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
Vvi16g0919 . . . . Adu05g03386 . Aed1g2271 . Aev05g2908 Aev09g2222 . Ahy19g3561 Aip05g03862 Aip09g04019 . . . Amo19g4436 . Apr6g0697 Arst5g04302 . Bach1g01169 . . . Bva03g01388 Bva04g01158 . . Cca02g02249 Cca08g00669 . . Dod02g3029 Dod06g0794 . . . . Gma10g02226 . . . Gso10g2096 . . . . Lal2g0922 . Lal24g0045 . . . . . . . . . Lapu7g02039 . . . . . . . . . . Lja2g2620 Lja5g0635 Mal1g2061 . . Mepo4g04234 . . . . Mtr1g3747 Mtr6g1459 . . Phco5g00701 Phco6g02471 . . . . Pste9g01172 Pste4g02951 . . . . . Pumo3g00956 Pvu4g1213 Pvu7g0730 Rops5g00891 Rops6g02728 . . Spst4g03198 Spst10g00960 Ssu7g0791 . . . Tpr1g0755 Tpr2g4411 . . . . Vian8g01066 Vian3g00638 . Vifa3g02910 Vimu8g02108 Vimu3g03038 Viun4g02164 Viun7g03250 . . Vra8g2228 .
Vvi16g0920 Acco01g0273 . Accr1g00084 . Adu05g03390 Adu09g02362 Aed1g2272 Aed7g0590 Aev05g2907 . . . Aip05g03864 Aip05g01430 Alju02g3621 . . . . Apr6g0696 Arst5g04305 Arst9g03116 Bach1g01168 . Bisa01g0759 . . . . . Cca02g02248 Cca08g00670 Dere06g1348 . Dod02g3028 . Enph12g0901 . Glsi01g1529 . Gma10g02225 . . . Gso10g2095 . . . . . Lal9g0813 . . Lal13g0041 . . . . . . Lapu4g00599 Lapu7g02037 . Lasa6g04084 Lele45g0182 Lele46g0201 . Lele48g1263 . . . . . Lja5g0636 Mal1g2062 . . Mepo4g04233 . Mesa1g04639 Mibi01g3372 . Mtr1g3746 Mtr6g1460 . Phac7g01081 Phco5g00702 Phco6g02470 Prci14g2131 . . . Pste9g01171 Pste4g02947 Pte16g00278 . Pte16g00278 . Pumo6g02571 . Pvu4g1212 Pvu7g0731 Rops5g00895 Rops6g02727 Seca10g03961 Seca10g03962 Spst4g03199 Spst10g00959 Ssu7g0792 . Sto10g2468 . Tpr1g0756 Tpr2g4409 . Trre1g05387 Tsu01g04408 . Vian8g01065 Vian3g00639 Vifa1g04359 . Vimu8g02109 Vimu3g03035 Viun4g02162 Viun7g03249 Vivi2g05436 Vivi1g04391 Vra8g2227 Vra1g1834
Vvi16g0921 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco5g00928 . . . . . Pste9g01029 . . . . . . . Pvu4g1027 . . . . . Spst4g03353 . . . . . . . . . . . . . . . Vimu8g02570 . . . . . . .
Vvi16g0922 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0923 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva03g01387 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja2g2623 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0924 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0925 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0926 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco5g00936 . . . . . . . . . . . . . Pvu4g1022 . . . . . Spst4g03357 . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0927 . . . . . Adu09g02361 Aed1g2274 . . . . . . . . . . . . . . Arst9g03115 . . . . Bva03g01386 Bva04g01159 . . Cca02g02246 . . . . . . . . . Gma10g02224 . . . Gso10g2094 . . . . . . . Lal12g0053 . . . . . . . . Lapu7g02036 . Lasa6g04083 . . . . . . . . . Lja5g0637 . . . Mepo4g04232 . Mesa1g04638 . . Mtr1g3745 . . . . Phco6g02469 . . . . . Pste4g02943 . . . Pte9g00345 . Pumo3g00957 . Pvu7g0732 . Rops6g02726 . Seca8g07379 . Spst10g00957 Ssu7g0793 . . . Tpr1g0757 . . Trre1g05385 Tsu01g04407 . . . . . . Vimu3g03034 . . . Vivi1g04393 . .
