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
Vvi1g0481 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva11g00630 . . . . . . . . . . . . . . . . . . . . . . . . . Lal15g0988 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto11g0575 . . . . . . . . . . . . . . . . . . .
Vvi1g0482 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0483 . . . . . . . . . . . . . . . . . . Apr7g1321 . . . . . . . . Bva11g00628 Car04g02885 . . . . . . . . . . . . . . . . . . . . Lal22g0927 . . . . . . . . . . . . . . . . . . . . . . Lja2g3234 . Mal1g5027 . . . . . . . Mtr1g0951 . . . . Phco8g03095 . . . . . Pste1g03083 . . . Pte12g00949 . . . Pvu3g0341 . . . . . Spst2g01968 . . Sto11g0572 Sto6g2645 Tpr1g3014 . . . Tsu01g01077 . . . . . . . . . . Vivi4g04535 . .
Vvi1g0484 Acco11g0200 . Accr9g01999 . . . . . . . . . . . Alju09g0238 . . . . Apr3g1598 Arst5g04111 . . . Bisa11g0519 . Bva01g01580 . Car06g01775 . . . Dere09g2176 . . . Enph13g0619 . Glsi05g0248 . . . . . . . . . . . . Lal23g0869 . Lal15g0730 . . . . . . Lapu3g02525 . Lasa7g02956 . Lele49g1197 Lele50g1643 Lele51g1218 Lele52g1598 . . . . . . . . Mepo2g03045 . . . Mibi12g0198 . . . . . Phco4g01814 . Prci10g2812 . . Psa7g2964 Pste3g04118 . Pte14g00427 . . . . . Pvu2g0979 . . . . . Spst3g02260 . . . . Sto6g2643 . . Trre7g01920 . . . . . . . Vimu11g02611 . . . Vivi5g03812 . . .
Vvi1g0485 Acco11g0198 . Accr9g02002 . . . . . . . . . . . Alju09g0236 . . . . Apr3g1597 . . . . Bisa11g0518 . Bva01g01579 Bva11g00626 Car06g01776 . . . Dere09g2178 . . . Enph13g0620 . Glsi05g0247 . . . . . . . . . . . . . Lal16g0767 Lal15g0731 . . . . . . . . Lasa7g02955 . Lele49g1196 Lele50g1645 Lele51g1216 Lele52g1600 . . . . . . . . Mepo2g03044 . . . Mibi12g0196 . . . . . Phco4g01815 . Prci10g2816 . . . Pste3g04117 . . . . . . . Pvu2g0980 . . . . . Spst3g02262 . . . . Sto6g2642 . . Trre7g01921 . . . . . . . Vimu11g02614 . . . Vivi5g03810 . . .
Vvi1g0486 . . . . . . . . . . . . . . . . . . . Apr3g1594 . . . . . . Bva01g01578 Bva11g00625 Car06g01779 . . . . . . . . . . . . . . . . . . . . . . Lal23g0868 Lal16g0768 Lal15g0732 . . . . . . Lapu3g02528 . Lasa7g02950 . . . . . . . . . . . . . Mepo2g03041 . . . . . . . . . Phco4g01820 . . . . . Pste3g04115 . . . . . . . Pvu2g0982 . . . . . Spst3g02264 . . . Sto11g0569 . . . Trre7g01924 . . . . . . . Vimu11g02618 . . . Vivi5g03807 . . .
Vvi1g0487 . . . . . . . . . . . . . . . . . . . Apr3g1592 . . . . . . Bva01g01577 Bva11g00624 Car06g01781 . . . . . . . . . . . . . . . . . . . . . . Lal23g0867 Lal16g0769 . . . . . . . Lapu3g02529 . Lasa7g02947 . . . . . . . . . . . . . . . . . . . . . . . Phco4g01821 . . . . . Pste3g04114 . . . . . . . Pvu2g0983 . . . . . Spst3g02266 . . . Sto11g0568 . . . . . . . . . . . Vimu11g02620 . . . Vivi5g03806 . . .
