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
Vvi3g0793 . . . . . Adu05g01358 . Aed11g1947 . Aev05g1262 . Ahy15g1328 . Aip05g01397 . . . . . Apr7g0005 . Arst5g01732 . . . . Bva13g00386 . . Car08g00031 . Cca06g02039 . . . Dod02g1408 . . . . . . . . . . . . . . . . . . . . . . . . . . . Lasa2g02521 . . . . . . . . . . . . . Mepo5g00037 . Mesa17g00032 . . . . . . . Phco4g00034 . . . . . Pste1g00699 . . . Pte19g00440 . Pumo8g02605 . Pvu2g0534 . . . Seca10g00054 . Spst2g00034 . Ssu2g3157 Sto2g0501 . . . . Trre9g00032 . . . Vian10g00029 . Vifa1g04046 . Vimu7g02172 . Viun2g02943 . Vivi2g04267 . Vra11g0032
Vvi3g0794 . . . . Adu09g02589 . Aed1g2017 . Aev09g2459 . Ahy19g3340 . Aip09g03805 . . . Amo19g4257 . Apr8g2407 Apr7g0004 Arst9g03437 . Bach11g00343 . . . Bva13g00387 Bva14g00479 Car04g01413 Car08g00032 Cca02g02493 Cca06g02038 . . Dod06g0500 . . . . . . . . . . . . . . . . . Lal12g0379 . . . . . . . Lapu7g02264 . Lasa6g04424 . . . . . . . . . Lja5g0449 . . Mal1g0583 Mepo4g04521 . Mesa1g04954 . . . . Mtr1g4019 Phac7g00694 . Phco6g02747 Phco4g00035 . . Psa6g4911 . Pste4g01236 . . . . . Pumo3g00680 . Pvu7g0462 Pvu2g0533 Rops6g03056 Rops1g02462 Seca8g07688 Seca10g00055 Spst10g01249 Spst2g00035 Ssu7g0523 . Sto2g0500 . . Tpr1g0491 Trre1g05765 . . Tsu01g04693 Vian3g00422 Vian10g00030 Vifa3g03294 Vifa3g03294 Vimu3g03343 Vimu7g02173 Viun7g03582 Viun2g02941 Vivi1g03959 . Vra8g2392 Vra11g0034
Vvi3g0795 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva13g00388 . . . . . . . . . . . . . . . . . . . . . . . . . Lal12g0378 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto2g0499 . . . . . . . . . . . . . . . . . . .
Vvi3g0796 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0797 . . . . . Adu05g01357 . Aed11g1946 . Aev05g1261 . Ahy15g1327 . Aip05g01396 . . . . . Apr7g0001 . Arst5g01731 . . . . Bva13g00389 . . Car08g00033 . Cca06g02037 . . . Dod02g1405 . . . . . . . . . . . . . . . . . . . . . . . . . . . Lasa2g02524 . . . . . . . . . . . . . Mepo5g00039 . . . . . . . . . Phco4g00036 . . . . . Pste1g00703 . . . . . Pumo8g02603 . Pvu2g0532 . Rops1g02460 . . . Spst2g00036 . Ssu2g3156 Sto2g0498 . . . . Trre9g00034 . . . Vian10g00031 . Vifa1g04045 . Vimu7g02174 . Viun2g02939 . Vivi2g04266 . Vra11g0035
Vvi3g0798 . . . . . . . . . Aev05g1260 . Ahy15g1325 . Aip05g01395 . . . . . . . . . . . . Bva13g00391 Bva14g00480 . . . . . . . Dod02g1404 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto2g0497 . . . . . . . . . . . . . . . . . . .
Vvi3g0799 . . . . . . . . Aev09g2458 . . . Aip09g03806 . . . Amo19g4256 . . . . . . . . . . . . . . . . . Dod06g0502 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mtr1g4018 . . . . . . Psa6g4910 . . . . . . . . . . . . . . . . . . . . Sto10g0372 . . . . . . . . . . . . . . . . . .
Vvi3g0800 . . . . Adu09g02588 . . . . . . . . . . . . . . . . . . . . . Bva13g00392 Bva14g00481 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lasa6g04423 . . . . . . . . . Lja5g0450 . . Mal1g0584 Mepo4g04520 . . . . . . Mtr1g4017 Phac7g00695 . Phco6g02746 . . . . . Pste4g01237 . . . . . Pumo3g00681 . Pvu7g0463 . Rops6g03055 . Seca8g07687 . Spst10g01248 . . . . . . Tpr1g0492 Trre1g05763 . . Tsu01g04692 Vian3g00423 . Vifa3g03291 . Vimu3g03342 . Viun7g03581 . Vivi1g03961 . . .
