Hierarchical alignments with the V. vinifera genome as reference

  Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Fabaceae genomes. We used P. vulgaris as a reference, and by comparing homologous gene locus maps and Ks values between P. vulgaris and other Fabaceae, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We created two hierarchical lists of homologous genes using P. vulgaris as a reference.
  The relevant gene ids can be obtained from the Fabaceae blast and match under the Tools module. This link is Fabaceae blast and match.
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Select Download Tree Vvi Acco_1 Acco_2 Accr_1 Accr_2 Adu_1 Adu_2 Aed_1 Aed_2 Aev_1 Aev_2 Ahy_1 Ahy_2 Aip_1 Aip_2 Alju_1 Alju_2 Amo_1 Amo_2 Apr_1 Apr_2 Arst_1 Arst_2 Bach_1 Bach_2 Bisa_1 Bisa_2 Bva_1 Bva_2 Car_1 Car_2 Cca_1 Cca_2 Dere_1 Dere_2 Dod_1 Dod_2 Enph_1 Enph_2 Glsi_1 Glsi_2 Gma_1 Gma_2 Gma_3 Gma_4 Gso_1 Gso_2 Gso_3 Gso_4 Lal_1 Lal_2 Lal_3 Lal_4 Lal_5 Lal_6 Lan_1 Lan_2 Lan_3 Lan_4 Lan_5 Lan_6 Lapu_1 Lapu_2 Lasa_1 Lasa_2 Lele_1 Lele_2 Lele_3 Lele_4 Lele_5 Lele_6 Lele_7 Lele_8 Lja_1 Lja_2 Mal_1 Mal_2 Mepo_1 Mepo_2 Mesa_1 Mesa_2 Mibi_1 Mibi_2 Mtr_1 Mtr_2 Phac_1 Phac_2 Phco_1 Phco_2 Prci_1 Prci_2 Psa_1 Psa_2 Pste_1 Pste_2 Pte_1 Pte_2 Pte_3 Pte_4 Pumo_1 Pumo_2 Pvu_1 Pvu_2 Rops_1 Rops_2 Seca_1 Seca_2 Spst_1 Spst_2 Ssu_1 Ssu_2 Sto_1 Sto_2 Tpr_1 Tpr_2 Trre_1 Trre_2 Tsu_1 Tsu_2 Vian_1 Vian_2 Vifa_1 Vifa_2 Vimu_1 Vimu_2 Viun_1 Viun_2 Vivi_1 Vivi_2 Vra_1 Vra_2
Vvi3g0813 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva13g00402 Bva14g00488 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto10g0376 . . . . . . . . . . . . . . . . . .
Vvi3g0814 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0815 . . . . . . Aed1g2029 . Aev09g2454 . Ahy19g3345 . Aip09g03812 . . . Amo19g4252 . Apr8g2401 . Arst9g03429 . . . . . . Bva14g00490 Car04g01405 . Cca02g02484 . . . Dod06g0507 . . . . . . . . . . . . . . . . Lal13g0366 . . . . . . . . Lapu7g02256 . Lasa6g04412 . . . . . . . . . Lja5g0455 . . Mal1g0592 Mepo4g04512 . Mesa1g04946 . . . . Mtr1g4011 . . Phco6g02736 . . . . . Pste4g01250 . . . . . Pumo3g00688 . Pvu7g0474 . . . . . . . . . . Sto10g0378 . Tpr1g0498 Trre1g05754 . . Tsu01g04687 Vian3g00429 . Vifa3g04972 . Vimu3g03335 . Viun7g03562 . Vivi4g05686 . Vra8g2386 .
