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
Vvi19g0180 . . . . . . . . Aev10g1331 . Ahy18g1411 Ahy13g1934 Aip08g01506 Aip03g02151 . . . . . Apr5g0141 . . . Bach9g00776 . . . Bva07g01708 . . . . . . Dod10g0955 . . . . . . . . . . . . . Lal9g0533 . Lal2g0597 Lal20g0354 . . Lan8g1368 . Lan8g1368 Lan8g1368 . . . . . . . . . . . . . . . Lja3g4855 . . . . . . . . . . . . . Phco9g01773 . . . . . . . . . . . Pumo11g00593 . Pvu11g1641 . Rops3g01991 . . . . . . . Sto4g2819 . . . . . . . . . . . Vimu5g00571 . . . Vivi7g00301 . .
Vvi19g0181 . . . . Adu08g02057 . Aed1g0564 . Aev10g1332 . Ahy18g1410 . Aip08g01503 . Alju02g0785 . Amo18g1666 . Apr2g0428 Apr5g0700 Arst8g02834 . . . . . . Bva07g01709 Car01g02012 . Cca10g01141 . . . Dod10g0956 . . . . . . . Gma12g02134 Gma13g02421 . . . . . . . Lal20g0353 . . . . . . . . . . Lasa1g04948 . . . . Lele12g0685 . . . . . . Mal4g1484 . Mepo6g03053 . Mesa5g01515 . Mibi01g0691 . Mtr2g2587 . Phac5g00973 . Phco10g00713 . . . Psa5g5541 . Pste3g02308 . . . . . . . Pvu5g0716 . . . . . . . Ssu8g1183 . . . Tpr7g3494 . Trre11g03331 . Tsu02g04341 . . . . . . . . . Vivi2g06144 . Vra5g2834 .
Vvi19g0182 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g0183 . . . . Adu08g02056 . Aed1g0565 . Aev10g1333 . Ahy18g1408 Ahy13g1930 Aip08g01502 Aip03g02147 . . . . Apr2g0427 . Arst8g02832 . Bach13g00755 . . . Bva09g00896 Bva07g01710 Car01g02013 . Cca10g01140 . . . Dod10g0957 . . . . . . . Gma12g02133 Gma13g02422 . . . . Lal9g0532 . Lal2g0596 Lal20g0352 Lal1g0584 Lal11g1449 Lan8g1369 . Lan8g1369 Lan8g1369 Lan8g1369 Lan8g1369 . . Lasa1g04949 . . . . . . . . . . . Mal4g1483 . Mepo6g03054 . Mesa5g01514 . . . Mtr2g2588 . Phac5g00974 . Phco10g00715 . . . Psa5g5542 . . . . . . . . . Pvu5g0717 . . . . . . . Ssu8g1182 . . Sto4g2820 Tpr7g3495 . Trre11g03329 . Tsu02g04342 . . . . . . . . . Vivi2g06145 . Vra5g2835 .
Vvi19g0184 . . . . Adu10g00223 . . . . . . . . . . . . . . . Arst10g00288 . Bach7g00542 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phac6g02588 . Phco11g00458 . . . . . Pste2g02075 . Pte19g00977 . . . Pumo2g00779 . Pvu6g1879 . Rops11g00610 . Seca6g04839 . Spst6g00827 . . . . . . . Trre3g00532 . . . Vian6g01733 . Vifa1g10408 . Vimu2g00708 . Viun6g02731 . Vivi1g08076 . . .
Vvi19g0185 . . . . . . Aed1g0566 Aed5g1206 Aev10g1334 . Ahy18g1407 . Aip08g01501 . . . . . Apr2g0426 Apr5g0140 . . . . . . Bva09g00895 Bva07g01711 . . Cca10g01139 Cca04g01458 . . Dod10g0958 . . . . . . . Gma12g02132 Gma13g02423 . . . . . . Lal2g0595 Lal20g0351 . . . . . . . . . . . . . . . . . . . . . . Mal4g1482 . . . . . . . Mtr2g2589 . . . . . . . Psa5g5543 . . . . . . . . . . . . . . . . . Ssu8g1181 Ssu3g1748 . Sto4g2821 Tpr7g3496 . . . Tsu02g04343 . . . . . . . . . . . . .
