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
Vvi17g0183 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0184 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0185 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0186 . . . . . Adu03g04061 . . . . . . . . . . . . . . . Arst3g05348 . Bach1g01435 . . Bva04g00893 Bva03g00766 . Car06g00149 . Cca09g02838 . . . . . . . . . Gma08g00529 Gma05g02390 . . . . . Lal15g0908 . Lal23g0703 . . . . . . . . . . Lapu3g03960 . Lasa7g05306 . . . . . . . . . Lja4g0009 . . . Mepo2g05117 . Mesa13g00014 . . Mtr8g3893 . . . . Phco4g03738 . . . . . . . . . . . Pumo6g00049 . Pvu2g3405 . Rops2g00044 . Seca12g07002 . Spst3g00650 . Ssu5g3508 . Sto8g4505 . . . Trre7g05987 Tsu02g00013 . . Vian1g04223 . Vifa6g04185 . Vimu11g04940 . Viun3g00045 . Vivi5g06479 . .
Vvi17g0187 . . . . Adu05g02782 Adu03g04060 Aed7g0289 Aed5g2656 . . . . . . . . . . Apr6g0987 . Arst5g03524 Arst5g03524 Bach1g01436 Bach1g01436 . . Bva04g00892 Bva03g00765 Car08g01616 Car06g00150 Cca08g00309 Cca09g02837 . . . . . . . . Gma07g00926 Gma08g00528 . . Gso7g0873 Gso7g0873 . . Lal15g0909 . . . Lal10g0946 . . . . . . . Lapu4g00264 Lapu3g03959 Lasa1g04163 Lasa7g05305 . . . . . . . . Lja2g2203 Lja4g0010 . Mal6g3319 Mepo7g00913 . Mesa22g02747 . . . . Mtr6g1822 Phac4g01956 . Phco5g00335 Phco4g03737 . . Psa1g0715 . Pste9g01428 . . Pte9g00149 . . Pumo6g02938 Pumo6g02938 Pvu4g1588 Pvu2g3404 Rops5g00373 Rops2g00046 Seca10g04735 Seca12g07001 Spst4g02839 Spst3g00651 Ssu5g3507 Ssu5g3507 . Sto8g4506 . . . . . Tsu06g03713 . Vian1g04222 Vifa1g07348 Vifa1g07348 Vimu8g01648 Vimu11g04938 Viun4g00398 Viun3g00046 Vivi4g00367 Vivi5g06480 Vra1g0683 .
Vvi17g0188 . . . . . . . . . . . . . . . . . . Apr6g0988 . . . . . . . Bva04g00891 . Car08g01617 . Cca08g00308 . . . . . . . . . Gma07g00925 . . . Gso7g0872 . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja2g2202 . . Mal6g3318 . . . . . . . Mtr6g1821 . . . . . . Psa1g0714 . . . . . . . . . . . . . . . . . . . . Sto8g4507 . . . . . . . . . . . . . . . . Vra1g0682 .
Vvi17g0189 . . . . . . Aed7g0286 . . . . . . . . . . . Apr6g0989 . . . Bach1g01437 . . . . Bva03g00764 Car08g01618 . Cca08g00307 . . . . . . . . . Gma07g00924 . . . Gso7g0871 . . . . . . Lal8g0476 . . . . . . . . Lapu4g00262 . Lasa1g04159 . . . . . . . . . Lja2g2200 . . Mal6g3316 Mepo7g00915 . Mesa22g02745 . . . . Mtr6g1820 . . Phco5g00333 . . . Psa1g0711 . Pste9g01429 . . Pte9g00147 . . Pumo6g02939 . Pvu4g1589 . Rops5g00369 . Seca10g04742 . Spst4g02837 . . . . Sto8g4512 . . Trre11g02056 . . Tsu06g03719 Vian8g01398 . Vifa1g07346 . Vimu8g01646 . Viun4g00393 . Vivi4g00363 . Vra1g0681 .
Vvi17g0190 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva03g00763 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0191 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto8g4504 . . . . . . . . . . . . . . . . . .
Vvi17g0192 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lal16g0930 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa7g0030 . . . . . . . . . . . . . . . . . . . Sto8g4503 . . . . . . . . . . . . . . . . . .
