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
Vvi16g1079 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1080 . . . . . . Aed1g2330 . . . . . . . . . . . . . . . . . . . . . . . Cca02g02189 . . . . . . . . . Gma09g01191 . . . Gso9g1028 . . . . . . . Lal12g0074 Lal13g0066 . . . . . . . . . . . . . . . . . . . Lja5g0690 Mal1g2126 . . . . . . . Mtr1g3680 . . . Phco9g01860 . . . Psa6g4442 . Pste1g04089 . . . . . Pumo11g00484 . Pvu11g1734 . . . . . Spst11g00513 . Ssu7g0857 . Sto10g2296 . Tpr1g0824 . . . Tsu01g04346 . . . . . Vimu5g00457 . . . . . Vra8g2173 .
Vvi16g1081 . . . . . Adu09g03039 . . Aev05g2828 Aev09g2157 Ahy15g3623 Ahy19g2844 Aip05g03938 Aip09g03305 . . . Amo19g3619 . . . Arst9g04075 . . . . Bva03g02487 . . . . . . . Dod02g2946 . . . . . Gma10g02170 . . . Gso10g2034 . . . . . . . . . . . . . . . . . . Lasa6g04003 . . . . . . . . . Lja5g0691 Mal1g2128 . . Mepo4g04179 . . . . Mtr1g3678 . . Phac7g01185 Phco9g01859 Phco6g02398 . . Psa6g4441 . Pste1g04087 . . . Pte16g00338 . Pumo11g00522 Pumo3g01090 Pvu11g1731 Pvu7g0801 . Rops6g02638 . Seca8g07317 Spst11g00516 Spst10g00891 . . Sto10g2278 . Tpr1g0825 . . Trre1g05304 Tsu01g04345 . Vian5g00259 Vian3g00689 . Vifa3g02832 Vimu5g00464 Vimu3g02966 . Viun7g03156 . Vivi1g04481 . .
Vvi16g1082 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Gma16g01514 . . . Gso16g1417 . . . . . . Lal24g0065 . . . . . . . . . . . . . . . . . . . . . Lja5g0692 Mal1g2129 . . . . . . . Mtr1g3677 . . . . . . . . . Pste1g04085 . . . . . Pumo11g00524 . Pvu11g1730 . . . . . Spst11g00523 . . . Sto10g2276 . Tpr1g0827 . . . Tsu01g04344 . Vian5g00260 . . . Vimu5g00465 . . . . . . .
Vvi16g1083 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Gma16g00264 . . . Gso16g0241 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1084 . . . . . . . Aed7g0682 . . Ahy17g2677 . Aip07g02922 . . . . . . Apr6g0608 . . . . . . . . . . . Cca08g00765 . . . . . . . . Gma16g01513 . . . Gso16g1416 . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja2g2708 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ssu9g0013 Sto10g2265 . . . . . . . . . . . . . . . . . . .
Vvi16g1085 . . . . . . . . . Aev09g2156 . Ahy19g2843 . Aip09g03304 . . . . . . . . . . . . Bva03g02488 . . . . . . . . Dod06g0866 . . . . . . . . . . . . . . . . Lal12g0075 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto10g2263 . . . . . . . . . . . . . . . . . . .
Vvi16g1086 . . . . Adu05g03460 . . Aed7g0685 Aev05g2826 . Ahy15g3624 . Aip05g03939 . . . . . . Apr6g0607 Arst5g04445 . Bach1g00040 . . . Bva03g02489 . . . . Cca08g00766 . . Dod02g2941 . . . . . Gma16g01512 . . . Gso16g1415 . . . . . . . . . . . . . . . Lapu4g00784 . Lasa1g02776 . . . . . . . . . Lja2g2709 . . . Mepo5g04016 . Mesa22g01278 . . . . . . . . . . . . . Pste9g01069 . . . . . Pumo6g02480 . Pvu4g1077 . Rops5g01005 . . . Spst4g01882 . . Ssu9g0012 . . . . Trre11g00957 . . . Vian8g00951 . Vifa1g04838 . . . Viun4g01972 . Vivi2g05175 . . Vra1g1675
Vvi16g1087 . . . . . . Aed1g2332 . . Aev09g2154 . Ahy19g2842 . Aip09g03303 . . . Amo19g3617 . Apr6g0606 . . . . . . Bva03g02490 . . . Cca02g02187 Cca08g00768 . . . . . . . . Gma10g02166 . . . Gso10g2032 . . . . Lal2g0970 . Lal24g0066 Lal12g0076 . . . . . . . . . Lasa1g02525 Lasa6g04002 . . . . . . . . Lja2g2711 Lja5g0693 . . . . Mesa22g01279 . . . . . . . . . . . Psa6g4438 . . . . . . . . . Pvu4g1073 Pvu7g0802 . . . . . . . . Sto10g2255 . . . . . . . . . . . . . . . . . Vra8g2171 .
