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
Vvi2g0572 . . . . . . Aed11g1640 . . . . . . . . . . . . . . . . . . . . . . . Cca06g01714 . . . . . . . . . . Gma11g00284 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco4g01382 . . . . . . . . . . . Pumo8g02221 . Pvu2g0634 . Rops1g02076 . Seca10g00446 . . . Ssu2g2767 . . . . . . . . . Vian10g00352 . . . Vimu7g02538 . Viun2g02460 . . . Vra11g0351 .
Vvi2g0573 . . . . . . . . . . . . . . . . . . Apr7g0673 . . . . . . . . . Car08g00290 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja2g0085 . Mal6g1600 . . . . . . . Mtr5g0399 . . . . . . . Psa2g4068 . . . . . . . . . . . . . . . . . . . Sto6g3363 . Tpr2g3786 . . . Tsu05g00364 . . . . . . . . . . . . .
Vvi2g0574 . . . . Adu05g01001 . . . . . . . . . . . . . . . Arst5g01250 . . . . . . . . . . . . . . . . . . . . Gma11g00286 . . . . . . . . . . . . . . . . . . Lapu2g00338 . . . . . . . . . . . . . . . Mepo5g00460 . Mesa17g00471 . . . . . Phac2g00984 . . . . . . . Pste1g00807 . . . . . Pumo8g02219 . Pvu2g0636 . Rops1g02074 . Seca10g00448 . . . . . . . . . Trre9g00490 . . . Vian10g00354 . . . Vimu7g02540 . Viun2g02457 . Vivi2g03720 . . .
Vvi2g0575 . . . . . . Aed11g1639 . . . . . . . . . . . . . . . . . . . . Bva11g02004 . . Cca06g01712 . . . . . . . . . . . . . . . . . Lal15g0268 . . . . . Lan18g0899 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ssu2g2765 . . . . . . . . . . . . . . . . . . . Vra11g0353 .
Vvi2g0576 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lal16g0331 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0577 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto6g3364 . . . . . . . . . . . . . . . . . . .
Vvi2g0578 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0579 . . . . . . Aed11g1637 Aed6g0518 . Aev01g0308 . Ahy11g1382 . Aip01g01488 . . . . Apr7g0675 Apr10g1578 . . Bach4g00257 . . . Bva08g00297 Bva11g02002 Car08g00292 Car07g01220 Cca06g01710 Cca11g01634 . . . Dod05g1398 . . . . Gma01g02120 Gma11g00288 Gma05g00540 Gma17g01290 Gso1g1793 Gso1g1793 Gso1g1793 Gso1g1793 Lal15g0267 . . . . Lal23g1220 Lan18g0900 . . . . Lan18g0900 Lapu2g00340 . . . . . . . . . . . Lja2g0089 Lja4g2523 Mal6g1597 Mal5g3891 Mepo5g00463 . Mesa17g00473 . . . Mtr5g0402 Mtr4g3616 . . . . . . . . . . . . . . Pumo8g02217 . Pvu2g0638 . Rops1g02067 . Seca12g01920 . . . Ssu2g2763 Ssu6g1594 Sto6g3368 Sto11g1949 Tpr2g3784 Tpr5g2671 Trre9g00495 . Tsu05g00366 Tsu04g02415 Vian10g00356 . . . Vimu7g02544 . Viun2g02454 . Vivi2g03715 . Vra11g0355 .
Vvi2g0580 . . . . . . . . . Aev01g0309 . Ahy11g1377 . Aip01g01484 . . . Amo11g1376 . Apr10g1579 . . . . . . . Bva11g02001 . . . . . . . Dod05g1397 . . . . . . Gma05g00541 Gma17g01291 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal5g3890 . . . . . . . Mtr4g3614 . . . . . . . . . . . . . . . . . . . . . . . . . . Sto6g3369 . . Tpr5g2670 . . . Tsu04g02413 . . . . . . . . . . . .