Vvi16g0928 . . . . . Adu09g02359 Aed1g2275 Aed11g1721 . Aev09g2218 . Ahy19g3566 . Aip09g04023 . . . Amo19g4433 . . . Arst9g03114 . . . . Bva03g01384 Bva04g01162 . . Cca02g02244 Cca06g01800 . . . Dod06g0799 . . . . Gma10g02223 . . . Gso10g2093 . . . . . . . . Lal13g0043 . . . . . . . Lapu7g02035 . Lasa6g04082 . . . . . . . . . Lja5g0639 Mal1g2064 . . Mepo4g04231 . Mesa1g04635 . . Mtr1g3743 . . . . Phco6g02467 . . . . . Pste4g02937 . . Pte16g00279 . . . . Pvu7g0733 . Rops6g02725 . Seca8g07376 . Spst10g00955 Ssu7g0794 Ssu2g2869 Sto10g2449 . Tpr1g0759 . . Trre1g05382 Tsu01g04405 . . Vian3g00641 . . . Vimu3g03032 . Viun7g03246 . Vivi1g04394 Vra8g2225 Vra11g0276
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Aed Aed11g1721 Chr11 20822148 20827496 +
Cca Cca06g01800 Chr06 33381384 33395410 +
Ssu Ssu2g2869 Chr2 89864008 89870655 +
Vra Vra11g0276 Chr11 1938704 1942492 -
Vvi Vvi16g0919 Chr16 17352540 17355619 +
Adu Adu05g03386 Chr05 106294847 106301097 +
Aed Aed1g2271 Chr1 18841752 18843757 +
Aev Aev05g2908 Chr05 29885007 29890443 -
Aev Aev09g2222 Chr09 24927999 24930086 -
Ahy Ahy19g3561 Chr19 158254061 158256921 +
Aip Aip05g03862 Chr05 146835299 146841568 +
Aip Aip09g04019 Chr09 146531521 146534320 +
Amo Amo19g4436 Chr19 161405745 161407765 -
Apr Apr6g0697 Chr6 10650929 10654990 -
Arst Arst5g04302 Chr5 104970589 104976839 +
Bach Bach1g01169 Chr1 24908642 24911539 -
Bva Bva03g01388 Chr03 13305071 13307686 -
Bva Bva04g01158 Chr04 7830399 7832327 +
Cca Cca02g02249 Chr02 43042876 43046319 -
Cca Cca08g00669 Chr08 12401786 12404619 +
Dod Dod02g3029 Chr02 63903556 63907811 -
Dod Dod06g0794 Chr06 9691642 9696745 +
Gma Gma10g02226 Chr10 49825316 49828691 -
Gso Gso10g2096 Chr10 47939193 47942789 -
Lal Lal2g0922 Chr2 6178373 6181967 -
Lal Lal24g0045 Chr24 295653 298120 +
Lapu Lapu7g02039 Chr7 36619899 36621990 -
Lja Lja2g2620 Chr2 35961934 35968371 +
Lja Lja5g0635 Chr5 5673536 5676464 +
Mal Mal1g2061 Chr1 27082243 27085341 +
Mepo Mepo4g04234 Chr4 52173768 52176673 -
Mtr Mtr1g3747 Chr1 49055276 49058436 -
Mtr Mtr6g1459 Chr6 23889646 23893850 +
Phco Phco5g00701 Chr5 7507725 7511335 +
Phco Phco6g02471 Chr6 46123951 46126450 -
Pste Pste9g01172 Chr9 9398471 9402000 -
Pste Pste4g02951 Chr4 20956560 20959722 -
Pumo Pumo3g00956 Chr3 14651950 14686069 +
Pvu Pvu4g1213 Chr4 37500922 37504514 -
Pvu Pvu7g0730 Chr7 6492628 6495088 +
Rops Rops5g00891 Chr5 17272550 17277698 +
