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
Vvi3g0553 . . . . . . . . Aev03g0200 . Ahy20g1514 . Aip10g01730 . . . Amo20g1669 . Apr3g1693 . . . . . . . Bva13g00258 . Car06g01684 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal7g3414 . . . . . . . Mtr4g2845 . . . . . . . Psa7g2776 . . . . . . . . . . . . . . . . . . . Sto2g0650 . . . . . Tsu02g03429 . . . . . . . . . . . . .
Vvi3g0554 . . . . . Adu10g03037 . . Aev03g0199 . Ahy20g1509 . Aip10g01724 . . . . . Apr3g1694 . . . . . . . Bva13g00257 Bva14g00335 Car06g01683 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu2g01762 . . . . . . . . . . . Lja2g3385 Mal7g3415 . . Mepo4g01252 . Mesa1g01378 . . Mtr4g2846 . . . . Phco8g03303 . . Psa7g2774 . . Pste1g03651 . . . . . Pumo8g00192 . Pvu3g0117 . Rops1g00251 . Seca10g05316 . Spst2g02146 . . Sto2g0652 Sto10g0216 . . . Trre1g01327 Tsu02g03430 . . Vian10g01815 . Vifa3g03842 . Vimu7g00372 . Viun2g00234 . Vivi4g03861 . .
Vvi3g0555 . Acco11g2190 . Accr9g00285 . Adu05g00718 . . Aev03g0198 Aev05g0595 Ahy20g1508 Ahy15g0695 Aip10g01721 Aip05g00709 . Alju09g2188 Amo20g1663 . Apr3g1695 . . Arst5g00903 . Bach4g00564 . Bisa11g1580 . Bva14g00334 Car06g01682 Car08g00534 . . . Dere09g0805 . Dod02g0654 . Enph13g0995 . Glsi05g1546 . . . . . . . . . . . . . . . . . . . . . Lapu2g00602 . Lasa2g03215 . . . . Lele49g0229 Lele50g0240 Lele51g0243 Lele52g0244 . Lja2g0378 Mal7g3416 . . . . Mesa17g00823 . Mibi12g1895 Mtr4g2847 . . Phac2g02419 . . . Prci10g0387 Psa7g2772 Psa2g3729 . Pste1g02522 . . . Pte12g00380 . Pumo8g01908 . Pvu2g0232 . Rops1g01729 . Seca10g00799 . Spst2g00726 . . Sto2g0653 . . . . Trre9g00931 Tsu02g03432 . . Vian10g00627 . Vifa1g07039 . Vimu7g02862 . Viun2g02060 . Vivi2g03201 . .
Vvi3g0556 . . . . . Adu03g00407 . . Aev04g3287 . Ahy13g0631 . Aip03g00663 . . . Amo13g0643 . Apr5g0247 . . Arst3g00544 . . . . Bva13g00255 Bva14g00332 Car06g03715 . Cca04g00497 . . . Dod03g3076 . . . . . . . Gma11g01136 Gma12g00438 . . . . . Lal2g0167 . . . . . . . . . . . Lapu11g00699 . Lasa7g01321 . . . . . . . . Lja3g0573 . Mal7g2454 . . Mepo2g02236 . Mesa13g02876 . . Mtr4g2025 . . . . Phco9g00576 . . Psa7g4755 . . Pste1g02040 . . . . . Pumo11g01733 . Pvu11g0522 . Rops3g00627 . Seca4g03632 . Spst2g02454 Ssu3g2772 . Sto2g0654 . Tpr3g2230 . . Trre7g02991 Tsu02g02295 . . Vian5g01439 . Vifa6g00870 . Vimu5g02274 . Viun11g02337 . Vivi5g02814 Vra2g0466 .
Vvi3g0557 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cca04g00496 . . . . . . . . . . . Gma11g01135 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ssu3g2773 . . . . . . . . . . . . . . . . . . . Vra2g0465 .
