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
Vvi3g0773 . . . . Adu09g02603 . Aed1g2003 . Aev09g2473 . Ahy19g3327 . Aip09g03790 . . . Amo19g4269 . Apr8g2423 . Arst9g03457 . Bach11g00329 . . . Bva13g00374 Bva14g00461 Car04g01426 . Cca02g02503 . . . Dod06g0482 . . . . . . . . . . . . . . . . Lal13g0380 Lal12g0389 Lal24g0298 . . . . . . Lapu7g02279 . Lasa6g04443 . . . . . . . . . Lja5g0436 . . Mal1g0563 Mepo4g04537 . Mesa1g04966 . . . . Mtr1g4038 Phac7g00672 . Phco6g02766 . . . Psa6g4928 . Pste4g01184 . . Pte9g01356 . . Pumo3g00665 . Pvu7g0446 . Rops6g03082 . Seca8g07707 . Spst10g01268 . Ssu7g0506 . Sto2g0513 . . Tpr1g0475 Trre1g05781 . . Tsu01g04710 Vian3g00407 . Vifa3g03316 . Vimu3g03361 . Viun7g03602 . Vivi1g03928 . Vra8g2406 .
Vvi3g0774 . . . . . Adu05g01361 . . . Aev05g1268 . Ahy15g1331 . Aip05g01400 . . . . . Apr7g0010 . Arst5g01736 . . . . . Bva14g00462 . Car08g00026 . Cca06g02046 . . . Dod02g1415 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mepo5g00029 . Mesa17g00025 . . . . . . . Phco4g00029 . . . . . Pste1g00675 . . . Pte19g00437 . Pumo8g02611 . Pvu2g0540 . Rops1g02471 . Seca10g00043 . Spst2g00029 . Ssu2g3166 . . . . . Trre9g00026 . . . Vian10g00024 . Vifa1g04057 . Vimu7g02167 . Viun2g02958 . Vivi2g04278 . Vra11g0027
Vvi3g0775 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva14g00463 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto10g0352 . . . . . . . . . . . . . . . . . .
Vvi3g0776 . . . . . Adu05g01040 . Aed11g1951 . Aev05g1267 . Ahy15g1329 . Aip05g01399 . . . . . Apr7g0009 . Arst5g01734 . . . . . Bva14g00464 . Car08g00027 . Cca06g02045 . . . Dod02g1414 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mepo5g00030 . Mesa17g00026 . . . . . . . Phco4g00030 . . . . . Pste1g00681 . . . . . Pumo8g02610 . Pvu2g0539 . Rops1g02470 . Seca10g00044 . Spst2g00030 . Ssu2g3165 Sto2g0512 . . . . Trre9g00027 . . . Vian10g00025 . Vifa1g04054 . Vimu7g02168 . Viun2g02947 . Vivi2g04274 . Vra11g0028
Vvi3g0777 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0778 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0779 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0780 . . . . Adu09g02602 . Aed1g2005 . Aev09g2471 . Ahy19g3329 . Aip09g03792 . . . Amo19g4268 . Apr8g2421 . Arst9g03455 . Bach11g00330 . . . Bva13g00375 Bva14g00467 Car04g01425 . Cca02g02502 . . . Dod06g0487 . . . . . . . . . . . . . . . . Lal13g0378 Lal12g0387 Lal24g0296 . . . . . . Lapu7g02277 . Lasa6g04440 . . . . . . . . . Lja5g0438 . . Mal1g0565 Mepo4g04534 . Mesa1g04965 . . . . Mtr1g4036 Phac7g00674 . Phco6g02763 . . . Psa6g4926 . Pste4g01191 . . Pte9g01354 . . Pumo3g00666 . Pvu7g0448 . Rops6g03080 . Seca8g07705 . Spst10g01265 . Ssu7g0508 . Sto2g0511 Sto10g0354 . Tpr1g0477 Trre1g05780 . . Tsu01g04709 Vian3g00409 . Vifa3g03313 . Vimu3g03359 . Viun7g03599 . Vivi1g03931 . Vra8g2404 .