Vvi16g1088 . . . . Adu08g00464 . . . . . . . . . . . . . . . Arst8g00594 . . . . . Bva12g01987 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja1g5737 . . . . . . . . . . . . Phco7g01386 . . . . . Pste2g03381 . . . . . . . Pvu9g1419 . . . . . Spst9g01426 . . . . . . . . . . . . . . . Vimu10g02434 . Viun9g02242 . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Apr Apr6g0608 Chr6 8752876 8755475 +
Vvi Vvi16g1079 Chr16 19171464 19171505 +
Vvi Vvi16g1080 Chr16 19171528 19172421 -
Aed Aed1g2330 Chr1 19322818 19323738 -
Cca Cca02g02189 Chr02 42407509 42408715 +
Gma Gma09g01191 Chr09 32561614 32563371 +
Gso Gso9g1028 Chr9 29426807 29428511 +
Lal Lal12g0074 Chr12 482642 483850 -
Lal Lal13g0066 Chr13 397142 402905 -
Lja Lja5g0690 Chr5 6201085 6202586 -
Mal Mal1g2126 Chr1 27781393 27782265 -
Mtr Mtr1g3680 Chr1 48493517 48494634 +
Phco Phco9g01860 Chr9 43114798 43115682 -
Psa Psa6g4442 Chr6 390661858 390663338 +
Pste Pste1g04089 Chr1 23932515 23935078 -
Pumo Pumo11g00484 Chr11 17696207 17698718 -
Pvu Pvu11g1734 Chr11 43710467 43711598 -
Spst Spst11g00513 Chr11 26931233 26932392 -
Ssu Ssu7g0857 Chr7 17556801 17557703 -
Sto Sto10g2296 Chr10 33095049 33095987 +
Tpr Tpr1g0824 Chr1 6879739 6880960 -
Tsu Tsu01g04346 Chr01 51416827 51417705 +
Vimu Vimu5g00457 Chr5 4495713 4496597 +
Vra Vra8g2173 Chr8 40114473 40115564 +
Vvi Vvi16g1081 Chr16 19180777 19188753 -
Adu Adu09g03039 Chr09 117989201 117991662 -
Aev Aev05g2828 Chr05 29304061 29310084 -
Aev Aev09g2157 Chr09 24552662 24557345 +
Ahy Ahy15g3623 Chr15 158994274 158995704 +
Ahy Ahy19g2844 Chr19 150718254 150720856 +
Aip Aip05g03938 Chr05 147603724 147605157 +
Aip Aip09g03305 Chr09 139450086 139451723 +
Amo Amo19g3619 Chr19 151138101 151139252 +
Arst Arst9g04075 Chr9 115868687 115870050 -
Bva Bva03g02487 Chr03 21000902 21001954 -
Dod Dod02g2946 Chr02 62293265 62366055 -
Gma Gma10g02170 Chr10 49246658 49247977 +
Gso Gso10g2034 Chr10 47367807 47368959 +
Lasa Lasa6g04003 Chr6 611225915 611226799 -
Lja Lja5g0691 Chr5 6207396 6208729 +
Mal Mal1g2128 Chr1 27796632 27797528 -
Mepo Mepo4g04179 Chr4 51721044 51722092 +
Mtr Mtr1g3678 Chr1 48482480 48483602 +
Phac Phac7g01185 Chr7 7616572 7617744 -
Phco Phco9g01859 Chr9 43093030 43094190 -
Phco Phco6g02398 Chr6 45371762 45372664 +
Psa Psa6g4441 Chr6 390551207 390552443 +
Pste Pste1g04087 Chr1 23903339 23905511 +
Pte Pte16g00338 Chr16 4464532 4465530 -
Pumo Pumo11g00522 Chr11 18696105 18697144 -
Pumo Pumo3g01090 Chr3 17398685 17399686 +
Pvu Pvu11g1731 Chr11 43676866 43678126 +
