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
Vvi17g0193 . . . . . . . . Aev05g3520 . Ahy15g2599 . Aip05g02905 . . . . . . . . . . . . . . . . . . . . . Dod02g3745 . . . . . . . . Gma09g01629 . . . . . . . Lal8g0475 Lal10g0947 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa1g0695 . . . . . . . . . . . . . . . . . . . . Sto8g4502 . . . . . . . . . . . . . . . . . .
Vvi17g0194 . . . . . . . . . . . . . . . . . . . Apr2g1595 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto8g4492 . . . . . . . . . . . . . . . . . .
Vvi17g0195 . . . . . . . . . . . . . . . . . . . Apr2g1594 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto8g4491 . . . . . . . . . . . . . . . . . .
Vvi17g0196 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lal8g0474 Lal10g0948 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa1g0700 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0197 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0198 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0199 Acco01g0586 . Accr1g00394 . Adu05g02778 . Aed7g0285 . . . . . . . . . . . Apr6g0990 . Arst5g03521 . Bach1g01439 . Bisa01g0453 . Bva04g00886 Bva03g00762 Car08g01619 . Cca08g00306 . Dere06g1705 . . . Enph12g1108 . Glsi01g1918 . Gma07g00923 . . Gma09g01633 Gso7g0870 . . Gso7g0870 . . . Lal8g0477 . Lal25g0483 . . . . . . . . Lasa1g04158 . Lele45g0403 Lele46g0422 Lele47g1001 Lele48g1066 . . . . Lja2g2197 . . Mal6g3312 Mepo7g00917 . Mesa22g02744 . Mibi01g3093 . . Mtr6g1819 . . . . Prci14g1778 . Psa1g0709 . Pste9g01430 . Pte16g00126 Pte9g00146 . . Pumo6g02941 . Pvu4g1590 . Rops5g00368 . Seca10g04744 . Spst4g02836 . . . . . . Tpr2g5241 Trre11g02057 . . Tsu06g03723 Vian8g01399 . Vifa1g07345 . Vimu8g01645 . Viun4g00391 . Vivi4g00361 . Vra1g0680 .
Vvi17g0200 Acco01g0589 . Accr1g00395 . Adu05g02777 . Aed7g0284 . . . Ahy15g2625 . Aip05g02936 . Alju02g3317 . . . Apr6g0991 . Arst5g03520 . . . Bisa01g0452 . . Bva03g00761 Car08g01620 . Cca08g00305 . Dere06g1707 . . . Enph12g1109 . Glsi01g1919 . Gma07g00922 . . Gma09g01637 Gso7g0869 . . Gso7g0869 . . . . . . . . . . . . . . Lasa1g04155 . Lele45g0404 Lele46g0423 Lele47g1000 Lele48g1065 . . . . . . . Mal6g3310 Mepo7g00918 . . . Mibi01g3092 . . Mtr6g1818 . . Phco5g00331 . Prci14g1776 . Psa1g0708 . Pste9g01431 . Pte16g00125 . . . Pumo6g02942 . Pvu4g1591 . Rops5g00367 . Seca10g04745 . Spst4g02835 . . . . . . . Trre11g02058 . . Tsu06g03724 Vian8g01401 . Vifa1g07344 . Vimu8g01642 . Viun4g00387 . Vivi4g00360 . Vra1g0678 .
Vvi17g0201 . . . . . Adu03g04059 . Aed5g2654 . . . . . . . . . . . Apr2g1588 . Arst3g05346 . Bach1g01440 . . . Bva03g00760 . Car06g00151 . Cca09g02836 . . . . . . . . . Gma08g00526 Gma05g02389 . . . . . . Lal16g0934 Lal23g0701 . . . . . . . . . . Lapu3g03957 . Lasa7g05303 . . . . . . . . . Lja4g0013 . . . Mepo2g05115 . Mesa13g00016 . . Mtr8g3891 . . . . Phco4g03735 . . . . . . . . . . . Pumo6g00052 . Pvu2g3402 . Rops2g00049 . Seca12g06998 . Spst3g00653 . Ssu5g3505 . Sto8g4513 . . . Trre7g05983 Tsu02g00017 . . Vian1g04220 . Vifa6g04180 . Vimu11g04936 . Viun3g00048 . Vivi5g06482 . .
