-binding protein coding region similar to U81287.1 Pisum sativum
LTR_gg_141+-
LTR_gg_142--
LTR_gg_143+ *-
LTR_gg_145--
RBIP sequences containing entire target site for PDR1 insertion
399-14-9-
399-3-6anthocyanidin reductase (BAN) gene protein coding region (maybe also Litchi chinensis ethylene receptor)
399-80-46 CACTA transposon
1794-2-
399-x131Medicago BAC AY224188, 5’ region of Selenium binding protein gene
399x149-
399-9xRepeated sequence - Intron of Mt nodulin25 gene
Birte-B1-
Birte-x165 Medicago hits
Birte-x28-
Birte-x34WD40/Leunig/STYLOSA gene protein coding region
Birte-x5-
281-x1Small dispersed repeat (initially found in GapN gene 3’ untranslated region)
281-x16-
281-x40Dispersed repeat, probable LINE retrotransposon
281-x44-
281-x5Ty3-gypsy group retrotransposon
1794-1Repeated sequence (Lotus, Medicago)
1794-x35Repeated sequence
1794-x7-
1794-x9-
2055-x10Ty-copia LTR retrotransposon (Mel76-like)
2055-x19Ty3-gypsy group retrotransposon
2055-x28Ogre Ty3-gypsy group retrotransposon
2055-x29-
2055-x36MIRE1-like Ty3-gypsy group retrotransposon
(2055NR1IDENTICAL TO MKRBIP4 (LTR retrotransposon))
2055NR16-
2055NR23-
2055NR33-
2055NR51 -
2055NR532 Medicago and 3 Arabidopsis hits
2385-x16Ty1-copia group retrotransposon
2385-x23-
2385-x463 Medicago and 1 Lotus hit
2385-x56Single Medicago hit
2385-x64Repeated sequence
1006-x19-
1006-x21-
1006-x36Hopscotch Ty1-copia group retrotransposon
1006-x50Cytosolic aldehyde dehydrogenase gene protein coding region (maize &Arabidopsis)
1006-x58-
1006-x6Ty3-gypsy group retrotransposon (like MIRE-1, e.g. AY196987)
1006-NR13-
1006NR2-
1006NR27-
1006NR32Repeated sequence - probably Ty-copia LTR retrotransposon (e.g.SMAB1585)
1006NR9-
95-x195 Medicago hits
95-x2-
95-x255 strong Medicago hits
95-x43-
64-x11Repeated sequence
64-x14-
64-x15Repeated sequence & AT hook motif mRNA
64-x29Ty1-copia LTR retrotransposon
64-x405 weak Medicago hits (eg AC146564)
64-x456 strong Medicago hits and many weaker hits in Lotus
64-x74-
64-x76Repeated sequence
45-x15-
45-x20-
45-x29Nicotiana cellulase & respiratory burst oxidase gene protein-coding regions
45-x31-
45-x33like Ogre Ty3-gypsy group retrotransposon
45-x38Ty1-copia LTR retrotransposon
45-x8Retrofit Ty1-copia LTR retrotransposon
2539-x7-
3150-x11tRNA splicing endonuclease (Arabidopsis (At1g65780) & strong Lotus hit (AP004913)
261-x1P sat gibberellin c20-oxidase region (AF138704) – non genic. Possibly P. sativum LTR?
261-x13Glycosyl hydrolase gene, protein-coding region
MKRBIP2Ty3-gypsy group retrotransposon
MKRBIP3Insertion in homologue of Medicago truncatula HCR6 gene, exon structure unknown
MKRBIP4Repeated sequence, possibly retroelement(identical to 2055nr1)
MKRBIP7Repeated sequence
Sequences 3’ to PDR1
399-R102-
399-R106-
399-R11-
399-R125-
399-R126-
399-R134-
399-R150-
399-R217-
399-R52-
399-R53-
399-R56-
399-R68-
399-R82 -
Birte-R18-
Birte-R22-
Birte-R30-
Birte-R31-
281-R13-
281-R32-
281-R42Region upstream of pea Legumin gene (non-repetitious)
1794-R12-
1794-R14 -
1794-R16PDR1 Ty1-copia group retrotransposon, nts 157-296
1794-R17-
1794-R2-
1794-R20Repeated sequence (like pSat28)
1794-R21-
1794-R24 -
1794-R27 -
1794-R3 -
1794-R30-
2055-R14-
2055-R15-
2055-R18Ogre Ty3-gypsy group retrotransposon
2055-R20-
2055-R21-
2055-R26 -
2055-R32 -
2055-R34 -
2055NR12 -
2055NR24-
2055NR33-
2055NR52Repeated sequence
2055NR55-
2055NR56R gene coding region
2055NR65 -
2385-R13-
2385-R14Ty1-copia group retrotransposon
2385-R17-
2385-R21-
2385-R26-
2385-R27Repeated sequence
2385-R29-
2385-R3-
2385-R35Repeated sequence outside Ogre Ty3-gypsy group retrotransposon
2385-R36Ty1-copia group retrotransposon
2385-R41-
2385-R43Artefact - polylinker
2385-R47 -
2385-R573 medicago hits
2385-R60-
2385-R61-
2385-R68Ty1-copia group retrotransposon
2385-R69-
2385-R7-
1006-R11-
1006-R12Ty3-gypsy group retrotransposon