Vvi19g0186 . . . . Adu08g02054 . Aed1g0567 . Aev10g1335 . Ahy18g1406 . Aip08g01500 . . . . . Apr2g0425 . Arst8g02830 . Bach13g00757 . . . Bva09g00894 Bva09g00894 Car01g02014 . Cca10g01138 . . . Dod10g0959 . . . . . . . Gma12g02131 Gma13g02424 . . . . . . . . . Lal11g1448 . . . . . . . . Lasa1g04951 . . . . . . . . . . . Mal4g1481 . Mepo6g03057 . Mesa5g01510 . . . Mtr2g2593 . Phac5g00975 . Phco10g00720 . . . Psa5g5544 Psa5g6271 Pste3g02313 . . . . . . . Pvu5g0719 . . . . . . . Ssu8g1180 . Sto7g0216 . Tpr7g3497 . Trre11g03325 . Tsu02g04344 . . . . . . . . . . . Vra5g2836 .
Vvi19g0187 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco9g01556 . . . . . . . . . . . . . Pvu11g1413 . . . . . Spst11g00816 . . . . . . . . . . . . . . . Vimu5g01319 . . . . . .
Vvi19g0188 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva07g01713 . . . Cca09g01837 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto4g2822 . . . . . . . . . . . . . . . . . .
Vvi19g0189 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco9g01564 . . . . . . . . . . . . . Pvu11g1416 . . . . . Spst11g00810 . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Adu Adu10g00223 Chr10 2780125 2781368 +
Arst Arst10g00288 Chr10 2415924 2416958 +
Bach Bach7g00542 Chr7 15806171 15806971 +
Phac Phac6g02588 Chr6 23925883 23927736 +
Phco Phco11g00458 Chr11 3141522 3142318 -
Pste Pste2g02075 Chr2 20930373 20931121 -
Pte Pte19g00977 Chr19 8603579 8604564 -
Pumo Pumo2g00779 Chr2 11983851 11984789 +
Pvu Pvu6g1879 Chr6 29041136 29042513 +
Rops Rops11g00610 Chr11 8729234 8730248 -
Seca Seca6g04839 Chr6 115800874 115805547 +
Spst Spst6g00827 Chr6 7591279 7592064 -
Trre Trre3g00532 Chr3 3668387 3669158 -
Vian Vian6g01733 Chr6 34779720 34780511 +
Vifa Vifa1g10408 Chr1 1738283846 1738284217 +
Vimu Vimu2g00708 Chr2 4315283 4316075 -
Viun Viun6g02731 Chr6 31215841 31216996 +
Vivi Vivi1g08076 Chr1 226501042 226503112 -
Vvi Vvi19g0180 Chr19 2066046 2074067 +
Aev Aev10g1331 Chr10 16832055 16836706 +
Ahy Ahy18g1411 Chr18 26966773 26970912 -
Ahy Ahy13g1934 Chr13 33348232 33361024 -
Aip Aip08g01506 Chr08 25681093 25685204 -
Aip Aip03g02151 Chr03 32105608 32117878 -
Apr Apr5g0141 Chr5 1236323 1244837 -
Bach Bach9g00776 Chr9 5449932 5454444 -
Bva Bva07g01708 Chr07 15967563 15972051 +
Dod Dod10g0955 Chr10 27515968 27521101 +
Lal Lal9g0533 Chr9 3577004 3582275 -
Lal Lal2g0597 Chr2 3579029 3587563 -
Lal Lal20g0354 Chr20 2840132 2848658 -
Lan Lan8g1368 Chr8 20534155 20546181 +
