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
Vvi1g0461 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car04g02897 . . . . . . . . . . . . . . . . . . . . Lal22g0924 . . . . . . . . . . . . . . . . . . . . . . Lja2g3217 . Mal1g5041 . . . . . . . Mtr1g0933 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto6g2663 Tpr1g3030 . . . Tsu01g01057 . . . . . . . . . . . . .
Vvi1g0462 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva11g00650 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja5g0379 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto11g0600 . . . . . . . . . . . . . . . . . . .
Vvi1g0463 . . . . . . . . . . . . . . . . . . Apr7g1337 . . . . . . . . Bva11g00649 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0464 . . . . . . . . . Aev03g0760 . Ahy13g3479 . Aip03g03931 . . . Amo13g4171 . Apr3g1625 . . . . . . Bva01g01612 Bva11g00648 . . . . . . . Dod04g0252 . . . . . . . . . . . . . . . Lal23g0871 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto6g2662 . . . . . . . . . . . . . . . . . .
Vvi1g0465 Acco11g0216 . Accr9g01975 . . . . . . . . . . . Alju09g0270 . . . . Apr3g1624 . . . . Bisa11g0555 . Bva01g01611 . Car06g01762 . . . Dere09g2147 . . . Enph13g0604 . Glsi05g0283 . . . . . . . . . . . . . Lal16g0754 Lal15g0720 . . . . . . . . Lasa7g02988 . . Lele50g1625 Lele51g1233 Lele52g1578 . . . . . . . . Mepo2g03069 . . . Mibi12g0217 . . . Phac2g01462 . Phco4g01787 . . . . Psa7g2936 Pste3g04139 . Pte14g00412 . . . . . Pvu2g0954 . . . . . . . . . Sto11g0596 Sto6g2661 . . Trre7g01889 . . . . . . . . . . . Vivi5g03853 . . .
Vvi1g0466 Acco11g0215 Acco05g1428 Accr9g01976 Accr3g01545 . Adu07g00954 . . . Aev03g0757 . Ahy13g3480 . Aip03g03933 Alju09g0269 Alju07g1393 . Amo13g4168 Apr7g1335 Apr3g1622 . Arst7g01303 . Bach3g01115 Bisa11g0542 Bisa05g1510 Bva01g01610 Bva11g00647 Car06g00063 . . . Dere09g2148 Dere05g1030 . Dod04g0251 Enph13g0605 Enph7g0372 Glsi05g0280 Glsi10g1694 . . . Gma18g00363 . . . . Lal6g1031 . . . Lal16g0756 Lal15g0721 . . . . . . . . Lasa7g02983 Lasa2g01555 Lele49g1213 . Lele51g1232 Lele52g1579 Lele25g1265 Lele26g1278 Lele27g0818 Lele28g1270 Lja2g3219 . Mal1g5038 . Mepo2g03066 Mepo7g02137 . Mesa17g03513 Mibi12g0216 Mibi08g1196 Mtr1g0937 . . Phac8g03100 Phco4g01790 Phco3g00609 Prci10g2781 Prci2g1997 Psa6g0985 . Pste3g04137 Pste8g01432 Pte14g00413 . . . . Pumo9g02443 Pvu2g0956 Pvu8g2420 . Rops9g00968 . Seca6g02304 Spst3g02240 Spst1g02235 . . Sto11g0592 Sto6g2660 Tpr1g3027 . Trre7g01891 Trre9g04193 Tsu01g01062 . . Vian7g01672 . Vifa1g01802 Vimu7g00080 Vimu1g01067 . Viun8g02179 Vivi5g03851 Vivi7g01903 . .
Vvi1g0467 . . . . . . . . . . . . . . . . . . . Apr3g1621 . . . . . . Bva01g01609 Bva11g00646 Car06g01765 . . . . . . . . . . . . . . . . . . . . . . Lal23g0870 . Lal15g0722 . . . . . . . . Lasa7g02982 . . . . . . . . . . . . . Mepo2g03065 . . . . . . . Phac2g01467 . Phco4g01791 . . . . Psa7g2947 Pste3g04136 . Pte14g00414 . . . . . Pvu2g0957 . . . . . Spst3g02241 . . . Sto11g0591 . . . Trre7g01894 . . . . . . . Vimu11g02587 . . . Vivi5g03850 . . .
