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
Vvi4g1554 Acco05g0050 . Accr3g02798 Accr9g00012 Adu07g00559 Adu05g00308 Aed11g1102 Aed7g1316 . . . . . . Alju07g0060 Alju09g2498 . . . Apr7g0291 Arst7g00830 Arst5g00381 . Bach4g00843 Bisa05g2241 Bisa11g1948 Bva08g00983 . . . Cca06g01155 Cca11g00967 . Dere09g1214 . . Enph7g1582 Enph13g0764 Glsi10g2427 Glsi05g1201 Gma11g00806 Gma01g01604 . Gma16g01052 Gso11g0745 Gso11g0745 . Gso11g0745 . . . . . . . . . . . . . Lapu2g01003 Lasa2g01958 Lasa2g03565 Lele25g2037 Lele26g2089 Lele27g0040 Lele28g2089 Lele49g0003 . Lele51g0004 . Lja2g0654 . Mal6g0868 Mal5g3207 Mepo7g02475 Mepo5g01128 Mesa17g03972 Mesa17g01195 Mibi08g0043 . Mtr5g1006 Mtr8g2287 . . Phco3g00904 Phco4g00739 Prci2g3878 . . . Pste8g00855 Pste1g03456 . . Pte14g00800 Pte12g00572 Pumo9g02133 Pumo8g01612 Pvu8g2162 Pvu2g1228 Rops9g00634 Rops1g01427 Seca6g03349 Seca12g03133 . Spst3g03697 Ssu2g2139 Ssu5g0839 Sto6g4053 Sto11g1370 Tpr2g1232 Tpr4g4406 Trre9g04637 Trre9g01448 Tsu05g00973 Tsu04g02712 Vian7g01416 Vian10g00914 Vifa1g02744 Vifa1g06275 Vimu1g00695 Vimu7g03216 Viun8g02525 Viun2g01697 Vivi7g03060 Vivi2g02721 Vra11g0883 .
Vvi4g1555 . . . . . Adu05g00307 Aed11g1101 Aed7g1317 . . . . Aip05g00267 . . . . . Apr3g0441 Apr7g0292 . Arst5g00380 . Bach4g00844 . . Bva08g00984 . . . Cca06g01154 Cca11g00970 . . . . . . . . Gma11g00807 Gma01g01603 . Gma16g01053 Gso11g0746 Gso11g0746 . Gso11g0746 . . . . . . . . . . . . . Lapu2g01002 . Lasa2g03566 . . . . . . . . Lja2g0655 . Mal6g0864 . . Mepo5g01130 . Mesa17g01196 . . Mtr5g1007 . . Phac2g01888 . Phco4g00738 . . Psa2g3349 . . Pste1g03466 . . . . . . . Pvu2g1229 . Rops1g01425 . Seca12g03134 . Spst3g03696 Ssu2g2138 Ssu5g0840 . Sto11g1368 Tpr2g1234 . . Trre9g01453 Tsu05g00975 . . Vian10g00915 . Vifa1g06272 . Vimu7g03217 . Viun2g01696 . Vivi2g02719 Vra11g0884 .
Vvi4g1556 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1557 . . . . . . . Aed7g1319 . . . . . . . . . . Apr3g0442 . . . . . . . . . . . . Cca11g00976 . . . . . . . . . . . Gma16g01069 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal5g3204 . . . . . . . Mtr8g2286 . . . . . . . . . . . . . . . . . . . . . . . . . Ssu5g0842 Sto6g4056 . . Tpr4g4408 . . . Tsu04g02716 . . . . . . . . . . . .
Vvi4g1558 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1559 . . . . Adu08g02645 . . . . . . . . . . . . . Apr1g0385 . Arst8g03654 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lal17g0784 . . . . . . . . . Lapu9g00869 . Lasa5g03438 . . . . . . . . . . . Mal2g1437 . Mepo3g06892 . Mesa9g04424 . . . Mtr3g3413 . Phac9g02615 . . . . . . . . . . . . . Pumo10g01770 . Pvu9g1623 . Rops10g00926 . Seca4g01856 . Spst9g01841 . . . Sto3g3271 . Tpr3g3221 . Trre5g04423 . Tsu07g01247 . . . Vifa2g03300 . Vimu10g01857 . Viun9g01668 . Vivi3g02338 . . .
