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
Vvi4g1224 . . . . . . . . . . . . . . . . . . Apr3g0309 . . . Bach10g00572 . . . Bva08g00791 . . . . . . . . . . . . . . . . . . . . . . Lal15g1489 . . . . . . . . . . Lapu3g01724 . Lasa4g02296 . . . . . . . . . . Lja4g3191 . Mal5g3388 Mepo1g02087 . . . . . . Mtr8g2458 Phac3g04036 . Phco8g00452 . . . . Psa4g2243 . . . . . . Pumo4g02160 . Pvu3g2651 . Rops2g03319 . Seca12g02800 . Spst3g03850 . . . Sto6g3869 . . Tpr4g4219 Trre15g02759 . . Tsu04g03453 Vian1g01798 . Vifa4g02395 . Vimu11g00677 . Viun3g03635 . Vivi1g03065 . . .
Vvi4g1225 . . . . . . . . . . . . . . . . . . Apr3g0310 . Arst1g00152 . . . . . . . . . . . . . . . . . . . . . Gma02g00478 Gma16g01239 . . . . Lal16g1844 . . . . . Lan6g1473 . . . . . . . Lasa4g02293 . . . . . . . . . . Lja4g3188 . Mal5g3385 . . Mesa29g02259 . . . . Mtr8g2456 Phac3g04043 . Phco8g00448 . . . . Psa4g2245 Pste7g01567 . . . . . . . Pvu3g2654 . . . . . Spst3g03847 . . . Sto6g3870 . . Tpr4g4221 Trre15g02751 . . . . . . . Vimu11g00681 . . . Vivi1g03073 . . .
Vvi4g1226 . . . . Adu01g00098 . . . . . . . . . . . . . Apr3g0311 . Arst1g00161 . Bach10g00575 . . . . . . . . . . . . . . . . . . . Gma02g00477 Gma16g01238 . . . . Lal16g1843 . . . . . Lan6g1474 . . . . . Lapu3g01739 . . . . . . . . . . . . Lja4g3186 . Mal5g3380 Mepo1g02093 . . . . . . Mtr8g2453 . . Phco8g00447 . . . . . Pste7g01568 . . . . . . . Pvu3g2655 . . . . . Spst3g03846 . . . Sto6g3871 . . Tpr4g4225 Trre15g02750 . . Tsu04g03462 . . . . Vimu11g00682 . . . . . . .
Vvi4g1227 . Acco11g2344 . Accr9g00151 . Adu05g00875 . . . . . . . . . Alju09g2349 . . . . . Arst5g01098 . Bach4g00698 . Bisa11g1750 . . . . . . . Dere09g0992 . . . Enph13g0884 . Glsi05g1382 . . . . . . . . . . . . . . . . . . . . . Lapu2g00728 . Lasa2g03371 . . . . Lele49g0114 Lele50g0128 . Lele52g0133 . . . . . Mepo5g00949 . Mesa17g00989 . Mibi12g2040 . . . . . . . . . . . Pste1g02943 . . . . . . . Pvu2g1160 . . . . . Spst2g00876 . . . . . . . Trre9g01122 . . . . . . . Vimu7g03020 . . . . . .
Vvi4g1228 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1229 . . . . . Adu05g00873 . . . . . . . . . . . . . . . Arst5g01096 . Bach4g00696 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lasa2g03368 . . . . . . . . . . . . . Mepo5g00947 . Mesa17g00987 . . . . . . . Phco4g00910 . . . . . Pste1g02937 . . . . . Pumo8g01771 . Pvu2g1724 . Rops1g01591 . Seca12g02825 . Spst2g00874 . . . . . . . Trre9g01119 . . . Vian10g00750 . Vifa1g06686 . Vimu7g03018 . Viun2g01905 . Vivi2g02968 . .