   
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Select Species Gene Chromosome Start End Strand
Vvi Vvi17g0183 Chr17 1691102 1691638 +
Vvi Vvi17g0184 Chr17 1703011 1706116 +
Vvi Vvi17g0185 Chr17 1708001 1709120 +
Vvi Vvi17g0186 Chr17 1714388 1715151 +
Adu Adu03g04061 Chr03 129707090 129707596 -
Arst Arst3g05348 Chr3 128471178 128471782 -
Bach Bach1g01435 Chr1 27843477 27843977 +
Bva Bva04g00893 Chr04 5883938 5884432 -
Bva Bva03g00766 Chr03 4582309 4582812 -
Car Car06g00149 Chr06 1794502 1795220 +
Cca Cca09g02838 Chr09 53957796 53958402 -
Gma Gma08g00529 Chr08 4333855 4334608 -
Gma Gma05g02390 Chr05 44702218 44702770 -
Lal Lal15g0908 Chr15 6885794 6886300 +
Lal Lal23g0703 Chr23 9687856 9688359 -
Lapu Lapu3g03960 Chr3 63003389 63003865 -
Lasa Lasa7g05306 Chr7 721662089 721662592 -
Lja Lja4g0009 Chr4 94241 94738 +
Mepo Mepo2g05117 Chr2 59008278 59009147 -
Mesa Mesa13g00014 Chr13 165392 165892 +
Mtr Mtr8g3893 Chr8 49538266 49539498 -
Phco Phco4g03738 Chr4 56792249 56792740 -
Pumo Pumo6g00049 Chr6 540281 541062 +
Pvu Pvu2g3405 Chr2 48858790 48859281 -
Rops Rops2g00044 Chr2 867326 867817 +
Seca Seca12g07002 Chr12 161975645 161976142 -
Spst Spst3g00650 Chr3 9982216 9982707 +
Ssu Ssu5g3508 Chr5 86004015 86004506 -
Sto Sto8g4505 Chr8 47773704 47774267 +
Trre Trre7g05987 Chr7 64143480 64149966 -
Tsu Tsu02g00013 Chr02 101562 102062 +
Vian Vian1g04223 Chr1 65139608 65140099 -
Vifa Vifa6g04185 Chr6 1374802783 1374803277 -
Vimu Vimu11g04940 Chr11 68837347 68840722 -
Viun Viun3g00045 Chr3 202431 204828 +
Vivi Vivi5g06479 Chr5 171441338 171442201 +
Vvi Vvi17g0187 Chr17 1717329 1718051 -
Adu Adu05g02782 Chr05 95638668 95639922 +
Adu Adu03g04060 Chr03 129703024 129704008 +
Aed Aed7g0289 Chr7 2077983 2078723 +
Aed Aed5g2656 Chr5 27116697 27117125 +
Apr Apr6g0987 Chr6 14471610 14472479 -
Arst Arst5g03524 Chr5 94296762 94298119 +
Arst Arst5g03524 Chr5 94296762 94298119 +
Bach Bach1g01436 Chr1 27848505 27849205 -
Bach Bach1g01436 Chr1 27848505 27849205 -
Bva Bva04g00892 Chr04 5881071 5881876 +
Bva Bva03g00765 Chr03 4578225 4579108 +
Car Car08g01616 Chr08 25681019 25682376 -
Car Car06g00150 Chr06 1797849 1801529 -
Cca Cca08g00309 Chr08 4570015 4571199 +
Cca Cca09g02837 Chr09 53953698 53954676 +
Gma Gma07g00926 Chr07 10200632 10201383 +
Gma Gma08g00528 Chr08 4330025 4330934 +
Gso Gso7g0873 Chr7 9973250 9974494 +
Gso Gso7g0873 Chr7 9973250 9974494 +
Lal Lal15g0909 Chr15 6889726 6890968 -
Lal Lal10g0946 Chr10 16794765 16802043 +
Lapu Lapu4g00264 Chr4 2680438 2681850 +
Lapu Lapu3g03959 Chr3 62994734 62995736 +
Lasa Lasa1g04163 Chr1 711714559 711715412 +
Lasa Lasa7g05305 Chr7 721593044 721593709 +
Lja Lja2g2203 Chr2 25122590 25123689 +
Lja Lja4g0010 Chr4 95557 96291 -
Mal Mal6g3319 Chr6 96274374 96275314 +
Mepo Mepo7g00913 Chr7 14252204 14253635 -
Mesa Mesa22g02747 Chr22 72843955 72844383 +
Mtr Mtr6g1822 Chr6 33167003 33168627 +
Phac Phac4g01956 Chr4 46314149 46315862 +
Phco Phco5g00335 Chr5 2902728 2903462 +
Phco Phco4g03737 Chr4 56789536 56790203 +
Psa Psa1g0715 Chr1 46425889 46426713 +
Pste Pste9g01428 Chr9 13630262 13631244 -
Pte Pte9g00149 Chr9 1623780 1624715 +
Pumo Pumo6g02938 Chr6 69745363 69746590 -
Pumo Pumo6g02938 Chr6 69745363 69746590 -