Vvi3g0781 . . . . Adu09g02601 . . . . . Ahy19g3330 . Aip09g03793 . . . Amo19g4267 . Apr8g2418 Apr7g0007 Arst9g03453 . Bach11g00331 . . . Bva13g00376 Bva14g00468 . . . . . . Dod06g0488 . . . . . . . . . . . . . . . . . . Lal24g0295 . . . . . . Lapu7g02274 . Lasa6g04436 . . . . . . . . . Lja5g0439 . . Mal1g0566 Mepo4g04533 . Mesa1g04964 . . . . Mtr1g4035 Phac7g00679 . Phco6g02760 . . . Psa6g4925 . Pste4g01201 . . . . . . . Pvu7g0451 . . . . . Spst10g01262 . . . Sto2g0510 . . Tpr1g0478 Trre1g05778 . . Tsu01g04706 . . . . Vimu3g03356 . . . Vivi1g03939 . . .
Vvi3g0782 . . . . Adu09g02600 . . . Aev09g2469 . Ahy19g3331 . Aip09g03794 . . . Amo19g4266 . Apr8g2417 . Arst9g03449 . Bach11g00332 . . . Bva13g00377 Bva14g00469 Car04g01424 . . . . . Dod06g0489 . . . . . . . . . . . . . . . . Lal13g0377 Lal12g0386 Lal24g0294 . . . . . . Lapu7g02273 . Lasa6g04435 . . . . . . . . . Lja5g0440 . . Mal1g0567 Mepo4g04532 . Mesa1g04963 . . . . Mtr1g4034 . . Phco6g02759 . . . . . Pste4g01202 . . . . . . . Pvu7g0452 . . . . . Spst10g01261 . . . Sto2g0509 Sto10g0355 . Tpr1g0479 . . . Tsu01g04705 . . . . Vimu3g03355 . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi3g0773 Chr3 7040975 7042039 -
Adu Adu09g02603 Chr09 113518991 113520031 +
Aed Aed1g2003 Chr1 16919585 16921875 -
Aev Aev09g2473 Chr09 26573863 26574924 +
Ahy Ahy19g3327 Chr19 156292924 156294920 -
Aip Aip09g03790 Chr09 144653125 144654168 -
Amo Amo19g4269 Chr19 159393429 159394472 +
Apr Apr8g2423 Chr8 34398703 34400765 +
Arst Arst9g03457 Chr9 111414748 111416729 +
Bach Bach11g00329 Chr11 2227318 2228349 -
Bva Bva13g00374 Chr13 1733092 1735099 -
Bva Bva14g00461 Chr14 2223077 2224821 -
Car Car04g01426 Chr04 14541114 14543092 +
Cca Cca02g02503 Chr02 46249463 46250539 +
Dod Dod06g0482 Chr06 5916011 5918224 -
Lal Lal13g0380 Chr13 2395345 2396370 +
Lal Lal12g0389 Chr12 2759761 2760801 +
Lal Lal24g0298 Chr24 2141470 2142507 +
Lapu Lapu7g02279 Chr7 39130809 39132925 +
Lasa Lasa6g04443 Chr6 642839523 642840566 +
Lja Lja5g0436 Chr5 3803267 3805306 -
Mal Mal1g0563 Chr1 6421979 6423049 -
Mepo Mepo4g04537 Chr4 55097975 55099933 +
Mesa Mesa1g04966 Chr1 76563420 76564496 +
Mtr Mtr1g4038 Chr1 51991476 51993503 +
Phac Phac7g00672 Chr7 3722320 3724496 -
Phco Phco6g02766 Chr6 49043589 49044656 +
Psa Psa6g4928 Chr6 430018561 430020950 +
Pste Pste4g01184 Chr4 8749575 8751373 -
Pte Pte9g01356 Chr9 34937911 34940361 -
Pumo Pumo3g00665 Chr3 9948661 9950773 -
Pvu Pvu7g0446 Chr7 3481713 3483820 -
Rops Rops6g03082 Chr6 53957848 53959903 +
Seca Seca8g07707 Chr8 174367390 174370187 +
Spst Spst10g01268 Chr10 13406662 13407732 +
Ssu Ssu7g0506 Chr7 9401202 9402245 -
