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
Vvi19g0010 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lasa4g01492 . . . . . . . . . . . . . Mepo1g03068 . Mesa29g03439 . . . . . Phac11g02294 . Phco9g01903 . . . . . . . . . . . . . Pvu11g1801 . . . Seca4g08064 . Spst11g00476 . . . . . . . Trre15g02423 . . . . . Vifa4g00281 . Vimu5g00992 . . . . . .
Vvi19g0011 . . . . . . . Aed4g1236 . . . . . . . . . . . . . . . . . . Bva09g01005 Bva07g01558 . . . Cca04g01582 . . . . . . . . . Gma15g02020 . . . . . . Lal9g0562 . . . . . Lan8g1332 . . . . . . . . Lasa4g01492 . . . . . . . . . . . Mal5g2252 . Mepo1g03068 . Mesa29g03439 . . . Mtr8g1565 . Phac11g02294 . Phco9g01903 . . . . . . . . . . . . . Pvu11g1801 . . . Seca4g08064 . Spst11g00476 . . . . . Tpr7g1351 . Trre15g02423 . Tsu08g01731 . . . Vifa4g00281 . Vimu5g00992 . . . . . .
Vvi19g0012 . . . . . . Aed1g0445 . . . . . . . . . . . . . . . . . . . . . . . Cca10g01250 . . . . . . . . . . . . Gma13g02331 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ssu8g1316 . . . . . . . . . . . . . . . . . . . Vra5g2374 .
Vvi19g0013 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g0014 . . . . . . . Aed4g1223 . . . . . . . . . . . . . . . . . . Bva09g00994 Bva09g00994 . . . Cca04g01580 . . . . . . . . . . . . . . . . . . Lal2g0654 . . . . . . . . . . . . . . . . . . . . . . Lja3g4913 . Mal5g2253 . Mepo1g03067 . Mesa29g03438 . . . Mtr8g1567 . . . Phco9g01902 . . . . . Pste1g04132 . . . . . . . Pvu11g1796 . . . Seca4g08083 . Spst11g00482 . . Sto7g0117 . . Tpr7g1349 . Trre15g01768 . Tsu08g01733 . . . Vifa4g00279 . . . . . . . .
Vvi19g0015 . . . . . . Aed1g0452 . Aev10g1224 . Ahy18g1622 . Aip08g01789 . . . Amo18g1971 . Apr2g0514 . . . . . . . . Bva07g01564 Car01g01921 . Cca10g01240 . . . Dod10g0841 . . . . . . Gma15g02316 . Gma13g02340 . . . . . . . Lal20g0402 . . . . . . . . . . . . . . . . . . . . . . Mal4g1702 . . . . . . . Mtr2g2443 . . . . . . . . Psa1g0186 . . . . . . . . . . . . . . . . Ssu8g1305 . . Sto4g2738 Tpr7g3357 . . . Tsu02g04145 . . . . . . . . . . . Vra5g2380 .
Vvi19g0016 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g0017 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g0018 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g0019 . . . . . . Aed1g0454 . Aev07g0300 . Ahy17g0494 . Aip07g00432 . . . . . Apr2g0513 Apr5g0740 . . . . . . Bva09g00993 Bva07g01566 Car01g01925 . Cca10g01238 Cca04g01570 . . Dod08g0355 . . . . . . Gma15g02315 . Gma13g02341 . . . . . Lal1g1587 Lal2g0651 . . . . . . . . . . . . . . . . . . . . . . Lja3g4912 Mal4g1701 Mal5g2254 . . . . . . Mtr2g2444 Mtr8g1568 . . . . . . . Psa1g0185 . . . . . . . . . . . . . . . . Ssu8g1303 . Sto7g0118 Sto4g2739 Tpr7g3356 Tpr7g1348 . . Tsu02g04146 Tsu08g01735 . . . . . . . . . . Vra5g2381 .