Rops Rops6g02728 Chr6 49030835 49036327 -
Spst Spst4g03198 Chr4 71634862 71638432 +
Spst Spst10g00960 Chr10 10332389 10335117 -
Ssu Ssu7g0791 Chr7 15870917 15902517 +
Tpr Tpr1g0755 Chr1 6377312 6380795 +
Tpr Tpr2g4411 Chr2 48174856 48181860 -
Vian Vian8g01066 Chr8 28104710 28108101 -
Vian Vian3g00638 Chr3 6453346 6455727 +
Vifa Vifa3g02910 Chr3 818093245 818095282 -
Vimu Vimu8g02108 Chr8 27310695 27313648 +
Vimu Vimu3g03038 Chr3 44252896 44255230 -
Viun Viun4g02164 Chr4 37144357 37147876 -
Viun Viun7g03250 Chr7 34739252 34741755 -
Vra Vra8g2228 Chr8 40587355 40589726 -
Vvi Vvi16g0920 Chr16 17357904 17397226 -
Acco Acco01g0273 Chr01 3017291 3044227 +
Accr Accr1g00084 Chr1 1719522 1732948 +
Adu Adu05g03390 Chr05 106311748 106326100 -
Adu Adu09g02362 Chr09 110820667 110833398 +
Aed Aed1g2272 Chr1 18854812 18881651 -
Aed Aed7g0590 Chr7 4333338 4353233 -
Aev Aev05g2907 Chr05 29868863 29880861 +
Aip Aip05g03864 Chr05 146851371 146865832 -
Aip Aip05g01430 Chr05 22054310 22059724 +
Alju Alju02g3621 Chr02 54997354 55021628 -
Apr Apr6g0696 Chr6 10598203 10632095 +
Arst Arst5g04305 Chr5 104987518 105001816 -
Arst Arst9g03116 Chr9 108717884 108730459 +
Bach Bach1g01168 Chr1 24877337 24897407 +
Bisa Bisa01g0759 Chr01 11942856 11973224 -
Cca Cca02g02248 Chr02 43010086 43029780 +
Cca Cca08g00670 Chr08 12430864 12452072 -
Dere Dere06g1348 Chr06 25883825 25911804 +
Dod Dod02g3028 Chr02 63883532 63901403 +
Enph Enph12g0901 Chr12 15655877 15683441 +
Glsi Glsi01g1529 Chr01 75622985 75647731 +
Gma Gma10g02225 Chr10 49799790 49819502 +
Gso Gso10g2095 Chr10 47913312 47933399 +
Lal Lal9g0813 Chr9 5866463 5884996 -
Lal Lal13g0041 Chr13 271258 294796 -
Lapu Lapu4g00599 Chr4 6367994 6393809 -
Lapu Lapu7g02037 Chr7 36572432 36594806 +
Lasa Lasa6g04084 Chr6 616736508 616760498 +
Lele Lele45g0182 Chr45 1501007 1521811 +
Lele Lele46g0201 Chr46 1214238 1232221 +
Lele Lele48g1263 Chr48 16999107 17015665 -
Lja Lja5g0636 Chr5 5678465 5696903 -
Mal Mal1g2062 Chr1 27086209 27101372 -
Mepo Mepo4g04233 Chr4 52153105 52173365 +
Mesa Mesa1g04639 Chr1 72277555 72293268 +
Mibi Mibi01g3372 Chr01 59119417 59141938 -
Mtr Mtr1g3746 Chr1 49038424 49055225 +
Mtr Mtr6g1460 Chr6 23908209 23934306 -
Phac Phac7g01081 Chr7 6819819 6847795 -
Phco Phco5g00702 Chr5 7556172 7577794 -
Phco Phco6g02470 Chr6 46089040 46112648 +
Prci Prci14g2131 Chr14 28627948 28659676 -
Pste Pste9g01171 Chr9 9356271 9378030 +
Pste Pste4g02947 Chr4 20902770 20932391 +