Vvi4g1560 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1561 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1562 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1563 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Lasa Lasa2g03565 Chr2 541802461 541805006 +
Pte Pte14g00800 Chr14 29507339 29512013 -
Pte Pte12g00572 Chr12 5135742 5139634 +
Spst Spst3g03697 Chr3 86970446 86974330 -
Vvi Vvi4g1554 Chr4 23597424 23599575 +
Acco Acco05g0050 Chr05 652178 655518 -
Accr Accr3g02798 Chr3 58472334 58475388 +
Accr Accr9g00012 Chr9 200441 202634 -
Adu Adu07g00559 Chr07 5818169 5822140 -
Adu Adu05g00308 Chr05 3253463 3259016 -
Aed Aed11g1102 Chr11 16618973 16623118 -
Aed Aed7g1316 Chr7 10910540 10914879 +
Alju Alju07g0060 Chr07 625110 628609 -
Alju Alju09g2498 Chr09 47795758 47800542 +
Apr Apr7g0291 Chr7 8251075 8254746 +
Arst Arst7g00830 Chr7 5967530 5971411 -
Arst Arst5g00381 Chr5 3272747 3278263 -
Bach Bach4g00843 Chr4 5611639 5614661 +
Bisa Bisa05g2241 Chr05 50934698 50937967 -
Bisa Bisa11g1948 Chr11 41882424 41885616 +
Bva Bva08g00983 Chr08 5009818 5013581 +
Cca Cca06g01155 Chr06 25900769 25904484 -
Cca Cca11g00967 Chr11 20640656 20644636 +
Dere Dere09g1214 Chr09 16033404 16037009 +
Enph Enph7g1582 Chr7 20946908 20950983 -
Enph Enph13g0764 Chr13 13980710 13986585 -
Glsi Glsi10g2427 Chr10 21875446 21883675 -
Glsi Glsi05g1201 Chr05 61568092 61571234 -
Gma Gma11g00806 Chr11 6749576 6753365 +
Gma Gma01g01604 Chr01 51677026 51681477 -
Gma Gma16g01052 Chr16 26591827 26595835 +
Gso Gso11g0745 Chr11 6685440 6689527 +
Gso Gso11g0745 Chr11 6685440 6689527 +
Gso Gso11g0745 Chr11 6685440 6689527 +
Lapu Lapu2g01003 Chr2 9398052 9402132 -
Lasa Lasa2g01958 Chr2 486538473 486541916 +
Lasa Lasa2g03565 Chr2 541802461 541805006 +
Lele Lele25g2037 Chr25 27747763 27750896 +
Lele Lele26g2089 Chr26 23949831 23952999 +
Lele Lele27g0040 Chr27 322467 325620 -
Lele Lele28g2089 Chr28 23826692 23829859 +
Lele Lele49g0003 Chr49 29575 32995 -
Lele Lele51g0004 Chr51 22900 26187 -
Lja Lja2g0654 Chr2 5931443 5935641 +
Mal Mal6g0868 Chr6 13011891 13015175 -
Mal Mal5g3207 Chr5 94062431 94065209 -
Mepo Mepo7g02475 Chr7 35922070 35926077 +
Mepo Mepo5g01128 Chr5 11413775 11417375 +
Mesa Mesa17g03972 Chr17 69004548 69008272 +
Mesa Mesa17g01195 Chr17 15389033 15392182 +
Mibi Mibi08g0043 Chr08 653256 656313 -
Mtr Mtr5g1006 Chr5 10065870 10069073 +
Mtr Mtr8g2287 Chr8 33167767 33171417 -
Phco Phco3g00904 Chr3 7615235 7618399 +
Phco Phco4g00739 Chr4 5655920 5659517 -
Prci Prci2g3878 Chr2 47843949 47847549 +
Pste Pste8g00855 Chr8 4406768 4410391 -
Pste Pste1g03456 Chr1 16104893 16110959 +
Pte Pte14g00800 Chr14 29507339 29512013 -
Pte Pte12g00572 Chr12 5135742 5139634 +
Pumo Pumo9g02133 Chr9 52564821 52568700 -
Pumo Pumo8g01612 Chr8 51441657 51446111 -
Pvu Pvu8g2162 Chr8 51998792 52002592 -