Sto Sto2g0513 Chr2 4413938 4414972 +
Tpr Tpr1g0475 Chr1 4002500 4004489 -
Trre Trre1g05781 Chr1 62681696 62682760 +
Tsu Tsu01g04710 Chr01 54405320 54407255 +
Vian Vian3g00407 Chr3 3835229 3836299 -
Vifa Vifa3g03316 Chr3 951540264 951541307 +
Vimu Vimu3g03361 Chr3 46977027 46978097 +
Viun Viun7g03602 Chr7 37218180 37220311 +
Vivi Vivi1g03928 Chr1 82831766 82833759 -
Vra Vra8g2406 Chr8 42223812 42225918 +
Vvi Vvi3g0774 Chr3 7045025 7047456 -
Adu Adu05g01361 Chr05 20617589 20619903 +
Aev Aev05g1268 Chr05 8912168 8914274 +
Ahy Ahy15g1331 Chr15 21953976 21956281 +
Aip Aip05g01400 Chr05 21127800 21130096 +
Apr Apr7g0010 Chr7 801634 804372 +
Arst Arst5g01736 Chr5 20666119 20668459 +
Bva Bva14g00462 Chr14 2225603 2228002 -
Car Car08g00026 Chr08 258006 260339 -
Cca Cca06g02046 Chr06 35676211 35678453 +
Dod Dod02g1415 Chr02 16968596 16971405 +
Mepo Mepo5g00029 Chr5 328026 330155 -
Mesa Mesa17g00025 Chr17 263318 265136 -
Phco Phco4g00029 Chr4 211485 213136 -
Pste Pste1g00675 Chr1 2132775 2135219 -
Pte Pte19g00437 Chr19 3470463 3473350 +
Pumo Pumo8g02611 Chr8 63303702 63308685 +
Pvu Pvu2g0540 Chr2 4805778 4807640 +
Rops Rops1g02471 Chr1 47780827 47783162 +
Seca Seca10g00043 Chr10 374202 376847 -
Spst Spst2g00029 Chr2 322376 324033 -
Ssu Ssu2g3166 Chr2 93925493 93927061 +
Trre Trre9g00026 Chr9 376678 378451 -
Vian Vian10g00024 Chr10 220198 221804 -
Vifa Vifa1g04057 Chr1 623416165 623417812 +
Vimu Vimu7g02167 Chr7 19165544 19167182 -
Viun Viun2g02958 Chr2 33671331 33674010 +
Vivi Vivi2g04278 Chr2 156516516 156520080 +
Vra Vra11g0027 Chr11 247303 249556 -
Vvi Vvi3g0775 Chr3 7051150 7055710 +
Bva Bva14g00463 Chr14 2228333 2231102 +
Sto Sto10g0352 Chr10 2793163 2796689 +
Vvi Vvi3g0776 Chr3 7056023 7059008 -
Adu Adu05g01040 Chr05 14034690 14036850 -
Aed Aed11g1951 Chr11 22236403 22240601 +
Aev Aev05g1267 Chr05 8907176 8908509 +
Ahy Ahy15g1329 Chr15 21926179 21927418 +
Aip Aip05g01399 Chr05 21103207 21104045 +
Apr Apr7g0009 Chr7 799088 800039 +
Arst Arst5g01734 Chr5 20626565 20627366 +
Bva Bva14g00464 Chr14 2231352 2232906 -
Car Car08g00027 Chr08 262684 264115 -
Cca Cca06g02045 Chr06 35671508 35672859 +
Dod Dod02g1414 Chr02 16963070 16964521 +
Mepo Mepo5g00030 Chr5 333119 338477 -
Mesa Mesa17g00026 Chr17 269059 271640 -
Phco Phco4g00030 Chr4 215580 216200 -
Pste Pste1g00681 Chr1 2151102 2153068 -
Pumo Pumo8g02610 Chr8 63299844 63300293 +
Pvu Pvu2g0539 Chr2 4803321 4804204 +
Rops Rops1g02470 Chr1 47776269 47777839 +
Seca Seca10g00044 Chr10 378807 380751 -
Spst Spst2g00030 Chr2 325963 326621 -
Ssu Ssu2g3165 Chr2 93917855 93918595 +
Sto Sto2g0512 Chr2 4410683 4412005 +
