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
Vvi18g0276 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva12g02079 . . . Cca03g01109 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto9g2894 . . . . . . . . . . . . . . . . . .
Vvi18g0277 . . . . . . Aed3g1536 . . . . . . . . . . . Apr9g0813 . . . . . . . . Bva12g02080 . . Cca05g00939 . . . . . . . . . . . Gma14g01404 Gma13g00174 . . . . . . . . . Lal22g0494 . . . . . . . . . . . . . . . . . . . Lja1g5835 . . . . . . . . . . . . . . . . . Psa5g0348 . . . . . . . . . . . . . . . . Ssu6g2299 . . Sto9g2896 . . . . . . . . . . . . . . . . Vra6g1373 .
Vvi18g0278 . Acco05g2738 . Accr3g00294 Adu08g02610 . Aed3g1537 . . . . . . . . Alju07g2695 . . Apr9g0814 . Arst8g03604 . Bach2g02365 . . Bisa05g0925 Bva06g02851 . Car04g02916 Car05g02540 Cca05g00940 . . Dere05g2523 . . . Enph7g1307 . Glsi10g1197 Gma04g02013 Gma06g01402 Gma14g01403 Gma13g00173 Gso4g1754 Gso4g1754 Gso4g1754 Gso4g1754 . . . . . Lal22g0493 . . . . . . . . . Lasa5g02805 . . . . . . . . . Lja1g5836 Mal1g5075 Mal2g1455 . . . . . Mibi08g2398 Mtr1g0903 Mtr3g3395 . Phac1g00976 Phco7g01745 Phco2g00820 . Prci2g0400 Psa6g0954 Psa5g1367 Pste2g00081 Pste8g01965 . . Pte3g01964 . . Pumo9g01188 Pvu9g1578 Pvu1g0746 . . . Seca8g02417 Spst9g01912 Spst8g01368 . . Sto5g0379 Sto9g2897 Tpr1g3064 Tpr3g3203 . . . Tsu07g01263 . Vian7g00235 . Vifa3g04049 . Vimu1g02283 . Viun8g01104 . Vivi4g04589 Vra6g1372 .
Vvi18g0279 . . . . . . Aed3g1538 . . . . . . . . . . . Apr9g0815 . . . . . . . Bva06g02848 Bva12g02082 Car04g02915 . Cca05g00941 . . . . . . . . . . . Gma14g01401 Gma13g00172 . . . . . . . Lal6g0543 Lal18g1118 . . . . . . . . . . Lasa5g02804 . . . . . . . . . Lja1g5837 Mal1g5073 . . . . . . . Mtr1g0904 . . Phac1g00977 . Phco2g00821 . . Psa6g0963 Psa5g2018 . Pste8g01964 . . . . . Pumo9g01189 . Pvu1g0747 . . . Seca8g02414 . Spst8g01367 Ssu6g2301 . . Sto9g2899 Tpr1g3063 . . . Tsu01g01027 . . . . Vifa3g04048 . Vimu1g02062 . Viun8g01107 . Vivi4g04588 . .
Vvi18g0280 . . . . . . . . . . . . . . . . . . . Apr1g0194 . . . . . . Bva06g02845 Bva12g02083 Car05g02159 . . Cca03g01114 . . . . . . . . Gma04g02370 . . . Gso4g2073 . . . . Lal17g0475 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mtr3g2957 . . . . . . . . . . . . . . . . . . . . . . . . . . Sto5g0380 . . Tpr2g4984 . . . Tsu07g02330 . . . . . . . . . . . .
Vvi18g0281 . . . . . . . Aed10g0317 . . . . . . . . . . . . . . . . . . Bva06g02844 Bva12g02084 . Car05g02542 . Cca03g01118 . . . . . . . . . Gma06g01026 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa5g2023 . . . . . . . . . . . . . . . . . Ssu1g2986 Sto5g0382 . . . . . . . . . . . . . . . . . . Vra5g0776
Vvi18g0282 . . . . Adu08g00583 . Aed3g1540 . Aev08g0930 . Ahy17g2810 . Aip07g03068 . . . Amo17g2711 . Apr9g0816 . Arst8g00748 . Bach12g00854 . . . Bva06g02843 Bva12g02085 . . Cca05g00942 . . . . . . . . . . . Gma14g01400 Gma13g00592 . . . . Lal4g0421 . . . . . Lan14g0599 . . . . . Lapu9g01475 . . . . . . . . . . . . Lja1g5838 . . . . . . . . . . Phac9g00891 . Phco7g01263 . . . . . Pste2g03123 . . . . . Pumo10g01259 . Pvu9g1306 . . . Seca4g02332 . Spst9g01315 . Ssu6g2303 . Sto5g0383 . . . . . . . Vian4g01524 . . . Vimu10g02275 . Viun9g02371 . Vivi3g03090 . . .