Vvi1g0468 . . . . . . . . . . . . . . . . . . Apr7g1334 . . . . . . . Bva01g01608 Bva11g00644 Car04g02893 . . . . . . . . . . . . . . . . . . . . Lal22g0926 . . . . . . . . . . . . . . . . . . . . . . Lja2g3220 . Mal1g5037 . . . . . . . Mtr1g0938 . . . . . . . Psa6g0986 . . . . . . . . . . . . . . . . . . . . Sto6g2659 Tpr1g3026 . . . Tsu01g01063 . . . . . . . . . . . . .
Vvi1g0469 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0470 . . . . . . . . . . . . . . . . . . Apr7g1333 . . . . . . . Bva01g01607 Bva11g00642 Car04g02892 . . . . . . . . . . . . . . . . . . . Lal6g1032 . . . . . . . . . . . . . . . . . . . . . . . Lja2g3221 . Mal1g5036 . . . . . . . Mtr1g0939 . . . . . . . Psa6g0987 . . . . . . . . . . . . . . . . . . . . . Tpr1g3025 . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi1g0461 Chr1 4265497 4268656 +
Car Car04g02897 Chr04 55965738 55970493 -
Lal Lal22g0924 Chr22 7323913 7329321 +
Lja Lja2g3217 Chr2 69812861 69819389 +
Mal Mal1g5041 Chr1 121284700 121289093 -
Mtr Mtr1g0933 Chr1 10738250 10743154 +
Sto Sto6g2663 Chr6 33752660 33757444 -
Tpr Tpr1g3030 Chr1 34700491 34704924 -
Tsu Tsu01g01057 Chr01 9746008 9751741 +
Vvi Vvi1g0462 Chr1 4273851 4277143 +
Bva Bva11g00650 Chr11 9780974 9784528 -
Lja Lja5g0379 Chr5 3361504 3364959 +
Sto Sto11g0600 Chr11 7098127 7104370 -
Vvi Vvi1g0463 Chr1 4278409 4287206 +
Apr Apr7g1337 Chr7 20456773 20461767 -
Bva Bva11g00649 Chr11 9776245 9780547 -
Vvi Vvi1g0464 Chr1 4330134 4331211 +
Aev Aev03g0760 Chr03 5879110 5881336 -
Ahy Ahy13g3479 Chr13 132665174 132666040 +
Aip Aip03g03931 Chr03 122285909 122286784 +
Amo Amo13g4171 Chr13 135284863 135285590 -
Apr Apr3g1625 Chr3 31706025 31707504 -
Bva Bva01g01612 Chr01 17428476 17430253 -
Bva Bva11g00648 Chr11 9768340 9770302 -
Dod Dod04g0252 Chr04 3086092 3087837 -
Lal Lal23g0871 Chr23 11048900 11051785 -
Sto Sto6g2662 Chr6 33740712 33743908 -
Vvi Vvi1g0465 Chr1 4353672 4357753 +
Acco Acco11g0216 Chr11 2806816 2809884 -
Accr Accr9g01975 Chr9 43094622 43097800 +
Alju Alju09g0270 Chr09 3649567 3652633 -
Apr Apr3g1624 Chr3 31665258 31668417 -
Bisa Bisa11g0555 Chr11 15181096 15184284 -
Bva Bva01g01611 Chr01 17408205 17411582 -
Car Car06g01762 Chr06 17447753 17451760 +
Dere Dere09g2147 Chr09 30542484 30545258 +
Enph Enph13g0604 Chr13 12343660 12347065 +
Glsi Glsi05g0283 Chr05 49720627 49723781 -
Lal Lal16g0754 Chr16 4870294 4873804 +
Lal Lal15g0720 Chr15 5022333 5027064 +
Lasa Lasa7g02988 Chr7 564705312 564708079 -
Lele Lele50g1625 Chr50 21308513 21311596 +
Lele Lele51g1233 Chr51 8142405 8145407 -
Lele Lele52g1578 Chr52 19658525 19661609 +
Mepo Mepo2g03069 Chr2 40349851 40352712 -