Trre Trre9g00027 Chr9 380770 381462 -
Vian Vian10g00025 Chr10 223737 224350 -
Vifa Vifa1g04054 Chr1 622972797 622973551 +
Vimu Vimu7g02168 Chr7 19168506 19170192 -
Viun Viun2g02947 Chr2 33659583 33660481 +
Vivi Vivi2g04274 Chr2 156467367 156468442 +
Vra Vra11g0028 Chr11 250794 252331 -
Vvi Vvi3g0777 Chr3 7065044 7065631 -
Vvi Vvi3g0778 Chr3 7072474 7072790 +
Vvi Vvi3g0779 Chr3 7076260 7076677 +
Vvi Vvi3g0780 Chr3 7082071 7097828 +
Adu Adu09g02602 Chr09 113491507 113497226 -
Aed Aed1g2005 Chr1 16930239 16936066 +
Aev Aev09g2471 Chr09 26558155 26563207 -
Ahy Ahy19g3329 Chr19 156306706 156312329 +
Aip Aip09g03792 Chr09 144666654 144672244 +
Amo Amo19g4268 Chr19 159365606 159371226 -
Apr Apr8g2421 Chr8 34383167 34389260 -
Arst Arst9g03455 Chr9 111387866 111393632 -
Bach Bach11g00330 Chr11 2235706 2239797 +
Bva Bva13g00375 Chr13 1741022 1745532 +
Bva Bva14g00467 Chr14 2242863 2248097 +
Car Car04g01425 Chr04 14518286 14524770 -
Cca Cca02g02502 Chr02 46230215 46235639 -
Dod Dod06g0487 Chr06 5950824 5955984 +
Lal Lal13g0378 Chr13 2383318 2388217 -
Lal Lal12g0387 Chr12 2744874 2750621 -
Lal Lal24g0296 Chr24 2126461 2131651 -
Lapu Lapu7g02277 Chr7 39114860 39120259 -
Lasa Lasa6g04440 Chr6 642667451 642672247 -
Lja Lja5g0438 Chr5 3815485 3822096 +
Mal Mal1g0565 Chr1 6438135 6444304 +
Mepo Mepo4g04534 Chr4 55066706 55073094 -
Mesa Mesa1g04965 Chr1 76546247 76552355 -
Mtr Mtr1g4036 Chr1 51969321 51976282 -
Phac Phac7g00674 Chr7 3734738 3740240 +
Phco Phco6g02763 Chr6 49026724 49031292 -
Psa Psa6g4926 Chr6 429908130 429914029 -
Pste Pste4g01191 Chr4 8774541 8779959 +
Pte Pte9g01354 Chr9 34915217 34920597 -
Pumo Pumo3g00666 Chr3 9964466 9970195 +
Pvu Pvu7g0448 Chr7 3494891 3499818 +
Rops Rops6g03080 Chr6 53941312 53947959 -
Seca Seca8g07705 Chr8 174343505 174349160 -
Spst Spst10g01265 Chr10 13392830 13397249 -
Ssu Ssu7g0508 Chr7 9420769 9426312 +
Sto Sto2g0511 Chr2 4389222 4394728 -
Sto Sto10g0354 Chr10 2810532 2816574 +
Tpr Tpr1g0477 Chr1 4019142 4025377 +
Trre Trre1g05780 Chr1 62662723 62667745 -
Tsu Tsu01g04709 Chr01 54385088 54391561 -
Vian Vian3g00409 Chr3 3845806 3850325 +
Vifa Vifa3g03313 Chr3 951072298 951076918 -
Vimu Vimu3g03359 Chr3 46963235 46967767 -
Viun Viun7g03599 Chr7 37202518 37207505 -
Vivi Vivi1g03931 Chr1 82866447 82872223 +
Vra Vra8g2404 Chr8 42209789 42214921 -
Vvi Vvi3g0781 Chr3 7099073 7099739 -
Adu Adu09g02601 Chr09 113489991 113490739 +
Ahy Ahy19g3330 Chr19 156313470 156314255 -
Aip Aip09g03793 Chr09 144673522 144674147 -
Amo Amo19g4267 Chr19 159364085 159364800 +
Apr Apr8g2418 Chr8 34374240 34375604 +
Apr Apr7g0007 Chr7 775114 775837 +
