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
Vvi2g0792 . . . . . . Aed6g0168 . Aev05g0146 . Ahy15g0103 . Aip05g00102 . . . . . Apr7g1762 Apr3g0641 . . . . . . Bva08g01142 Bva11g01296 . . Cca06g00972 Cca11g00817 . . Dod02g0153 . . . . . Gma01g00147 Gma09g01913 . . Gso1g0145 Gso1g0145 . . Lal15g0399 Lal16g0448 . . . . Lan18g0771 Lan18g0771 . . . . . . . . . . . . . . . . Lja2g0829 . Mal6g0692 . . . . . . . Mtr5g1230 . . . . . . . Psa2g3108 . . . . . . . . . . . . . . . . . Ssu2g1953 . Sto6g4178 Sto11g1307 Tpr2g1483 . . . Tsu05g01251 . . . . . . . . . . . Vra11g1061 .
Vvi2g0793 . . . . . . Aed6g0167 . . . Ahy15g0104 . Aip05g00103 . . . . . Apr7g1763 Apr3g0640 . . . . . . Bva08g01141 Bva11g01297 . Car07g01920 Cca06g00973 Cca11g00818 . . . . . . . . Gma01g00146 Gma09g01914 . . Gso1g0144 Gso1g0144 . . Lal15g0398 Lal16g0447 . . . . . . . . . . . . . . . . . . . . . . Lja2g0828 . Mal6g0690 Mal5g2761 . . . . . . Mtr5g1226 Mtr8g2044 . . . . . . Psa2g3113 Psa4g2834 . . . . . . . . . . . . . . . . Ssu2g1956 . . Sto11g1306 . Tpr4g4709 . . . Tsu04g02928 . . . . . . . . . . Vra11g1060 .
Vvi2g0794 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0795 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto6g4175 . . . . . . . . . . . . . . . . . . .
Vvi2g0796 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0797 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0798 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0799 . . . . Adu05g00113 . Aed6g0165 . . . Ahy15g0106 . Aip05g00104 . Alju09g1297 . . . Apr7g1766 . Arst5g00143 . . . Bisa11g2094 . . . . . Cca06g00974 . Dere09g1371 . Dod02g0156 . Enph13g1656 . Glsi05g1044 . . Gma09g01916 . . . . . . . Lal16g0446 . . . . . . . . . . Lapu2g00845 . Lasa2g03755 . . Lele50g0952 . Lele52g0930 . . . . Lja2g0825 . Mal6g0688 . Mepo5g01369 . Mesa17g01499 . Mibi12g1081 . Mtr5g1224 . Phac2g02202 . Phco4g00522 . Prci10g1468 . Psa2g3118 . Pste1g00899 . . . . . Pumo8g01389 . Pvu2g1429 . Rops1g01257 . Seca10g01301 . Spst2g01227 . Ssu2g1958 . Sto6g4174 . Tpr2g1477 . Trre9g01854 . Tsu05g01243 . Vian10g01093 . Vifa1g05855 . Vimu7g03493 . Viun2g01434 . Vivi2g02403 . Vra11g1058 .
Vvi2g0800 Acco11g1280 . . . . . . . . . . . . . Alju09g1298 . . . Apr7g1767 . . . . . Bisa11g2093 . . . . . Cca06g00975 . Dere09g1370 . . . Enph13g1655 . Glsi05g1045 . Gma01g00143 . . . . . . . . . . . . . . . . . . . . . Lasa2g03754 . . Lele50g0950 Lele51g0918 Lele52g0928 . . . . . . Mal6g0687 . Mepo5g01368 . Mesa17g01497 . . . Mtr5g1223 . Phac2g02200 . . . Prci10g1467 . Psa2g3119 . Pste1g00893 . . . . . Pumo8g01390 . Pvu2g1428 . Rops1g01258 . . . Spst2g01226 . Ssu2g1959 . Sto6g4173 . Tpr2g1476 . Trre9g01853 . Tsu05g01242 . . . Vifa1g05857 . . . Viun2g01436 . Vivi2g02406 . Vra11g1057 .