Vvi17g0202 . . . . Adu05g02769 . Aed7g0281 . . . Ahy15g2633 . Aip05g02945 . . . . . Apr6g0995 . Arst5g03515 . . . . . . . Car08g01623 Car06g00155 Cca08g00302 . . . . . . . . . Gma07g00918 . . Gma09g01639 Gso7g0865 . . Gso7g0865 . . . Lal8g0479 . . . . . . . . Lapu4g00253 . Lasa1g04149 . . . . . . . . . Lja2g2191 . . Mal6g3304 Mepo7g00923 . Mesa22g02737 . . . . Mtr6g1812 . . Phco5g00326 . . . . . Pste9g01436 . . Pte9g00139 . . Pumo6g02946 . Pvu4g1597 . Rops5g00360 . Seca10g04756 . Spst4g02832 . Ssu5g3501 . . . . . Trre11g02077 . . Tsu06g03731 Vian8g01405 . Vifa1g07333 . Vimu8g01637 . Viun4g00383 . Vivi4g00356 . Vra1g0675 .
   
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Select Species Gene Chromosome Start End Strand
Vvi Vvi17g0193 Chr17 1821384 1823776 -
Aev Aev05g3520 Chr05 34406960 34409532 -
Ahy Ahy15g2599 Chr15 141400434 141404627 +
Aip Aip05g02905 Chr05 130543940 130547988 +
Dod Dod02g3745 Chr02 76338839 76342857 -
Gma Gma09g01629 Chr09 41646700 41650507 +
Lal Lal8g0475 Chr8 3184003 3187830 +
Lal Lal10g0947 Chr10 16803584 16807210 -
Psa Psa1g0695 Chr1 45513375 45517344 +
Sto Sto8g4502 Chr8 47732968 47737145 +
Vvi Vvi17g0194 Chr17 1830227 1832876 +
Apr Apr2g1595 Chr2 21701797 21706620 +
Sto Sto8g4492 Chr8 47658857 47663461 -
Vvi Vvi17g0195 Chr17 1833242 1853582 -
Apr Apr2g1594 Chr2 21697882 21709113 -
Sto Sto8g4491 Chr8 47653572 47658459 +
Vvi Vvi17g0196 Chr17 1857595 1861330 -
Lal Lal8g0474 Chr8 3177479 3183470 +
Lal Lal10g0948 Chr10 16808424 16811256 -
Psa Psa1g0700 Chr1 45658234 45662657 -
Vvi Vvi17g0197 Chr17 1868119 1879021 -
Vvi Vvi17g0198 Chr17 1884478 1897769 -
Vvi Vvi17g0199 Chr17 1901239 1903652 +
Acco Acco01g0586 Chr01 6859246 6861706 +
Accr Accr1g00394 Chr1 7556935 7559395 +
Adu Adu05g02778 Chr05 95593935 95596533 -
Aed Aed7g0285 Chr7 2044081 2045832 -
Apr Apr6g0990 Chr6 14511637 14514283 +
Arst Arst5g03521 Chr5 94252040 94254616 -
Bach Bach1g01439 Chr1 27884520 27886515 +
Bisa Bisa01g0453 Chr01 6463633 6466300 -
Bva Bva04g00886 Chr04 5842786 5845081 +
Bva Bva03g00762 Chr03 4551674 4553993 -
Car Car08g01619 Chr08 25742082 25745156 +
Cca Cca08g00306 Chr08 4520236 4523057 -
Dere Dere06g1705 Chr06 31731740 31734353 +
Enph Enph12g1108 Chr12 17954645 17957538 +
Glsi Glsi01g1918 Chr01 82639376 82643917 +
Gma Gma07g00923 Chr07 10159109 10162154 -
Gma Gma09g01633 Chr09 41698863 41702628 +
Gso Gso7g0870 Chr7 9932136 9935171 -
Gso Gso7g0870 Chr7 9932136 9935171 -
Lal Lal8g0477 Chr8 3207466 3210449 +
Lal Lal25g0483 Chr25 3350208 3353736 +
Lasa Lasa1g04158 Chr1 711222718 711224562 -
Lele Lele45g0403 Chr45 3142247 3149613 +
Lele Lele46g0422 Chr46 2850392 2852529 +
Lele Lele47g1001 Chr47 15945111 15947215 -
Lele Lele48g1066 Chr48 15493438 15495502 -
Lja Lja2g2197 Chr2 25049621 25052086 +
Mal Mal6g3312 Chr6 96148316 96150822 -
Mepo Mepo7g00917 Chr7 14309404 14312224 +
Mesa Mesa22g02744 Chr22 72794412 72796816 -
Mibi Mibi01g3093 Chr01 54743328 54745676 -