Arst Arst9g03453 Chr9 111386359 111387028 +
Bach Bach11g00331 Chr11 2240992 2241658 -
Bva Bva13g00376 Chr13 1746990 1747662 -
Bva Bva14g00468 Chr14 2249345 2250082 -
Dod Dod06g0488 Chr06 5958437 5959778 -
Lal Lal24g0295 Chr24 2124638 2126193 +
Lapu Lapu7g02274 Chr7 39102539 39104304 +
Lasa Lasa6g04436 Chr6 642638140 642638862 +
Lja Lja5g0439 Chr5 3838550 3839954 -
Mal Mal1g0566 Chr1 6447777 6448526 -
Mepo Mepo4g04533 Chr4 55063351 55064325 +
Mesa Mesa1g04964 Chr1 76542635 76543444 +
Mtr Mtr1g4035 Chr1 51964287 51965218 +
Phac Phac7g00679 Chr7 3748879 3751046 -
Phco Phco6g02760 Chr6 49009858 49016451 +
Psa Psa6g4925 Chr6 429871212 429872470 +
Pste Pste4g01201 Chr4 8829750 8832498 -
Pvu Pvu7g0451 Chr7 3508488 3510206 -
Spst Spst10g01262 Chr10 13381817 13383217 +
Sto Sto2g0510 Chr2 4384070 4385905 +
Tpr Tpr1g0478 Chr1 4026805 4027894 -
Trre Trre1g05778 Chr1 62657843 62658616 +
Tsu Tsu01g04706 Chr01 54381274 54382040 +
Vimu Vimu3g03356 Chr3 46945286 46946486 +
Vivi Vivi1g03939 Chr1 83081604 83082457 -
Vvi Vvi3g0782 Chr3 7103653 7113572 -
Adu Adu09g02600 Chr09 113482441 113487290 +
Aev Aev09g2469 Chr09 26544396 26547708 +
Ahy Ahy19g3331 Chr19 156317438 156322448 -
Aip Aip09g03794 Chr09 144677206 144682097 -
Amo Amo19g4266 Chr19 159356691 159360336 +
Apr Apr8g2417 Chr8 34368288 34371432 +
Arst Arst9g03449 Chr9 111378849 111383707 +
Bach Bach11g00332 Chr11 2243697 2247176 -
Bva Bva13g00377 Chr13 1749557 1755265 -
Bva Bva14g00469 Chr14 2252423 2258379 -
Car Car04g01424 Chr04 14505370 14509634 +
Dod Dod06g0489 Chr06 5963117 5968458 -
Lal Lal13g0377 Chr13 2377574 2382490 +
Lal Lal12g0386 Chr12 2738303 2743118 +
Lal Lal24g0294 Chr24 2115954 2122070 +
Lapu Lapu7g02273 Chr7 39093405 39100233 +
Lasa Lasa6g04435 Chr6 642455846 642458109 +
Lja Lja5g0440 Chr5 3845174 3849197 -
Mal Mal1g0567 Chr1 6452205 6456242 -
Mepo Mepo4g04532 Chr4 55053275 55057104 +
Mesa Mesa1g04963 Chr1 76534953 76538516 +
Mtr Mtr1g4034 Chr1 51955170 51960722 +
Phco Phco6g02759 Chr6 49002853 49007097 +
Pste Pste4g01202 Chr4 8834774 8839776 -
Pvu Pvu7g0452 Chr7 3512488 3518991 -
Spst Spst10g01261 Chr10 13372976 13379001 +
Sto Sto2g0509 Chr2 4373363 4378116 +
Sto Sto10g0355 Chr10 2817953 2827222 -
Tpr Tpr1g0479 Chr1 4036470 4041308 -
Tsu Tsu01g04705 Chr01 54370881 54375779 +
Vimu Vimu3g03355 Chr3 46938043 46942689 +
Psa Psa6g4925 Chr6 429871212 429872470 +
Aev Aev09g2471 Chr09 26558155 26563207 -
Ahy Ahy19g3329 Chr19 156306706 156312329 +
Aip Aip09g03792 Chr09 144666654 144672244 +
Amo Amo19g4268 Chr19 159365606 159371226 -
Dod Dod06g0487 Chr06 5950824 5955984 +
Psa Psa6g4926 Chr6 429908130 429914029 -