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
Vvi4g0794 Acco05g1213 Acco10g1442 Accr3g01742 Accr4g01313 Adu07g01124 . . Aed3g1974 . Aev07g2235 . Ahy17g1274 . Aip07g01208 Alju07g1165 Alju08g1364 . . . . Arst7g01514 . Bach3g01031 Bach12g01287 Bisa05g2136 Bisa09g0480 . . . . . Cca05g01382 Dere05g1164 Dere04g2025 . Dod08g0907 Enph7g0210 Enph1g0936 Glsi10g1825 . . . . . . . . . . . . . . . . . . . . . Lapu6g02242 Lapu6g02242 Lasa2g01408 Lasa5g01595 Lele25g1388 Lele26g1412 Lele27g0698 Lele28g1397 Lele01g1075 Lele02g1101 Lele03g1080 Lele04g1089 . . . . Mepo7g02008 Mepo3g05280 Mesa17g03323 Mesa9g02549 Mibi08g1001 Mibi05g1270 . . Phac8g03227 Phac6g01147 Phco3g00506 Phco11g01569 Prci2g2271 Prci8g0567 . . Pste8g01560 Pste7g01875 . . . . Pumo9g02555 . Pvu8g2514 Pvu6g0872 Rops9g01105 Rops11g03368 Seca6g02453 Seca8g01267 Spst8g00269 Spst6g00250 . Ssu6g2804 Sto5g1762 Sto9g2333 . . . Trre5g00769 . . Vian7g01754 Vian6g00774 Vifa1g01563 Vifa2g01428 Vimu1g01207 Vimu2g01948 Viun8g02053 Viun6g01377 Vivi7g01696 . . Vra6g0791
Vvi4g0795 . . . . . Adu01g00595 . . . . . . . . . . . . . . . Arst1g00813 . Bach12g01286 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu6g02241 . Lasa5g01598 . . . . . . . . . . . . . Mepo3g05284 . Mesa9g02555 . . . . . Phac6g01148 . Phco11g01568 . . . . . Pste7g01876 . . . . . . . Pvu6g0873 . Rops11g03369 . Seca6g02452 . Spst6g00251 . . Sto5g1761 . . . . Trre5g00768 . . . Vian6g00775 . Vifa2g01431 . Vimu2g01947 . Viun6g01378 . Vivi3g04933 . .
Vvi4g0796 . Acco10g1441 . Accr4g01314 Adu07g01123 Adu01g00596 . Aed3g1975 . Aev07g2236 . Ahy17g1273 . Aip07g01207 . Alju08g1365 . . . . Arst7g01513 Arst1g00814 Bach3g01032 Bach12g01285 . Bisa09g0481 . . . . . Cca05g01384 . Dere04g2027 . Dod08g0906 . . . Glsi08g0517 . . . . . . . . . . . . . . . . . . . . Lapu6g02240 Lapu6g02240 Lasa2g01409 Lasa5g01600 . . . . Lele01g1076 Lele02g1102 Lele03g1081 Lele04g1090 . . . . Mepo7g02012 Mepo3g05286 Mesa17g03326 Mesa9g02557 . Mibi05g1271 . . Phac8g03226 Phac6g01149 Phco3g00507 Phco11g01567 . Prci8g0568 . . Pste8g01559 Pste7g01878 . Pte8g00549 . Pte8g00549 Pumo9g02554 . Pvu8g2513 Pvu6g0874 Rops9g01104 Rops11g03370 Seca6g02451 Seca8g01266 Spst8g00270 Spst6g00252 . Ssu6g2805 . Sto9g2334 . . . Trre5g00763 . . Vian7g01753 Vian6g00776 Vifa1g01570 Vifa2g01435 Vimu1g01206 Vimu2g01945 Viun8g02054 Viun6g01379 . . . Vra6g0790