Pvu Pvu2g1228 Chr2 24123993 24128210 +
Rops Rops9g00634 Chr9 8961845 8965110 -
Rops Rops1g01427 Chr1 31565558 31570281 -
Seca Seca6g03349 Chr6 100572620 100576198 -
Seca Seca12g03133 Chr12 62284035 62287197 +
Spst Spst3g03697 Chr3 86970446 86974330 -
Ssu Ssu2g2139 Chr2 77204151 77209972 -
Ssu Ssu5g0839 Chr5 21766190 21768455 -
Sto Sto6g4053 Chr6 44197897 44201185 +
Sto Sto11g1370 Chr11 13225532 13227989 -
Tpr Tpr2g1232 Chr2 14436000 14438359 +
Tpr Tpr4g4406 Chr4 51449059 51453017 +
Trre Trre9g04637 Chr9 53444729 53448502 +
Trre Trre9g01448 Chr9 12384676 12388000 +
Tsu Tsu05g00973 Chr05 8450472 8453034 +
Tsu Tsu04g02712 Chr04 30926227 30929637 +
Vian Vian7g01416 Chr7 22646199 22649024 -
Vian Vian10g00914 Chr10 9411805 9415379 +
Vifa Vifa1g02744 Chr1 428516731 428520007 +
Vifa Vifa1g06275 Chr1 980332042 980334037 -
Vimu Vimu1g00695 Chr1 4447107 4450803 -
Vimu Vimu7g03216 Chr7 27251560 27254019 +
Viun Viun8g02525 Chr8 34722890 34726309 +
Viun Viun2g01697 Chr2 26520505 26524223 -
Vivi Vivi7g03060 Chr7 95318874 95322740 -
Vivi Vivi2g02721 Chr2 121801540 121803968 -
Vra Vra11g0883 Chr11 7537972 7541376 +
Vvi Vvi4g1555 Chr4 23601285 23604295 -
Adu Adu05g00307 Chr05 3247665 3251328 +
Aed Aed11g1101 Chr11 16609900 16615221 +
Aed Aed7g1317 Chr7 10915026 10919066 -
Aip Aip05g00267 Chr05 2944081 2947787 -
Apr Apr3g0441 Chr3 8793620 8797569 +
Apr Apr7g0292 Chr7 8259732 8265762 -
Arst Arst5g00380 Chr5 3266952 3270453 +
Bach Bach4g00844 Chr4 5616475 5618841 -
Bva Bva08g00984 Chr08 5014904 5017917 -
Cca Cca06g01154 Chr06 25884793 25891916 +
Cca Cca11g00970 Chr11 20793874 20796295 +
Gma Gma11g00807 Chr11 6761961 6766422 -
Gma Gma01g01603 Chr01 51663093 51667975 +
Gma Gma16g01053 Chr16 26604394 26607321 -
Gso Gso11g0746 Chr11 6698151 6702462 -
Gso Gso11g0746 Chr11 6698151 6702462 -
Gso Gso11g0746 Chr11 6698151 6702462 -
Lapu Lapu2g01002 Chr2 9380729 9383995 +
Lasa Lasa2g03566 Chr2 542005050 542007861 -
Lja Lja2g0655 Chr2 5938778 5944991 -
Mal Mal6g0864 Chr6 12948060 12953076 +
Mepo Mepo5g01130 Chr5 11435852 11441803 -
Mesa Mesa17g01196 Chr17 15420874 15426087 -
Mtr Mtr5g1007 Chr5 10084126 10088787 -
Phac Phac2g01888 Chr2 20973098 20974659 -
Phco Phco4g00738 Chr4 5641024 5646878 +
Psa Psa2g3349 Chr2 376658075 376662250 +
Pste Pste1g03466 Chr1 16155993 16162057 -
Pvu Pvu2g1229 Chr2 24149251 24154956 -
Rops Rops1g01425 Chr1 31522616 31529617 +
Seca Seca12g03134 Chr12 62294696 62299771 -
Spst Spst3g03696 Chr3 86964656 86966784 +
Ssu Ssu2g2138 Chr2 77184213 77193946 +
Ssu Ssu5g0840 Chr5 21830110 21832257 -
Sto Sto11g1368 Chr11 13220293 13222570 +
Tpr Tpr2g1234 Chr2 14458121 14463584 -
Trre Trre9g01453 Chr9 12407066 12412259 -
Tsu Tsu05g00975 Chr05 8462271 8467829 -
Vian Vian10g00915 Chr10 9433946 9438045 -
Vifa Vifa1g06272 Chr1 979588111 979591232 +