Vvi2g0801 . . . . . . . . . . . . . . . . . . . Apr3g0635 . . . . . . Bva08g01139 Bva11g01299 . . . Cca11g00819 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ssu5g0970 . Sto11g1304 . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Lal Lal16g0447 Chr16 2762844 2772314 +
Lal Lal15g0398 Chr15 2700174 2709737 +
Vvi Vvi2g0792 Chr2 7942404 7943694 -
Aed Aed6g0168 Chr6 1485154 1486462 +
Aev Aev05g0146 Chr05 1139634 1140758 -
Ahy Ahy15g0103 Chr15 1184073 1186431 -
Aip Aip05g00102 Chr05 1171622 1174040 -
Apr Apr7g1762 Chr7 24911349 24913313 -
Apr Apr3g0641 Chr3 16196511 16197613 +
Bva Bva08g01142 Chr08 5865767 5866852 +
Bva Bva11g01296 Chr11 13348714 13349820 -
Cca Cca06g00972 Chr06 23466457 23468191 -
Cca Cca11g00817 Chr11 15634976 15636412 -
Dod Dod02g0153 Chr02 2225314 2226434 -
Gma Gma01g00147 Chr01 1620919 1623411 +
Gma Gma09g01913 Chr09 44747470 44749764 -
Gso Gso1g0145 Chr1 1634109 1636689 +
Gso Gso1g0145 Chr1 1634109 1636689 +
Lal Lal15g0399 Chr15 2714837 2716757 +
Lal Lal16g0448 Chr16 2781955 2784391 +
Lan Lan18g0771 Chr18 13144468 13146523 -
Lan Lan18g0771 Chr18 13144468 13146523 -
Lja Lja2g0829 Chr2 7735879 7737890 +
Mal Mal6g0692 Chr6 9795602 9797321 +
Mtr Mtr5g1230 Chr5 12599238 12601434 +
Psa Psa2g3108 Chr2 356841735 356844267 -
Ssu Ssu2g1953 Chr2 72111198 72113208 -
Sto Sto6g4178 Chr6 45054248 45055492 +
Sto Sto11g1307 Chr11 12712367 12713616 +
Tpr Tpr2g1483 Chr2 17461777 17464114 +
Tsu Tsu05g01251 Chr05 11278833 11280600 +
Vra Vra11g1061 Chr11 9833527 9835879 +
Vvi Vvi2g0793 Chr2 7964138 7972385 -
Aed Aed6g0167 Chr6 1471235 1479573 +
Ahy Ahy15g0104 Chr15 1197502 1204316 -
Aip Aip05g00103 Chr05 1184662 1191748 -
Apr Apr7g1763 Chr7 24921513 24930035 -
Apr Apr3g0640 Chr3 16162653 16193580 +
Bva Bva08g01141 Chr08 5854771 5862169 +
Bva Bva11g01297 Chr11 13353317 13360936 -
Car Car07g01920 Chr07 21928919 21941312 -
Cca Cca06g00973 Chr06 23482715 23492212 -
Cca Cca11g00818 Chr11 15673247 15690892 -
Gma Gma01g00146 Chr01 1601649 1611370 +
Gma Gma09g01914 Chr09 44766451 44774174 -
Gso Gso1g0144 Chr1 1614939 1624681 +
Gso Gso1g0144 Chr1 1614939 1624681 +
Lal Lal15g0398 Chr15 2700174 2709737 +
Lal Lal16g0447 Chr16 2762844 2772314 +
Lja Lja2g0828 Chr2 7710458 7720449 +
Mal Mal6g0690 Chr6 9771997 9782206 +
Mal Mal5g2761 Chr5 82166331 82188875 -
Mtr Mtr5g1226 Chr5 12561975 12571395 +
Mtr Mtr8g2044 Chr8 30302504 30316311 +
Psa Psa2g3113 Chr2 357193848 357199227 -
Psa Psa4g2834 Chr4 226826393 226831384 -
Ssu Ssu2g1956 Chr2 72137494 72144304 -
Sto Sto11g1306 Chr11 12702463 12707869 +
Tpr Tpr4g4709 Chr4 55493623 55506596 -
Tsu Tsu04g02928 Chr04 35590456 35609049 +
Vra Vra11g1060 Chr11 9805816 9813259 +
Vvi Vvi2g0794 Chr2 7997844 7999451 +
Vvi Vvi2g0795 Chr2 8014905 8022371 -
Sto Sto6g4175 Chr6 45030829 45034243 +
Vvi Vvi2g0796 Chr2 8042005 8046755 +
Vvi Vvi2g0797 Chr2 8058691 8059614 -
Vvi Vvi2g0798 Chr2 8071720 8071824 +
Vvi Vvi2g0799 Chr2 8123287 8139000 +
Adu Adu05g00113 Chr05 1239535 1242976 +
Aed Aed6g0165 Chr6 1453931 1459627 -
Ahy Ahy15g0106 Chr15 1246018 1249958 +
Aip Aip05g00104 Chr05 1215087 1219043 +
Alju Alju09g1297 Chr09 36645104 36649989 +
Apr Apr7g1766 Chr7 24967733 24973061 +
Arst Arst5g00143 Chr5 1259515 1262883 +
Bisa Bisa11g2094 Chr11 44062186 44073667 -
Cca Cca06g00974 Chr06 23521319 23526035 +
