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
Vvi3g0503 . . . . . . . . Aev08g0755 Aev05g0628 Ahy20g1676 Ahy15g0664 Aip10g01951 Aip05g00674 . . . . Apr3g1676 . . . . . . . Bva13g00283 Bva14g00356 Car06g01707 Car08g00510 . . . . . Dod02g0685 . . . . . . . . . . . . . . . . . . . . . . . . . Lapu3g02457 . . . . . . . . . . . Lja2g0352 Mal7g3387 . . . . . . . Mtr4g2822 . . . . Phco8g00033 . . Psa7g2810 Psa2g3762 . . . . . . . . . Pvu3g3034 . . . . . . . . Sto2g0617 Sto10g0204 Tpr4g1859 . . . Tsu02g03397 . . . . . . Vimu11g01078 . . . . . .
Vvi3g0504 . . . . . . . . . . Ahy20g1675 . Aip10g01949 . . . Amo20g2006 . Apr3g1677 . . . . . . . Bva13g00282 Bva14g00355 Car06g01706 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu3g02456 . . . . . . . . . . . . Mal7g3388 . . . . . . . Mtr4g2823 . . . . Phco8g00034 . . Psa7g2809 . . . . . Pte3g01837 . . . . Pvu3g3033 . . . . . . . . Sto2g0618 Sto10g0205 Tpr4g1858 . . . Tsu02g03398 . . . . . . Vimu11g01077 . . . . . .
Vvi3g0505 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0506 . . . . . Adu03g00406 . . . . . . . . . . . . . . . Arst3g00542 . . . Bisa02g3996 . . . . Cca04g00500 . . Dere07g1128 . . . Enph8g1112 . Glsi04g0034 . . . Gma12g00441 . . . . . . . . . . . . . . . . . Lapu11g00696 . . . . . . . Lele30g1371 Lele31g1520 Lele32g0022 Lja3g0576 . . . . . . . . Mibi07g0018 . . . . . Phco9g00582 . Prci6g0051 Psa7g4757 . . . . . . . . Pumo11g01729 . Pvu11g0528 . Rops3g00631 . Seca4g08866 . Spst2g02451 Ssu3g2770 . . . . . . . . . . . . . . Vimu5g02268 . Viun11g02333 . . Vra2g0470 .
Vvi3g0507 . . . . . . . . . . Ahy20g1670 . Aip10g01945 . . . . . Apr3g1678 . . . . . . . Bva13g00281 Bva14g00354 Car06g01705 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu3g02455 . . . . . . . . . . . . Mal7g3389 . . . . . . . Mtr4g2824 . . . . Phco8g00040 . . Psa7g2806 . . . . . Pte3g01838 . . . . Pvu3g3029 . . . . . . . . Sto2g0620 Sto10g0206 Tpr4g1857 . . . Tsu02g03399 . . . . . . . . . . . . .
Vvi3g0508 . . . . . . . . . . . . Aip10g01943 . . . Amo20g2001 . . . . . . . . . Bva13g00280 Bva14g00353 Car06g01704 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal7g3390 . . . . . . . Mtr4g2825 . . . . . . . Psa7g2805 . . . . . . . . . . . . . . . . . . . . . Tpr4g1856 . . . Tsu02g03400 . . . . . . . . . . . . .
Vvi3g0509 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0510 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0511 . . . . . . . . . . . . Aip10g01941 . . . . . Apr3g1679 . . . . . . . Bva13g00279 Bva14g00352 Car06g01703 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal7g3392 . . . . . . . Mtr4g2826 . . . . . . . Psa7g2804 . . . . . . . . . . . . . . . . . . . Sto2g0623 . Tpr4g1854 . . . Tsu02g03402 . . . . . . . . . . . . .
Vvi3g0512 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Pste1g03622 . . . . . . . Pvu3g0130 . . . . . . . . . . . . . . . . . . . . . Vimu7g00344 . . . Vivi4g03845 . .