Vvi3g0558 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0559 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0560 . . . . . . . . . . . . . . . . . . Apr5g0248 . . . . . . . . Bva14g00330 . . . . . . . . . . . . . . . Gma12g00437 . . . . . . . . . . . . . . . . . . . Lasa7g01320 . . . . . . . . Lja3g0571 . . . . Mepo2g02237 . Mesa13g02875 . . . . . . . Phco9g00575 . . . . . . . . . . . Pumo11g01734 . Pvu11g0521 . Rops3g00626 . Seca4g03631 . . . . . . . . . Trre7g02990 . . . Vian5g01440 . Vifa6g00869 . . . Viun11g02339 . . . .
Vvi3g0561 . . . . . Adu10g03000 . . . . . . . . . . . . . . . . . . . . Bva13g00254 Bva14g00329 Car06g03717 . . . . . . . . . . . . . . . . . . . Lal1g0269 . . . . . Lan13g0269 . . . . . . Lapu2g01763 . . . . . . . . . . . Lja2g3387 Mal7g2459 . . Mepo4g01255 . Mesa1g01381 . . Mtr4g2028 . . . . Phco8g03304 . . . . . Pste1g03654 . . . . . Pumo8g00191 . Pvu3g0116 . Rops1g00253 . Seca10g05314 . Spst2g02147 . . . Sto10g0236 Tpr3g2233 . . Trre1g01329 Tsu02g02298 . . Vian10g01816 . Vifa3g03841 . Vimu7g00374 . Viun2g00230 . Vivi4g03862 . .
Vvi3g0562 . . . . . . . . Aev04g3290 . Ahy13g0634 . Aip03g00664 . . . Amo13g0645 . Apr5g0249 . . . . . . . . . . . Cca04g00495 . . . Dod03g3079 . . . . . . . Gma11g01134 Gma12g00436 . . . . . . Lal9g0175 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ssu3g2774 . Sto2g0655 Sto10g0217 . . . . . . . . . . . . . . . . Vra2g0464 .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi3g0553 Chr3 4819253 4820290 -
Aev Aev03g0200 Chr03 1567713 1569105 +
Ahy Ahy20g1514 Chr20 43578860 43580805 +
Aip Aip10g01730 Chr10 40729401 40731087 +
Amo Amo20g1669 Chr20 47146317 47148078 +
Apr Apr3g1693 Chr3 32567165 32569304 -
Bva Bva13g00258 Chr13 1233263 1234624 +
Car Car06g01684 Chr06 16612007 16614260 +
Mal Mal7g3414 Chr7 99115967 99117775 -
Mtr Mtr4g2845 Chr4 42107690 42109417 -
Psa Psa7g2776 Chr7 198926424 198928029 +
Sto Sto2g0650 Chr2 5519598 5520989 -
Tsu Tsu02g03429 Chr02 38362805 38365455 -
Vvi Vvi3g0554 Chr3 4827356 4844436 +
Adu Adu10g03037 Chr10 106349617 106356317 -
Aev Aev03g0199 Chr03 1557299 1566090 -
Ahy Ahy20g1509 Chr20 43396339 43405324 -
Aip Aip10g01724 Chr10 40554327 40563686 -
Apr Apr3g1694 Chr3 32573780 32586071 +
Bva Bva13g00257 Chr13 1223819 1231935 -
Bva Bva14g00335 Chr14 1659323 1666558 -
Car Car06g01683 Chr06 16593336 16604610 -
Lapu Lapu2g01762 Chr2 31285703 31305798 +
Lja Lja2g3385 Chr2 77475413 77486967 +
Mal Mal7g3415 Chr7 99122897 99134713 +
