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
Vvi1g0571 . Acco12g0145 . Accr10g01851 . . . . . . . . . . . Alju12g1938 . . . . . . . . . . Bva01g01466 . Car04g02837 . Cca06g00202 . . Dere13g1938 . . . Enph14g0719 . Glsi09g1872 . . . . . . . . . . . . . . . . . . . . . Lapu2g01703 . . . . . . Lele53g1353 Lele54g1327 Lele55g0124 Lele56g0128 Lja2g3313 . Mal1g4961 . . . . . . Mibi10g1887 Mtr1g1023 . . . . Phco8g03244 . Prci5g2318 Psa6g1197 . . Pste1g03443 . . Pte14g00507 Pte12g00849 . Pumo8g00287 . Pvu3g0171 . Rops1g00128 . Seca10g05398 . Spst2g02078 Ssu2g1139 . . . Tpr1g2961 . . Trre1g01231 Tsu01g01141 . . . . Vifa3g03910 . Vimu7g00279 . Viun2g00322 . Vivi4g04432 Vra11g1400 .
Vvi1g0572 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva01g01465 . Car04g02835 . Cca06g00200 . . . . . . . . . Gma02g00771 . . . Gso2g0708 . . . Lal6g1089 . . . . . Lan11g1070 . . . . . . Lapu2g01705 . . . . . . . . . . Lja2g3315 . Mal1g4959 . . . . . . . Mtr1g1025 . . . . Phco8g03246 . . Psa6g1194 . . Pste1g03458 . . Pte14g00511 Pte12g00847 . Pumo8g00284 . Pvu3g0169 . Rops1g00147 . Seca10g05396 . Spst2g02080 Ssu2g1137 . Sto11g0421 . Tpr1g2959 . . Trre1g01236 Tsu01g01142 . . Vian10g01765 . Vifa3g03904 . Vimu7g00282 . Viun2g00320 . Vivi4g04429 Vra11g1568 .
Vvi1g0573 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0574 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lal6g1090 . . . . . Lan11g1071 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0575 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Dere13g1939 . . . Enph14g0718 . Glsi09g1877 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco8g03247 . . . . . . . . . . . . . Pvu3g0168 . . . . . Spst2g02081 . . . . . . . . . . . . . . . Vimu7g00283 . . . . . .
Vvi1g0576 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0577 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva01g01456 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco8g03248 . . . . . . . . . . . . . Pvu3g0167 . . . . . Spst2g02082 . . Sto11g0419 . . . . . . . . . . . . Vimu7g00284 . . . . . .
Vvi1g0578 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva01g01455 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0579 . . . . Adu03g03996 . . Aed7g1832 . Aev03g3381 . Ahy13g3941 . Aip03g04374 . . . Amo13g4968 . Apr2g1509 Arst5g01955 . . . . . Bva01g01454 Bva11g00533 Car06g00223 . . Cca01g00069 . . . Dod04g3118 . . . . . . . Gma18g00043 . . . . . . . . Lal16g0975 Lal15g0954 . . . . . . Lapu3g03891 . Lasa7g05185 . . . . . . . . . . Lja4g0085 . Mal5g0347 Mepo2g05017 . . . . . . Mtr8g3806 . . Phco4g03656 . . . . . Pste3g00073 . . . . . Pumo6g00134 . Pvu2g3318 . Rops2g00131 . Seca10g05390 . Spst3g00731 . . Ssu9g1837 Sto11g0416 . . Tpr3g0298 Trre7g05890 . . Tsu02g00098 . . Vifa6g04049 . Vimu11g04846 . Viun3g00141 . Vivi5g06611 . . .