Vvi3g0816 . . . . Adu09g02580 . Aed1g2031 . Aev09g2453 . Ahy19g3346 . Aip09g03813 . . . . . Apr8g2400 . Arst9g03428 . Bach11g00355 . . . Bva13g00404 Bva14g00491 . . Cca02g02482 . . . Dod06g0508 . . . . . . . . . . . . . . . . . . . . . . . . . Lapu7g02255 . . . . . . . . . . . Lja5g0456 . . . . . . . . . . . . . Phco6g02735 . . . . . Pste4g01252 . . Pte9g01344 . . Pumo3g00689 . Pvu7g0475 . Rops6g03045 . Seca8g07673 . Spst10g01237 . Ssu7g0530 . Sto2g0490 Sto10g0380 . . . . . . Vian3g00430 . . . Vimu3g03334 . Viun7g03561 . . . Vra8g2384 .
Vvi3g0817 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto2g0488 . . . . . . . . . . . . . . . . . . .
Vvi3g0818 . . . . . Adu05g01351 Aed1g2032 Aed11g1943 Aev09g2452 . Ahy19g3347 Ahy15g1318 Aip09g03814 Aip05g01390 . . Amo19g4251 . Apr8g2399 . Arst9g03426 . . . . . Bva13g00406 Bva14g00494 Car04g01404 Car08g00036 Cca02g02480 Cca06g02035 . . Dod06g0509 Dod02g1400 . . . . . . . . . . . . . . . Lal13g0365 Lal12g0373 Lal24g0288 . . . . . . . . Lasa6g04408 Lasa2g02528 . . . . . . . . Lja5g0457 . . Mal1g0593 Mepo4g04511 Mepo5g00042 Mesa1g04945 Mesa17g00037 . . . Mtr1g4010 Phac7g00713 . Phco6g02734 Phco4g00039 . . Psa6g4905 . Pste4g01265 Pste1g00724 . Pte9g01343 . . Pumo3g00690 Pumo8g02599 Pvu7g0476 Pvu2g0529 Rops6g03037 Rops1g02456 Seca8g07672 Seca10g00060 Spst10g01234 Spst2g00039 Ssu7g0531 Ssu2g3153 Sto2g0487 Sto10g0381 . Tpr1g0499 Trre1g05753 Trre9g00037 . Tsu01g04686 Vian3g00431 Vian10g00034 Vifa3g03276 Vifa3g03276 Vimu3g03333 Vimu7g02176 Viun7g03560 Viun2g02934 Vivi1g03984 Vivi2g04260 Vra8g2383 Vra11g0039
Vvi3g0819 . . . . Adu09g02579 . . . Aev09g2451 . Ahy19g3348 . Aip09g03815 . . . . . Apr8g2398 . Arst9g03424 . . . . . . Bva14g00495 . . Cca02g02479 . . . Dod06g0510 . . . . . . . . . . . . . . . . . . Lal24g0287 . . . . . . Lapu7g02254 . Lasa6g04407 . . . . . . . . . Lja5g0458 . . Mal1g0594 Mepo4g04510 . . . . . . Mtr1g4009 Phac7g00715 . Phco6g02732 . . . Psa6g4904 . Pste4g01271 . . . . . . . Pvu7g0477 . . . . . Spst10g01232 . . . Sto2g0483 . . Tpr1g0500 Trre1g05752 . . Tsu01g04685 Vian3g00432 . . . Vimu3g03332 . Viun7g03559 . Vivi1g03985 . . .