Lan Lan8g1368 Chr8 20534155 20546181 +
Lan Lan8g1368 Chr8 20534155 20546181 +
Lja Lja3g4855 Chr3 90609753 90616078 -
Phco Phco9g01773 Chr9 41662001 41686375 -
Pumo Pumo11g00593 Chr11 20669777 20677555 -
Pvu Pvu11g1641 Chr11 41631501 41644945 -
Rops Rops3g01991 Chr3 35727054 35742863 -
Sto Sto4g2819 Chr4 28994239 29002845 +
Vimu Vimu5g00571 Chr5 6106042 6123164 -
Vivi Vivi7g00301 Chr7 17392924 17399013 +
Vvi Vvi19g0181 Chr19 2075818 2079272 +
Adu Adu08g02057 Chr08 34395277 34399331 -
Aed Aed1g0564 Chr1 7148420 7153078 +
Aev Aev10g1332 Chr10 16837810 16841320 +
Ahy Ahy18g1410 Chr18 26915827 26920289 -
Aip Aip08g01503 Chr08 25624273 25629385 -
Alju Alju02g0785 Chr02 5794061 5799129 -
Amo Amo18g1666 Chr18 33599231 33604082 +
Apr Apr2g0428 Chr2 4984570 4989868 -
Apr Apr5g0700 Chr5 9550524 9552644 +
Arst Arst8g02834 Chr8 38761840 38766189 -
Bva Bva07g01709 Chr07 15972769 15976789 +
Car Car01g02012 Chr01 45361377 45365213 +
Cca Cca10g01141 Chr10 14559031 14562613 -
Dod Dod10g0956 Chr10 27521752 27528128 +
Gma Gma12g02134 Chr12 42193079 42198183 -
Gma Gma13g02421 Chr13 38963240 38968628 +
Lal Lal20g0353 Chr20 2834188 2838642 -
Lasa Lasa1g04948 Chr1 808746124 808748793 +
Lele Lele12g0685 Chr12 15077890 15082141 -
Mal Mal4g1484 Chr4 22719633 22723699 -
Mepo Mepo6g03053 Chr6 42157028 42162670 +
Mesa Mesa5g01515 Chr5 22010769 22015100 -
Mibi Mibi01g0691 Chr01 6577771 6581095 -
Mtr Mtr2g2587 Chr2 38851830 38856796 +
Phac Phac5g00973 Chr5 11134481 11141452 +
Phco Phco10g00713 Chr10 8699428 8705170 +
Psa Psa5g5541 Chr5 481419557 481423240 +
Pste Pste3g02308 Chr3 16334334 16340901 +
Pvu Pvu5g0716 Chr5 11149862 11156222 +
Ssu Ssu8g1183 Chr8 21083827 21089230 -
Tpr Tpr7g3494 Chr7 43424237 43428776 +
Trre Trre11g03331 Chr11 45363386 45366828 -
Tsu Tsu02g04341 Chr02 51983093 51986744 +
Vivi Vivi2g06144 Chr2 195436977 195441170 +
Vra Vra5g2834 Chr5 36240864 36251974 +
Vvi Vvi19g0182 Chr19 2082214 2094788 -
Vvi Vvi19g0183 Chr19 2107497 2109764 +
Adu Adu08g02056 Chr08 34370453 34373036 -
Aed Aed1g0565 Chr1 7159034 7161295 +
Aev Aev10g1333 Chr10 16848818 16851196 +
Ahy Ahy18g1408 Chr18 26859396 26862485 -
Ahy Ahy13g1930 Chr13 33289439 33291049 +
Aip Aip08g01502 Chr08 25576934 25579553 -
Aip Aip03g02147 Chr03 32049560 32051773 +
Apr Apr2g0427 Chr2 4976163 4979097 -
Arst Arst8g02832 Chr8 38737221 38739679 -
Bach Bach13g00755 Chr13 13134148 13136298 +
Bva Bva09g00896 Chr09 4622767 4625225 -
Bva Bva07g01710 Chr07 15979553 15981118 +
Car Car01g02013 Chr01 45382692 45385364 +