Vvi4g0797 Acco05g1221 . Accr3g01726 . Adu07g01122 . . Aed3g1976 . Aev07g2237 . Ahy17g1272 . Aip07g01206 Alju07g1172 . . . . . Arst7g01511 . Bach3g01033 . Bisa05g2141 . . . . . . Cca05g01385 Dere05g1160 . . Dod08g0905 Enph7g0213 . Glsi10g1822 . . . . . . . . . . . . . . . . . . . . . . . Lasa2g01410 . . Lele26g1409 . Lele28g1394 . . . . . . . . Mepo7g02013 . Mesa17g03327 . . . . . Phac8g03225 . Phco3g00508 . Prci2g2268 . . . Pste8g01558 . . Pte8g00550 . . Pumo9g02553 . Pvu8g2512 . Rops9g01101 . Seca8g01265 . Spst8g00271 . . Ssu6g2806 Sto5g1759 . . . . . . . Vian7g01752 . Vifa1g01571 . Vimu1g01205 . Viun8g02056 . . . . Vra6g0789
Vvi4g0798 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g0799 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g0800 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g0801 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g0802 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g0803 . . . . . Adu01g00600 . . . Aev08g0520 . Ahy20g2129 . Aip10g02514 . . . Amo20g2749 . . . Arst1g00817 . . . . . . . . . . . . . Dod09g1906 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco11g01566 . . . . . Pste7g01879 . . . Pte8g00551 . . . Pvu6g0875 . Rops11g03372 . Seca6g02449 . Spst6g00253 . . . . . . . . . . . Vian6g00777 . . . Vimu2g01944 . Viun6g01381 . . . .
   
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Select Species Gene Chromosome Start End Strand
Vvi Vvi4g0794 Chr4 9417305 9419563 +
Acco Acco05g1213 Chr05 25116811 25119198 +
Acco Acco10g1442 Chr10 28168460 28171773 -
Accr Accr3g01742 Chr3 22739794 22742196 -
Accr Accr4g01313 Chr4 12871003 12873136 +
Adu Adu07g01124 Chr07 16300324 16303188 -
Aed Aed3g1974 Chr3 23892251 23895150 +
Aev Aev07g2235 Chr07 23339030 23341233 +
Ahy Ahy17g1274 Chr17 19788005 19791254 -
Aip Aip07g01208 Chr07 18034308 18037213 -
Alju Alju07g1165 Chr07 35164249 35166646 +
Alju Alju08g1364 Chr08 10499434 10501331 +
Arst Arst7g01514 Chr7 16409617 16412471 -
Bach Bach3g01031 Chr3 20802929 20805291 +
Bach Bach12g01287 Chr12 8952677 8955017 -
Bisa Bisa05g2136 Chr05 47665430 47667907 +
Bisa Bisa09g0480 Chr09 7024768 7027633 +
Cca Cca05g01382 Chr05 32089919 32092737 +
Dere Dere05g1164 Chr05 18676622 18678988 -
Dere Dere04g2025 Chr04 23243031 23259269 +
Dod Dod08g0907 Chr08 11099812 11102607 -
Enph Enph7g0210 Chr7 7887946 7890326 +
Enph Enph1g0936 Chr1 35667441 35669573 +
Glsi Glsi10g1825 Chr10 12650014 12652815 -
Lapu Lapu6g02242 Chr6 21869243 21872079 -
Lapu Lapu6g02242 Chr6 21869243 21872079 -
Lasa Lasa2g01408 Chr2 454356053 454358409 +
Lasa Lasa5g01595 Chr5 386596970 386599232 +
Lele Lele25g1388 Chr25 9937440 9939835 -
Lele Lele26g1412 Chr26 9907104 9909493 -
Lele Lele27g0698 Chr27 14980488 14982868 +
Lele Lele28g1397 Chr28 10092933 10095297 -