Pte Pte16g00278 Chr16 3690012 3710402 -
Pte Pte16g00278 Chr16 3690012 3710402 -
Pumo Pumo6g02571 Chr6 60162428 60181396 +
Pvu Pvu4g1212 Chr4 37441356 37461707 +
Pvu Pvu7g0731 Chr7 6507524 6528807 -
Rops Rops5g00895 Chr5 17350631 17394102 -
Rops Rops6g02727 Chr6 48987932 49013593 +
Seca Seca10g03961 Chr10 84548018 84563106 +
Seca Seca10g03962 Chr10 84569971 84577719 +
Spst Spst4g03199 Chr4 71649745 71668461 -
Spst Spst10g00959 Chr10 10321841 10330690 +
Ssu Ssu7g0792 Chr7 15930385 15963004 -
Sto Sto10g2468 Chr10 34942080 34964384 +
Tpr Tpr1g0756 Chr1 6380890 6399087 -
Tpr Tpr2g4409 Chr2 48121062 48140699 +
Trre Trre1g05387 Chr1 59554027 59572119 +
Tsu Tsu01g04408 Chr01 51876542 51893288 +
Vian Vian8g01065 Chr8 28061759 28081722 +
Vian Vian3g00639 Chr3 6466085 6486047 -
Vifa Vifa1g04359 Chr1 677076378 677103103 -
Vimu Vimu8g02109 Chr8 27346748 27369112 -
Vimu Vimu3g03035 Chr3 44226976 44246508 +
Viun Viun4g02162 Chr4 37099882 37119293 +
Viun Viun7g03249 Chr7 34708882 34729077 +
Vivi Vivi2g05436 Chr2 179366542 179396251 +
Vivi Vivi1g04391 Chr1 93736807 93760942 -
Vra Vra8g2227 Chr8 40554721 40581141 +
Vra Vra1g1834 Chr1 34973408 34996097 +
Vvi Vvi16g0921 Chr16 17423020 17425185 -
Phco Phco5g00928 Chr5 13828275 13829768 -
Pste Pste9g01029 Chr9 7015127 7024851 +
Pvu Pvu4g1027 Chr4 27358643 27363188 +
Spst Spst4g03353 Chr4 73519966 73523358 -
Vimu Vimu8g02570 Chr8 34904897 34907018 -
Vvi Vvi16g0922 Chr16 17429551 17447121 -
Vvi Vvi16g0923 Chr16 17447965 17448333 -
Bva Bva03g01387 Chr03 13275851 13299041 +
Lja Lja2g2623 Chr2 35996861 36017662 -
Vvi Vvi16g0924 Chr16 17450061 17455539 -
Vvi Vvi16g0925 Chr16 17463449 17469612 -
Vvi Vvi16g0926 Chr16 17491816 17493993 -
Phco Phco5g00936 Chr5 14075111 14077888 +
Pvu Pvu4g1022 Chr4 27028009 27029889 +
Spst Spst4g03357 Chr4 73563347 73565221 +
Vvi Vvi16g0927 Chr16 17513133 17521083 -
Adu Adu09g02361 Chr09 110812804 110820136 +
Aed Aed1g2274 Chr1 18905212 18907813 -
Arst Arst9g03115 Chr9 108709963 108717177 +
Bva Bva03g01386 Chr03 13265975 13273458 +
Bva Bva04g01159 Chr04 7837322 7845879 -
Cca Cca02g02246 Chr02 42978185 42990435 +
Gma Gma10g02224 Chr10 49788474 49797201 +
Gso Gso10g2094 Chr10 47902528 47911365 +
Lal Lal12g0053 Chr12 355932 362509 -
Lapu Lapu7g02036 Chr7 36557494 36569007 +
Lasa Lasa6g04083 Chr6 616441625 616447771 +
Lja Lja5g0637 Chr5 5709594 5717402 -
Mepo Mepo4g04232 Chr4 52141210 52151254 +