Cca Cca10g01140 Chr10 14548860 14551562 -
Dod Dod10g0957 Chr10 27532238 27535016 +
Gma Gma12g02133 Chr12 42183315 42185672 -
Gma Gma13g02422 Chr13 38974541 38976841 +
Lal Lal9g0532 Chr9 3573147 3574565 -
Lal Lal2g0596 Chr2 3576448 3577893 -
Lal Lal20g0352 Chr20 2826599 2828599 -
Lal Lal1g0584 Chr1 3741671 3743218 -
Lal Lal11g1449 Chr11 17824167 17826110 -
Lan Lan8g1369 Chr8 20560460 20562335 +
Lan Lan8g1369 Chr8 20560460 20562335 +
Lan Lan8g1369 Chr8 20560460 20562335 +
Lan Lan8g1369 Chr8 20560460 20562335 +
Lan Lan8g1369 Chr8 20560460 20562335 +
Lasa Lasa1g04949 Chr1 808904454 808906613 +
Mal Mal4g1483 Chr4 22666542 22668752 -
Mepo Mepo6g03054 Chr6 42170999 42173643 +
Mesa Mesa5g01514 Chr5 21997934 22000027 -
Mtr Mtr2g2588 Chr2 38864170 38866658 +
Phac Phac5g00974 Chr5 11144090 11148090 +
Phco Phco10g00715 Chr10 8709753 8711900 +
Psa Psa5g5542 Chr5 481431931 481435375 +
Pvu Pvu5g0717 Chr5 11160229 11162980 +
Ssu Ssu8g1182 Chr8 21074649 21076788 -
Sto Sto4g2820 Chr4 29011676 29014408 +
Tpr Tpr7g3495 Chr7 43436259 43438896 +
Trre Trre11g03329 Chr11 45338127 45340322 -
Tsu Tsu02g04342 Chr02 52004416 52006932 +
Vivi Vivi2g06145 Chr2 195452508 195455104 +
Vra Vra5g2835 Chr5 36255683 36258969 +
Vvi Vvi19g0184 Chr19 2112872 2113818 +
Adu Adu10g00223 Chr10 2780125 2781368 +
Arst Arst10g00288 Chr10 2415924 2416958 +
Bach Bach7g00542 Chr7 15806171 15806971 +
Phac Phac6g02588 Chr6 23925883 23927736 +
Phco Phco11g00458 Chr11 3141522 3142318 -
Pste Pste2g02075 Chr2 20930373 20931121 -
Pte Pte19g00977 Chr19 8603579 8604564 -
Pumo Pumo2g00779 Chr2 11983851 11984789 +
Pvu Pvu6g1879 Chr6 29041136 29042513 +
Rops Rops11g00610 Chr11 8729234 8730248 -
Seca Seca6g04839 Chr6 115800874 115805547 +
Spst Spst6g00827 Chr6 7591279 7592064 -
Trre Trre3g00532 Chr3 3668387 3669158 -
Vian Vian6g01733 Chr6 34779720 34780511 +
Vifa Vifa1g10408 Chr1 1738283846 1738284217 +
Vimu Vimu2g00708 Chr2 4315283 4316075 -
Viun Viun6g02731 Chr6 31215841 31216996 +
Vivi Vivi1g08076 Chr1 226501042 226503112 -
Vvi Vvi19g0185 Chr19 2114858 2118984 -
Aed Aed1g0566 Chr1 7164912 7168303 -
Aed Aed5g1206 Chr5 10790681 10792663 -
Aev Aev10g1334 Chr10 16853970 16856757 -
Ahy Ahy18g1407 Chr18 26848002 26851579 +
Aip Aip08g01501 Chr08 25564832 25568446 +
Apr Apr2g0426 Chr2 4970279 4973392 +
Apr Apr5g0140 Chr5 1233898 1236346 +
Bva Bva09g00895 Chr09 4618138 4621235 +
Bva Bva07g01711 Chr07 15983618 15985690 -
Cca Cca10g01139 Chr10 14538654 14543586 +