Lele Lele01g1075 Chr01 6289037 6297155 +
Lele Lele02g1101 Chr02 6984880 6987068 +
Lele Lele03g1080 Chr03 6287307 6289597 +
Lele Lele04g1089 Chr04 6834236 6836431 +
Mepo Mepo7g02008 Chr7 30335242 30338311 +
Mepo Mepo3g05280 Chr3 66189275 66191994 +
Mesa Mesa17g03323 Chr17 58612879 58615427 +
Mesa Mesa9g02549 Chr9 53163526 53165987 +
Mibi Mibi08g1001 Chr08 23396054 23398463 +
Mibi Mibi05g1270 Chr05 15262615 15264957 +
Phac Phac8g03227 Chr8 40617709 40620798 -
Phac Phac6g01147 Chr6 15265359 15268058 +
Phco Phco3g00506 Chr3 3919950 3922191 +
Phco Phco11g01569 Chr11 11949434 11951738 -
Prci Prci2g2271 Chr2 17878835 17882210 -
Prci Prci8g0567 Chr8 3704312 3707120 +
Pste Pste8g01560 Chr8 8899215 8901883 -
Pste Pste7g01875 Chr7 17199117 17201473 +
Pumo Pumo9g02555 Chr9 60535221 60537906 -
Pvu Pvu8g2514 Chr8 55712693 55715294 -
Pvu Pvu6g0872 Chr6 20233891 20236537 +
Rops Rops9g01105 Chr9 18129327 18132296 -
Rops Rops11g03368 Chr11 64791818 64794485 +
Seca Seca6g02453 Chr6 87222666 87225401 -
Seca Seca8g01267 Chr8 19732382 19735324 -
Spst Spst8g00269 Chr8 2359502 2361762 +
Spst Spst6g00250 Chr6 2572697 2574982 +
Ssu Ssu6g2804 Chr6 65119457 65121772 +
Sto Sto5g1762 Chr5 12746537 12749182 -
Sto Sto9g2333 Chr9 26598563 26601053 +
Trre Trre5g00769 Chr5 5257115 5259395 -
Vian Vian7g01754 Chr7 27492197 27494404 -
Vian Vian6g00774 Chr6 24782173 24784429 +
Vifa Vifa1g01563 Chr1 257690057 257692138 +
Vifa Vifa2g01428 Chr2 388664362 388666735 +
Vimu Vimu1g01207 Chr1 9440980 9443696 -
Vimu Vimu2g01948 Chr2 14164811 14169065 -
Viun Viun8g02053 Chr8 31079567 31082069 +
Viun Viun6g01377 Chr6 22498012 22500660 +
Vivi Vivi7g01696 Chr7 74925391 74928145 +
Vra Vra6g0791 Chr6 7748024 7750616 -
Vvi Vvi4g0795 Chr4 9420772 9426033 -
Adu Adu01g00595 Chr01 8183259 8186756 -
Arst Arst1g00813 Chr1 8187036 8190486 -
Bach Bach12g01286 Chr12 8947247 8951305 +
Lapu Lapu6g02241 Chr6 21864974 21868913 +
Lasa Lasa5g01598 Chr5 386681931 386685224 -
Mepo Mepo3g05284 Chr3 66209762 66212525 -
Mesa Mesa9g02555 Chr9 53207942 53210737 -
Phac Phac6g01148 Chr6 15268513 15272527 -
Phco Phco11g01568 Chr11 11944990 11948434 +
Pste Pste7g01876 Chr7 17202509 17206226 -
Pvu Pvu6g0873 Chr6 20236973 20240957 -
Rops Rops11g03369 Chr11 64795040 64799566 -
Seca Seca6g02452 Chr6 87218059 87221855 +
Spst Spst6g00251 Chr6 2576386 2579979 -
Sto Sto5g1761 Chr5 12741025 12746234 +
Trre Trre5g00768 Chr5 5255090 5255963 +
Vian Vian6g00775 Chr6 24785526 24788795 -
Vifa Vifa2g01431 Chr2 388746039 388749808 -
Vimu Vimu2g01947 Chr2 14158961 14162225 +
Viun Viun6g01378 Chr6 22501149 22505073 -