Mibi Mibi12g0217 Chr12 4348616 4351892 -
Phac Phac2g01462 Chr2 12984370 12988089 +
Phco Phco4g01787 Chr4 33440286 33443239 +
Psa Psa7g2936 Chr7 210017377 210020882 -
Pste Pste3g04139 Chr3 36878361 36881585 -
Pte Pte14g00412 Chr14 21915619 21918884 +
Pvu Pvu2g0954 Chr2 16556078 16559423 +
Sto Sto11g0596 Chr11 7076044 7078975 -
Sto Sto6g2661 Chr6 33719992 33722992 -
Trre Trre7g01889 Chr7 14755339 14758040 +
Vivi Vivi5g03853 Chr5 133302386 133305660 -
Vvi Vvi1g0466 Chr1 4359718 4362886 +
Acco Acco11g0215 Chr11 2800447 2802576 -
Acco Acco05g1428 Chr05 29994000 29995775 -
Accr Accr9g01976 Chr9 43120174 43122124 +
Accr Accr3g01545 Chr3 18398834 18400482 +
Adu Adu07g00954 Chr07 13049852 13053019 +
Aev Aev03g0757 Chr03 5851175 5855563 -
Ahy Ahy13g3480 Chr13 132691827 132694360 +
Aip Aip03g03933 Chr03 122312076 122314489 +
Alju Alju09g0269 Chr09 3639886 3641923 -
Alju Alju07g1393 Chr07 39289420 39291033 -
Amo Amo13g4168 Chr13 135256320 135258952 -
Apr Apr7g1335 Chr7 20437039 20440911 -
Apr Apr3g1622 Chr3 31650395 31652722 -
Arst Arst7g01303 Chr7 13207528 13210761 +
Bach Bach3g01115 Chr3 21410650 21411609 -
Bisa Bisa11g0542 Chr11 14807790 14809903 -
Bisa Bisa05g1510 Chr05 27460910 27463093 -
Bva Bva01g01610 Chr01 17402580 17404264 -
Bva Bva11g00647 Chr11 9755774 9757676 -
Car Car06g00063 Chr06 817358 820796 -
Dere Dere09g2148 Chr09 30583397 30586346 +
Dere Dere05g1030 Chr05 16598442 16599779 +
Dod Dod04g0251 Chr04 3067232 3070530 -
Enph Enph13g0605 Chr13 12349611 12352892 +
Enph Enph7g0372 Chr7 9947723 9949654 -
Glsi Glsi05g0280 Chr05 49584349 49586163 -
Glsi Glsi10g1694 Chr10 11451002 11452291 +
Gma Gma18g00363 Chr18 3162167 3165322 +
Lal Lal6g1031 Chr6 7434220 7436814 +
Lal Lal16g0756 Chr16 4878309 4880091 +
Lal Lal15g0721 Chr15 5039617 5042317 +
Lasa Lasa7g02983 Chr7 564671695 564673129 -
Lasa Lasa2g01555 Chr2 465654358 465655651 -
Lele Lele49g1213 Chr49 8111548 8113253 -
Lele Lele51g1232 Chr51 8137345 8137953 -
Lele Lele52g1579 Chr52 19666558 19668171 +
Lele Lele25g1265 Chr25 8514876 8516451 +
Lele Lele26g1278 Chr26 8432210 8433907 +
Lele Lele27g0818 Chr27 16226922 16228502 -
Lele Lele28g1270 Chr28 8478871 8480400 +
Lja Lja2g3219 Chr2 69865664 69870687 +
Mal Mal1g5038 Chr1 121221194 121224565 -
Mepo Mepo2g03066 Chr2 40327635 40329432 -
Mepo Mepo7g02137 Chr7 31844455 31847728 -
Mesa Mesa17g03513 Chr17 61837229 61840053 -
Mibi Mibi12g0216 Chr12 4339000 4340714 -
Mibi Mibi08g1196 Chr08 27267833 27270012 -
Mtr Mtr1g0937 Chr1 10819134 10821936 +
Phac Phac8g03100 Chr8 39738815 39741545 +
Phco Phco4g01790 Chr4 33609704 33611326 +
Phco Phco3g00609 Chr3 4892580 4894455 -
Prci Prci10g2781 Chr10 36244528 36246748 +