   
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Select Species Gene Chromosome Start End Strand
Vvi Vvi19g0010 Chr19 101199 109904 +
Lasa Lasa4g01492 Chr4 188272246 188293388 +
Mepo Mepo1g03068 Chr1 34398704 34411898 +
Mesa Mesa29g03439 Chr29 53761896 53774553 +
Phac Phac11g02294 Chr11 34019957 34030854 +
Phco Phco9g01903 Chr9 43810430 43820613 +
Pvu Pvu11g1801 Chr11 44718440 44729883 +
Seca Seca4g08064 Chr4 189596138 189604092 -
Spst Spst11g00476 Chr11 25818244 25833599 -
Trre Trre15g02423 Chr15 20084040 20093930 +
Vifa Vifa4g00281 Chr4 60362021 60384033 +
Vimu Vimu5g00992 Chr5 15219080 15221782 -
Vvi Vvi19g0011 Chr19 114759 145225 +
Aed Aed4g1236 Chr4 12568451 12581930 +
Bva Bva09g01005 Chr09 5129721 5136196 +
Bva Bva07g01558 Chr07 15149283 15152390 -
Cca Cca04g01582 Chr04 23667091 23677618 +
Gma Gma15g02020 Chr15 34254605 34281411 +
Lal Lal9g0562 Chr9 3806552 3813954 +
Lan Lan8g1332 Chr8 20177310 20184904 -
Lasa Lasa4g01492 Chr4 188272246 188293388 +
Mal Mal5g2252 Chr5 56975839 57040187 -
Mepo Mepo1g03068 Chr1 34398704 34411898 +
Mesa Mesa29g03439 Chr29 53761896 53774553 +
Mtr Mtr8g1565 Chr8 21617820 21633176 -
Phac Phac11g02294 Chr11 34019957 34030854 +
Phco Phco9g01903 Chr9 43810430 43820613 +
Pvu Pvu11g1801 Chr11 44718440 44729883 +
Seca Seca4g08064 Chr4 189596138 189604092 -
Spst Spst11g00476 Chr11 25818244 25833599 -
Tpr Tpr7g1351 Chr7 14339142 14354594 +
Trre Trre15g02423 Chr15 20084040 20093930 +
Tsu Tsu08g01731 Chr08 20957654 20968548 -
Vifa Vifa4g00281 Chr4 60362021 60384033 +
Vimu Vimu5g00992 Chr5 15219080 15221782 -
Vvi Vvi19g0012 Chr19 147249 149194 +
Aed Aed1g0445 Chr1 6151206 6152658 -
Cca Cca10g01250 Chr10 16587002 16588374 +
Gma Gma13g02331 Chr13 38079410 38080996 -
Ssu Ssu8g1316 Chr8 24414838 24417790 +
Vra Vra5g2374 Chr5 30775931 30777220 -
Vvi Vvi19g0013 Chr19 150637 151440 -
Vvi Vvi19g0014 Chr19 153742 156440 -
Aed Aed4g1223 Chr4 12291328 12294627 -
Bva Bva09g00994 Chr09 5098866 5101325 +
Bva Bva09g00994 Chr09 5098866 5101325 +
Cca Cca04g01580 Chr04 23611208 23614847 +
Lal Lal2g0654 Chr2 3925956 3928044 +
Lja Lja3g4913 Chr3 91198871 91201726 +
Mal Mal5g2253 Chr5 57083806 57086016 -
Mepo Mepo1g03067 Chr1 34370173 34373850 +
Mesa Mesa29g03438 Chr29 53749768 53751880 +
Mtr Mtr8g1567 Chr8 21714106 21717422 -
Phco Phco9g01902 Chr9 43743918 43749393 +
Pste Pste1g04132 Chr1 24814133 24817624 +
Pvu Pvu11g1796 Chr11 44526802 44532963 +
Seca Seca4g08083 Chr4 190210022 190214157 -