Vvi1g0580 . Acco12g0139 . Accr10g01855 . . . . . Aev03g3383 . Ahy13g3942 . Aip03g04377 . Alju12g1942 . Amo13g4971 Apr7g0079 . . . . Bach10g01420 . . Bva01g01452 Bva11g00532 Car06g00221 . Cca06g00197 . . Dere13g1942 . Dod04g2220 . Enph14g0715 . Glsi09g1886 Gma02g00772 . . . Gso2g0709 . . . Lal6g1091 . . . Lal16g0974 . Lan11g1072 . . . Lan11g1072 . . Lapu2g01708 . . . . . . . . . . Lja2g3317 Lja4g0083 Mal1g4950 Mal5g0349 . Mepo4g01154 . Mesa1g01283 . Mibi10g1892 Mtr1g1028 Mtr8g3808 . . . Phco8g03249 . Prci5g2329 Psa6g1192 . . Pste1g03465 . . . . . Pumo8g00279 Pvu2g1055 Pvu3g0166 . Rops1g00155 . Seca10g05388 . Spst2g02083 Ssu2g1133 . Sto11g0405 . Tpr1g2957 Tpr3g0296 . Trre1g01240 Tsu01g01145 Tsu02g00096 . Vian10g01767 . Vifa3g03903 . Vimu7g00285 . Viun2g00314 . Vivi4g04423 Vra11g1394 .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi1g0571 Chr1 5627438 5633436 +
Acco Acco12g0145 Chr12 1271307 1276104 -
Accr Accr10g01851 Chr10 43002223 43021712 +
Alju Alju12g1938 Chr12 40400244 40406127 +
Bva Bva01g01466 Chr01 16200565 16201416 -
Car Car04g02837 Chr04 55111400 55116759 -
Cca Cca06g00202 Chr06 4916001 4922247 -
Dere Dere13g1938 Chr13 26380696 26388796 +
Enph Enph14g0719 Chr14 9214380 9223737 -
Glsi Glsi09g1872 Chr09 20404266 20416451 +
Lapu Lapu2g01703 Chr2 30788762 30796355 +
Lele Lele53g1353 Chr53 21723886 21731951 +
Lele Lele54g1327 Chr54 18330299 18338180 +
Lele Lele55g0124 Chr55 804090 811156 -
Lele Lele56g0128 Chr56 1232634 1245745 -
Lja Lja2g3313 Chr2 75133973 75145574 +
Mal Mal1g4961 Chr1 119845538 119849552 -
Mibi Mibi10g1887 Chr10 41968078 41969416 +
Mtr Mtr1g1023 Chr1 11608805 11612918 +
Phco Phco8g03244 Chr8 47120091 47125314 +
Prci Prci5g2318 Chr5 40150273 40158826 +
Psa Psa6g1197 Chr6 47754856 47758510 -
Pste Pste1g03443 Chr1 16052620 16056695 +
Pte Pte14g00507 Chr14 24624777 24630025 -
Pte Pte12g00849 Chr12 9987591 9989614 -
Pumo Pumo8g00287 Chr8 8527591 8530313 -
Pvu Pvu3g0171 Chr3 1516886 1524476 -
Rops Rops1g00128 Chr1 3765424 3776288 +
Seca Seca10g05398 Chr10 122718534 122726049 -
Spst Spst2g02078 Chr2 19965039 19970098 +
Ssu Ssu2g1139 Chr2 51729717 51731449 -
Tpr Tpr1g2961 Chr1 33980257 33989090 -
Trre Trre1g01231 Chr1 9353702 9358062 +
Tsu Tsu01g01141 Chr01 10545623 10554688 +
Vifa Vifa3g03910 Chr3 1154332616 1154336478 -
Vimu Vimu7g00279 Chr7 3398659 3405726 +
Viun Viun2g00322 Chr2 6355630 6372153 -
Vivi Vivi4g04432 Chr4 171114592 171118591 -
Vra Vra11g1400 Chr11 16980219 16986126 -
Vvi Vvi1g0572 Chr1 5652583 5659082 +
Bva Bva01g01465 Chr01 16185426 16191621 -
Car Car04g02835 Chr04 55093602 55102843 -
Cca Cca06g00200 Chr06 4888006 4898902 -
Gma Gma02g00771 Chr02 7545250 7556047 +
Gso Gso2g0708 Chr2 7411534 7421903 +
Lal Lal6g1089 Chr6 8027856 8039033 +
Lan Lan11g1070 Chr11 13699434 13709691 +
Lapu Lapu2g01705 Chr2 30806133 30814762 +
Lja Lja2g3315 Chr2 75179096 75186408 +
Mal Mal1g4959 Chr1 119834792 119839669 -