Vvi3g0820 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0821 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0822 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi3g0813 Chr3 7564327 7579267 -
Bva Bva13g00402 Chr13 1858198 1862702 -
Bva Bva14g00488 Chr14 2335094 2340535 -
Sto Sto10g0376 Chr10 3009110 3016039 -
Vvi Vvi3g0814 Chr3 7603570 7604263 -
Vvi Vvi3g0815 Chr3 7652632 7660938 +
Aed Aed1g2029 Chr1 17087330 17091006 +
Aev Aev09g2454 Chr09 26444789 26448565 -
Ahy Ahy19g3345 Chr19 156406187 156409179 +
Aip Aip09g03812 Chr09 144762416 144765395 +
Amo Amo19g4252 Chr19 159256651 159259456 -
Apr Apr8g2401 Chr8 34266225 34270676 -
Arst Arst9g03429 Chr9 111285278 111288228 -
Bva Bva14g00490 Chr14 2347241 2352349 +
Car Car04g01405 Chr04 14358169 14362079 -
Cca Cca02g02484 Chr02 45981879 45986416 -
Dod Dod06g0507 Chr06 6124591 6128839 +
Lal Lal13g0366 Chr13 2301376 2305789 -
Lapu Lapu7g02256 Chr7 38919987 38935124 -
Lasa Lasa6g04412 Chr6 640746667 640749703 -
Lja Lja5g0455 Chr5 3979080 3983675 +
Mal Mal1g0592 Chr1 6804180 6808093 +
Mepo Mepo4g04512 Chr4 54849563 54853475 -
Mesa Mesa1g04946 Chr1 76346837 76350807 -
Mtr Mtr1g4011 Chr1 51712978 51717373 -
Phco Phco6g02736 Chr6 48826211 48830739 -
Pste Pste4g01250 Chr4 9173433 9177711 +
Pumo Pumo3g00688 Chr3 10255804 10260320 +
Pvu Pvu7g0474 Chr7 3719065 3724526 +
Sto Sto10g0378 Chr10 3031829 3036171 +
Tpr Tpr1g0498 Chr1 4197477 4202405 +
Trre Trre1g05754 Chr1 62432066 62436252 -
Tsu Tsu01g04687 Chr01 54187450 54191375 -
Vian Vian3g00429 Chr3 4031372 4035787 +
Vifa Vifa3g04972 Chr3 1444831346 1444835162 -
Vimu Vimu3g03335 Chr3 46775254 46780166 -
Viun Viun7g03562 Chr7 37001878 37006597 -
Vivi Vivi4g05686 Chr4 193176771 193181049 -
Vra Vra8g2386 Chr8 42035145 42039696 -
Vvi Vvi3g0816 Chr3 7674046 7675558 +
Adu Adu09g02580 Chr09 113385971 113387928 -
Aed Aed1g2031 Chr1 17098696 17100618 +
Aev Aev09g2453 Chr09 26441274 26443023 -
Ahy Ahy19g3346 Chr19 156409756 156411847 +
Aip Aip09g03813 Chr09 144765938 144768502 +
Apr Apr8g2400 Chr8 34261194 34262715 -
Arst Arst9g03428 Chr9 111282732 111284757 -
Bach Bach11g00355 Chr11 2365902 2367557 +
Bva Bva13g00404 Chr13 1870704 1873031 +
Bva Bva14g00491 Chr14 2353386 2355623 +
Cca Cca02g02482 Chr02 45968076 45969718 -
Dod Dod06g0508 Chr06 6133051 6135438 +
Lapu Lapu7g02255 Chr7 38908399 38910497 -
Lja Lja5g0456 Chr5 3986771 3988844 +
Phco Phco6g02735 Chr6 48816436 48817992 -
Pste Pste4g01252 Chr4 9208350 9210267 +
Pte Pte9g01344 Chr9 34847236 34849438 -
Pumo Pumo3g00689 Chr3 10270489 10272469 +
Pvu Pvu7g0475 Chr7 3731781 3733953 +