Pvu Pvu7g0801 Chr7 7269770 7270959 -
Rops Rops6g02638 Chr6 47371084 47372127 -
Seca Seca8g07317 Chr8 169818889 169819779 +
Spst Spst11g00516 Chr11 26977147 26978167 +
Spst Spst10g00891 Chr10 9666066 9667019 +
Sto Sto10g2278 Chr10 32889965 32890867 -
Tpr Tpr1g0825 Chr1 6881608 6882792 -
Trre Trre1g05304 Chr1 59003481 59005119 +
Tsu Tsu01g04345 Chr01 51410862 51416112 +
Vian Vian5g00259 Chr5 5423050 5424124 -
Vian Vian3g00689 Chr3 7048366 7049268 -
Vifa Vifa3g02832 Chr3 795538332 795539210 +
Vimu Vimu5g00464 Chr5 4569284 4570845 -
Vimu Vimu3g02966 Chr3 43757647 43759394 +
Viun Viun7g03156 Chr7 34212179 34213312 +
Vivi Vivi1g04481 Chr1 95379866 95381092 -
Vvi Vvi16g1082 Chr16 19193725 19194618 -
Gma Gma16g01514 Chr16 35012437 35013937 +
Gso Gso16g1417 Chr16 34155589 34157150 +
Lal Lal24g0065 Chr24 397460 398350 -
Lja Lja5g0692 Chr5 6230088 6231726 -
Mal Mal1g2129 Chr1 27812550 27813437 -
Mtr Mtr1g3677 Chr1 48478993 48480140 +
Pste Pste1g04085 Chr1 23866748 23870171 -
Pumo Pumo11g00524 Chr11 18799417 18800863 +
Pvu Pvu11g1730 Chr11 43645622 43646833 +
Spst Spst11g00523 Chr11 27194557 27197909 -
Sto Sto10g2276 Chr10 32880042 32881028 +
Tpr Tpr1g0827 Chr1 6892601 6893675 -
Tsu Tsu01g04344 Chr01 51391436 51392688 -
Vian Vian5g00260 Chr5 5483966 5497271 -
Vimu Vimu5g00465 Chr5 4594316 4595419 -
Vvi Vvi16g1083 Chr16 19198071 19200931 -
Gma Gma16g00264 Chr16 2804695 2813807 -
Gso Gso16g0241 Chr16 2777855 2780884 -
Vvi Vvi16g1084 Chr16 19205060 19207096 -
Aed Aed7g0682 Chr7 5058399 5059334 -
Ahy Ahy17g2677 Chr17 124043802 124048344 +
Aip Aip07g02922 Chr07 115175983 115181783 +
Apr Apr6g0608 Chr6 8752876 8755475 +
Cca Cca08g00765 Chr08 14989729 14991810 -
Gma Gma16g01513 Chr16 35006472 35010064 +
Gso Gso16g1416 Chr16 34149470 34152558 +
Lja Lja2g2708 Chr2 39389094 39391170 -
Ssu Ssu9g0013 Chr9 2617445 2618203 +
Sto Sto10g2265 Chr10 32746699 32748723 +
Vvi Vvi16g1085 Chr16 19209266 19213829 -
Aev Aev09g2156 Chr09 24546490 24547740 +
Ahy Ahy19g2843 Chr19 150709925 150714215 +
Aip Aip09g03304 Chr09 139442055 139446073 +
Bva Bva03g02488 Chr03 21004072 21008021 -
Dod Dod06g0866 Chr06 10789253 10793619 -
Lal Lal12g0075 Chr12 485281 489027 -
Sto Sto10g2263 Chr10 32722100 32733491 +
Vvi Vvi16g1086 Chr16 19214898 19218689 +
Adu Adu05g03460 Chr05 107068036 107069674 -
Aed Aed7g0685 Chr7 5068638 5071483 -
Aev Aev05g2826 Chr05 29297492 29298882 +
Ahy Ahy15g3624 Chr15 158996302 158998179 -
Aip Aip05g03939 Chr05 147605459 147607246 -
Apr Apr6g0607 Chr6 8749035 8751904 +