Vimu Vimu7g03217 Chr7 27264274 27265311 -
Viun Viun2g01696 Chr2 26508289 26512374 +
Vivi Vivi2g02719 Chr2 121751465 121754645 +
Vra Vra11g0884 Chr11 7559822 7564488 -
Vvi Vvi4g1556 Chr4 23609768 23610145 -
Vvi Vvi4g1557 Chr4 23611042 23617786 +
Aed Aed7g1319 Chr7 10935281 10941301 +
Apr Apr3g0442 Chr3 8878121 8893797 +
Cca Cca11g00976 Chr11 21043073 21057984 +
Gma Gma16g01069 Chr16 26918120 26928886 +
Mal Mal5g3204 Chr5 93993069 93997780 -
Mtr Mtr8g2286 Chr8 33148768 33154500 -
Ssu Ssu5g0842 Chr5 21876512 21895222 +
Sto Sto6g4056 Chr6 44212942 44218024 +
Tpr Tpr4g4408 Chr4 51470741 51475548 +
Tsu Tsu04g02716 Chr04 30957320 30962955 +
Vvi Vvi4g1558 Chr4 23618680 23618934 +
Vvi Vvi4g1559 Chr4 23620810 23623902 +
Adu Adu08g02645 Chr08 42544609 42554335 -
Apr Apr1g0385 Chr1 4817056 4829446 +
Arst Arst8g03654 Chr8 46917357 46926998 -
Lal Lal17g0784 Chr17 5718703 5735182 -
Lapu Lapu9g00869 Chr9 13043130 13051228 -
Lasa Lasa5g03438 Chr5 562250471 562279967 -
Mal Mal2g1437 Chr2 17211818 17223986 +
Mepo Mepo3g06892 Chr3 82622710 82627286 -
Mesa Mesa9g04424 Chr9 77567685 77578568 -
Mtr Mtr3g3413 Chr3 48024107 48036455 -
Phac Phac9g02615 Chr9 24686190 24700744 -
Pumo Pumo10g01770 Chr10 23330600 23345235 -
Pvu Pvu9g1623 Chr9 22820718 22834865 -
Rops Rops10g00926 Chr10 20410584 20422314 +
Seca Seca4g01856 Chr4 31114012 31119724 +
Spst Spst9g01841 Chr9 23415632 23432790 +
Sto Sto3g3271 Chr3 37421544 37431149 -
Tpr Tpr3g3221 Chr3 35382141 35393551 -
Trre Trre5g04423 Chr5 46248874 46259196 -
Tsu Tsu07g01247 Chr07 10817118 10824512 +
Vifa Vifa2g03300 Chr2 948323151 948340124 -
Vimu Vimu10g01857 Chr10 26545543 26555609 -
Viun Viun9g01668 Chr9 25180877 25193116 +
Vivi Vivi3g02338 Chr3 39374039 39395057 +
Vvi Vvi4g1560 Chr4 23624397 23627302 +
Vvi Vvi4g1561 Chr4 23627352 23629497 +
Vvi Vvi4g1562 Chr4 23629551 23631286 +
Vvi Vvi4g1563 Chr4 23632649 23632834 -
Adu Adu08g02645 Chr08 42544609 42554335 -
Arst Arst8g03654 Chr8 46917357 46926998 -
Lapu Lapu9g00869 Chr9 13043130 13051228 -
Lasa Lasa5g03438 Chr5 562250471 562279967 -
Mal Mal2g1437 Chr2 17211818 17223986 +
Mepo Mepo3g06892 Chr3 82622710 82627286 -
Mesa Mesa9g04424 Chr9 77567685 77578568 -
Mtr Mtr3g3413 Chr3 48024107 48036455 -
Phac Phac9g02615 Chr9 24686190 24700744 -
Pumo Pumo10g01770 Chr10 23330600 23345235 -
Pvu Pvu9g1623 Chr9 22820718 22834865 -
Rops Rops10g00926 Chr10 20410584 20422314 +
Seca Seca4g01856 Chr4 31114012 31119724 +
Spst Spst9g01841 Chr9 23415632 23432790 +
Sto Sto3g3271 Chr3 37421544 37431149 -
Tpr Tpr3g3221 Chr3 35382141 35393551 -
Trre Trre5g04423 Chr5 46248874 46259196 -
Tsu Tsu07g01247 Chr07 10817118 10824512 +
Vifa Vifa2g03300 Chr2 948323151 948340124 -
Vimu Vimu10g01857 Chr10 26545543 26555609 -
Viun Viun9g01668 Chr9 25180877 25193116 +
Vivi Vivi3g02338 Chr3 39374039 39395057 +