Prci Prci2g1997 Chr2 15071133 15073020 +
Psa Psa6g0985 Chr6 37958106 37959631 +
Pste Pste3g04137 Chr3 36854264 36856384 -
Pste Pste8g01432 Chr8 7826532 7829775 +
Pte Pte14g00413 Chr14 21953730 21956328 +
Pumo Pumo9g02443 Chr9 58740517 58743703 +
Pvu Pvu2g0956 Chr2 16605926 16608010 +
Pvu Pvu8g2420 Chr8 54819037 54821397 +
Rops Rops9g00968 Chr9 15820027 15822198 +
Seca Seca6g02304 Chr6 84514297 84514971 +
Spst Spst3g02240 Chr3 64809111 64810567 +
Spst Spst1g02235 Chr1 30820974 30823888 +
Sto Sto11g0592 Chr11 7059237 7061521 -
Sto Sto6g2660 Chr6 33709317 33710327 -
Tpr Tpr1g3027 Chr1 34670544 34673592 -
Trre Trre7g01891 Chr7 14771183 14772641 +
Trre Trre9g04193 Chr9 49686642 49689410 -
Tsu Tsu01g01062 Chr01 9778031 9781383 +
Vian Vian7g01672 Chr7 26192092 26193889 +
Vifa Vifa1g01802 Chr1 292774588 292775706 -
Vimu Vimu7g00080 Chr7 1022134 1026471 -
Vimu Vimu1g01067 Chr1 7933987 7935882 +
Viun Viun8g02179 Chr8 32018881 32021135 -
Vivi Vivi5g03851 Chr5 133267167 133269157 -
Vivi Vivi7g01903 Chr7 78895563 78897488 -
Vvi Vvi1g0467 Chr1 4368625 4384287 -
Apr Apr3g1621 Chr3 31639355 31647381 +
Bva Bva01g01609 Chr01 17393765 17402249 +
Bva Bva11g00646 Chr11 9746832 9754632 +
Car Car06g01765 Chr06 17470055 17479005 -
Lal Lal23g0870 Chr23 11037067 11045270 +
Lal Lal15g0722 Chr15 5046136 5054403 -
Lasa Lasa7g02982 Chr7 564545317 564558610 +
Mepo Mepo2g03065 Chr2 40315200 40322263 +
Phac Phac2g01467 Chr2 13046240 13054242 -
Phco Phco4g01791 Chr4 33641776 33649480 -
Psa Psa7g2947 Chr7 211150334 211158187 -
Pste Pste3g04136 Chr3 36839336 36847166 +
Pte Pte14g00414 Chr14 21960029 22010899 -
Pvu Pvu2g0957 Chr2 16623066 16630933 -
Spst Spst3g02241 Chr3 64813984 64820752 -
Sto Sto11g0591 Chr11 7047774 7054541 +
Trre Trre7g01894 Chr7 14806087 14813040 -
Vimu Vimu11g02587 Chr11 45975847 45982589 -
Vivi Vivi5g03850 Chr5 133228191 133235492 +
Vvi Vvi1g0468 Chr1 4389565 4394725 -
Apr Apr7g1334 Chr7 20429740 20435575 +
Bva Bva01g01608 Chr01 17374852 17382822 +
Bva Bva11g00644 Chr11 9734090 9736167 +
Car Car04g02893 Chr04 55932853 55940124 +
Lal Lal22g0926 Chr22 7342889 7351629 -
Lja Lja2g3220 Chr2 69871368 69894946 -
Mal Mal1g5037 Chr1 121212956 121219513 +
Mtr Mtr1g0938 Chr1 10822368 10828063 -
Psa Psa6g0986 Chr6 37959899 37962700 -
Sto Sto6g2659 Chr6 33695379 33701127 +
Tpr Tpr1g3026 Chr1 34660203 34670037 +
Tsu Tsu01g01063 Chr01 9781413 9786841 -
Vvi Vvi1g0469 Chr1 4401593 4401895 +
Vvi Vvi1g0470 Chr1 4423908 4425008 -
Apr Apr7g1333 Chr7 20422612 20423892 +
Bva Bva01g01607 Chr01 17357712 17358907 +
Bva Bva11g00642 Chr11 9721367 9722479 +
Car Car04g02892 Chr04 55908770 55910303 +