Mepo Mepo4g01252 Chr4 16080207 16091068 +
Mesa Mesa1g01378 Chr1 18950453 18958069 +
Mtr Mtr4g2846 Chr4 42123709 42135317 +
Phco Phco8g03303 Chr8 47673005 47692787 +
Psa Psa7g2774 Chr7 198694345 198714774 -
Pste Pste1g03651 Chr1 17488387 17504129 +
Pumo Pumo8g00192 Chr8 6129473 6146376 -
Pvu Pvu3g0117 Chr3 1054609 1067305 -
Rops Rops1g00251 Chr1 7058651 7077303 +
Seca Seca10g05316 Chr10 121265962 121285965 -
Spst Spst2g02146 Chr2 20422869 20444544 +
Sto Sto2g0652 Chr2 5529358 5538110 +
Sto Sto10g0216 Chr10 1816230 1833355 +
Trre Trre1g01327 Chr1 9931472 9937565 +
Tsu Tsu02g03430 Chr02 38397160 38406955 +
Vian Vian10g01815 Chr10 29976957 29993973 +
Vifa Vifa3g03842 Chr3 1130248630 1130254153 -
Vimu Vimu7g00372 Chr7 4204584 4220884 +
Viun Viun2g00234 Chr2 4472334 4508487 -
Vivi Vivi4g03861 Chr4 157959823 157965239 +
Vvi Vvi3g0555 Chr3 4854093 4857037 +
Acco Acco11g2190 Chr11 35690159 35693370 +
Accr Accr9g00285 Chr9 3185798 3189426 -
Adu Adu05g00718 Chr05 8470386 8472757 +
Aev Aev03g0198 Chr03 1554126 1556084 -
Aev Aev05g0595 Chr05 4115350 4117209 -
Ahy Ahy20g1508 Chr20 43279211 43281666 -
Ahy Ahy15g0695 Chr15 9290615 9293069 +
Aip Aip10g01721 Chr10 40431914 40434015 -
Aip Aip05g00709 Chr05 8962527 8967244 +
Alju Alju09g2188 Chr09 45278407 45281731 +
Amo Amo20g1663 Chr20 46994927 46997259 -
Apr Apr3g1695 Chr3 32587789 32590499 +
Arst Arst5g00903 Chr5 8495553 8497947 +
Bach Bach4g00564 Chr4 3801279 3803326 +
Bisa Bisa11g1580 Chr11 36580691 36583520 +
Bva Bva14g00334 Chr14 1655790 1658520 -
Car Car06g01682 Chr06 16588369 16591060 -
Car Car08g00534 Chr08 4518322 4520853 +
Dere Dere09g0805 Chr09 10948562 10951554 +
Dod Dod02g0654 Chr02 8540532 8544255 -
Enph Enph13g0995 Chr13 15947434 15950317 -
Glsi Glsi05g1546 Chr05 63927320 63929678 -
Lapu Lapu2g00602 Chr2 5246001 5250132 +
Lasa Lasa2g03215 Chr2 525565822 525569346 +
Lele Lele49g0229 Chr49 1353778 1356444 -
Lele Lele50g0240 Chr50 1429420 1432904 -
Lele Lele51g0243 Chr51 1380056 1382646 -
Lele Lele52g0244 Chr52 1447140 1450865 -
Lja Lja2g0378 Chr2 3464118 3467380 +
Mal Mal7g3416 Chr7 99136703 99139620 +
Mesa Mesa17g00823 Chr17 10495710 10499528 -
Mibi Mibi12g1895 Chr12 35241057 35243862 +
Mtr Mtr4g2847 Chr4 42159515 42162776 +
Phac Phac2g02419 Chr2 25769884 25774057 +
Prci Prci10g0387 Chr10 2631881 2635497 -
Psa Psa7g2772 Chr7 198659246 198664036 -
Psa Psa2g3729 Chr2 397998273 398001550 -
Pste Pste1g02522 Chr1 9368914 9371940 +
Pte Pte12g00380 Chr12 3151370 3154705 +
Pumo Pumo8g01908 Chr8 55586145 55589011 -