Mtr Mtr6g1819 Chr6 33106256 33108924 -
Prci Prci14g1778 Chr14 25203142 25205912 -
Psa Psa1g0709 Chr1 46234614 46237436 -
Pste Pste9g01430 Chr9 13688212 13690990 +
Pte Pte16g00126 Chr16 1415179 1417610 -
Pte Pte9g00146 Chr9 1585895 1588381 -
Pumo Pumo6g02941 Chr6 69809001 69809390 +
Pvu Pvu4g1590 Chr4 43119230 43122061 +
Rops Rops5g00368 Chr5 6400174 6402506 -
Seca Seca10g04744 Chr10 109051321 109052314 +
Spst Spst4g02836 Chr4 68063680 68065788 -
Tpr Tpr2g5241 Chr2 58976297 58979722 +
Trre Trre11g02057 Chr11 23100744 23103105 +
Tsu Tsu06g03723 Chr06 49213750 49216990 +
Vian Vian8g01399 Chr8 33214114 33216597 +
Vifa Vifa1g07345 Chr1 1132731238 1132733008 -
Vimu Vimu8g01645 Chr8 22282072 22284532 -
Viun Viun4g00391 Chr4 2602084 2605175 -
Vivi Vivi4g00361 Chr4 8202023 8204184 -
Vra Vra1g0680 Chr1 8020506 8023351 -
Vvi Vvi17g0200 Chr17 1904122 1909229 -
Acco Acco01g0589 Chr01 6866115 6868243 -
Accr Accr1g00395 Chr1 7564062 7567971 -
Adu Adu05g02777 Chr05 95584222 95588483 +
Aed Aed7g0284 Chr7 2024443 2034465 +
Ahy Ahy15g2625 Chr15 141850374 141854971 -
Aip Aip05g02936 Chr05 130985213 130989453 -
Alju Alju02g3317 Chr02 50991917 50995772 +
Apr Apr6g0991 Chr6 14514867 14518626 -
Arst Arst5g03520 Chr5 94242206 94246827 +
Bisa Bisa01g0452 Chr01 6457192 6461752 +
Bva Bva03g00761 Chr03 4548839 4550947 +
Car Car08g01620 Chr08 25745835 25750742 -
Cca Cca08g00305 Chr08 4511685 4516848 +
Dere Dere06g1707 Chr06 31739983 31744386 -
Enph Enph12g1109 Chr12 17958132 17962626 -
Glsi Glsi01g1919 Chr01 82644974 82654128 -
Gma Gma07g00922 Chr07 10153040 10156921 +
Gma Gma09g01637 Chr09 41812279 41816774 +
Gso Gso7g0869 Chr7 9925935 9930032 +
Gso Gso7g0869 Chr7 9925935 9930032 +
Lasa Lasa1g04155 Chr1 711217698 711221994 +
Lele Lele45g0404 Chr45 3151166 3154742 -
Lele Lele46g0423 Chr46 2853700 2868889 -
Lele Lele47g1000 Chr47 15940945 15943913 +
Lele Lele48g1065 Chr48 15487549 15492572 +
Mal Mal6g3310 Chr6 96120149 96124955 +
Mepo Mepo7g00918 Chr7 14313717 14319111 -
Mibi Mibi01g3092 Chr01 54738381 54742222 +
Mtr Mtr6g1818 Chr6 33099311 33104915 +
Phco Phco5g00331 Chr5 2822960 2826643 +
Prci Prci14g1776 Chr14 25196923 25201172 +
Psa Psa1g0708 Chr1 46224715 46229704 +
Pste Pste9g01431 Chr9 13693122 13697885 -
Pte Pte16g00125 Chr16 1411095 1414535 +
Pumo Pumo6g02942 Chr6 69814614 69819270 -
Pvu Pvu4g1591 Chr4 43123947 43127891 -
Rops Rops5g00367 Chr5 6393753 6398797 +
Seca Seca10g04745 Chr10 109054751 109059958 -
Spst Spst4g02835 Chr4 68058153 68062207 +
Trre Trre11g02058 Chr11 23104322 23108814 -
Tsu Tsu06g03724 Chr06 49219641 49223431 -
Vian Vian8g01401 Chr8 33226797 33230805 -
Vifa Vifa1g07344 Chr1 1132692729 1132704588 +
Vimu Vimu8g01642 Chr8 22267453 22271552 +
Viun Viun4g00387 Chr4 2569718 2574315 +
Vivi Vivi4g00360 Chr4 8197200 8201084 +
Vra Vra1g0678 Chr1 8007638 8012092 +
Vvi Vvi17g0201 Chr17 1919351 1929815 +
Adu Adu03g04059 Chr03 129696552 129701821 -