Vvi4g1230 . . . . . Adu05g00872 . . . . . . . . . . . . . . . Arst5g01095 . Bach4g00695 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lasa2g03367 . . . . . . . . . . . . . Mepo5g00946 . . . . . . . Phac2g02612 . Phco4g00911 . . . . . Pste1g02936 . . . . . Pumo8g01772 . Pvu2g1723 . Rops1g01592 . . . Spst2g00872 . . . . . . . . . . . Vian10g00749 . Vifa1g06692 . Vimu7g03017 . Viun2g01906 . Vivi2g02969 . .
Vvi4g1231 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1232 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1233 . . . . . Adu05g00871 . . . . . . . . . . . . . . . Arst5g01094 . Bach4g00693 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lasa2g03365 . . . . . . . . . . . . . Mepo5g00945 . Mesa17g00985 . . . . . Phac2g02611 . Phco4g00912 . . . . . Pste1g02934 . . . . . Pumo8g01773 . Pvu2g1722 . Rops1g01594 . Seca10g00933 . Spst2g00870 . . . . . . . Trre9g01114 . . . Vian10g00748 . Vifa1g06693 . Vimu7g03012 . Viun2g01907 . Vivi2g02970 . .
   
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Select Species Gene Chromosome Start End Strand
Vvi Vvi4g1224 Chr4 19138680 19139249 +
Apr Apr3g0309 Chr3 5966911 5969386 +
Bach Bach10g00572 Chr10 4066528 4067124 +
Bva Bva08g00791 Chr08 4064279 4066894 +
Lal Lal15g1489 Chr15 17050526 17054085 +
Lapu Lapu3g01724 Chr3 27197355 27202836 +
Lasa Lasa4g02296 Chr4 456307880 456308488 -
Lja Lja4g3191 Chr4 60376833 60378898 -
Mal Mal5g3388 Chr5 97874059 97874658 -
Mepo Mepo1g02087 Chr1 21477224 21481692 +
Mtr Mtr8g2458 Chr8 35031258 35033980 -
Phac Phac3g04036 Chr3 39855590 39859152 +
Phco Phco8g00452 Chr8 4226654 4227247 -
Psa Psa4g2243 Chr4 180266062 180268724 +
Pumo Pumo4g02160 Chr4 31432778 31435266 +
Pvu Pvu3g2651 Chr3 48524901 48528383 +
Rops Rops2g03319 Chr2 60981444 60984517 -
Seca Seca12g02800 Chr12 49564402 49565252 +
Spst Spst3g03850 Chr3 88547785 88548381 -
Sto Sto6g3869 Chr6 43076192 43076788 +
Tpr Tpr4g4219 Chr4 49276693 49278383 +
Trre Trre15g02759 Chr15 23489868 23490479 -
Tsu Tsu04g03453 Chr04 43713061 43715636 +
Vian Vian1g01798 Chr1 21180730 21181323 +
Vifa Vifa4g02395 Chr4 724137484 724138092 -
Vimu Vimu11g00677 Chr11 7215559 7220486 +
Viun Viun3g03635 Chr3 43240425 43243244 -
Vivi Vivi1g03065 Chr1 67621655 67624828 +
Vvi Vvi4g1225 Chr4 19143417 19150047 +
Apr Apr3g0310 Chr3 5978181 6002159 +
Arst Arst1g00152 Chr1 1273075 1280836 -
Gma Gma02g00478 Chr02 4830931 4841354 -
Gma Gma16g01239 Chr16 30476314 30481786 -
Lal Lal16g1844 Chr16 17497834 17503643 -
Lan Lan6g1473 Chr6 21585627 21591920 +
Lasa Lasa4g02293 Chr4 456282406 456288062 -