Vvi1g0488 Acco11g0194 . Accr9g02005 . . . . . . . . . . . Alju09g0234 . . . Apr7g1318 Apr3g1589 . . . . Bisa11g0516 . Bva01g01576 Bva11g00623 Car06g01783 . Cca06g00288 . Dere09g2180 . . . Enph13g0622 . Glsi05g0244 . . . . . . . . . Lal6g1040 Lal22g0928 . Lal23g0866 . Lal15g0735 . . . . . . Lapu3g02531 . Lasa7g02945 . Lele49g1194 . Lele51g1214 . . . . . . . Mal1g5014 . Mepo2g03040 . . . Mibi12g0195 . Mtr1g0967 . . . Phco4g01824 . Prci10g2818 . . Psa7g2976 Pste1g01488 . . . . . . . Pvu2g0985 . . . . . Spst3g02268 . Ssu2g1227 . Sto11g0562 Sto6g2640 . . . . . . . . . . Vimu11g02622 . . . Vivi2g02089 . . .
Vvi1g0489 . . . . . . . . . . . . . . . . . . . Apr3g1588 . . . . . . Bva01g01574 Bva11g00622 Car06g01784 . . . . . . . . . . . . . . . . . . . . . . . . Lal15g0736 . . . . . . Lapu3g02532 . Lasa7g02944 . . . . . . . . . . . . . Mepo2g03039 . . . . . . . . . Phco4g01829 . . . . Psa7g2979 Pste3g04109 . . . . . . . Pvu2g0986 . . . . . Spst3g02270 . . . Sto11g0561 . . . Trre7g01927 . . . . . . . Vimu11g02623 . . . Vivi5g03803 . . .
Vvi1g0490 . . . . . . . . . . . . . . . . . . . Apr3g1587 . . . . . . Bva01g01573 Bva11g00621 Car06g01785 . . . . . . . . . . . . . . . . . . . . . . Lal23g0865 Lal16g0770 Lal15g0737 . . . . . . Lapu3g02533 . Lasa7g02943 . . . . . . . . . . . . . Mepo2g03038 . . . . . . . . . Phco4g01830 . . . . . Pste3g04108 . . . . . . . Pvu2g0987 . . . . . Spst3g02271 . . . Sto11g0560 . . . Trre7g01928 . . . . . . . Vimu11g02624 . . . Vivi5g03801 . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi1g0481 Chr1 4565691 4571201 -
Bva Bva11g00630 Chr11 9635218 9641974 +
Lal Lal15g0988 Chr15 7892286 7894946 +
Sto Sto11g0575 Chr11 6881705 6886902 +
Vvi Vvi1g0482 Chr1 4583341 4584933 -
Vvi Vvi1g0483 Chr1 4586268 4590991 -
Apr Apr7g1321 Chr7 20299849 20303321 +
Bva Bva11g00628 Chr11 9626481 9631217 +
Car Car04g02885 Chr04 55734093 55766364 +
Lal Lal22g0927 Chr22 7354119 7359200 -
Lja Lja2g3234 Chr2 71119831 71126295 +
Mal Mal1g5027 Chr1 120952504 120954808 +
Mtr Mtr1g0951 Chr1 10980231 10983046 -
Phco Phco8g03095 Chr8 45316020 45318766 +
Pste Pste1g03083 Chr1 13820549 13824665 +
Pte Pte12g00949 Chr12 13497860 13500885 +
Pvu Pvu3g0341 Chr3 3264030 3267310 -
Spst Spst2g01968 Chr2 18708307 18711712 +
Sto Sto11g0572 Chr11 6862416 6865879 +
Sto Sto6g2645 Chr6 33518784 33529917 +
Tpr Tpr1g3014 Chr1 34546722 34549398 +
Tsu Tsu01g01077 Chr01 9961124 9963886 -