Dere Dere09g1371 Chr09 17782397 17787748 -
Dod Dod02g0156 Chr02 2277777 2281352 +
Enph Enph13g1656 Chr13 22579012 22584605 -
Glsi Glsi05g1044 Chr05 60305844 60318559 +
Gma Gma09g01916 Chr09 44792167 44795072 +
Lal Lal16g0446 Chr16 2744783 2753516 -
Lapu Lapu2g00845 Chr2 7714144 7723513 +
Lasa Lasa2g03755 Chr2 553139020 553143585 -
Lele Lele50g0952 Chr50 6016739 6022418 -
Lele Lele52g0930 Chr52 6058551 6060919 -
Lja Lja2g0825 Chr2 7684137 7686983 -
Mal Mal6g0688 Chr6 9739622 9745717 -
Mepo Mepo5g01369 Chr5 14188592 14193574 -
Mesa Mesa17g01499 Chr17 20355167 20360639 -
Mibi Mibi12g1081 Chr12 25952125 25954177 +
Mtr Mtr5g1224 Chr5 12535886 12543173 -
Phac Phac2g02202 Chr2 23662123 23668109 -
Phco Phco4g00522 Chr4 3762115 3764034 +
Prci Prci10g1468 Chr10 9882357 9887790 -
Psa Psa2g3118 Chr2 357616866 357621846 +
Pste Pste1g00899 Chr1 2782239 2793581 -
Pumo Pumo8g01389 Chr8 46471071 46476418 +
Pvu Pvu2g1429 Chr2 27149680 27155632 -
Rops Rops1g01257 Chr1 28831632 28837054 +
Seca Seca10g01301 Chr10 13012099 13017693 -
Spst Spst2g01227 Chr2 10833355 10837422 -
Ssu Ssu2g1958 Chr2 72190751 72196838 +
Sto Sto6g4174 Chr6 45015446 45020792 -
Tpr Tpr2g1477 Chr2 17374132 17392906 -
Trre Trre9g01854 Chr9 17678473 17684228 -
Tsu Tsu05g01243 Chr05 11176308 11182123 -
Vian Vian10g01093 Chr10 12705093 12711343 -
Vifa Vifa1g05855 Chr1 917742254 917746655 +
Vimu Vimu7g03493 Chr7 29578177 29583715 -
Viun Viun2g01434 Chr2 24830961 24836712 +
Vivi Vivi2g02403 Chr2 110884071 110888908 +
Vra Vra11g1058 Chr11 9765397 9771352 -
Vvi Vvi2g0800 Chr2 8161666 8163969 +
Acco Acco11g1280 Chr11 26882493 26884730 +
Alju Alju09g1298 Chr09 36657365 36659900 +
Apr Apr7g1767 Chr7 24994727 25000197 +
Bisa Bisa11g2093 Chr11 44044909 44049322 -
Cca Cca06g00975 Chr06 23529041 23531959 +
Dere Dere09g1370 Chr09 17761495 17763877 -
Enph Enph13g1655 Chr13 22571769 22574461 -
Glsi Glsi05g1045 Chr05 60318999 60323119 +
Gma Gma01g00143 Chr01 1573536 1581338 -
Lasa Lasa2g03754 Chr2 553114818 553116812 -
Lele Lele50g0950 Chr50 6005865 6008090 -
Lele Lele51g0918 Chr51 5706744 5714412 -
Lele Lele52g0928 Chr52 6045618 6054291 -
Mal Mal6g0687 Chr6 9734026 9736470 -
Mepo Mepo5g01368 Chr5 14179511 14185227 -
Mesa Mesa17g01497 Chr17 20300954 20303089 -
Mtr Mtr5g1223 Chr5 12528415 12534588 -
Phac Phac2g02200 Chr2 23653204 23658968 -
Prci Prci10g1467 Chr10 9878588 9880807 -
Psa Psa2g3119 Chr2 357658359 357666361 +
Pste Pste1g00893 Chr1 2754789 2760537 -
Pumo Pumo8g01390 Chr8 46482709 46484922 +
Pvu Pvu2g1428 Chr2 27132279 27138483 -
Rops Rops1g01258 Chr1 28839734 28845238 +
Spst Spst2g01226 Chr2 10827940 10830141 -
Ssu Ssu2g1959 Chr2 72201247 72203451 +
Sto Sto6g4173 Chr6 45011316 45013571 -
Tpr Tpr2g1476 Chr2 17366954 17372855 -
Trre Trre9g01853 Chr9 17672314 17675981 -
Tsu Tsu05g01242 Chr05 11168310 11172657 -
Vifa Vifa1g05857 Chr1 917945524 917953362 +
Viun Viun2g01436 Chr2 24840198 24850025 +
Vivi Vivi2g02406 Chr2 111009207 111017589 +
Vra Vra11g1057 Chr11 9749720 9762968 -
Vvi Vvi2g0801 Chr2 8170908 8173925 -
Apr Apr3g0635 Chr3 16017331 16019647 +
Bva Bva08g01139 Chr08 5844943 5847317 +
Bva Bva11g01299 Chr11 13366755 13369444 -
Cca Cca11g00819 Chr11 15746434 15751519 -
Ssu Ssu5g0970 Chr5 29813376 29817185 -
Sto Sto11g1304 Chr11 12689182 12691513 +