Vvi18g0283 . . . . . . Aed3g1541 . . . . . . . . . . . Apr9g0818 . . . . . . . Bva06g02842 Bva12g02086 . . Cca05g00943 . . . . . . . . . . . . Gma13g00593 . . . . . . . . Lal18g1121 Lal22g0492 . . . . . . . . . . . . . . . . . . Lja1g5037 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ssu6g2304 . Sto5g0384 Sto9g2905 . . . . . . . . . . . . . . . . . .
Vvi18g0284 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva06g02841 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto5g0385 . . . . . . . . . . . . . . . . . . .
Vvi18g0285 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva06g02840 Bva12g02087 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto5g0386 Sto9g2906 . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Mal Mal2g1455 Chr2 17487273 17490380 +
Mtr Mtr3g3395 Chr3 47818559 47835189 -
Psa Psa5g1367 Chr5 107002137 107008217 +
Tpr Tpr3g3203 Chr3 35201206 35204674 -
Tsu Tsu07g01263 Chr07 11026588 11029520 +
Vvi Vvi18g0276 Chr18 2677372 2684290 -
Bva Bva12g02079 Chr12 16246389 16250274 -
Cca Cca03g01109 Chr03 26818208 26828020 -
Sto Sto9g2894 Chr9 30262085 30266587 -
Vvi Vvi18g0277 Chr18 2688559 2731306 +
Aed Aed3g1536 Chr3 19807407 19821132 +
Apr Apr9g0813 Chr9 15614386 15633328 +
Bva Bva12g02080 Chr12 16251530 16260722 +
Cca Cca05g00939 Chr05 25114855 25140284 +
Gma Gma14g01404 Chr14 29702508 29707574 -
Gma Gma13g00174 Chr13 10506729 10537953 -
Lal Lal22g0494 Chr22 3257636 3267896 -
Lja Lja1g5835 Chr1 104835718 104848667 +
Psa Psa5g0348 Chr5 25140744 25149430 +
Ssu Ssu6g2299 Chr6 52134474 52158747 +
Sto Sto9g2896 Chr9 30278074 30287299 +
Vra Vra6g1373 Chr6 26990630 27024023 -
Vvi Vvi18g0278 Chr18 2734694 2737407 -
Acco Acco05g2738 Chr05 42648676 42650823 +
Accr Accr3g00294 Chr3 3205929 3208067 -
Adu Adu08g02610 Chr08 42203792 42211912 -
Aed Aed3g1537 Chr3 19820260 19824868 -
Alju Alju07g2695 Chr07 52466388 52468506 +
Apr Apr9g0814 Chr9 15632831 15635894 -
Arst Arst8g03604 Chr8 46576273 46579115 -
Bach Bach2g02365 Chr2 30019214 30021954 -
Bisa Bisa05g0925 Chr05 15886174 15890062 -
Bva Bva06g02851 Chr06 17851245 17854289 +
Car Car04g02916 Chr04 56270163 56274102 +
Car Car05g02540 Chr05 70483675 70487787 -
Cca Cca05g00940 Chr05 25140766 25143766 -
Dere Dere05g2523 Chr05 35750934 35753398 +
Enph Enph7g1307 Chr7 18555701 18558664 +
Glsi Glsi10g1197 Chr10 8065411 8077508 +
Gma Gma04g02013 Chr04 50571611 50575242 +
Gma Gma06g01402 Chr06 13274384 13277946 -
Gma Gma14g01403 Chr14 29697535 29700542 +
Gma Gma13g00173 Chr13 10502953 10506849 +
Gso Gso4g1754 Chr4 47657863 47661951 +
Gso Gso4g1754 Chr4 47657863 47661951 +
Gso Gso4g1754 Chr4 47657863 47661951 +
Gso Gso4g1754 Chr4 47657863 47661951 +
Lal Lal22g0493 Chr22 3253396 3262242 +
Lasa Lasa5g02805 Chr5 509071119 509072960 +
Lja Lja1g5836 Chr1 104848520 104852111 -
Mal Mal1g5075 Chr1 122273386 122276700 +
Mal Mal2g1455 Chr2 17487273 17490380 +
Mibi Mibi08g2398 Chr08 41721363 41723690 +