Rops Rops6g03045 Chr6 53577630 53579473 -
Seca Seca8g07673 Chr8 174029346 174032229 -
Spst Spst10g01237 Chr10 13130360 13132620 -
Ssu Ssu7g0530 Chr7 9755129 9756772 +
Sto Sto2g0490 Chr2 4237388 4239602 -
Sto Sto10g0380 Chr10 3041061 3042687 +
Vian Vian3g00430 Chr3 4040211 4041796 +
Vimu Vimu3g03334 Chr3 46770357 46771926 -
Viun Viun7g03561 Chr7 36994741 36997007 -
Vra Vra8g2384 Chr8 42019787 42021746 -
Vvi Vvi3g0817 Chr3 7693498 7695038 -
Sto Sto2g0488 Chr2 4222573 4233503 +
Vvi Vvi3g0818 Chr3 7704824 7705724 +
Adu Adu05g01351 Chr05 20372497 20373643 -
Aed Aed1g2032 Chr1 17111983 17112774 +
Aed Aed11g1943 Chr11 22195942 22196491 -
Aev Aev09g2452 Chr09 26428801 26429807 -
Ahy Ahy19g3347 Chr19 156423480 156424868 +
Ahy Ahy15g1318 Chr15 21585599 21586930 -
Aip Aip09g03814 Chr09 144778322 144779615 +
Aip Aip05g01390 Chr05 20790105 20791276 -
Amo Amo19g4251 Chr19 159240954 159242258 -
Apr Apr8g2399 Chr8 34249880 34251512 -
Arst Arst9g03426 Chr9 111270955 111272266 -
Bva Bva13g00406 Chr13 1880812 1881709 +
Bva Bva14g00494 Chr14 2372617 2374542 +
Car Car04g01404 Chr04 14340090 14341407 -
Car Car08g00036 Chr08 319507 320483 +
Cca Cca02g02480 Chr02 45927239 45928568 -
Cca Cca06g02035 Chr06 35604989 35611013 -
Dod Dod06g0509 Chr06 6150464 6151999 +
Dod Dod02g1400 Chr02 16844419 16845908 -
Lal Lal13g0365 Chr13 2298697 2300080 -
Lal Lal12g0373 Chr12 2659072 2661473 -
Lal Lal24g0288 Chr24 2072380 2073697 -
Lasa Lasa6g04408 Chr6 640125758 640126583 +
Lasa Lasa2g02528 Chr2 504013955 504014644 +
Lja Lja5g0457 Chr5 3996982 3998725 +
Mal Mal1g0593 Chr1 6830320 6831203 +
Mepo Mepo4g04511 Chr4 54842324 54843510 -
Mepo Mepo5g00042 Chr5 417978 419702 +
Mesa Mesa1g04945 Chr1 76339175 76339931 -
Mesa Mesa17g00037 Chr17 357656 358392 +
Mtr Mtr1g4010 Chr1 51707658 51709012 -
Phac Phac7g00713 Chr7 3981824 3983129 +
Phco Phco6g02734 Chr6 48785247 48787436 -
Phco Phco4g00039 Chr4 263237 264113 +
Psa Psa6g4905 Chr6 428102615 428104561 +
Pste Pste4g01265 Chr4 9302565 9303569 +
Pste Pste1g00724 Chr1 2273956 2275383 +
Pte Pte9g01343 Chr9 34842389 34843931 -
Pumo Pumo3g00690 Chr3 10296785 10297897 +
Pumo Pumo8g02599 Chr8 63206812 63207783 -
Pvu Pvu7g0476 Chr7 3761709 3763244 +
Pvu Pvu2g0529 Chr2 4742807 4744245 -
Rops Rops6g03037 Chr6 53484298 53485696 -
Rops Rops1g02456 Chr1 47581018 47581920 -
Seca Seca8g07672 Chr8 174014523 174016153 -
Seca Seca10g00060 Chr10 539256 540497 +
Spst Spst10g01234 Chr10 13119616 13121484 -
Spst Spst2g00039 Chr2 371111 377053 +
Ssu Ssu7g0531 Chr7 9794686 9795543 +
Ssu Ssu2g3153 Chr2 93797221 93797974 -
Sto Sto2g0487 Chr2 4212158 4213044 -