Vvi2g0581 . Acco12g1612 . Accr10g00471 . Adu01g01475 Aed11g1636 Aed6g0520 . Aev01g0311 . Ahy11g1374 . Aip01g01473 . Alju12g0514 . Amo11g1362 . . . Arst1g01959 . Bach10g00227 . Bisa01g1136 . Bva11g02000 . . Cca06g01708 Cca11g01631 . Dere13g0214 . Dod05g1396 . Enph14g0235 . Glsi09g0171 Gma01g02119 . . . Gso1g1792 . . . . . . Lal15g1340 Lal16g1288 . . . . . . . . . . Lasa4g02867 . . . . Lele53g0361 Lele54g0368 Lele55g1127 Lele56g1075 . . . Mal5g3889 . Mepo1g01601 . . . Mibi10g0466 . Mtr4g3613 . . . Phco8g00750 . Prci5g0567 . . . Pste6g01408 . . Pte14g01189 Pte12g00158 . Pumo4g01642 . Pvu3g2250 . Rops2g04247 . Seca12g01922 . Spst3g04328 Ssu2g2761 Ssu6g1596 . . . Tpr5g2669 . Trre15g03225 . Tsu04g02408 . Vian1g01389 . Vifa4g02970 . Vimu7g02547 . Viun3g04192 . Vivi1g02453 Vra11g0356 Vra7g1400
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi2g0572 Chr2 4949418 4950534 +
Aed Aed11g1640 Chr11 20326369 20331231 -
Cca Cca06g01714 Chr06 32459555 32460562 -
Gma Gma11g00284 Chr11 2260198 2261706 +
Phco Phco4g01382 Chr4 11928779 11930244 -
Pumo Pumo8g02221 Chr8 59314670 59316535 -
Pvu Pvu2g0634 Chr2 6704172 6705363 +
Rops Rops1g02076 Chr1 41716539 41718102 -
Seca Seca10g00446 Chr10 3880500 3882063 +
Ssu Ssu2g2767 Chr2 88379843 88381026 -
Vian Vian10g00352 Chr10 3167311 3168387 +
Vimu Vimu7g02538 Chr7 21583866 21584880 +
Viun Viun2g02460 Chr2 31179280 31180720 -
Vra Vra11g0351 Chr11 2526741 2528018 +
Vvi Vvi2g0573 Chr2 4952685 4956004 -
Apr Apr7g0673 Chr7 13520810 13523855 -
Car Car08g00290 Chr08 2276991 2279888 -
Lja Lja2g0085 Chr2 651157 656013 -
Mal Mal6g1600 Chr6 29769376 29773527 +
Mtr Mtr5g0399 Chr5 3608247 3611576 -
Psa Psa2g4068 Chr2 418338254 418340868 +
Sto Sto6g3363 Chr6 39683581 39686630 -
Tpr Tpr2g3786 Chr2 40795605 40799067 +
Tsu Tsu05g00364 Chr05 2707936 2710413 -
Vvi Vvi2g0574 Chr2 4957898 4960773 -
Adu Adu05g01001 Chr05 13286102 13289320 -
Arst Arst5g01250 Chr5 13329556 13333110 -
Gma Gma11g00286 Chr11 2266002 2270719 -
Lapu Lapu2g00338 Chr2 2771990 2777071 -
Mepo Mepo5g00460 Chr5 3993403 3995241 -
Mesa Mesa17g00471 Chr17 5462685 5465826 -
Phac Phac2g00984 Chr2 6346656 6350176 +
Pste Pste1g00807 Chr1 2516177 2523948 -
Pumo Pumo8g02219 Chr8 59306104 59310444 +
Pvu Pvu2g0636 Chr2 6721298 6725543 -
Rops Rops1g02074 Chr1 41702168 41705656 +
Seca Seca10g00448 Chr10 3893955 3896938 -
Trre Trre9g00490 Chr9 3497897 3500713 -
Vian Vian10g00354 Chr10 3173569 3176881 -
Vimu Vimu7g02540 Chr7 21589659 21592790 -
Viun Viun2g02457 Chr2 31171901 31175287 +
Vivi Vivi2g03720 Chr2 147705584 147709448 +
Vvi Vvi2g0575 Chr2 4962612 4965728 -
Aed Aed11g1639 Chr11 20324835 20327447 +
Bva Bva11g02004 Chr11 16983965 16986745 +
Cca Cca06g01712 Chr06 32449950 32452729 +
Lal Lal15g0268 Chr15 1831138 1835524 +