Mtr Mtr1g0903 Chr1 10407146 10410829 -
Mtr Mtr3g3395 Chr3 47818559 47835189 -
Phac Phac1g00976 Chr1 8929179 8932622 -
Phco Phco7g01745 Chr7 17632454 17637414 +
Phco Phco2g00820 Chr2 9327008 9330001 -
Prci Prci2g0400 Chr2 2851526 2854287 -
Psa Psa6g0954 Chr6 36796185 36799245 -
Psa Psa5g1367 Chr5 107002137 107008217 +
Pste Pste2g00081 Chr2 283045 286301 -
Pste Pste8g01965 Chr8 15200079 15203502 +
Pte Pte3g01964 Chr3 31428834 31433391 -
Pumo Pumo9g01188 Chr9 35552004 35555845 -
Pvu Pvu9g1578 Chr9 22194415 22199545 +
Pvu Pvu1g0746 Chr1 9706299 9711569 -
Seca Seca8g02417 Chr8 51622859 51625772 +
Spst Spst9g01912 Chr9 26862158 26865966 -
Spst Spst8g01368 Chr8 12805210 12808185 +
Sto Sto5g0379 Chr5 2349204 2351264 -
Sto Sto9g2897 Chr9 30287871 30290379 -
Tpr Tpr1g3064 Chr1 35115564 35119294 +
Tpr Tpr3g3203 Chr3 35201206 35204674 -
Tsu Tsu07g01263 Chr07 11026588 11029520 +
Vian Vian7g00235 Chr7 7263438 7266443 +
Vifa Vifa3g04049 Chr3 1194109200 1194111566 +
Vimu Vimu1g02283 Chr1 33215911 33218877 +
Viun Viun8g01104 Chr8 13719158 13722727 -
Vivi Vivi4g04589 Chr4 173769931 173772788 +
Vra Vra6g1372 Chr6 26987437 26990801 +
Vvi Vvi18g0279 Chr18 2748042 2754460 -
Aed Aed3g1538 Chr3 19836979 19844012 -
Apr Apr9g0815 Chr9 15655606 15667073 -
Bva Bva06g02848 Chr06 17842716 17849653 +
Bva Bva12g02082 Chr12 16262798 16266937 -
Car Car04g02915 Chr04 56250205 56255590 +
Cca Cca05g00941 Chr05 25150204 25157661 -
Gma Gma14g01401 Chr14 29641554 29648265 +
Gma Gma13g00172 Chr13 10483351 10489994 +
Lal Lal6g0543 Chr6 3487685 3494755 +
Lal Lal18g1118 Chr18 14149796 14155209 -
Lasa Lasa5g02804 Chr5 509011642 509014203 -
Lja Lja1g5837 Chr1 104873166 104879143 -
Mal Mal1g5073 Chr1 122017253 122019183 +
Mtr Mtr1g0904 Chr1 10439590 10448226 -
Phac Phac1g00977 Chr1 8933588 8950129 -
Phco Phco2g00821 Chr2 9361337 9369750 -
Psa Psa6g0963 Chr6 36879685 36898468 -
Psa Psa5g2018 Chr5 155958539 155961056 +
Pste Pste8g01964 Chr8 15188363 15196024 +
Pumo Pumo9g01189 Chr9 35567651 35574590 -
Pvu Pvu1g0747 Chr1 9737465 9743912 -
Seca Seca8g02414 Chr8 51592528 51599095 +
Spst Spst8g01367 Chr8 12784823 12793384 +
Ssu Ssu6g2301 Chr6 52161971 52199768 -
Sto Sto9g2899 Chr9 30294157 30298746 -
Tpr Tpr1g3063 Chr1 35097746 35108002 +
Tsu Tsu01g01027 Chr01 9430649 9438858 -
Vifa Vifa3g04048 Chr3 1193911756 1193915274 +
Vimu Vimu1g02062 Chr1 28811595 28818442 +
Viun Viun8g01107 Chr8 13773964 13792654 -
Vivi Vivi4g04588 Chr4 173753562 173758503 +
Vvi Vvi18g0280 Chr18 2761290 2771892 +
Apr Apr1g0194 Chr1 2127809 2133863 +
Bva Bva06g02845 Chr06 17834292 17838213 -
Bva Bva12g02083 Chr12 16271682 16276190 +
Car Car05g02159 Chr05 66841302 66850050 +
Cca Cca03g01114 Chr03 26997622 26998224 -
Gma Gma04g02370 Chr04 54104668 54110714 -
Gso Gso4g2073 Chr4 51176762 51182783 -
Lal Lal17g0475 Chr17 3262549 3267673 +
Mtr Mtr3g2957 Chr3 43428596 43435171 +
Sto Sto5g0380 Chr5 2353404 2360676 +