   
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Select Species Gene Chromosome Start End Strand
Vvi Vvi3g0503 Chr3 4300203 4305386 +
Aev Aev08g0755 Chr08 4352589 4355281 +
Aev Aev05g0628 Chr05 4342477 4345910 -
Ahy Ahy20g1676 Chr20 73579350 73582632 -
Ahy Ahy15g0664 Chr15 8823706 8826826 +
Aip Aip10g01951 Chr10 69461127 69464335 -
Aip Aip05g00674 Chr05 8495842 8498832 +
Apr Apr3g1676 Chr3 32331658 32338361 +
Bva Bva13g00283 Chr13 1334700 1338250 -
Bva Bva14g00356 Chr14 1764277 1767830 -
Car Car06g01707 Chr06 16832582 16837152 -
Car Car08g00510 Chr08 4299268 4303597 +
Dod Dod02g0685 Chr02 8942896 8947129 -
Lapu Lapu3g02457 Chr3 46475158 46487966 -
Lja Lja2g0352 Chr2 3237240 3242105 +
Mal Mal7g3387 Chr7 98686937 98690909 +
Mtr Mtr4g2822 Chr4 41888799 41894352 +
Phco Phco8g00033 Chr8 328048 332373 +
Psa Psa7g2810 Chr7 201534662 201538146 -
Psa Psa2g3762 Chr2 400025989 400030721 -
Pvu Pvu3g3034 Chr3 52022776 52028130 -
Sto Sto2g0617 Chr2 5240600 5244511 +
Sto Sto10g0204 Chr10 1699891 1703607 +
Tpr Tpr4g1859 Chr4 19470802 19479037 -
Tsu Tsu02g03397 Chr02 38010543 38016558 +
Vimu Vimu11g01078 Chr11 11456189 11460490 -
Vvi Vvi3g0504 Chr3 4306562 4311189 +
Ahy Ahy20g1675 Chr20 73428118 73432370 -
Aip Aip10g01949 Chr10 69315381 69319848 -
Amo Amo20g2006 Chr20 79305264 79309560 -
Apr Apr3g1677 Chr3 32340361 32344774 +
Bva Bva13g00282 Chr13 1329495 1333838 -
Bva Bva14g00355 Chr14 1758505 1763009 -
Car Car06g01706 Chr06 16824856 16829377 -
Lapu Lapu3g02456 Chr3 46473777 46479926 -
Mal Mal7g3388 Chr7 98695500 98699217 +
Mtr Mtr4g2823 Chr4 41897746 41902217 +
Phco Phco8g00034 Chr8 335123 339542 +
Psa Psa7g2809 Chr7 201510998 201514490 -
Pte Pte3g01837 Chr3 29227944 29232413 +
Pvu Pvu3g3033 Chr3 52015510 52020461 -
Sto Sto2g0618 Chr2 5248231 5253085 +
Sto Sto10g0205 Chr10 1710945 1715131 +
Tpr Tpr4g1858 Chr4 19461851 19467203 -
Tsu Tsu02g03398 Chr02 38024257 38028701 +
Vimu Vimu11g01077 Chr11 11448340 11452746 -
Vvi Vvi3g0505 Chr3 4315325 4317586 +
Vvi Vvi3g0506 Chr3 4323418 4325277 +
Adu Adu03g00406 Chr03 3776351 3778460 -
Arst Arst3g00542 Chr3 3782399 3784421 -
Bisa Bisa02g3996 Chr02 94335978 94336850 -
Cca Cca04g00500 Chr04 4907937 4909071 +
Dere Dere07g1128 Chr07 14636885 14638234 -
Enph Enph8g1112 Chr8 19149544 19153298 -
Glsi Glsi04g0034 Chr04 391864 392789 +
Gma Gma12g00441 Chr12 3598327 3600089 +
Lapu Lapu11g00696 Chr11 10058313 10059387 -
Lele Lele30g1371 Chr30 15863233 15863996 -
Lele Lele31g1520 Chr31 20392316 20392986 -
Lele Lele32g0022 Chr32 161567 162330 +
Lja Lja3g0576 Chr3 5670633 5671581 +
Mibi Mibi07g0018 Chr07 743294 744167 +
Phco Phco9g00582 Chr9 4224954 4225792 +
Prci Prci6g0051 Chr6 391640 392474 +