Vivi Vivi4g04535 Chr4 172725850 172728686 +
Vvi Vvi1g0484 Chr1 4612464 4628112 +
Acco Acco11g0200 Chr11 2515539 2526603 -
Accr Accr9g01999 Chr9 43441388 43452354 +
Alju Alju09g0238 Chr09 3205641 3217965 -
Apr Apr3g1598 Chr3 31192580 31223593 -
Arst Arst5g04111 Chr5 102846216 102855429 +
Bisa Bisa11g0519 Chr11 13973983 14010106 -
Bva Bva01g01580 Chr01 17178552 17190601 -
Car Car06g01775 Chr06 17617757 17634596 +
Dere Dere09g2176 Chr09 31135859 31150454 +
Enph Enph13g0619 Chr13 12519050 12537459 +
Glsi Glsi05g0248 Chr05 48180694 48246759 -
Lal Lal23g0869 Chr23 11003167 11019120 -
Lal Lal15g0730 Chr15 5117291 5135073 +
Lapu Lapu3g02525 Chr3 47316171 47339765 +
Lasa Lasa7g02956 Chr7 562629657 562648739 -
Lele Lele49g1197 Chr49 7949558 7966112 -
Lele Lele50g1643 Chr50 21480178 21490555 +
Lele Lele51g1218 Chr51 8017462 8020578 -
Lele Lele52g1598 Chr52 19873155 19884982 +
Mepo Mepo2g03045 Chr2 40083530 40099105 -
Mibi Mibi12g0198 Chr12 3957412 3971438 -
Phco Phco4g01814 Chr4 34880801 34909952 +
Prci Prci10g2812 Chr10 36594037 36608024 +
Psa Psa7g2964 Chr7 215422914 215443408 -
Pste Pste3g04118 Chr3 36408810 36429289 -
Pte Pte14g00427 Chr14 22263159 22275721 +
Pvu Pvu2g0979 Chr2 17163692 17193014 +
Spst Spst3g02260 Chr3 65510707 65512540 +
Sto Sto6g2643 Chr6 33486936 33501991 -
Trre Trre7g01920 Chr7 15086103 15100770 +
Vimu Vimu11g02611 Chr11 46346280 46359952 +
Vivi Vivi5g03812 Chr5 132251812 132272675 -
Vvi Vvi1g0485 Chr1 4638568 4649195 -
Acco Acco11g0198 Chr11 2504844 2507058 +
Accr Accr9g02002 Chr9 43460967 43467369 -
Alju Alju09g0236 Chr09 3188767 3193486 +
Apr Apr3g1597 Chr3 31170571 31186578 +
Bisa Bisa11g0518 Chr11 13931368 13953972 +
Bva Bva01g01579 Chr01 17172812 17177566 +
Bva Bva11g00626 Chr11 9615686 9620373 +
Car Car06g01776 Chr06 17637108 17643857 -
Dere Dere09g2178 Chr09 31206001 31214128 +
Enph Enph13g0620 Chr13 12538068 12553619 -
Glsi Glsi05g0247 Chr05 48138781 48159748 +
Lal Lal16g0767 Chr16 4954372 4970933 -
Lal Lal15g0731 Chr15 5133170 5141626 -
Lasa Lasa7g02955 Chr7 562607064 562613765 +
Lele Lele49g1196 Chr49 7937343 7948510 +
Lele Lele50g1645 Chr50 21499094 21503439 -
Lele Lele51g1216 Chr51 7994863 8005877 +
Lele Lele52g1600 Chr52 19895072 19899426 -
Mepo Mepo2g03044 Chr2 40074351 40082012 +
Mibi Mibi12g0196 Chr12 3944082 3948506 +
Phco Phco4g01815 Chr4 34911816 34917862 -
Prci Prci10g2816 Chr10 36626104 36635626 -
Pste Pste3g04117 Chr3 36400604 36407573 +