Lan Lan18g0899 Chr18 14265345 14269206 -
Ssu Ssu2g2765 Chr2 88370540 88373754 +
Vra Vra11g0353 Chr11 2532500 2535764 -
Vvi Vvi2g0576 Chr2 4974774 4978172 -
Lal Lal16g0331 Chr16 1993785 1997344 +
Vvi Vvi2g0577 Chr2 4983447 4986517 +
Sto Sto6g3364 Chr6 39687545 39690228 +
Vvi Vvi2g0578 Chr2 4989461 4989778 +
Vvi Vvi2g0579 Chr2 5025265 5026125 -
Aed Aed11g1637 Chr11 20307019 20307870 +
Aed Aed6g0518 Chr6 4459258 4460115 -
Aev Aev01g0308 Chr01 2575450 2576352 -
Ahy Ahy11g1382 Chr11 51898602 51899982 +
Aip Aip01g01488 Chr01 49054558 49054938 +
Apr Apr7g0675 Chr7 13545555 13546678 -
Apr Apr10g1578 Chr10 28304611 28305622 -
Bach Bach4g00257 Chr4 1664577 1665491 -
Bva Bva08g00297 Chr08 1454858 1456249 -
Bva Bva11g02002 Chr11 16974146 16975192 +
Car Car08g00292 Chr08 2289892 2290874 -
Car Car07g01220 Chr07 11034486 11035371 -
Cca Cca06g01710 Chr06 32409434 32410805 +
Cca Cca11g01634 Chr11 40202827 40204999 +
Dod Dod05g1398 Chr05 38225651 38226918 -
Gma Gma01g02120 Chr01 56564239 56565304 +
Gma Gma11g00288 Chr11 2297460 2298611 -
Gma Gma05g00540 Chr05 5224125 5224964 -
Gma Gma17g01290 Chr17 11494927 11495802 -
Gso Gso1g1793 Chr1 54749367 54750461 +
Gso Gso1g1793 Chr1 54749367 54750461 +
Gso Gso1g1793 Chr1 54749367 54750461 +
Gso Gso1g1793 Chr1 54749367 54750461 +
Lal Lal15g0267 Chr15 1827128 1828051 +
Lal Lal23g1220 Chr23 13444399 13445280 -
Lan Lan18g0900 Chr18 14274351 14275583 -
Lan Lan18g0900 Chr18 14274351 14275583 -
Lapu Lapu2g00340 Chr2 2798195 2799703 -
Lja Lja2g0089 Chr2 677366 678560 -
Lja Lja4g2523 Chr4 31382781 31383807 -
Mal Mal6g1597 Chr6 29733203 29734081 +
Mal Mal5g3891 Chr5 107967823 107968653 +
Mepo Mepo5g00463 Chr5 4024492 4025659 -
Mesa Mesa17g00473 Chr17 5500115 5500708 -
Mtr Mtr5g0402 Chr5 3642963 3644330 -
Mtr Mtr4g3616 Chr4 49905344 49906462 +
Pumo Pumo8g02217 Chr8 59265646 59266804 +
Pvu Pvu2g0638 Chr2 6790707 6791591 -
Rops Rops1g02067 Chr1 41622805 41623884 +
Seca Seca12g01920 Chr12 22730094 22730984 -
Ssu Ssu2g2763 Chr2 88309400 88310266 +
Ssu Ssu6g1594 Chr6 26386717 26387583 -
Sto Sto6g3368 Chr6 39706132 39707028 -
Sto Sto11g1949 Chr11 18276946 18279914 +
Tpr Tpr2g3784 Chr2 40777731 40778937 +
Tpr Tpr5g2671 Chr5 48908385 48909212 +
Trre Trre9g00495 Chr9 3589051 3589929 -
Tsu Tsu05g00366 Chr05 2734102 2735131 -
Tsu Tsu04g02415 Chr04 27118416 27124216 +
Vian Vian10g00356 Chr10 3203240 3204118 -
Vimu Vimu7g02544 Chr7 21622481 21624196 -
Viun Viun2g02454 Chr2 31150899 31152135 +
Vivi Vivi2g03715 Chr2 147560971 147562355 +
Vra Vra11g0355 Chr11 2557427 2558720 -
Vvi Vvi2g0580 Chr2 5037096 5037740 +
Aev Aev01g0309 Chr01 2585504 2586232 +
Ahy Ahy11g1377 Chr11 51405458 51409011 -
Aip Aip01g01484 Chr01 48653735 48657219 -
Amo Amo11g1376 Chr11 48832997 48838166 -
Apr Apr10g1579 Chr10 28321052 28325528 +
