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
Vvi4g1234 . . . . . . Aed11g1249 . . Aev08g0244 . Ahy17g2336 . Aip07g02499 . . . . . . . Arst5g01093 . . . . . . . . Cca06g01301 . . . . Dod08g2226 . . . . . . . . . . . . Lal16g1841 . . . . . Lan6g1476 . . . . . . . . . . . . . . . . . . Lja4g3179 . Mal5g3371 . Mepo5g00940 . . . . . Mtr8g2444 . . . . . . . . . . . . . . . . . Pvu2g1721 . . . . . Spst2g00869 . . . Sto11g1516 . Tpr4g4231 . . . Tsu04g03470 . . . . . Vimu7g03011 . . . . Vra11g0740 .
Vvi4g1235 . . . . . . . . . Aev08g0243 . Ahy17g2335 . Aip07g02498 . . . Amo17g2209 . Apr7g1064 . Arst5g01092 . . . . . . . . . . . . . Dod08g2227 . . . . Gma11g00664 Gma01g01738 . . Gso11g0616 Gso11g0616 . . . . Lal23g1441 . . . . . . . . . . . . Lasa2g03363 . . . . . . . . . . Mal6g1079 . . Mepo5g00939 . Mesa17g00983 . . Mtr5g0831 . . Phac2g02609 . Phco4g00914 . . . . . Pste1g02926 . . . . . . . Pvu2g1719 . . . . . Spst2g00868 . . . . Tpr2g1045 . . Trre9g01110 . . . . . . . Vimu7g03010 . . . Vivi2g02972 . .
Vvi4g1236 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1237 . . . . . Adu05g00869 . . Aev05g0465 . Ahy15g0844 . Aip05g00863 . . . . . . . . Arst5g01091 . Bach4g00690 . . Bva08g00799 . . . . . . . Dod02g0514 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lasa2g03362 . . . . . . . . Lja2g0508 . . . . Mepo5g00938 . . . . . . . Phac2g02608 . Phco4g00915 . . Psa2g3564 . . Pste1g02925 . . . . . . . Pvu2g1718 . . . . . Spst2g00867 . . Sto6g3881 . . . . Trre9g01109 . . . Vian10g00745 . Vifa1g06700 . Vimu7g03009 . . . Vivi2g02974 . .
Vvi4g1238 . . . . . Adu03g04560 . . . Aev08g0235 . Ahy17g2330 . Aip07g02491 . . . Amo17g2199 . . . Arst5g01089 . Bach4g00689 . Bisa07g0072 . . . . . . . Dere02g3056 . Dod08g2230 . . . Glsi11g2989 . . . . . . . . . . . . . . . . . . . . . . . Lasa2g03361 . . . . . Lele14g0322 Lele15g2091 . . . . . . Mepo2g03891 . Mesa13g01251 . . . . . . . Phco4g00916 . Prci3g0208 . . . Pste1g02923 . . . . . . . Pvu2g1717 . . . . . . . . . . . . . Trre7g04554 . . . . . . . Vimu7g03008 . . . . . .
Vvi4g1239 . . . . Adu01g00102 . . . . . . . . . . . . . Apr3g0314 . Arst1g00163 . Bach10g00578 . . . . . . . . . . . . . . . . . . . Gma02g00473 Gma16g01233 . . . . . . . . . . . . . . . . Lapu3g01744 . Lasa4g02289 . . . . . . . . . . . . . Mepo1g02097 . . . . . . . Phac3g04051 . Phco8g00444 . . . . Psa4g2255 Pste7g01579 . . Pte12g00484 . . . . Pvu3g2658 . . . Seca12g02818 . Spst3g03839 . . . . . . . Trre15g02738 . . . . . Vifa4g02382 . Vimu11g00688 . Viun3g03626 . . . . .
Vvi4g1240 . . . . . Adu05g00867 . . . . . . . . . . . . . . . Arst5g01086 . Bach4g00687 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lasa2g03360 . . . . . . . . . . . . . Mepo5g00936 . Mesa17g00980 . . . . . Phac2g02605 . Phco4g00917 . . . . . Pste1g02919 . . . . . Pumo8g01779 . Pvu2g1716 . Rops1g01603 . Seca10g00928 . Spst2g00866 . . . . . . . Trre9g01104 . . . Vian10g00743 . Vifa1g06704 . Vimu7g03006 . Viun2g01913 . Vivi2g02977 . .