Mtr Mtr1g1025 Chr1 11620142 11626006 +
Phco Phco8g03246 Chr8 47135233 47143740 +
Psa Psa6g1194 Chr6 47614575 47620313 -
Pste Pste1g03458 Chr1 16113684 16123066 +
Pte Pte14g00511 Chr14 24798041 24798672 +
Pte Pte12g00847 Chr12 9908561 9914284 -
Pumo Pumo8g00284 Chr8 8439423 8505562 -
Pvu Pvu3g0169 Chr3 1501098 1508313 -
Rops Rops1g00147 Chr1 4344485 4369380 +
Seca Seca10g05396 Chr10 122652043 122663608 -
Spst Spst2g02080 Chr2 19975971 19983740 +
Ssu Ssu2g1137 Chr2 51687652 51688137 -
Sto Sto11g0421 Chr11 5409255 5416750 -
Tpr Tpr1g2959 Chr1 33954383 33960953 -
Trre Trre1g01236 Chr1 9400401 9404782 +
Tsu Tsu01g01142 Chr01 10564450 10570945 +
Vian Vian10g01765 Chr10 29413258 29418765 +
Vifa Vifa3g03904 Chr3 1152919128 1152923208 -
Vimu Vimu7g00282 Chr7 3420664 3436266 +
Viun Viun2g00320 Chr2 6313988 6320637 -
Vivi Vivi4g04429 Chr4 171077419 171082766 -
Vra Vra11g1568 Chr11 19617276 19618919 +
Vvi Vvi1g0573 Chr1 5660726 5661950 -
Vvi Vvi1g0574 Chr1 5664184 5665866 -
Lal Lal6g1090 Chr6 8050497 8054242 -
Lan Lan11g1071 Chr11 13723801 13727718 -
Vvi Vvi1g0575 Chr1 5673027 5681127 -
Dere Dere13g1939 Chr13 26418926 26422678 -
Enph Enph14g0718 Chr14 9207231 9210587 +
Glsi Glsi09g1877 Chr09 20539571 20544698 +
Phco Phco8g03247 Chr8 47151973 47154504 -
Pvu Pvu3g0168 Chr3 1494079 1496941 +
Spst Spst2g02081 Chr2 19987058 19989721 -
Vimu Vimu7g00283 Chr7 3442031 3445143 +
Vvi Vvi1g0576 Chr1 5681821 5683503 -
Vvi Vvi1g0577 Chr1 5687062 5688738 +
Bva Bva01g01456 Chr01 16077354 16080325 -
Phco Phco8g03248 Chr8 47155661 47159128 -
Pvu Pvu3g0167 Chr3 1487949 1491549 +
Spst Spst2g02082 Chr2 19990225 19991810 -
Sto Sto11g0419 Chr11 5395872 5397859 +
Vimu Vimu7g00284 Chr7 3449705 3450561 -
Vvi Vvi1g0578 Chr1 5695230 5696103 -
Bva Bva01g01455 Chr01 16066916 16070293 +
Vvi Vvi1g0579 Chr1 5701636 5706168 -
Adu Adu03g03996 Chr03 129095025 129101075 -
Aed Aed7g1832 Chr7 21667233 21671111 +
Aev Aev03g3381 Chr03 31454385 31458841 -
Ahy Ahy13g3941 Chr13 138796125 138802314 -
Aip Aip03g04374 Chr03 128139934 128145959 -
Amo Amo13g4968 Chr13 148698757 148705061 -
Apr Apr2g1509 Chr2 21040928 21047850 -
Arst Arst5g01955 Chr5 25999947 26001941 -
Bva Bva01g01454 Chr01 16049283 16056771 +
Bva Bva11g00533 Chr11 8897485 8904418 +
Car Car06g00223 Chr06 2385970 2391389 +
Cca Cca01g00069 Chr01 714392 719810 +
Dod Dod04g3118 Chr04 54863329 54871492 -
Gma Gma18g00043 Chr18 355333 360382 +
Lal Lal16g0975 Chr16 6489944 6502671 +
Lal Lal15g0954 Chr15 7430581 7439978 +
Lapu Lapu3g03891 Chr3 62427642 62434180 -
Lasa Lasa7g05185 Chr7 714445971 714454184 -
Lja Lja4g0085 Chr4 660250 667313 +
Mal Mal5g0347 Chr5 5463594 5472774 -
Mepo Mepo2g05017 Chr2 58153864 58160663 -
Mtr Mtr8g3806 Chr8 48707852 48711868 -
Phco Phco4g03656 Chr4 56261195 56268556 -
Pste Pste3g00073 Chr3 350040 356634 +
Pumo Pumo6g00134 Chr6 1553112 1560272 +
Pvu Pvu2g3318 Chr2 48136283 48142735 -