Tpr Tpr2g4984 Chr2 55604347 55611575 +
Tsu Tsu07g02330 Chr07 26376102 26383302 +
Vvi Vvi18g0281 Chr18 2777880 2784606 +
Aed Aed10g0317 Chr10 2540316 2546636 +
Bva Bva06g02844 Chr06 17823063 17828539 -
Bva Bva12g02084 Chr12 16282594 16288146 +
Car Car05g02542 Chr05 70497948 70502619 +
Cca Cca03g01118 Chr03 27073659 27079405 -
Gma Gma06g01026 Chr06 9589247 9594492 +
Psa Psa5g2023 Chr5 156140673 156146112 -
Ssu Ssu1g2986 Chr1 78457327 78462202 -
Sto Sto5g0382 Chr5 2373705 2378124 +
Vra Vra5g0776 Chr5 13295768 13301602 -
Vvi Vvi18g0282 Chr18 2791946 2797838 +
Adu Adu08g00583 Chr08 10498659 10502011 -
Aed Aed3g1540 Chr3 19863543 19868884 +
Aev Aev08g0930 Chr08 5517144 5519963 -
Ahy Ahy17g2810 Chr17 126893501 126896892 -
Aip Aip07g03068 Chr07 117918422 117921812 -
Amo Amo17g2711 Chr17 127819522 127822524 -
Apr Apr9g0816 Chr9 15695697 15701390 +
Arst Arst8g00748 Chr8 10469653 10472944 -
Bach Bach12g00854 Chr12 6031876 6035729 -
Bva Bva06g02843 Chr06 17817964 17822233 -
Bva Bva12g02085 Chr12 16288840 16292711 +
Cca Cca05g00942 Chr05 25176050 25181846 +
Gma Gma14g01400 Chr14 29605151 29615611 -
Gma Gma13g00592 Chr13 18986687 18991427 +
Lal Lal4g0421 Chr4 2929356 2933053 +
Lan Lan14g0599 Chr14 12795236 12799238 -
Lapu Lapu9g01475 Chr9 29133132 29144369 -
Lja Lja1g5838 Chr1 104892107 104907463 +
Phac Phac9g00891 Chr9 6771878 6777525 +
Phco Phco7g01263 Chr7 11241758 11247574 +
Pste Pste2g03123 Chr2 31137439 31149183 +
Pumo Pumo10g01259 Chr10 16547568 16564363 +
Pvu Pvu9g1306 Chr9 18760310 18767201 +
Seca Seca4g02332 Chr4 39758076 39760106 +
Spst Spst9g01315 Chr9 12773899 12782711 +
Ssu Ssu6g2303 Chr6 52206188 52216220 +
Sto Sto5g0383 Chr5 2381259 2385485 +
Vian Vian4g01524 Chr4 30446591 30452330 -
Vimu Vimu10g02275 Chr10 33221427 33228487 +
Viun Viun9g02371 Chr9 33199595 33203384 -
Vivi Vivi3g03090 Chr3 52357015 52360577 -
Vvi Vvi18g0283 Chr18 2802996 2805108 -
Aed Aed3g1541 Chr3 19869602 19872803 -
Apr Apr9g0818 Chr9 15734244 15738615 -
Bva Bva06g02842 Chr06 17814655 17817061 +
Bva Bva12g02086 Chr12 16294456 16297058 -
Cca Cca05g00943 Chr05 25181850 25185751 -
Gma Gma13g00593 Chr13 19018530 19022447 -
Lal Lal18g1121 Chr18 14171913 14181001 -
Lal Lal22g0492 Chr22 3249310 3251787 +
Lja Lja1g5037 Chr1 70938487 70941684 +
Ssu Ssu6g2304 Chr6 52220237 52224052 -
Sto Sto5g0384 Chr5 2387282 2389429 -
Sto Sto9g2905 Chr9 30327373 30329095 -
Vvi Vvi18g0284 Chr18 2813326 2821580 +
Bva Bva06g02841 Chr06 17803822 17809169 -
Sto Sto5g0385 Chr5 2399915 2404802 +
Vvi Vvi18g0285 Chr18 2822316 2827158 -
Bva Bva06g02840 Chr06 17798755 17803564 +
Bva Bva12g02087 Chr12 16303554 16309607 -
Sto Sto5g0386 Chr5 2405644 2410952 -
Sto Sto9g2906 Chr9 30340637 30345241 -
Apr Apr9g0814 Chr9 15632831 15635894 -
Sto Sto9g2897 Chr9 30287871 30290379 -
Apr Apr9g0813 Chr9 15614386 15633328 +
Gma Gma13g00174 Chr13 10506729 10537953 -
Sto Sto9g2896 Chr9 30278074 30287299 +