Bva Bva11g02001 Chr11 16968451 16971115 -
Dod Dod05g1397 Chr05 38217261 38222092 -
Gma Gma05g00541 Chr05 5235456 5238774 +
Gma Gma17g01291 Chr17 11504575 11505240 +
Mal Mal5g3890 Chr5 107930916 107931599 -
Mtr Mtr4g3614 Chr4 49874462 49879388 -
Sto Sto6g3369 Chr6 39712529 39714303 +
Tpr Tpr5g2670 Chr5 48898819 48903333 -
Tsu Tsu04g02413 Chr04 27100249 27104430 -
Vvi Vvi2g0581 Chr2 5062795 5070823 +
Acco Acco12g1612 Chr12 26526854 26536684 +
Accr Accr10g00471 Chr10 7846660 7855324 -
Adu Adu01g01475 Chr01 39903894 39916874 -
Aed Aed11g1636 Chr11 20284468 20292789 -
Aed Aed6g0520 Chr6 4489311 4499528 +
Aev Aev01g0311 Chr01 2617906 2629929 +
Ahy Ahy11g1374 Chr11 50605234 50617406 -
Aip Aip01g01473 Chr01 47812802 47821817 -
Alju Alju12g0514 Chr12 6763164 6772895 -
Amo Amo11g1362 Chr11 48115967 48127654 -
Arst Arst1g01959 Chr1 40366013 40378081 -
Bach Bach10g00227 Chr10 1606296 1613390 +
Bisa Bisa01g1136 Chr01 18973497 18981978 -
Bva Bva11g02000 Chr11 16951213 16958098 -
Cca Cca06g01708 Chr06 32364636 32374905 -
Cca Cca11g01631 Chr11 40132023 40148442 -
Dere Dere13g0214 Chr13 3219344 3229315 +
Dod Dod05g1396 Chr05 38164825 38180699 -
Enph Enph14g0235 Chr14 4459134 4469991 +
Glsi Glsi09g0171 Chr09 1280209 1289471 +
Gma Gma01g02119 Chr01 56527145 56537226 -
Gso Gso1g1792 Chr1 54712980 54723260 -
Lal Lal15g1340 Chr15 15452491 15463794 -
Lal Lal16g1288 Chr16 9104550 9115009 +
Lasa Lasa4g02867 Chr4 534806681 534814439 -
Lele Lele53g0361 Chr53 3210885 3220448 -
Lele Lele54g0368 Chr54 3215471 3224404 -
Lele Lele55g1127 Chr55 17694828 17704353 +
Lele Lele56g1075 Chr56 14139991 14148873 +
Mal Mal5g3889 Chr5 107888342 107899485 -
Mepo Mepo1g01601 Chr1 15772829 15783822 +
Mibi Mibi10g0466 Chr10 8152748 8163149 -
Mtr Mtr4g3613 Chr4 49834954 49846026 -
Phco Phco8g00750 Chr8 7541270 7550681 +
Prci Prci5g0567 Chr5 7449183 7460518 -
Pste Pste6g01408 Chr6 6114447 6125116 +
Pte Pte14g01189 Chr14 33285984 33292818 -
Pte Pte12g00158 Chr12 1292499 1299639 +
Pumo Pumo4g01642 Chr4 20831309 20841876 +
Pvu Pvu3g2250 Chr3 43548650 43558232 +
Rops Rops2g04247 Chr2 77336337 77345549 +
Seca Seca12g01922 Chr12 22841447 22853570 +
Spst Spst3g04328 Chr3 94868782 94882757 -
Ssu Ssu2g2761 Chr2 88238703 88248641 -
Ssu Ssu6g1596 Chr6 26422282 26433429 +
Tpr Tpr5g2669 Chr5 48852049 48862737 -
Trre Trre15g03225 Chr15 30841049 30850097 +
Tsu Tsu04g02408 Chr04 27046392 27057158 -
Vian Vian1g01389 Chr1 15232988 15242521 +
Vifa Vifa4g02970 Chr4 949872308 949877526 -
Vimu Vimu7g02547 Chr7 21641245 21650166 +
Viun Viun3g04192 Chr3 49514887 49522586 -
Vivi Vivi1g02453 Chr1 51648511 51656927 +
Vra Vra11g0356 Chr11 2573006 2586131 +
Vra Vra7g1400 Chr7 31142743 31153193 -
Seca Seca12g01922 Chr12 22841447 22853570 +
Vimu Vimu7g02547 Chr7 21641245 21650166 +