Rops Rops2g00131 Chr2 2026312 2034338 +
Seca Seca10g05390 Chr10 122554087 122561361 +
Spst Spst3g00731 Chr3 10942414 10948244 +
Ssu Ssu9g1837 Chr9 55752195 55756588 -
Sto Sto11g0416 Chr11 5359357 5367797 +
Tpr Tpr3g0298 Chr3 3304457 3311442 +
Trre Trre7g05890 Chr7 63534982 63543054 -
Tsu Tsu02g00098 Chr02 716158 723364 +
Vifa Vifa6g04049 Chr6 1335187012 1335192250 -
Vimu Vimu11g04846 Chr11 68295928 68296257 -
Viun Viun3g00141 Chr3 728601 734599 +
Vivi Vivi5g06611 Chr5 173175753 173183016 +
Vvi Vvi1g0580 Chr1 5723080 5726397 -
Acco Acco12g0139 Chr12 1215097 1218770 +
Accr Accr10g01855 Chr10 43050214 43053739 -
Aev Aev03g3383 Chr03 31465822 31468840 -
Ahy Ahy13g3942 Chr13 138805117 138809301 -
Aip Aip03g04377 Chr03 128149175 128153450 -
Alju Alju12g1942 Chr12 40448889 40452390 -
Amo Amo13g4971 Chr13 148707741 148712019 -
Apr Apr7g0079 Chr7 3176592 3181003 +
Bach Bach10g01420 Chr10 13649431 13653001 -
Bva Bva01g01452 Chr01 16034376 16038695 +
Bva Bva11g00532 Chr11 8881854 8885929 +
Car Car06g00221 Chr06 2373157 2377334 +
Cca Cca06g00197 Chr06 4804479 4809274 +
Dere Dere13g1942 Chr13 26452294 26455804 -
Dod Dod04g2220 Chr04 46069168 46077726 +
Enph Enph14g0715 Chr14 9175383 9186662 +
Glsi Glsi09g1886 Chr09 20877846 20881252 -
Gma Gma02g00772 Chr02 7558812 7562482 -
Gso Gso2g0709 Chr2 7424271 7429281 -
Lal Lal6g1091 Chr6 8066798 8070304 -
Lal Lal16g0974 Chr16 6484297 6488499 +
Lan Lan11g1072 Chr11 13747896 13751581 -
Lan Lan11g1072 Chr11 13747896 13751581 -
Lapu Lapu2g01708 Chr2 30831422 30836663 -
Lja Lja2g3317 Chr2 75197647 75201871 +
Lja Lja4g0083 Chr4 644535 649101 +
Mal Mal1g4950 Chr1 119689077 119692558 +
Mal Mal5g0349 Chr5 5484474 5487992 -
Mepo Mepo4g01154 Chr4 15080812 15084862 -
Mesa Mesa1g01283 Chr1 17795761 17799223 -
Mibi Mibi10g1892 Chr10 42012171 42015631 -
Mtr Mtr1g1028 Chr1 11685277 11689536 -
Mtr Mtr8g3808 Chr8 48724065 48727841 -
Phco Phco8g03249 Chr8 47162353 47165885 -
Prci Prci5g2329 Chr5 40186001 40192531 -
Psa Psa6g1192 Chr6 47531756 47534654 +
Pste Pste1g03465 Chr1 16152975 16157519 -
Pumo Pumo8g00279 Chr8 8332249 8336901 +
Pvu Pvu2g1055 Chr2 20432797 20434066 +
Pvu Pvu3g0166 Chr3 1479494 1483979 +
Rops Rops1g00155 Chr1 4616411 4620982 -
Seca Seca10g05388 Chr10 122525890 122529515 +
Spst Spst2g02083 Chr2 19993918 19997154 -
Ssu Ssu2g1133 Chr2 51571827 51575139 +
Sto Sto11g0405 Chr11 5165717 5169307 +
Tpr Tpr1g2957 Chr1 33931012 33935622 +
Tpr Tpr3g0296 Chr3 3291848 3296531 +
Trre Trre1g01240 Chr1 9425155 9428334 -
Tsu Tsu01g01145 Chr01 10582589 10594676 -
Tsu Tsu02g00096 Chr02 697388 702083 +
Vian Vian10g01767 Chr10 29438244 29441387 -
Vifa Vifa3g03903 Chr3 1152841144 1152843866 +
Vimu Vimu7g00285 Chr7 3457813 3460985 -
Viun Viun2g00314 Chr2 6284633 6288784 +
Vivi Vivi4g04423 Chr4 171024479 171027947 +
Vra Vra11g1394 Chr11 16919602 16923819 +
Adu Adu03g03996 Chr03 129095025 129101075 -