Lal Lal6g1032 Chr6 7448757 7449884 -
Lja Lja2g3221 Chr2 69950941 69952594 +
Mal Mal1g5036 Chr1 121199007 121200110 +
Mtr Mtr1g0939 Chr1 10832019 10833502 -
Psa Psa6g0987 Chr6 38017563 38019984 +
Tpr Tpr1g3025 Chr1 34652337 34653724 +
Car Car06g01762 Chr06 17447753 17451760 +
Acco Acco05g1428 Chr05 29994000 29995775 -
Acco Acco05g1428 Chr05 29994000 29995775 -
Accr Accr3g01545 Chr3 18398834 18400482 +
Accr Accr3g01545 Chr3 18398834 18400482 +
Adu Adu07g00954 Chr07 13049852 13053019 +
Aev Aev03g0757 Chr03 5851175 5855563 -
Ahy Ahy13g3480 Chr13 132691827 132694360 +
Aip Aip03g03933 Chr03 122312076 122314489 +
Alju Alju07g1393 Chr07 39289420 39291033 -
Alju Alju07g1393 Chr07 39289420 39291033 -
Amo Amo13g4168 Chr13 135256320 135258952 -
Arst Arst7g01303 Chr7 13207528 13210761 +
Bach Bach3g01115 Chr3 21410650 21411609 -
Bisa Bisa05g1510 Chr05 27460910 27463093 -
Bisa Bisa05g1510 Chr05 27460910 27463093 -
Dere Dere05g1030 Chr05 16598442 16599779 +
Dere Dere05g1030 Chr05 16598442 16599779 +
Dod Dod04g0251 Chr04 3067232 3070530 -
Enph Enph7g0372 Chr7 9947723 9949654 -
Enph Enph7g0372 Chr7 9947723 9949654 -
Glsi Glsi10g1694 Chr10 11451002 11452291 +
Glsi Glsi10g1694 Chr10 11451002 11452291 +
Lasa Lasa2g01555 Chr2 465654358 465655651 -
Lele Lele25g1265 Chr25 8514876 8516451 +
Lele Lele26g1278 Chr26 8432210 8433907 +
Lele Lele27g0818 Chr27 16226922 16228502 -
Lele Lele28g1270 Chr28 8478871 8480400 +
Lele Lele25g1265 Chr25 8514876 8516451 +
Lele Lele26g1278 Chr26 8432210 8433907 +
Lele Lele27g0818 Chr27 16226922 16228502 -
Lele Lele28g1270 Chr28 8478871 8480400 +
Mepo Mepo7g02137 Chr7 31844455 31847728 -
Mesa Mesa17g03513 Chr17 61837229 61840053 -
Mibi Mibi08g1196 Chr08 27267833 27270012 -
Mibi Mibi08g1196 Chr08 27267833 27270012 -
Phac Phac8g03100 Chr8 39738815 39741545 +
Phco Phco3g00609 Chr3 4892580 4894455 -
Prci Prci2g1997 Chr2 15071133 15073020 +
Prci Prci2g1997 Chr2 15071133 15073020 +
Pste Pste8g01432 Chr8 7826532 7829775 +
Pumo Pumo9g02443 Chr9 58740517 58743703 +
Pvu Pvu8g2420 Chr8 54819037 54821397 +
Rops Rops9g00968 Chr9 15820027 15822198 +
Seca Seca6g02304 Chr6 84514297 84514971 +
Spst Spst1g02235 Chr1 30820974 30823888 +
Trre Trre9g04193 Chr9 49686642 49689410 -
Vian Vian7g01672 Chr7 26192092 26193889 +
Vifa Vifa1g01802 Chr1 292774588 292775706 -
Vimu Vimu1g01067 Chr1 7933987 7935882 +
Viun Viun8g02179 Chr8 32018881 32021135 -
Vivi Vivi7g01903 Chr7 78895563 78897488 -
Aev Aev03g0760 Chr03 5879110 5881336 -
Ahy Ahy13g3479 Chr13 132665174 132666040 +
Aip Aip03g03931 Chr03 122285909 122286784 +
Amo Amo13g4171 Chr13 135284863 135285590 -
Dod Dod04g0252 Chr04 3086092 3087837 -