Psa Psa7g4757 Chr7 414505234 414507137 +
Pumo Pumo11g01729 Chr11 48898371 48901766 -
Pvu Pvu11g0528 Chr11 4385181 4386182 +
Rops Rops3g00631 Chr3 7797662 7812556 +
Seca Seca4g08866 Chr4 211591253 211593094 +
Spst Spst2g02451 Chr2 24152663 24153612 -
Ssu Ssu3g2770 Chr3 82012355 82013298 -
Vimu Vimu5g02268 Chr5 33801958 33802380 -
Viun Viun11g02333 Chr11 37538948 37544601 -
Vra Vra2g0470 Chr2 3622191 3626810 +
Vvi Vvi3g0507 Chr3 4328078 4329175 +
Ahy Ahy20g1670 Chr20 73295148 73296444 -
Aip Aip10g01945 Chr10 69201056 69202212 -
Apr Apr3g1678 Chr3 32364955 32366105 +
Bva Bva13g00281 Chr13 1325683 1327167 -
Bva Bva14g00354 Chr14 1754216 1755676 -
Car Car06g01705 Chr06 16814542 16815708 -
Lapu Lapu3g02455 Chr3 46459832 46461160 -
Mal Mal7g3389 Chr7 98708414 98709400 +
Mtr Mtr4g2824 Chr4 41907690 41908992 +
Phco Phco8g00040 Chr8 372081 372998 +
Psa Psa7g2806 Chr7 201340646 201342107 -
Pte Pte3g01838 Chr3 29235002 29237411 +
Pvu Pvu3g3029 Chr3 51994042 51994911 -
Sto Sto2g0620 Chr2 5258114 5264917 +
Sto Sto10g0206 Chr10 1722206 1723327 +
Tpr Tpr4g1857 Chr4 19454695 19456048 -
Tsu Tsu02g03399 Chr02 38039761 38040880 +
Vvi Vvi3g0508 Chr3 4335011 4339676 -
Aip Aip10g01943 Chr10 69039167 69041880 +
Amo Amo20g2001 Chr20 79037023 79040044 +
Bva Bva13g00280 Chr13 1322024 1323556 +
Bva Bva14g00353 Chr14 1748528 1751906 +
Car Car06g01704 Chr06 16805994 16810284 +
Mal Mal7g3390 Chr7 98733278 98737966 -
Mtr Mtr4g2825 Chr4 41913512 41918394 -
Psa Psa7g2805 Chr7 201288285 201293764 +
Tpr Tpr4g1856 Chr4 19444875 19449930 +
Tsu Tsu02g03400 Chr02 38045686 38051060 -
Vvi Vvi3g0509 Chr3 4346016 4349456 +
Vvi Vvi3g0510 Chr3 4355495 4358711 -
Vvi Vvi3g0511 Chr3 4360065 4361414 +
Aip Aip10g01941 Chr10 68504886 68506362 -
Apr Apr3g1679 Chr3 32375328 32377508 +
Bva Bva13g00279 Chr13 1319033 1320991 -
Bva Bva14g00352 Chr14 1746173 1747993 -
Car Car06g01703 Chr06 16798136 16800100 -
Mal Mal7g3392 Chr7 98763675 98765006 +
Mtr Mtr4g2826 Chr4 41921858 41923842 +
Psa Psa7g2804 Chr7 201175074 201177335 -
Sto Sto2g0623 Chr2 5286464 5287849 +
Tpr Tpr4g1854 Chr4 19436303 19438349 -
Tsu Tsu02g03402 Chr02 38064842 38066809 +
Vvi Vvi3g0512 Chr3 4365445 4367733 -
Pste Pste1g03622 Chr1 17237806 17245788 -
Pvu Pvu3g0130 Chr3 1176914 1179539 +
Vimu Vimu7g00344 Chr7 4002703 4005024 -
Vivi Vivi4g03845 Chr4 157809699 157815136 -
Gma Gma12g00441 Chr12 3598327 3600089 +
Aev Aev05g0628 Chr05 4342477 4345910 -
Ahy Ahy15g0664 Chr15 8823706 8826826 +
Aip Aip05g00674 Chr05 8495842 8498832 +
Car Car08g00510 Chr08 4299268 4303597 +
Dod Dod02g0685 Chr02 8942896 8947129 -
Lja Lja2g0352 Chr2 3237240 3242105 +
Pte Pte3g01837 Chr3 29227944 29232413 +