Vvi3g0801 . . . . Adu09g02587 . Aed1g2021 . . . . . . . . . . . . . . . . . . . . Bva14g00482 Car04g01412 . Cca02g02492 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu7g02263 . Lasa6g04422 . . . . . . . . . . . . Mal1g0585 Mepo4g04519 . . . . . . Mtr1g4015 . . Phco6g02745 . . . Psa6g4909 . . . . . . . Pumo3g00682 . Pvu7g0464 . Rops6g03048 . Seca8g07685 . Spst10g01247 . . . . Sto10g0373 . Tpr1g0493 Trre1g05762 . . Tsu01g04691 . . Vifa3g03288 . . . . . Vivi1g03962 . Vra8g2391 .
Vvi3g0802 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi3g0793 Chr3 7291905 7300545 +
Adu Adu05g01358 Chr05 20534834 20537379 -
Aed Aed11g1947 Chr11 22222057 22223920 -
Aev Aev05g1262 Chr05 8878211 8881102 -
Ahy Ahy15g1328 Chr15 21893441 21896032 -
Aip Aip05g01397 Chr05 21062746 21065314 -
Apr Apr7g0005 Chr7 296537 299645 -
Arst Arst5g01732 Chr5 20583422 20585894 -
Bva Bva13g00386 Chr13 1801206 1804227 +
Car Car08g00031 Chr08 288072 292081 +
Cca Cca06g02039 Chr06 35640730 35644395 -
Dod Dod02g1408 Chr02 16916375 16920090 -
Lasa Lasa2g02521 Chr2 503916256 503916963 +
Mepo Mepo5g00037 Chr5 372555 374871 +
Mesa Mesa17g00032 Chr17 314807 316957 +
Phco Phco4g00034 Chr4 233410 235471 +
Pste Pste1g00699 Chr1 2197934 2201408 +
Pte Pte19g00440 Chr19 3490846 3495329 +
Pumo Pumo8g02605 Chr8 63274243 63276479 -
Pvu Pvu2g0534 Chr2 4774424 4776886 -
Seca Seca10g00054 Chr10 477641 481592 +
Spst Spst2g00034 Chr2 341275 343453 +
Ssu Ssu2g3157 Chr2 93858387 93862338 -
Sto Sto2g0501 Chr2 4299729 4304590 -
Trre Trre9g00032 Chr9 409440 412197 +
Vian Vian10g00029 Chr10 240609 243429 +
Vifa Vifa1g04046 Chr1 620990341 620993363 -
Vimu Vimu7g02172 Chr7 19187123 19189229 +
Viun Viun2g02943 Chr2 33638972 33641357 -
Vivi Vivi2g04267 Chr2 156339295 156342418 -
Vra Vra11g0032 Chr11 269111 271502 +
Vvi Vvi3g0794 Chr3 7303589 7311099 -
Adu Adu09g02589 Chr09 113414999 113417013 +
Aed Aed1g2017 Chr1 17011981 17015612 -
Aev Aev09g2459 Chr09 26486257 26488304 +
Ahy Ahy19g3340 Chr19 156380184 156382274 -
Aip Aip09g03805 Chr09 144738269 144740348 -
Amo Amo19g4257 Chr19 159287846 159290717 +
Apr Apr8g2407 Chr8 34308737 34311455 +
Apr Apr7g0004 Chr7 292726 296179 +
Arst Arst9g03437 Chr9 111311317 111313427 +
Bach Bach11g00343 Chr11 2304433 2306543 -
Bva Bva13g00387 Chr13 1804511 1806976 -
Bva Bva14g00479 Chr14 2301128 2304084 -
Car Car04g01413 Chr04 14420021 14423925 +
Car Car08g00032 Chr08 292597 295633 -
Cca Cca02g02493 Chr02 46116086 46118567 +
Cca Cca06g02038 Chr06 35637714 35640068 +
Dod Dod06g0500 Chr06 6072324 6074815 -
Lal Lal12g0379 Chr12 2694290 2698597 +
Lapu Lapu7g02264 Chr7 39022701 39025821 +
Lasa Lasa6g04424 Chr6 641687453 641690010 +
Lja Lja5g0449 Chr5 3935610 3938470 -
Mal Mal1g0583 Chr1 6730357 6733577 -