Pvu Pvu2g0980 Chr2 17194049 17200761 -
Spst Spst3g02262 Chr3 65523056 65523454 -
Sto Sto6g2642 Chr6 33474560 33481237 +
Trre Trre7g01921 Chr7 15102538 15107869 -
Vimu Vimu11g02614 Chr11 46386911 46394682 -
Vivi Vivi5g03810 Chr5 132242196 132248655 +
Vvi Vvi1g0486 Chr1 4650831 4654688 -
Apr Apr3g1594 Chr3 31129939 31140298 +
Bva Bva01g01578 Chr01 17162658 17170898 +
Bva Bva11g00625 Chr11 9606788 9615148 +
Car Car06g01779 Chr06 17654575 17660880 -
Lal Lal23g0868 Chr23 10992240 11001104 +
Lal Lal16g0768 Chr16 4971393 4977413 -
Lal Lal15g0732 Chr15 5142407 5147903 -
Lapu Lapu3g02528 Chr3 47388561 47397313 -
Lasa Lasa7g02950 Chr7 562445638 562449983 +
Mepo Mepo2g03041 Chr2 40057083 40063825 +
Phco Phco4g01820 Chr4 35039438 35046574 -
Pste Pste3g04115 Chr3 36366920 36374669 +
Pvu Pvu2g0982 Chr2 17291736 17298687 -
Spst Spst3g02264 Chr3 65630651 65638547 -
Sto Sto11g0569 Chr11 6817536 6825697 +
Trre Trre7g01924 Chr7 15127265 15134624 -
Vimu Vimu11g02618 Chr11 46420997 46429196 -
Vivi Vivi5g03807 Chr5 132213393 132217786 +
Vvi Vvi1g0487 Chr1 4661986 4662452 +
Apr Apr3g1592 Chr3 31105145 31105844 -
Bva Bva01g01577 Chr01 17154936 17155731 -
Bva Bva11g00624 Chr11 9594920 9595757 -
Car Car06g01781 Chr06 17685409 17686413 +
Lal Lal23g0867 Chr23 10979932 10982643 -
Lal Lal16g0769 Chr16 4977858 4978836 +
Lapu Lapu3g02529 Chr3 47421693 47424145 +
Lasa Lasa7g02947 Chr7 561917859 561918331 -
Phco Phco4g01821 Chr4 35132694 35133160 +
Pste Pste3g04114 Chr3 36323129 36324064 -
Pvu Pvu2g0983 Chr2 17351848 17352611 +
Spst Spst3g02266 Chr3 65648663 65650526 +
Sto Sto11g0568 Chr11 6788750 6789870 -
Vimu Vimu11g02620 Chr11 46476407 46479120 +
Vivi Vivi5g03806 Chr5 132139655 132140469 -
Vvi Vvi1g0488 Chr1 4666066 4672105 +
Acco Acco11g0194 Chr11 2475819 2484192 -
Accr Accr9g02005 Chr9 43482483 43489411 +
Alju Alju09g0234 Chr09 3173219 3181276 -
Apr Apr7g1318 Chr7 20275245 20286063 -
Apr Apr3g1589 Chr3 31044600 31051669 +
Bisa Bisa11g0516 Chr11 13884634 13899784 -
Bva Bva01g01576 Chr01 17146791 17152415 -
Bva Bva11g00623 Chr11 9586912 9592787 -
Car Car06g01783 Chr06 17696895 17704085 +
Cca Cca06g00288 Chr06 7590779 7626597 -
Dere Dere09g2180 Chr09 31233787 31244346 +
Enph Enph13g0622 Chr13 12566106 12574138 +
Glsi Glsi05g0244 Chr05 48061189 48075568 -
Lal Lal6g1040 Chr6 7520556 7533195 +
Lal Lal22g0928 Chr22 7366021 7373829 +
Lal Lal23g0866 Chr23 10969560 10978079 -
Lal Lal15g0735 Chr15 5159977 5167766 +