Arst Arst5g04445 Chr5 105743779 105745410 -
Bach Bach1g00040 Chr1 427597 429955 +
Bva Bva03g02489 Chr03 21008741 21011724 -
Cca Cca08g00766 Chr08 14993321 14996313 -
Dod Dod02g2941 Chr02 62189324 62191317 +
Gma Gma16g01512 Chr16 34999685 35003538 +
Gso Gso16g1415 Chr16 34143018 34146737 +
Lapu Lapu4g00784 Chr4 18724955 18727166 -
Lasa Lasa1g02776 Chr1 542718693 542720516 +
Lja Lja2g2709 Chr2 39397032 39399868 -
Mepo Mepo5g04016 Chr5 50184708 50188376 -
Mesa Mesa22g01278 Chr22 24846764 24847165 +
Pste Pste9g01069 Chr9 7693557 7697019 +
Pumo Pumo6g02480 Chr6 56982790 56991872 +
Pvu Pvu4g1077 Chr4 29907077 29910437 +
Rops Rops5g01005 Chr5 20171405 20174831 +
Spst Spst4g01882 Chr4 59391114 59402399 -
Ssu Ssu9g0012 Chr9 2608532 2612689 +
Trre Trre11g00957 Chr11 8374414 8377813 -
Vian Vian8g00951 Chr8 24167408 24179176 +
Vifa Vifa1g04838 Chr1 756079989 756081530 +
Viun Viun4g01972 Chr4 34915252 34917538 +
Vivi Vivi2g05175 Chr2 174344166 174346135 -
Vra Vra1g1675 Chr1 30604356 30606706 +
Vvi Vvi16g1087 Chr16 19219262 19225074 -
Aed Aed1g2332 Chr1 19331245 19339552 -
Aev Aev09g2154 Chr09 24537605 24543121 +
Ahy Ahy19g2842 Chr19 150701210 150708328 +
Aip Aip09g03303 Chr09 139434357 139439922 +
Amo Amo19g3617 Chr19 151114985 151121828 +
Apr Apr6g0606 Chr6 8718679 8725440 -
Bva Bva03g02490 Chr03 21012571 21019742 -
Cca Cca02g02187 Chr02 42387159 42394233 +
Cca Cca08g00768 Chr08 15005923 15013913 -
Gma Gma10g02166 Chr10 49218403 49224663 +
Gso Gso10g2032 Chr10 47336018 47344010 +
Lal Lal2g0970 Chr2 6519959 6529892 -
Lal Lal24g0066 Chr24 401914 414902 -
Lal Lal12g0076 Chr12 489349 496186 -
Lasa Lasa1g02525 Chr1 335203823 335209738 +
Lasa Lasa6g04002 Chr6 611219841 611225525 +
Lja Lja2g2711 Chr2 39438276 39448933 -
Lja Lja5g0693 Chr5 6233585 6248400 -
Mesa Mesa22g01279 Chr22 24860101 24866222 -
Psa Psa6g4438 Chr6 390416561 390424548 +
Pvu Pvu4g1073 Chr4 29623208 29629409 -
Pvu Pvu7g0802 Chr7 7274326 7281929 -
Sto Sto10g2255 Chr10 32635327 32647880 +
Vra Vra8g2171 Chr8 40079431 40086288 +
Vvi Vvi16g1088 Chr16 19231180 19234145 +
Adu Adu08g00464 Chr08 8413014 8416371 +
Arst Arst8g00594 Chr8 8384798 8388264 +
Bva Bva12g01987 Chr12 15732507 15733473 +
Lja Lja1g5737 Chr1 101845777 101848363 +
Phco Phco7g01386 Chr7 12607911 12611112 -
Pste Pste2g03381 Chr2 33876724 33881847 -
Pvu Pvu9g1419 Chr9 20134058 20139975 -
Spst Spst9g01426 Chr9 14208175 14210695 -
Vimu Vimu10g02434 Chr10 35304727 35306946 -
Viun Viun9g02242 Chr9 31871413 31875050 +
Sto Sto10g2265 Chr10 32746699 32748723 +