Mepo Mepo4g04521 Chr4 54948171 54951802 +
Mesa Mesa1g04954 Chr1 76428086 76430679 +
Mtr Mtr1g4019 Chr1 51811451 51814920 +
Phac Phac7g00694 Chr7 3830617 3833474 -
Phco Phco6g02747 Chr6 48924126 48926602 +
Phco Phco4g00035 Chr4 237184 239221 -
Psa Psa6g4911 Chr6 428391372 428394245 +
Pste Pste4g01236 Chr4 9044430 9047469 -
Pumo Pumo3g00680 Chr3 10103306 10107053 -
Pvu Pvu7g0462 Chr7 3589954 3592934 -
Pvu Pvu2g0533 Chr2 4770990 4773991 +
Rops Rops6g03056 Chr6 53765383 53767878 +
Rops Rops1g02462 Chr1 47675868 47679477 +
Seca Seca8g07688 Chr8 174189339 174192119 +
Seca Seca10g00055 Chr10 481757 491947 -
Spst Spst10g01249 Chr10 13299920 13302703 +
Spst Spst2g00035 Chr2 345302 347338 -
Ssu Ssu7g0523 Chr7 9590732 9593034 -
Sto Sto2g0500 Chr2 4295984 4298702 +
Tpr Tpr1g0491 Chr1 4135525 4138677 -
Trre Trre1g05765 Chr1 62538642 62541231 +
Tsu Tsu01g04693 Chr01 54266822 54269944 +
Vian Vian3g00422 Chr3 3955116 3957985 -
Vian Vian10g00030 Chr10 244741 246525 -
Vifa Vifa3g03294 Chr3 945477992 945481575 +
Vifa Vifa3g03294 Chr3 945477992 945481575 +
Vimu Vimu3g03343 Chr3 46863043 46864629 +
Vimu Vimu7g02173 Chr7 19201117 19202916 -
Viun Viun7g03582 Chr7 37111783 37114909 +
Viun Viun2g02941 Chr2 33636031 33638338 +
Vivi Vivi1g03959 Chr1 83505064 83508688 -
Vra Vra8g2392 Chr8 42112541 42115542 +
Vra Vra11g0034 Chr11 282156 284673 -
Vvi Vvi3g0795 Chr3 7320680 7324112 -
Bva Bva13g00388 Chr13 1807630 1808602 -
Lal Lal12g0378 Chr12 2691233 2694124 +
Sto Sto2g0499 Chr2 4292918 4294377 +
Vvi Vvi3g0796 Chr3 7321597 7321927 +
Vvi Vvi3g0797 Chr3 7326096 7339940 -
Adu Adu05g01357 Chr05 20529460 20533431 +
Aed Aed11g1946 Chr11 22210301 22214435 +
Aev Aev05g1261 Chr05 8872873 8877440 +
Ahy Ahy15g1327 Chr15 21887856 21892267 +
Aip Aip05g01396 Chr05 21057384 21061371 +
Apr Apr7g0001 Chr7 18525 23402 +
Arst Arst5g01731 Chr5 20577883 20582183 +
Bva Bva13g00389 Chr13 1808970 1813658 -
Car Car08g00033 Chr08 296619 301117 -
Cca Cca06g02037 Chr06 35630041 35634718 +
Dod Dod02g1405 Chr02 16905528 16910580 +
Lasa Lasa2g02524 Chr2 503922680 503924962 -
Mepo Mepo5g00039 Chr5 377121 381629 -
Phco Phco4g00036 Chr4 240668 245301 -
Pste Pste1g00703 Chr1 2206966 2209051 -
Pumo Pumo8g02603 Chr8 63264620 63268178 +
Pvu Pvu2g0532 Chr2 4764935 4769697 +
Rops Rops1g02460 Chr1 47667922 47673002 +
Spst Spst2g00036 Chr2 348792 353418 -
Ssu Ssu2g3156 Chr2 93846417 93850723 +
Sto Sto2g0498 Chr2 4287428 4289083 +
Trre Trre9g00034 Chr9 427358 431951 -
Vian Vian10g00031 Chr10 248089 252078 -
Vifa Vifa1g04045 Chr1 620861552 620866339 +
Vimu Vimu7g02174 Chr7 19204815 19208791 -
Viun Viun2g02939 Chr2 33629961 33634896 +
Vivi Vivi2g04266 Chr2 156311580 156328626 +
Vra Vra11g0035 Chr11 286000 290351 -