Vivi Vivi3g04933 Chr3 94393495 94397450 -
Vvi Vvi4g0796 Chr4 9458118 9458873 +
Acco Acco10g1441 Chr10 28159376 28160119 -
Accr Accr4g01314 Chr4 12878163 12878906 +
Adu Adu07g01123 Chr07 16285565 16286338 -
Adu Adu01g00596 Chr01 8193187 8194407 +
Aed Aed3g1975 Chr3 23897054 23897818 +
Aev Aev07g2236 Chr07 23347046 23347837 +
Ahy Ahy17g1273 Chr17 19781778 19783047 -
Aip Aip07g01207 Chr07 18029871 18030932 -
Alju Alju08g1365 Chr08 10511100 10511840 +
Arst Arst7g01513 Chr7 16394842 16395888 -
Arst Arst1g00814 Chr1 8196809 8198060 +
Bach Bach3g01032 Chr3 20808532 20809299 +
Bach Bach12g01285 Chr12 8944310 8945071 -
Bisa Bisa09g0481 Chr09 7031872 7032630 +
Cca Cca05g01384 Chr05 32116733 32117877 +
Dere Dere04g2027 Chr04 23265414 23266175 +
Dod Dod08g0906 Chr08 11092593 11093665 -
Glsi Glsi08g0517 Chr08 4316509 4317264 +
Lapu Lapu6g02240 Chr6 21858206 21861707 -
Lapu Lapu6g02240 Chr6 21858206 21861707 -
Lasa Lasa2g01409 Chr2 454396206 454396982 +
Lasa Lasa5g01600 Chr5 386809852 386810601 +
Lele Lele01g1076 Chr01 6299201 6299950 +
Lele Lele02g1102 Chr02 7011544 7012296 +
Lele Lele03g1081 Chr03 6291590 6292339 +
Lele Lele04g1090 Chr04 6852175 6852927 +
Mepo Mepo7g02012 Chr7 30359274 30360461 +
Mepo Mepo3g05286 Chr3 66221997 66223126 +
Mesa Mesa17g03326 Chr17 58635607 58636383 +
Mesa Mesa9g02557 Chr9 53228307 53229065 +
Mibi Mibi05g1271 Chr05 15269270 15270025 +
Phac Phac8g03226 Chr8 40614401 40615481 -
Phac Phac6g01149 Chr6 15274900 15276344 +
Phco Phco3g00507 Chr3 3924807 3925586 +
Phco Phco11g01567 Chr11 11941626 11942357 -
Prci Prci8g0568 Chr8 3708765 3709987 +
Pste Pste8g01559 Chr8 8893748 8894527 -
Pste Pste7g01878 Chr7 17211867 17212598 +
Pte Pte8g00549 Chr8 27052816 27053735 +
Pte Pte8g00549 Chr8 27052816 27053735 +
Pumo Pumo9g02554 Chr9 60530694 60531685 -
Pvu Pvu8g2513 Chr8 55709082 55709858 -
Pvu Pvu6g0874 Chr6 20243196 20244188 +
Rops Rops9g01104 Chr9 18125850 18126626 -
Rops Rops11g03370 Chr11 64816677 64817411 +
Seca Seca6g02451 Chr6 87207498 87208241 -
Seca Seca8g01266 Chr8 19710696 19711472 -
Spst Spst8g00270 Chr8 2364151 2364933 +
Spst Spst6g00252 Chr6 2582036 2582767 +
Ssu Ssu6g2805 Chr6 65125851 65126615 +
Sto Sto9g2334 Chr9 26604907 26605671 +
Trre Trre5g00763 Chr5 5238067 5239052 -
Vian Vian7g01753 Chr7 27489228 27490016 -
Vian Vian6g00776 Chr6 24793476 24794207 +
Vifa Vifa1g01570 Chr1 258740593 258741375 +
Vifa Vifa2g01435 Chr2 389598213 389598977 -
Vimu Vimu1g01206 Chr1 9438001 9438792 -
Vimu Vimu2g01945 Chr2 14148034 14149996 -
Viun Viun8g02054 Chr8 31084446 31085586 +
Viun Viun6g01379 Chr6 22507982 22509049 +