Pvu Pvu2g0232 Chr2 2451929 2455854 +
Rops Rops1g01729 Chr1 36104146 36108163 -
Seca Seca10g00799 Chr10 7625554 7626493 +
Spst Spst2g00726 Chr2 6066257 6071336 +
Sto Sto2g0653 Chr2 5541219 5543764 +
Trre Trre9g00931 Chr9 7174299 7178044 +
Tsu Tsu02g03432 Chr02 38420174 38422877 +
Vian Vian10g00627 Chr10 5997565 6001358 +
Vifa Vifa1g07039 Chr1 1088029284 1088031917 -
Vimu Vimu7g02862 Chr7 24166461 24168696 +
Viun Viun2g02060 Chr2 28869635 28873409 -
Vivi Vivi2g03201 Chr2 133306371 133309681 -
Vvi Vvi3g0556 Chr3 4857382 4858284 -
Adu Adu03g00407 Chr03 3780299 3783588 -
Aev Aev04g3287 Chr04 31959946 31961530 -
Ahy Ahy13g0631 Chr13 6591278 6593177 -
Aip Aip03g00663 Chr03 6498120 6504024 -
Amo Amo13g0643 Chr13 7973192 7975353 -
Apr Apr5g0247 Chr5 2211016 2212424 -
Arst Arst3g00544 Chr3 3786385 3787887 -
Bva Bva13g00255 Chr13 1218045 1220089 +
Bva Bva14g00332 Chr14 1650077 1651536 +
Car Car06g03715 Chr06 68855742 68857612 -
Cca Cca04g00497 Chr04 4895091 4897172 +
Dod Dod03g3076 Chr03 63439996 63441768 -
Gma Gma11g01136 Chr11 9578203 9579625 +
Gma Gma12g00438 Chr12 3579508 3582129 +
Lal Lal2g0167 Chr2 1003393 1004296 +
Lapu Lapu11g00699 Chr11 10074298 10075816 -
Lasa Lasa7g01321 Chr7 323487979 323488891 +
Lja Lja3g0573 Chr3 5650259 5652214 +
Mal Mal7g2454 Chr7 85062066 85065386 -
Mepo Mepo2g02236 Chr2 32096296 32098324 -
Mesa Mesa13g02876 Chr13 33783533 33785098 +
Mtr Mtr4g2025 Chr4 33748234 33750544 -
Phco Phco9g00576 Chr9 4166301 4167653 +
Psa Psa7g4755 Chr7 414441492 414442508 -
Pste Pste1g02040 Chr1 6379961 6381394 +
Pumo Pumo11g01733 Chr11 48924494 48925866 -
Pvu Pvu11g0522 Chr11 4354664 4356492 +
Rops Rops3g00627 Chr3 7780416 7782457 +
Seca Seca4g03632 Chr4 62811647 62814047 +
Spst Spst2g02454 Chr2 24180361 24181664 -
Ssu Ssu3g2772 Chr3 82032863 82034214 -
Sto Sto2g0654 Chr2 5544657 5546365 -
Tpr Tpr3g2230 Chr3 20912608 20914088 -
Trre Trre7g02991 Chr7 27070982 27072163 +
Tsu Tsu02g02295 Chr02 23204471 23205529 -
Vian Vian5g01439 Chr5 37017493 37018805 -
Vifa Vifa6g00870 Chr6 299332128 299333032 +
Vimu Vimu5g02274 Chr5 33822355 33823666 -
Viun Viun11g02337 Chr11 37567270 37569159 -
Vivi Vivi5g02814 Chr5 114974372 114976048 -
Vra Vra2g0466 Chr2 3608840 3610688 +
Vvi Vvi3g0557 Chr3 4860063 4864155 +
Cca Cca04g00496 Chr04 4890746 4893618 -
Gma Gma11g01135 Chr11 9565617 9576055 -
Ssu Ssu3g2773 Chr3 82036159 82038322 +
Vra Vra2g0465 Chr2 3602513 3607348 -
Vvi Vvi3g0558 Chr3 4866536 4866772 +
Vvi Vvi3g0559 Chr3 4870222 4872315 -
Vvi Vvi3g0560 Chr3 4874233 4875104 +