Spst Spst11g00482 Chr11 26531995 26533450 -
Sto Sto7g0117 Chr7 905147 907129 -
Tpr Tpr7g1349 Chr7 14328684 14331962 +
Trre Trre15g01768 Chr15 14204463 14207630 -
Tsu Tsu08g01733 Chr08 21028583 21031253 -
Vifa Vifa4g00279 Chr4 59825892 59826834 +
Vvi Vvi19g0015 Chr19 157208 162887 +
Aed Aed1g0452 Chr1 6292647 6295858 +
Aev Aev10g1224 Chr10 15905501 15909657 +
Ahy Ahy18g1622 Chr18 38890351 38893584 -
Aip Aip08g01789 Chr08 39019464 39022615 -
Amo Amo18g1971 Chr18 46571118 46574008 -
Apr Apr2g0514 Chr2 5942446 5945620 -
Bva Bva07g01564 Chr07 15186950 15189273 +
Car Car01g01921 Chr01 43788665 43792307 +
Cca Cca10g01240 Chr10 16361104 16364890 -
Dod Dod10g0841 Chr10 24166800 24171442 +
Gma Gma15g02316 Chr15 49019114 49022332 -
Gma Gma13g02340 Chr13 38138855 38141980 +
Lal Lal20g0402 Chr20 3226696 3233531 -
Mal Mal4g1702 Chr4 29958480 29961572 -
Mtr Mtr2g2443 Chr2 36798821 36803243 +
Psa Psa1g0186 Chr1 10936328 10939620 -
Ssu Ssu8g1305 Chr8 24111295 24114374 -
Sto Sto4g2738 Chr4 28350331 28353147 +
Tpr Tpr7g3357 Chr7 41680798 41685646 -
Tsu Tsu02g04145 Chr02 48623973 48628813 +
Vra Vra5g2380 Chr5 30888769 30892716 +
Vvi Vvi19g0016 Chr19 176298 176841 +
Vvi Vvi19g0017 Chr19 195093 195411 -
Vvi Vvi19g0018 Chr19 202365 210949 -
Vvi Vvi19g0019 Chr19 224590 233939 +
Aed Aed1g0454 Chr1 6309841 6315252 +
Aev Aev07g0300 Chr07 1714059 1718197 -
Ahy Ahy17g0494 Chr17 4782973 4788440 -
Aip Aip07g00432 Chr07 3715671 3719167 -
Apr Apr2g0513 Chr2 5920523 5925367 -
Apr Apr5g0740 Chr5 10257490 10263147 -
Bva Bva09g00993 Chr09 5090254 5094823 -
Bva Bva07g01566 Chr07 15202587 15207226 +
Car Car01g01925 Chr01 43810453 43815082 +
Cca Cca10g01238 Chr10 16304270 16308961 -
Cca Cca04g01570 Chr04 23074440 23084209 -
Dod Dod08g0355 Chr08 3835085 3838490 -
Gma Gma15g02315 Chr15 48938270 48943403 -
Gma Gma13g02341 Chr13 38155415 38159302 +
Lal Lal1g1587 Chr1 18261458 18266562 +
Lal Lal2g0651 Chr2 3899282 3903758 -
Lja Lja3g4912 Chr3 91185450 91191945 -
Mal Mal4g1701 Chr4 29899644 29904487 -
Mal Mal5g2254 Chr5 57100585 57105844 +
Mtr Mtr2g2444 Chr2 36807158 36812094 +
Mtr Mtr8g1568 Chr8 21719892 21725355 +
Psa Psa1g0185 Chr1 10911055 10915672 -
Ssu Ssu8g1303 Chr8 23997685 24001848 +
Sto Sto7g0118 Chr7 913746 918284 +
Sto Sto4g2739 Chr4 28368113 28370621 +
Tpr Tpr7g3356 Chr7 41669391 41674277 -
Tpr Tpr7g1348 Chr7 14318903 14325003 -
Tsu Tsu02g04146 Chr02 48636373 48641324 +
Tsu Tsu08g01735 Chr08 21039213 21044771 +
Vra Vra5g2381 Chr5 30925798 30930640 +