Lja Lja4g3188 Chr4 60346669 60354657 -
Mal Mal5g3385 Chr5 97836707 97844704 -
Mesa Mesa29g02259 Chr29 31003464 31012512 -
Mtr Mtr8g2456 Chr8 35013529 35021554 -
Phac Phac3g04043 Chr3 39890497 39898599 +
Phco Phco8g00448 Chr8 4200527 4208158 -
Psa Psa4g2245 Chr4 180472415 180478277 +
Pste Pste7g01567 Chr7 14363090 14367625 +
Pvu Pvu3g2654 Chr3 48543992 48552888 +
Spst Spst3g03847 Chr3 88513475 88521702 -
Sto Sto6g3870 Chr6 43079747 43085528 +
Tpr Tpr4g4221 Chr4 49290336 49303102 +
Trre Trre15g02751 Chr15 23434431 23440305 -
Vimu Vimu11g00681 Chr11 7239140 7246290 +
Vivi Vivi1g03073 Chr1 67651923 67658797 +
Vvi Vvi4g1226 Chr4 19151167 19152416 -
Adu Adu01g00098 Chr01 1383168 1385702 -
Apr Apr3g0311 Chr3 6009613 6011950 -
Arst Arst1g00161 Chr1 1383150 1385689 -
Bach Bach10g00575 Chr10 4079463 4081129 -
Gma Gma02g00477 Chr02 4826691 4830505 +
Gma Gma16g01238 Chr16 30472879 30475780 +
Lal Lal16g1843 Chr16 17494824 17498271 +
Lan Lan6g1474 Chr6 21592459 21595698 -
Lapu Lapu3g01739 Chr3 27821057 27822834 -
Lja Lja4g3186 Chr4 60262514 60265972 +
Mal Mal5g3380 Chr5 97790770 97792836 +
Mepo Mepo1g02093 Chr1 21506507 21508496 -
Mtr Mtr8g2453 Chr8 34984984 34986793 +
Phco Phco8g00447 Chr8 4197983 4199576 +
Pste Pste7g01568 Chr7 14368782 14371002 -
Pvu Pvu3g2655 Chr3 48553486 48555473 -
Spst Spst3g03846 Chr3 88503223 88504809 +
Sto Sto6g3871 Chr6 43088131 43089070 -
Tpr Tpr4g4225 Chr4 49354097 49356159 -
Trre Trre15g02750 Chr15 23432057 23434057 +
Tsu Tsu04g03462 Chr04 43757598 43759742 -
Vimu Vimu11g00682 Chr11 7247226 7248884 -
Vvi Vvi4g1227 Chr4 19153446 19160809 -
Acco Acco11g2344 Chr11 36840508 36844994 +
Accr Accr9g00151 Chr9 1731292 1733454 -
Adu Adu05g00875 Chr05 10873932 10876493 +
Alju Alju09g2349 Chr09 46517842 46520038 +
Arst Arst5g01098 Chr5 10898320 10900719 +
Bach Bach4g00698 Chr4 4626875 4629737 +
Bisa Bisa11g1750 Chr11 39081527 39084412 +
Dere Dere09g0992 Chr09 12873196 12875824 +
Enph Enph13g0884 Chr13 15002583 15009183 -
Glsi Glsi05g1382 Chr05 62809543 62812277 -
Lapu Lapu2g00728 Chr2 6377539 6383281 +
Lasa Lasa2g03371 Chr2 532277622 532281375 +
Lele Lele49g0114 Chr49 702248 704701 -
Lele Lele50g0128 Chr50 783338 785853 -
Lele Lele52g0133 Chr52 779689 783927 -
Mepo Mepo5g00949 Chr5 9199817 9204750 +
Mesa Mesa17g00989 Chr17 12498068 12502189 +
Mibi Mibi12g2040 Chr12 36812121 36815813 +
Pste Pste1g02943 Chr1 12751472 12755692 +
Pvu Pvu2g1160 Chr2 22900543 22904324 -
Spst Spst2g00876 Chr2 7398032 7402060 +
Trre Trre9g01122 Chr9 9016032 9019570 +
Vimu Vimu7g03020 Chr7 25434101 25438038 +
Vvi Vvi4g1228 Chr4 19164272 19178094 -