Apr Apr5g0248 Chr5 2214994 2217020 +
Bva Bva14g00330 Chr14 1638336 1643084 -
Gma Gma12g00437 Chr12 3577087 3578688 -
Lasa Lasa7g01320 Chr7 323425255 323426301 -
Lja Lja3g0571 Chr3 5633164 5636337 -
Mepo Mepo2g02237 Chr2 32102289 32104173 +
Mesa Mesa13g02875 Chr13 33769366 33770759 -
Phco Phco9g00575 Chr9 4156253 4164370 -
Pumo Pumo11g01734 Chr11 48927901 48930302 +
Pvu Pvu11g0521 Chr11 4351357 4353334 -
Rops Rops3g00626 Chr3 7771365 7773078 -
Seca Seca4g03631 Chr4 62806287 62808302 -
Trre Trre7g02990 Chr7 27066448 27067668 -
Vian Vian5g01440 Chr5 37023156 37024521 +
Vifa Vifa6g00869 Chr6 299310708 299311761 -
Viun Viun11g02339 Chr11 37570425 37572176 +
Vvi Vvi3g0561 Chr3 4879760 4881663 +
Adu Adu10g03000 Chr10 106055869 106058441 -
Bva Bva13g00254 Chr13 1211939 1215681 -
Bva Bva14g00329 Chr14 1634000 1637065 -
Car Car06g03717 Chr06 68864296 68867673 +
Lal Lal1g0269 Chr1 1578917 1582280 -
Lan Lan13g0269 Chr13 1701308 1704385 -
Lapu Lapu2g01763 Chr2 31311715 31317927 +
Lja Lja2g3387 Chr2 77583192 77586191 +
Mal Mal7g2459 Chr7 85324927 85327559 +
Mepo Mepo4g01255 Chr4 16157353 16161420 +
Mesa Mesa1g01381 Chr1 19023414 19026833 +
Mtr Mtr4g2028 Chr4 33762718 33765818 +
Phco Phco8g03304 Chr8 47696575 47701440 +
Pste Pste1g03654 Chr1 17518689 17525127 +
Pumo Pumo8g00191 Chr8 6106000 6113512 -
Pvu Pvu3g0116 Chr3 1046578 1051766 -
Rops Rops1g00253 Chr1 7082037 7085679 +
Seca Seca10g05314 Chr10 121218695 121221959 -
Spst Spst2g02147 Chr2 20447618 20452846 +
Sto Sto10g0236 Chr10 1979613 1982116 -
Tpr Tpr3g2233 Chr3 20944554 20947754 +
Trre Trre1g01329 Chr1 9939207 9942647 +
Tsu Tsu02g02298 Chr02 23247529 23250696 +
Vian Vian10g01816 Chr10 29998187 30003371 +
Vifa Vifa3g03841 Chr3 1130027951 1130031876 -
Vimu Vimu7g00374 Chr7 4231248 4232963 +
Viun Viun2g00230 Chr2 4448512 4454104 -
Vivi Vivi4g03862 Chr4 157974894 157979228 +
Vvi Vvi3g0562 Chr3 4883296 4887736 +
Aev Aev04g3290 Chr04 31972846 31975387 +
Ahy Ahy13g0634 Chr13 6626644 6629474 +
Aip Aip03g00664 Chr03 6526504 6529890 +
Amo Amo13g0645 Chr13 8013115 8026122 +
Apr Apr5g0249 Chr5 2220682 2224453 +
Cca Cca04g00495 Chr04 4877858 4881663 -
Dod Dod03g3079 Chr03 63470262 63472715 +
Gma Gma11g01134 Chr11 9558983 9562226 -
Gma Gma12g00436 Chr12 3565767 3572470 -
Lal Lal9g0175 Chr9 1088667 1091476 -
Ssu Ssu3g2774 Chr3 82059657 82062558 +
Sto Sto2g0655 Chr2 5551246 5555432 +
Sto Sto10g0217 Chr10 1833729 1835364 +
Vra Vra2g0464 Chr2 3597312 3600981 -
Sto Sto10g0236 Chr10 1979613 1982116 -