Aed Aed5g2654 Chr5 27109557 27117324 -
Apr Apr2g1588 Chr2 21665891 21671623 -
Arst Arst3g05346 Chr3 128460698 128465900 -
Bach Bach1g01440 Chr1 27889428 27893808 +
Bva Bva03g00760 Chr03 4536254 4540812 -
Car Car06g00151 Chr06 1805587 1811281 +
Cca Cca09g02836 Chr09 53944651 53948874 -
Gma Gma08g00526 Chr08 4322617 4325966 -
Gma Gma05g02389 Chr05 44695666 44698477 -
Lal Lal16g0934 Chr16 6199794 6205023 +
Lal Lal23g0701 Chr23 9679137 9687177 -
Lapu Lapu3g03957 Chr3 62985653 62989576 -
Lasa Lasa7g05303 Chr7 721405664 721411406 -
Lja Lja4g0013 Chr4 109291 113289 +
Mepo Mepo2g05115 Chr2 58987633 58994814 -
Mesa Mesa13g00016 Chr13 201698 206195 +
Mtr Mtr8g3891 Chr8 49521951 49528302 -
Phco Phco4g03735 Chr4 56782324 56787157 -
Pumo Pumo6g00052 Chr6 569186 573163 +
Pvu Pvu2g3402 Chr2 48848269 48853063 -
Rops Rops2g00049 Chr2 897407 902361 +
Seca Seca12g06998 Chr12 161939812 161946321 -
Spst Spst3g00653 Chr3 10000891 10004908 +
Ssu Ssu5g3505 Chr5 85979920 85984199 -
Sto Sto8g4513 Chr8 47836681 47842610 +
Trre Trre7g05983 Chr7 64120567 64124739 -
Tsu Tsu02g00017 Chr02 112521 117486 +
Vian Vian1g04220 Chr1 65124238 65128564 -
Vifa Vifa6g04180 Chr6 1373922021 1373926901 -
Vimu Vimu11g04936 Chr11 68826901 68831142 -
Viun Viun3g00048 Chr3 215410 219417 +
Vivi Vivi5g06482 Chr5 171461863 171467764 +
Vvi Vvi17g0202 Chr17 1966859 1969611 -
Adu Adu05g02769 Chr05 95378955 95381484 +
Aed Aed7g0281 Chr7 1990968 1993397 +
Ahy Ahy15g2633 Chr15 142153015 142155555 -
Aip Aip05g02945 Chr05 131288965 131291483 -
Apr Apr6g0995 Chr6 14594883 14597076 -
Arst Arst5g03515 Chr5 94037069 94039585 +
Car Car08g01623 Chr08 25831745 25834069 -
Car Car06g00155 Chr06 1836974 1838014 -
Cca Cca08g00302 Chr08 4408832 4411368 +
Gma Gma07g00918 Chr07 10086115 10088104 +
Gma Gma09g01639 Chr09 41870211 41872006 -
Gso Gso7g0865 Chr7 9855389 9860267 +
Gso Gso7g0865 Chr7 9855389 9860267 +
Lal Lal8g0479 Chr8 3237048 3239338 -
Lapu Lapu4g00253 Chr4 2533033 2535579 +
Lasa Lasa1g04149 Chr1 710267569 710268648 +
Lja Lja2g2191 Chr2 24937981 24940951 +
Mal Mal6g3304 Chr6 95972232 95974339 +
Mepo Mepo7g00923 Chr7 14423070 14425816 -
Mesa Mesa22g02737 Chr22 72615066 72617103 +
Mtr Mtr6g1812 Chr6 33009083 33011669 +
Phco Phco5g00326 Chr5 2760456 2762488 +
Pste Pste9g01436 Chr9 13773524 13776208 -
Pte Pte9g00139 Chr9 1513220 1515641 -
Pumo Pumo6g02946 Chr6 69884825 69887915 -
Pvu Pvu4g1597 Chr4 43186492 43189050 -
Rops Rops5g00360 Chr5 6305617 6307805 +
Seca Seca10g04756 Chr10 109318237 109320816 -
Spst Spst4g02832 Chr4 67990310 67992324 +
Ssu Ssu5g3501 Chr5 85905698 85906610 +
Trre Trre11g02077 Chr11 23500971 23505047 -
Tsu Tsu06g03731 Chr06 49381196 49384227 -
Vian Vian8g01405 Chr8 33316225 33317860 -
Vifa Vifa1g07333 Chr1 1128701055 1128702269 +
Vimu Vimu8g01637 Chr8 22217366 22219490 +
Viun Viun4g00383 Chr4 2512656 2515052 +
Vivi Vivi4g00356 Chr4 7913352 7914809 +
Vra Vra1g0675 Chr1 7958259 7960640 +