Vvi4g1241 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1242 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1243 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi4g1234 Chr4 19231762 19237649 +
Aed Aed11g1249 Chr11 17666233 17672226 +
Aev Aev08g0244 Chr08 1372194 1376359 -
Ahy Ahy17g2336 Chr17 112807539 112812409 -
Aip Aip07g02499 Chr07 104743558 104748066 -
Arst Arst5g01093 Chr5 10854252 10859922 -
Cca Cca06g01301 Chr06 27750691 27756572 +
Dod Dod08g2226 Chr08 49980878 49987071 +
Lal Lal16g1841 Chr16 17484882 17493581 +
Lan Lan6g1476 Chr6 21607502 21614477 -
Lja Lja4g3179 Chr4 60124214 60130088 +
Mal Mal5g3371 Chr5 97607302 97612548 +
Mepo Mepo5g00940 Chr5 9111255 9114225 -
Mtr Mtr8g2444 Chr8 34897789 34903543 +
Pvu Pvu2g1721 Chr2 30942687 30945153 -
Spst Spst2g00869 Chr2 7337498 7342444 -
Sto Sto11g1516 Chr11 14359397 14363823 +
Tpr Tpr4g4231 Chr4 49438536 49445046 -
Tsu Tsu04g03470 Chr04 43843037 43849073 -
Vimu Vimu7g03011 Chr7 25371494 25376534 -
Vra Vra11g0740 Chr11 5972842 5978516 -
Vvi Vvi4g1235 Chr4 19239087 19241394 -
Aev Aev08g0243 Chr08 1371066 1371638 +
Ahy Ahy17g2335 Chr17 112805895 112806683 +
Aip Aip07g02498 Chr07 104742209 104743144 +
Amo Amo17g2209 Chr17 113227526 113228609 +
Apr Apr7g1064 Chr7 17594861 17596721 +
Arst Arst5g01092 Chr5 10851961 10853967 +
Dod Dod08g2227 Chr08 49987210 49989084 -
Gma Gma11g00664 Chr11 5532898 5535439 +
Gma Gma01g01738 Chr01 53063622 53066894 -
Gso Gso11g0616 Chr11 5488624 5491117 +
Gso Gso11g0616 Chr11 5488624 5491117 +
Lal Lal23g1441 Chr23 14816786 14819481 +
Lasa Lasa2g03363 Chr2 531996465 531998102 +
Mal Mal6g1079 Chr6 16460575 16463111 -
Mepo Mepo5g00939 Chr5 9108356 9110586 +
Mesa Mesa17g00983 Chr17 12426138 12432305 +
Mtr Mtr5g0831 Chr5 8153883 8156495 +
Phac Phac2g02609 Chr2 27293037 27295590 +
Phco Phco4g00914 Chr4 7249798 7251979 -
Pste Pste1g02926 Chr1 12642916 12647209 +
Pvu Pvu2g1719 Chr2 30934887 30937288 +
Spst Spst2g00868 Chr2 7332112 7333542 +
Tpr Tpr2g1045 Chr2 12297482 12300811 +
Trre Trre9g01110 Chr9 8911832 8913835 +
Vimu Vimu7g03010 Chr7 25367871 25370345 +
Vivi Vivi2g02972 Chr2 128373295 128375356 -
Vvi Vvi4g1236 Chr4 19244850 19249887 -
Vvi Vvi4g1237 Chr4 19254503 19255701 -
Adu Adu05g00869 Chr05 10820310 10829695 +
Aev Aev05g0465 Chr05 3241610 3243414 -
Ahy Ahy15g0844 Chr15 12156127 12158343 +
Aip Aip05g00863 Chr05 11765307 11767492 +
Arst Arst5g01091 Chr5 10847785 10849978 +
Bach Bach4g00690 Chr4 4582081 4584130 +
Bva Bva08g00799 Chr08 4117082 4119553 +
Dod Dod02g0514 Chr02 6711972 6715126 -
Lasa Lasa2g03362 Chr2 531987351 531988860 +
Lja Lja2g0508 Chr2 4597441 4599577 +
Mepo Mepo5g00938 Chr5 9105127 9106549 +
Phac Phac2g02608 Chr2 27289100 27291274 +
Phco Phco4g00915 Chr4 7254764 7257048 -
Psa Psa2g3564 Chr2 388468649 388469740 -
Pste Pste1g02925 Chr1 12636186 12636692 +
Pvu Pvu2g1718 Chr2 30930694 30932542 +
Spst Spst2g00867 Chr2 7328937 7329948 +
Sto Sto6g3881 Chr6 43151005 43152481 +
Trre Trre9g01109 Chr9 8905693 8907517 +
Vian Vian10g00745 Chr10 7281484 7282499 +
Vifa Vifa1g06700 Chr1 1039385159 1039390305 -
Vimu Vimu7g03009 Chr7 25362485 25363496 +
Vivi Vivi2g02974 Chr2 128378371 128380680 -
Vvi Vvi4g1238 Chr4 19266368 19268623 -
Adu Adu03g04560 Chr03 134922596 134930912 -
Aev Aev08g0235 Chr08 1338793 1341097 +
Ahy Ahy17g2330 Chr17 112395814 112398467 +
Aip Aip07g02491 Chr07 104392892 104395211 +