Sto Sto10g0381 Chr10 3061536 3062395 +
Tpr Tpr1g0499 Chr1 4205913 4207249 +
Trre Trre1g05753 Chr1 62428008 62429002 -
Trre Trre9g00037 Chr9 459298 460042 +
Tsu Tsu01g04686 Chr01 54181822 54183122 -
Vian Vian3g00431 Chr3 4060114 4060951 +
Vian Vian10g00034 Chr10 267533 268329 +
Vifa Vifa3g03276 Chr3 939353383 939354235 +
Vifa Vifa3g03276 Chr3 939353383 939354235 +
Vimu Vimu3g03333 Chr3 46752442 46753297 -
Vimu Vimu7g02176 Chr7 19223217 19224593 +
Viun Viun7g03560 Chr7 36976824 36978139 -
Viun Viun2g02934 Chr2 33611302 33612651 -
Vivi Vivi1g03984 Chr1 83972899 83974058 -
Vivi Vivi2g04260 Chr2 156216349 156217616 -
Vra Vra8g2383 Chr8 42004273 42005454 -
Vra Vra11g0039 Chr11 315531 317459 +
Vvi Vvi3g0819 Chr3 7710938 7711665 -
Adu Adu09g02579 Chr09 113370705 113372060 +
Aev Aev09g2451 Chr09 26424915 26425600 +
Ahy Ahy19g3348 Chr19 156427445 156428291 -
Aip Aip09g03815 Chr09 144781971 144783077 -
Apr Apr8g2398 Chr8 34245734 34247409 +
Arst Arst9g03424 Chr9 111267416 111268220 +
Bva Bva14g00495 Chr14 2377829 2378900 -
Cca Cca02g02479 Chr02 45923010 45923694 +
Dod Dod06g0510 Chr06 6154749 6155830 -
Lal Lal24g0287 Chr24 2067086 2072145 +
Lapu Lapu7g02254 Chr7 38880068 38880772 +
Lasa Lasa6g04407 Chr6 640111721 640112272 +
Lja Lja5g0458 Chr5 4013744 4015680 -
Mal Mal1g0594 Chr1 6835114 6835824 -
Mepo Mepo4g04510 Chr4 54838836 54839856 +
Mtr Mtr1g4009 Chr1 51703450 51704388 +
Phac Phac7g00715 Chr7 3984641 3988055 -
Phco Phco6g02732 Chr6 48781730 48782396 +
Psa Psa6g4904 Chr6 428047745 428050612 +
Pste Pste4g01271 Chr4 9348261 9349268 -
Pvu Pvu7g0477 Chr7 3766607 3767571 -
Spst Spst10g01232 Chr10 13110019 13117086 +
Sto Sto2g0483 Chr2 4192123 4193423 +
Tpr Tpr1g0500 Chr1 4211406 4212284 -
Trre Trre1g05752 Chr1 62421888 62422604 +
Tsu Tsu01g04685 Chr01 54175960 54177155 +
Vian Vian3g00432 Chr3 4063866 4064455 -
Vimu Vimu3g03332 Chr3 46749020 46753792 +
Viun Viun7g03559 Chr7 36973396 36974279 +
Vivi Vivi1g03985 Chr1 83986941 83987665 -
Vvi Vvi3g0820 Chr3 7716202 7726782 -
Vvi Vvi3g0821 Chr3 7739421 7740245 -
Vvi Vvi3g0822 Chr3 7742108 7743757 -
Aev Aev09g2452 Chr09 26428801 26429807 -
Ahy Ahy19g3347 Chr19 156423480 156424868 +
Aip Aip09g03814 Chr09 144778322 144779615 +
Amo Amo19g4251 Chr19 159240954 159242258 -
Dod Dod06g0509 Chr06 6150464 6151999 +
Aev Aev09g2454 Chr09 26444789 26448565 -
Ahy Ahy19g3345 Chr19 156406187 156409179 +
Aip Aip09g03812 Chr09 144762416 144765395 +
Amo Amo19g4252 Chr19 159256651 159259456 -
Dod Dod06g0507 Chr06 6124591 6128839 +
Vifa Vifa3g04972 Chr3 1444831346 1444835162 -
Vivi Vivi4g05686 Chr4 193176771 193181049 -