Cca Cca04g01458 Chr04 20210627 20215167 -
Dod Dod10g0958 Chr10 27538954 27543290 -
Gma Gma12g02132 Chr12 42175726 42179665 +
Gma Gma13g02423 Chr13 38988268 38991252 -
Lal Lal2g0595 Chr2 3570631 3572732 +
Lal Lal20g0351 Chr20 2821656 2825076 +
Mal Mal4g1482 Chr4 22656986 22660967 +
Mtr Mtr2g2589 Chr2 38871582 38875477 -
Psa Psa5g5543 Chr5 481451337 481455371 -
Ssu Ssu8g1181 Chr8 21062197 21070749 +
Ssu Ssu3g1748 Chr3 53322883 53325423 +
Sto Sto4g2821 Chr4 29019975 29023188 -
Tpr Tpr7g3496 Chr7 43444801 43449470 -
Tsu Tsu02g04343 Chr02 52012832 52017153 -
Vvi Vvi19g0186 Chr19 2124359 2125710 -
Adu Adu08g02054 Chr08 34354891 34356906 +
Aed Aed1g0567 Chr1 7184170 7186057 -
Aev Aev10g1335 Chr10 16857898 16859663 -
Ahy Ahy18g1406 Chr18 26845484 26847377 +
Aip Aip08g01500 Chr08 25562238 25564275 +
Apr Apr2g0425 Chr2 4967314 4968626 +
Arst Arst8g02830 Chr8 38721561 38723371 +
Bach Bach13g00757 Chr13 13142079 13143152 -
Bva Bva09g00894 Chr09 4616164 4617681 +
Bva Bva09g00894 Chr09 4616164 4617681 +
Car Car01g02014 Chr01 45385382 45387553 -
Cca Cca10g01138 Chr10 14527738 14529294 +
Dod Dod10g0959 Chr10 27543999 27545740 -
Gma Gma12g02131 Chr12 42172252 42174109 +
Gma Gma13g02424 Chr13 38992810 38994186 -
Lal Lal11g1448 Chr11 17821943 17823788 +
Lasa Lasa1g04951 Chr1 809016227 809017327 -
Mal Mal4g1481 Chr4 22650128 22651803 +
Mepo Mepo6g03057 Chr6 42192057 42193887 -
Mesa Mesa5g01510 Chr5 21969246 21970902 +
Mtr Mtr2g2593 Chr2 38903020 38905135 -
Phac Phac5g00975 Chr5 11155419 11158008 -
Phco Phco10g00720 Chr10 8730658 8732010 -
Psa Psa5g5544 Chr5 481473708 481475409 -
Psa Psa5g6271 Chr5 533735130 533736870 +
Pste Pste3g02313 Chr3 16364184 16365794 -
Pvu Pvu5g0719 Chr5 11169170 11170813 -
Ssu Ssu8g1180 Chr8 21057749 21059209 +
Sto Sto7g0216 Chr7 1552551 1553881 +
Tpr Tpr7g3497 Chr7 43451239 43454474 -
Trre Trre11g03325 Chr11 45311990 45313806 +
Tsu Tsu02g04344 Chr02 52019126 52021126 -
Vra Vra5g2836 Chr5 36264627 36266494 -
Vvi Vvi19g0187 Chr19 2128632 2130017 +
Phco Phco9g01556 Chr9 36276643 36278028 +
Pvu Pvu11g1413 Chr11 31458570 31460415 +
Spst Spst11g00816 Chr11 32257045 32258430 -
Vimu Vimu5g01319 Chr5 23359042 23360515 +
Vvi Vvi19g0188 Chr19 2131717 2132340 +
Bva Bva07g01713 Chr07 15989247 15990629 +
Cca Cca09g01837 Chr09 43109828 43114916 -
Sto Sto4g2822 Chr4 29029855 29033071 +
Vvi Vvi19g0189 Chr19 2134035 2135411 -
Phco Phco9g01564 Chr9 36472110 36473428 +
Pvu Pvu11g1416 Chr11 31593884 31595529 +
Spst Spst11g00810 Chr11 32122195 32126122 -