Amo Amo17g2199 Chr17 112878065 112881753 +
Arst Arst5g01089 Chr5 10844439 10846399 +
Bach Bach4g00689 Chr4 4578995 4580866 +
Bisa Bisa07g0072 Chr07 1493065 1497430 +
Dere Dere02g3056 Chr02 36469027 36471516 +
Dod Dod08g2230 Chr08 50022837 50026484 -
Glsi Glsi11g2989 Chr11 24967938 24970534 +
Lasa Lasa2g03361 Chr2 531976548 531978111 +
Lele Lele14g0322 Chr14 14808645 14809232 +
Lele Lele15g2091 Chr15 13613474 13617357 -
Mepo Mepo2g03891 Chr2 48120192 48127110 -
Mesa Mesa13g01251 Chr13 14831683 14836285 +
Phco Phco4g00916 Chr4 7257297 7259709 -
Prci Prci3g0208 Chr3 2822737 2824802 -
Pste Pste1g02923 Chr1 12630499 12632782 +
Pvu Pvu2g1717 Chr2 30927189 30929695 +
Trre Trre7g04554 Chr7 53537450 53540363 -
Vimu Vimu7g03008 Chr7 25359807 25360473 +
Vvi Vvi4g1239 Chr4 19273071 19318911 +
Adu Adu01g00102 Chr01 1448035 1459344 -
Apr Apr3g0314 Chr3 6125849 6174943 -
Arst Arst1g00163 Chr1 1447754 1459446 -
Bach Bach10g00578 Chr10 4108684 4125619 -
Gma Gma02g00473 Chr02 4747595 4766298 +
Gma Gma16g01233 Chr16 30334661 30363193 +
Lapu Lapu3g01744 Chr3 28331879 28374949 -
Lasa Lasa4g02289 Chr4 454136324 454151180 +
Mepo Mepo1g02097 Chr1 21548716 21553207 -
Phac Phac3g04051 Chr3 39967274 39990393 -
Phco Phco8g00444 Chr8 4101528 4130309 +
Psa Psa4g2255 Chr4 183091272 183104507 -
Pste Pste7g01579 Chr7 14524524 14554179 -
Pte Pte12g00484 Chr12 4361128 4368239 -
Pvu Pvu3g2658 Chr3 48615312 48641111 -
Seca Seca12g02818 Chr12 50750570 50750894 -
Spst Spst3g03839 Chr3 88402961 88440074 +
Trre Trre15g02738 Chr15 23240158 23262214 +
Vifa Vifa4g02382 Chr4 718894534 718908075 +
Vimu Vimu11g00688 Chr11 7365610 7368993 -
Viun Viun3g03626 Chr3 43055878 43085032 +
Vvi Vvi4g1240 Chr4 19328329 19343256 +
Adu Adu05g00867 Chr05 10792340 10802068 -
Arst Arst5g01086 Chr5 10816380 10822669 -
Bach Bach4g00687 Chr4 4561218 4567806 -
Lasa Lasa2g03360 Chr2 531962044 531971098 -
Mepo Mepo5g00936 Chr5 9087844 9096110 -
Mesa Mesa17g00980 Chr17 12403423 12410478 -
Phac Phac2g02605 Chr2 27278102 27284742 -
Phco Phco4g00917 Chr4 7261440 7267522 +
Pste Pste1g02919 Chr1 12598740 12605937 -
Pumo Pumo8g01779 Chr8 53878027 53884143 +
Pvu Pvu2g1716 Chr2 30919312 30925884 -
Rops Rops1g01603 Chr1 34202486 34214467 +
Seca Seca10g00928 Chr10 8879741 8887809 -
Spst Spst2g00866 Chr2 7308113 7325829 -
Trre Trre9g01104 Chr9 8870801 8878288 -
Vian Vian10g00743 Chr10 7260990 7274477 -
Vifa Vifa1g06704 Chr1 1039423295 1039437675 +
Vimu Vimu7g03006 Chr7 25348794 25354900 -
Viun Viun2g01913 Chr2 27870048 27876773 +
Vivi Vivi2g02977 Chr2 128393215 128401459 +
Vvi Vvi4g1241 Chr4 19345123 19345407 +
Vvi Vvi4g1242 Chr4 19345474 19346094 +
Vvi Vvi4g1243 Chr4 19351522 19352094 +
Aev Aev08g0244 Chr08 1372194 1376359 -
Ahy Ahy17g2336 Chr17 112807539 112812409 -
Aip Aip07g02499 Chr07 104743558 104748066 -
Dod Dod08g2226 Chr08 49980878 49987071 +
Dod Dod08g2226 Chr08 49980878 49987071 +
Aev Aev08g0243 Chr08 1371066 1371638 +
Ahy Ahy17g2335 Chr17 112805895 112806683 +
Aip Aip07g02498 Chr07 104742209 104743144 +
Amo Amo17g2209 Chr17 113227526 113228609 +
Dod Dod08g2227 Chr08 49987210 49989084 -
Dod Dod08g2227 Chr08 49987210 49989084 -
Aev Aev08g0235 Chr08 1338793 1341097 +
Ahy Ahy17g2330 Chr17 112395814 112398467 +
Aip Aip07g02491 Chr07 104392892 104395211 +
Amo Amo17g2199 Chr17 112878065 112881753 +
Dod Dod08g2230 Chr08 50022837 50026484 -