Pvu Pvu4g1588 Chr4 43075614 43076874 -
Pvu Pvu2g3404 Chr2 48856767 48857706 +
Rops Rops5g00373 Chr5 6449023 6450113 +
Rops Rops2g00046 Chr2 876245 877118 -
Seca Seca10g04735 Chr10 108971817 108972989 -
Seca Seca12g07001 Chr12 161971179 161972036 +
Spst Spst4g02839 Chr4 68115360 68116111 +
Spst Spst3g00651 Chr3 9996716 9997378 -
Ssu Ssu5g3507 Chr5 85992854 85993509 +
Ssu Ssu5g3507 Chr5 85992854 85993509 +
Sto Sto8g4506 Chr8 47781588 47782313 -
Tsu Tsu06g03713 Chr06 49123311 49124419 -
Vian Vian1g04222 Chr1 65132804 65133468 +
Vifa Vifa1g07348 Chr1 1133009663 1133010350 +
Vifa Vifa1g07348 Chr1 1133009663 1133010350 +
Vimu Vimu8g01648 Chr8 22323759 22324493 +
Vimu Vimu11g04938 Chr11 68835035 68835845 +
Viun Viun4g00398 Chr4 2658915 2660164 +
Viun Viun3g00046 Chr3 210093 211076 -
Vivi Vivi4g00367 Chr4 8272448 8273618 +
Vivi Vivi5g06480 Chr5 171448806 171449782 -
Vra Vra1g0683 Chr1 8061722 8062884 +
Vvi Vvi17g0188 Chr17 1721767 1723034 -
Apr Apr6g0988 Chr6 14476042 14479107 -
Bva Bva04g00891 Chr04 5873112 5876313 +
Car Car08g01617 Chr08 25685351 25688156 -
Cca Cca08g00308 Chr08 4561091 4566225 +
Gma Gma07g00925 Chr07 10190879 10196888 +
Gso Gso7g0872 Chr7 9965476 9970009 +
Lja Lja2g2202 Chr2 25116238 25119868 +
Mal Mal6g3318 Chr6 96265604 96268707 +
Mtr Mtr6g1821 Chr6 33160747 33164402 +
Psa Psa1g0714 Chr1 46385309 46388386 +
Sto Sto8g4507 Chr8 47792700 47798452 -
Vra Vra1g0682 Chr1 8053176 8058382 +
Vvi Vvi17g0189 Chr17 1751559 1773113 +
Aed Aed7g0286 Chr7 2046697 2069529 -
Apr Apr6g0989 Chr6 14482911 14510093 +
Bach Bach1g01437 Chr1 27865379 27880958 +
Bva Bva03g00764 Chr03 4556777 4571156 -
Car Car08g01618 Chr08 25690841 25711329 +
Cca Cca08g00307 Chr08 4526005 4554256 -
Gma Gma07g00924 Chr07 10165213 10189434 -
Gso Gso7g0871 Chr7 9938239 9962629 -
Lal Lal8g0476 Chr8 3188244 3206539 +
Lapu Lapu4g00262 Chr4 2636639 2668090 -
Lasa Lasa1g04159 Chr1 711373957 711394915 -
Lja Lja2g2200 Chr2 25074769 25096733 -
Mal Mal6g3316 Chr6 96224480 96249555 -
Mepo Mepo7g00915 Chr7 14275232 14298011 +
Mesa Mesa22g02745 Chr22 72807422 72827762 -
Mtr Mtr6g1820 Chr6 33122176 33142160 -
Phco Phco5g00333 Chr5 2849312 2893808 -
Psa Psa1g0711 Chr1 46281820 46300511 -
Pste Pste9g01429 Chr9 13644373 13682180 +
Pte Pte9g00147 Chr9 1590455 1610468 -
Pumo Pumo6g02939 Chr6 69773180 69799264 +
Pvu Pvu4g1589 Chr4 43090741 43116648 +
Rops Rops5g00369 Chr5 6404271 6431366 -
Seca Seca10g04742 Chr10 109013901 109047822 +
Spst Spst4g02837 Chr4 68067483 68102556 -
Sto Sto8g4512 Chr8 47815044 47832253 +
Trre Trre11g02056 Chr11 23082867 23098005 +
Tsu Tsu06g03719 Chr06 49161016 49183453 +
Vian Vian8g01398 Chr8 33172739 33211859 +
Vifa Vifa1g07346 Chr1 1132841124 1132857387 -
Vimu Vimu8g01646 Chr8 22286438 22311304 -
Viun Viun4g00393 Chr4 2607022 2639299 -
Vivi Vivi4g00363 Chr4 8210175 8228022 -
Vra Vra1g0681 Chr1 8025067 8049048 -
Vvi Vvi17g0190 Chr17 1774080 1775152 -
Bva Bva03g00763 Chr03 4555141 4556391 +
Vvi Vvi17g0191 Chr17 1776563 1784446 +
Sto Sto8g4504 Chr8 47759393 47764150 -
Vvi Vvi17g0192 Chr17 1793718 1816394 +
Lal Lal16g0930 Chr16 6171686 6181208 -
Psa Psa7g0030 Chr7 857995 866670 -
Sto Sto8g4503 Chr8 47739374 47747474 -