Vra Vra6g0790 Chr6 7744194 7745348 -
Vvi Vvi4g0797 Chr4 9493851 9539085 -
Acco Acco05g1221 Chr05 25264415 25272659 -
Accr Accr3g01726 Chr3 22362471 22372706 +
Adu Adu07g01122 Chr07 16275262 16281032 +
Aed Aed3g1976 Chr3 23900726 23906460 -
Aev Aev07g2237 Chr07 23350840 23356827 +
Ahy Ahy17g1272 Chr17 19769542 19775338 +
Aip Aip07g01206 Chr07 18016899 18022569 +
Alju Alju07g1172 Chr07 35286220 35299185 -
Arst Arst7g01511 Chr7 16384551 16390355 +
Bach Bach3g01033 Chr3 20810307 20816438 -
Bisa Bisa05g2141 Chr05 47727367 47741686 -
Cca Cca05g01385 Chr05 32121015 32131150 -
Dere Dere05g1160 Chr05 18643109 18654276 +
Dod Dod08g0905 Chr08 11082524 11090425 +
Enph Enph7g0213 Chr7 7923819 7931929 -
Glsi Glsi10g1822 Chr10 12625823 12634338 +
Lasa Lasa2g01410 Chr2 454418713 454425130 -
Lele Lele26g1409 Chr26 9885071 9891491 +
Lele Lele28g1394 Chr28 10070347 10077403 +
Mepo Mepo7g02013 Chr7 30360988 30370779 -
Mesa Mesa17g03327 Chr17 58639079 58647187 -
Phac Phac8g03225 Chr8 40605556 40614104 +
Phco Phco3g00508 Chr3 3927265 3934487 -
Prci Prci2g2268 Chr2 17822982 17831785 +
Pste Pste8g01558 Chr8 8878792 8891682 +
Pte Pte8g00550 Chr8 27054818 27061053 -
Pumo Pumo9g02553 Chr9 60521634 60529453 +
Pvu Pvu8g2512 Chr8 55700018 55708330 +
Rops Rops9g01101 Chr9 18108666 18116739 +
Seca Seca8g01265 Chr8 19697599 19706358 +
Spst Spst8g00271 Chr8 2366135 2379549 -
Ssu Ssu6g2806 Chr6 65129601 65139951 -
Sto Sto5g1759 Chr5 12716720 12730830 -
Vian Vian7g01752 Chr7 27474400 27487594 +
Vifa Vifa1g01571 Chr1 258772048 258779824 -
Vimu Vimu1g01205 Chr1 9431603 9437035 +
Viun Viun8g02056 Chr8 31086000 31094207 -
Vra Vra6g0789 Chr6 7734905 7743873 +
Vvi Vvi4g0798 Chr4 9507682 9509678 -
Vvi Vvi4g0799 Chr4 9566853 9572147 -
Vvi Vvi4g0800 Chr4 9646797 9657823 +
Vvi Vvi4g0801 Chr4 9678647 9680193 +
Vvi Vvi4g0802 Chr4 9681505 9686915 -
Vvi Vvi4g0803 Chr4 9696115 9697317 +
Adu Adu01g00600 Chr01 8209826 8211747 +
Aev Aev08g0520 Chr08 2934222 2935658 +
Ahy Ahy20g2129 Chr20 119029681 119032490 -
Aip Aip10g02514 Chr10 111688117 111689743 -
Amo Amo20g2749 Chr20 125990463 125993114 -
Arst Arst1g00817 Chr1 8213093 8215490 +
Dod Dod09g1906 Chr09 40606531 40609911 -
Phco Phco11g01566 Chr11 11938323 11939573 -
Pste Pste7g01879 Chr7 17214053 17215300 +
Pte Pte8g00551 Chr8 27087990 27090442 +
Pvu Pvu6g0875 Chr6 20245755 20247558 +
Rops Rops11g03372 Chr11 64837335 64838486 +
Seca Seca6g02449 Chr6 87196564 87199022 -
Spst Spst6g00253 Chr6 2584351 2585598 +
Vian Vian6g00777 Chr6 24797463 24798713 +
Vimu Vimu2g01944 Chr2 14143164 14146958 -
Viun Viun6g01381 Chr6 22510125 22513331 +