Mesa Mesa1g04638 Chr1 72245772 72257764 +
Mtr Mtr1g3745 Chr1 49026118 49036380 +
Phco Phco6g02469 Chr6 46075488 46086850 +
Pste Pste4g02943 Chr4 20858588 20875822 +
Pte Pte9g00345 Chr9 4105282 4113028 -
Pumo Pumo3g00957 Chr3 14696025 14731060 -
Pvu Pvu7g0732 Chr7 6535971 6547869 -
Rops Rops6g02726 Chr6 48976086 48987437 +
Seca Seca8g07379 Chr8 170616637 170643077 +
Spst Spst10g00957 Chr10 10287430 10299676 +
Ssu Ssu7g0793 Chr7 15969661 15982620 -
Tpr Tpr1g0757 Chr1 6401391 6405620 -
Trre Trre1g05385 Chr1 59548120 59552576 +
Tsu Tsu01g04407 Chr01 51873171 51875787 +
Vimu Vimu3g03034 Chr3 44212874 44224026 +
Vivi Vivi1g04393 Chr1 93863173 93869478 +
Vvi Vvi16g0928 Chr16 17535854 17540133 +
Adu Adu09g02359 Chr09 110789522 110791814 -
Aed Aed1g2275 Chr1 18911106 18914042 +
Aed Aed11g1721 Chr11 20822148 20827496 +
Aev Aev09g2218 Chr09 24884776 24886778 -
Ahy Ahy19g3566 Chr19 158327528 158330712 +
Aip Aip09g04023 Chr09 146584948 146587217 +
Amo Amo19g4433 Chr19 161365171 161368338 -
Arst Arst9g03114 Chr9 108686504 108689725 -
Bva Bva03g01384 Chr03 13257695 13262022 -
Bva Bva04g01162 Chr04 7852857 7857048 +
Cca Cca02g02244 Chr02 42969977 42972593 -
Cca Cca06g01800 Chr06 33381384 33395410 +
Dod Dod06g0799 Chr06 9787184 9789729 +
Gma Gma10g02223 Chr10 49772857 49776986 -
Gso Gso10g2093 Chr10 47887345 47891529 -
Lal Lal13g0043 Chr13 296002 299053 +
Lapu Lapu7g02035 Chr7 36549135 36553684 -
Lasa Lasa6g04082 Chr6 616163663 616166537 -
Lja Lja5g0639 Chr5 5757152 5761302 +
Mal Mal1g2064 Chr1 27129785 27132707 +
Mepo Mepo4g04231 Chr4 52128363 52133102 -
Mesa Mesa1g04635 Chr1 72217482 72221054 -
Mtr Mtr1g3743 Chr1 48997841 49002793 -
Phco Phco6g02467 Chr6 46063028 46066242 -
Pste Pste4g02937 Chr4 20792664 20797124 -
Pte Pte16g00279 Chr16 3748581 3751271 +
Pvu Pvu7g0733 Chr7 6554185 6558265 +
Rops Rops6g02725 Chr6 48945355 48950775 -
Seca Seca8g07376 Chr8 170586275 170591087 -
Spst Spst10g00955 Chr10 10277537 10280164 -
Ssu Ssu7g0794 Chr7 16014858 16018138 +
Ssu Ssu2g2869 Chr2 89864008 89870655 +
Sto Sto10g2449 Chr10 34748492 34753745 -
Tpr Tpr1g0759 Chr1 6419710 6423915 +
Trre Trre1g05382 Chr1 59522016 59524991 -
Tsu Tsu01g04405 Chr01 51850319 51855113 -
Vian Vian3g00641 Chr3 6519429 6532981 +
Vimu Vimu3g03032 Chr3 44194326 44197504 -
Viun Viun7g03246 Chr7 34680749 34684833 -
Vivi Vivi1g04394 Chr1 93904099 93909021 +
Vra Vra8g2225 Chr8 40533234 40537389 -
Vra Vra11g0276 Chr11 1938704 1942492 -