Lapu Lapu3g02531 Chr3 47429907 47437105 +
Lasa Lasa7g02945 Chr7 561806088 561812126 -
Lele Lele49g1194 Chr49 7926368 7931432 -
Lele Lele51g1214 Chr51 7982872 7988262 -
Mal Mal1g5014 Chr1 120788443 120797806 +
Mepo Mepo2g03040 Chr2 40033078 40039267 -
Mibi Mibi12g0195 Chr12 3908435 3908869 -
Mtr Mtr1g0967 Chr1 11139915 11148208 -
Phco Phco4g01824 Chr4 35246298 35252285 +
Prci Prci10g2818 Chr10 36649616 36659544 +
Psa Psa7g2976 Chr7 216652551 216659422 +
Pste Pste1g01488 Chr1 4687435 4692644 -
Pvu Pvu2g0985 Chr2 17366512 17373433 +
Spst Spst3g02268 Chr3 65661507 65667298 +
Ssu Ssu2g1227 Chr2 53750296 53755599 -
Sto Sto11g0562 Chr11 6764177 6773082 -
Sto Sto6g2640 Chr6 33461110 33464927 -
Vimu Vimu11g02622 Chr11 46482883 46488593 +
Vivi Vivi2g02089 Chr2 97593427 97596995 -
Vvi Vvi1g0489 Chr1 4673863 4683400 +
Apr Apr3g1588 Chr3 31033783 31037303 -
Bva Bva01g01574 Chr01 17139310 17142271 -
Bva Bva11g00622 Chr11 9581695 9585961 -
Car Car06g01784 Chr06 17706423 17710099 +
Lal Lal15g0736 Chr15 5168970 5173410 +
Lapu Lapu3g02532 Chr3 47440056 47443700 +
Lasa Lasa7g02944 Chr7 561780426 561782601 -
Mepo Mepo2g03039 Chr2 40026928 40031028 -
Phco Phco4g01829 Chr4 35381124 35391892 +
Psa Psa7g2979 Chr7 217265022 217268596 -
Pste Pste3g04109 Chr3 36290024 36293997 -
Pvu Pvu2g0986 Chr2 17386170 17395150 +
Spst Spst3g02270 Chr3 65693499 65696556 +
Sto Sto11g0561 Chr11 6754365 6759741 -
Trre Trre7g01927 Chr7 15183480 15186862 +
Vimu Vimu11g02623 Chr11 46491097 46493571 +
Vivi Vivi5g03803 Chr5 132104400 132107310 -
Vvi Vvi1g0490 Chr1 4685930 4687592 -
Apr Apr3g1587 Chr3 31017638 31019488 +
Bva Bva01g01573 Chr01 17132815 17135429 +
Bva Bva11g00621 Chr11 9575370 9578210 +
Car Car06g01785 Chr06 17716310 17718540 -
Lal Lal23g0865 Chr23 10963192 10966668 +
Lal Lal16g0770 Chr16 4980680 4983441 -
Lal Lal15g0737 Chr15 5177038 5179459 -
Lapu Lapu3g02533 Chr3 47455294 47457238 +
Lasa Lasa7g02943 Chr7 561633098 561634931 -
Mepo Mepo2g03038 Chr2 40015679 40018474 +
Phco Phco4g01830 Chr4 35420476 35422398 +
Pste Pste3g04108 Chr3 36279678 36281934 -
Pvu Pvu2g0987 Chr2 17408377 17410875 +
Spst Spst3g02271 Chr3 65699802 65701756 +
Sto Sto11g0560 Chr11 6745799 6749020 +
Trre Trre7g01928 Chr7 15199224 15201882 -
Vimu Vimu11g02624 Chr11 46503713 46505941 +
Vivi Vivi5g03801 Chr5 132084363 132086790 -
Lal Lal23g0866 Chr23 10969560 10978079 -
Mal Mal1g5014 Chr1 120788443 120797806 +
Mtr Mtr1g0967 Chr1 11139915 11148208 -