Vvi Vvi4g1229 Chr4 19181749 19186571 +
Adu Adu05g00873 Chr05 10858813 10861975 -
Arst Arst5g01096 Chr5 10883205 10886361 -
Bach Bach4g00696 Chr4 4614144 4617473 -
Lasa Lasa2g03368 Chr2 532202674 532207996 -
Mepo Mepo5g00947 Chr5 9166842 9174151 -
Mesa Mesa17g00987 Chr17 12474765 12481942 -
Phco Phco4g00910 Chr4 7204982 7209811 +
Pste Pste1g02937 Chr1 12710987 12723907 -
Pumo Pumo8g01771 Chr8 53819710 53823472 +
Pvu Pvu2g1724 Chr2 30982295 30989780 -
Rops Rops1g01591 Chr1 34077447 34080724 +
Seca Seca12g02825 Chr12 50960300 50965386 -
Spst Spst2g00874 Chr2 7370740 7373857 -
Trre Trre9g01119 Chr9 8983602 8990332 -
Vian Vian10g00750 Chr10 7342572 7348710 -
Vifa Vifa1g06686 Chr1 1036291312 1036297068 +
Vimu Vimu7g03018 Chr7 25414340 25420799 -
Viun Viun2g01905 Chr2 27809848 27814116 +
Vivi Vivi2g02968 Chr2 128223334 128229449 +
Vvi Vvi4g1230 Chr4 19189535 19193911 +
Adu Adu05g00872 Chr05 10845879 10849456 -
Arst Arst5g01095 Chr5 10870332 10873853 -
Bach Bach4g00695 Chr4 4606610 4611379 -
Lasa Lasa2g03367 Chr2 532073948 532078586 -
Mepo Mepo5g00946 Chr5 9157477 9162375 -
Phac Phac2g02612 Chr2 27330413 27335547 -
Phco Phco4g00911 Chr4 7216778 7222622 +
Pste Pste1g02936 Chr1 12692772 12700919 -
Pumo Pumo8g01772 Chr8 53828557 53836278 +
Pvu Pvu2g1723 Chr2 30961420 30967617 -
Rops Rops1g01592 Chr1 34085423 34092645 +
Spst Spst2g00872 Chr2 7361714 7365244 -
Vian Vian10g00749 Chr10 7315306 7320408 -
Vifa Vifa1g06692 Chr1 1038088111 1038092604 +
Vimu Vimu7g03017 Chr7 25401453 25406556 -
Viun Viun2g01906 Chr2 27823730 27829604 +
Vivi Vivi2g02969 Chr2 128321989 128331933 +
Vvi Vvi4g1231 Chr4 19196984 19199755 -
Vvi Vvi4g1232 Chr4 19219673 19220035 +
Vvi Vvi4g1233 Chr4 19222201 19223454 -
Adu Adu05g00871 Chr05 10842729 10844105 +
Arst Arst5g01094 Chr5 10867089 10868553 +
Bach Bach4g00693 Chr4 4599004 4600235 +
Lasa Lasa2g03365 Chr2 532071339 532072431 +
Mepo Mepo5g00945 Chr5 9153141 9156004 +
Mesa Mesa17g00985 Chr17 12455698 12458268 +
Phac Phac2g02611 Chr2 27317190 27318973 +
Phco Phco4g00912 Chr4 7231890 7234181 -
Pste Pste1g02934 Chr1 12686202 12688115 +
Pumo Pumo8g01773 Chr8 53838950 53840573 -
Pvu Pvu2g1722 Chr2 30951468 30953175 +
Rops Rops1g01594 Chr1 34123858 34124922 -
Seca Seca10g00933 Chr10 8940999 8942530 +
Spst Spst2g00870 Chr2 7348228 7349390 +
Trre Trre9g01114 Chr9 8951468 8953188 +
Vian Vian10g00748 Chr10 7309826 7310989 +
Vifa Vifa1g06693 Chr1 1038093404 1038094518 -
Vimu Vimu7g03012 Chr7 25385779 25386948 +
Viun Viun2g01907 Chr2 27832963 27834809 -
Vivi Vivi2g02970 Chr2 128332080 128334417 -