Vvi Vvi3g0798 Chr3 7342268 7356731 +
Aev Aev05g1260 Chr05 8868381 8870534 -
Ahy Ahy15g1325 Chr15 21766441 21769514 -
Aip Aip05g01395 Chr05 20961821 20964347 -
Bva Bva13g00391 Chr13 1814778 1817936 +
Bva Bva14g00480 Chr14 2305929 2308991 +
Dod Dod02g1404 Chr02 16890917 16893222 -
Sto Sto2g0497 Chr2 4280222 4284370 -
Vvi Vvi3g0799 Chr3 7374686 7382382 +
Aev Aev09g2458 Chr09 26479196 26482188 -
Aip Aip09g03806 Chr09 144742185 144745529 +
Amo Amo19g4256 Chr19 159281669 159284084 -
Dod Dod06g0502 Chr06 6081527 6084815 +
Mtr Mtr1g4018 Chr1 51801914 51804912 -
Psa Psa6g4910 Chr6 428367838 428370602 +
Sto Sto10g0372 Chr10 2982367 2985563 +
Vvi Vvi3g0800 Chr3 7385745 7389061 +
Adu Adu09g02588 Chr09 113409073 113410853 -
Bva Bva13g00392 Chr13 1818627 1822064 +
Bva Bva14g00481 Chr14 2309933 2313349 +
Lasa Lasa6g04423 Chr6 641651672 641654155 +
Lja Lja5g0450 Chr5 3943126 3946831 +
Mal Mal1g0584 Chr1 6743400 6746220 +
Mepo Mepo4g04520 Chr4 54925987 54928772 -
Mtr Mtr1g4017 Chr1 51795223 51798670 -
Phac Phac7g00695 Chr7 3837518 3848936 +
Phco Phco6g02746 Chr6 48915138 48918723 -
Pste Pste4g01237 Chr4 9062232 9075159 +
Pumo Pumo3g00681 Chr3 10128337 10131896 +
Pvu Pvu7g0463 Chr7 3597642 3601307 +
Rops Rops6g03055 Chr6 53747838 53751085 -
Seca Seca8g07687 Chr8 174156453 174160294 -
Spst Spst10g01248 Chr10 13292868 13296200 -
Tpr Tpr1g0492 Chr1 4143775 4162681 +
Trre Trre1g05763 Chr1 62517407 62521683 -
Tsu Tsu01g04692 Chr01 54255023 54263393 -
Vian Vian3g00423 Chr3 3961164 3966060 +
Vifa Vifa3g03291 Chr3 944728676 944731171 -
Vimu Vimu3g03342 Chr3 46855106 46859952 -
Viun Viun7g03581 Chr7 37102696 37105717 -
Vivi Vivi1g03961 Chr1 83524033 83526531 +
Vvi Vvi3g0801 Chr3 7389633 7402240 +
Adu Adu09g02587 Chr09 113408755 113409042 -
Aed Aed1g2021 Chr1 17033928 17037257 +
Bva Bva14g00482 Chr14 2315453 2319344 +
Car Car04g01412 Chr04 14400724 14404220 -
Cca Cca02g02492 Chr02 46097736 46101368 -
Lapu Lapu7g02263 Chr7 39014417 39017588 -
Lasa Lasa6g04422 Chr6 641651654 641654155 +
Mal Mal1g0585 Chr1 6747674 6750670 +
Mepo Mepo4g04519 Chr4 54921178 54922285 -
Mtr Mtr1g4015 Chr1 51762444 51766864 -
Phco Phco6g02745 Chr6 48908973 48913289 -
Psa Psa6g4909 Chr6 428348889 428352961 +
Pumo Pumo3g00682 Chr3 10134188 10139462 +
Pvu Pvu7g0464 Chr7 3604059 3608344 +
Rops Rops6g03048 Chr6 53643486 53646694 -
Seca Seca8g07685 Chr8 174149003 174151207 +
Spst Spst10g01247 Chr10 13285349 13291064 -
Sto Sto10g0373 Chr10 2988598 2999595 +
Tpr Tpr1g0493 Chr1 4147022 4150387 +
Trre Trre1g05762 Chr1 62517407 62522016 -
Tsu Tsu01g04691 Chr01 54224622 54247666 -
Vifa Vifa3g03288 Chr3 942726425 942729158 +
Vivi Vivi1g03962 Chr1 83530731 83534216 -
Vra Vra8g2391 Chr8 42104486 42108333 -
Vvi Vvi3g0802 Chr3 7415296 7415825 +