1006-R14-
1006-R15-
1006-R18-
1006-R20 -
1006-R27Repetitious, probably Tmgr-like retrotransposon
1006-R29-
1006-R46-
1006-R55-
1006-R56-
1006-R69-
1006NR7-
95-R12 Repeated sequence
95-R21 -
95-R42-
95-R45-
95-R6-
64-R17Tpv2-like Ty1-copia group retrotransposon
64-R20Arabidopsis AAM60906 gene protein coding region
64-R24Repetitious, probably Tmgr-like retrotransposon
64-R81Ty3-gypsy group retrotransposon
64-R86-
64-R88-
45-R11-
45-R13-
45-R7-
261R10-
261R12-
261R6-
2539R9-
2539R11-
3147R10-
3150R18pea GapN locus (see 281x1)
PPT_aa_123+ *Homologous to region of Ogre Ty3-gypsy group retrotransposon between end of protein and right LTR
PPT_aa_127+-
PPT_aa_140--
PPT_aa_141- *Ty3-gypsy group retrotransposon homologous to Ogre
PPT_ac_161- *Repeat found in pea Pra2 gene AB007911 etc (see PPT_gg_270+)
PPT_ac_162- *-
PPT_ac_163+Coding region of homologue of Arabidopsis unknown protein mRNA AY140050
PPT_ac_164+-
PPT_ac_165--
PPT_ac_166+Coding region homologous to Zea mays multidrug resistance associated protein AY186245 posn 753
PPT_ac_168--
PPT_ac_169-PDR1 Ty1-copia AND cyclops-2 Ty3-gypsy group retrotransposon
PPT_ag_173+-
PPT_ag_174--
PPT_ag_176--
PPT_ag_179+-
PPT_ag_181--
PPT_ag_182+Repeated sequence
PPT_ag_183-PDR1 Ty1-copia group retrotransposon position 3755
PPT_ag_184+ *-
PPT_at_87--
PPT_at_89--
PPT_at_108--
PPT_at_113+ *-
PPT_ca_205--
PPT_ca_206+-
PPT_ca_209+-
PPT_ca_210+R gene e.g. tomato AF118127 coding sequence
PPT_ca_212-Coding region of homologue of U94782 Helianthus annuus unconventional myosin (hamy2) mRNA
PPT_ca_214+Ty3-gypsy group retrotransposon
PPT_ca_216- *Repeated sequence
PPT_cc_253+Coding region of homologue of BT014082 Lycopersicon esculentum clone 133182F, mRNA etc
PPT_cg_245+-
PPT_cg_246-Repeated sequence
PPT_cg_247--
PPT_cg_248-Repeated sequence
PPT_cg_249- *-
PPT_ct_261+ *Coding region of homologue of AY150478 A. thaliana putative cleavage and polyadenylation specificity factor (At1g61010) etc mRNA
PPT_ct_262+-
PPT_ct_263+ *Ty3-gypsy group retrotransposon homologous to Ogre
PPT_ct_266+Single hit to Medicago AC148775
PPT_ga_222+ *-
PPT_ga_223+Coding region of homologue of Ricinus communis eukaryotic release factor 3 mRNA Accession rcerf3 .em_pl
PPT_gc_231+7 Medicago hits
PPT_gc_232+ *Ty3-gypsy group retrotransposon related to Cyclops 2
PPT_gg_269-8 Medicago hits, + insertion in region homologous to the upstream region of pea hsp70 gene pshsp70ct.em_pl
PPT_gg_270+ *Repeat found in pea Pra2 gene AB007911 etc
PPT_gg_271+-
PPT_gt_187+ *AF155761.1 Pisum sativum clone Psat24 repetitive sequence
PPT_gt_188-4 M.edicago hits including AY372418.1 Medicago truncatula HCR6 gene (no annotation)
PPT_gt_189--
PPT_gt_192-Hopscotch Ty1-copia group retrotransposon
PPT_gt_193+ *-
PPT_gt_194- *-
PPT_gt_195--
PPT_gt_197+-
PPT_gt_198+ *-
PPT_gt_199+ *-
PPT_ta_28--
PPT_ta_56+Homologous to Arabidopsis unknown mRNA protein coding region BT005734
PPT_ta_57+-
PPT_ta_58+-
PPT_ta_59+-
PPT_ta_60--
PPT_ta_61+ *-
PPT_ta_62- *-
PPT_tc_68+-
PPT_tc_69- *Repeated sequence
PPT_tc_70+Repeated sequence (pSat12 related)
PPT_tc_71- *-
PPT_tc_72-Repeated sequence found in Ogre Ty3-gypsy group retrotransposon
PPT_tc_73+-
PPT_tg_159+Repeated sequence related to Vicia faba TaqI element AJ222868
PPT_tt_9-Close homologue of coding region of AJ006041.1 Arabidopsis thaliana mRNA for DYW8 protein (R gene?)
PPT_tt_11--
PPT_tt_12-C terminus of coding region of homologue to rice cDNA AK106680
PPT_tt_76+-
PPT_tt_77+ *Low copy element homologous to apparently intergenic region of Lotus LCO580823
PPT_tt_78+Repeated sequence
PPT_tt_79+ *-
PPT_tt_95+ *-
* = No LTR detected in sequence
- = No significant hit in the databases (BLAST and TBLASTX)
yellow = Repeat sequence
Green = Gene protein coding region
Grey = Low copy insertion and/or gene non-protein coding region (intron, promoter, 5’ utr, 3’ utr region)