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
Vvi4g0274 . . . . Adu10g02118 . . . . Aev08g1259 . Ahy20g2332 . Aip10g02759 . . . Amo20g3073 Apr5g1164 . Arst10g02698 . Bach12g00583 . . . Bva10g00253 Bva06g02504 . . . . . . . Dod09g1031 . . . . . . Gma04g00705 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco7g00864 . . . . Psa6g0763 . . . . . . . . Pvu9g1058 . . . . . Spst9g00898 . . . . . . . . . . . . . . . Vimu10g02817 . . . Vivi4g04945 . . .
Vvi4g0275 . . . . . . . Aed3g1957 . Aev08g1260 . Ahy20g2333 . Aip10g02760 . . . . Apr5g1165 . . . . . . . . Bva06g02503 . . Cca03g01471 Cca05g01364 . . . Dod09g1030 . . . . . . Gma04g00704 . . . . . Lal21g0388 . . . . . Lan3g1480 . . . . . . . . . . . . . . . . . . Lja5g2156 . . . . . . . . . . . . . . . . . Psa6g0764 . . . . . . . . . . . . . . . . Ssu1g3348 Ssu6g2786 . Sto9g3230 . . . . . . . . . . . . . . . . Vra5g1098 Vra6g0817
Vvi4g0276 Acco10g2098 . Accr4g00691 . Adu10g02122 . . . . Aev08g1263 . Ahy20g2337 . Aip10g02762 Alju08g0710 . . . Apr5g1167 . Arst10g02706 . Bach12g00581 . Bisa09g1308 . Bva10g00256 Bva06g02502 . . Cca03g01473 . Dere04g0673 . . Dod09g1028 . . Glsi08g1484 . . . Gma04g00703 Gma06g00692 . . . . Lal21g0387 . . . . . Lan3g1479 . . . . . Lapu9g01799 . Lasa5g04197 . Lele01g0563 . Lele03g0566 . . . . . Lja1g3772 . . . Mepo3g07541 . Mesa9g05227 . Mibi05g0627 . . . . . Phco7g00861 . . . . . Pste2g02036 . . . . . Pumo10g00882 . Pvu9g1052 . Rops10g01512 . Seca4g00805 . Spst9g00895 . Ssu1g3350 . Sto5g0735 Sto9g3231 . . Trre5g05365 . . . Vian4g01879 . Vifa2g04144 . Vimu10g02820 . Viun9g02924 . Vivi3g00022 . Vra5g1100 .
Vvi4g0277 . . . . . . . . . . . . . . . . . . Apr5g1168 Apr9g0260 . . . . . . Bva10g00257 Bva06g02501 . . Cca03g01474 . . . . . . . . . . . Gma04g00702 Gma06g00691 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja1g3773 Lja5g2151 . . . . . . . . . . . . . . . . . Psa6g0765 . . . . . . . . . . . . . . . . Ssu1g3351 . Sto5g0736 Sto9g3232 . . . . . . . . . . . . . . . . Vra5g1101 .
Vvi4g0278 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g0279 . . . . Adu08g02397 . . . . . . . . . . . . . Apr5g1169 . Arst8g03295 . Bach12g00579 . . . Bva10g00258 Bva06g02500 . . Cca03g01475 . . . . . . . . . . . Gma04g00701 Gma06g00690 . . . . Lal21g0386 . Lal17g0280 . . . Lan3g1477 . Lan3g1477 . . . Lapu9g01801 . Lasa5g04192 . . . . . . . . . Lja1g3774 . . . . . Mesa9g05223 . . . . . Phac9g00541 . Phco7g00859 . . . Psa5g0561 . Pste2g02034 . . . . . Pumo10g00880 . Pvu9g1050 . Rops10g01508 . Seca4g00807 . Spst9g00892 . Ssu1g3352 . Sto5g0737 . . . Trre5g05362 . . . Vian4g01881 . Vifa2g04142 . Vimu10g02822 . Viun9g02928 . Vivi3g00019 . Vra5g1102 .
Vvi4g0280 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva10g00259 . . . . . . . . . . . . . . Gma17g01856 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa6g0767 . . . . . . . . . . . . . . . . . . Sto5g0738 . . . . . . . . . . . . . . . . . . .
Vvi4g0281 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g0282 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja5g2122 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g0283 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi4g0274 Chr4 2388754 2390093 -
Adu Adu10g02118 Chr10 93153597 93156949 -
Aev Aev08g1259 Chr08 7886301 7888467 -
Ahy Ahy20g2332 Chr20 126851141 126856787 -
Aip Aip10g02759 Chr10 118927290 118930165 -
Amo Amo20g3073 Chr20 134521277 134524418 -
Apr Apr5g1164 Chr5 16137888 16140204 -
Arst Arst10g02698 Chr10 92438416 92441860 -
Bach Bach12g00583 Chr12 3973896 3975436 +
Bva Bva10g00253 Chr10 3590193 3592396 -
Bva Bva06g02504 Chr06 15884502 15886446 +
Dod Dod09g1031 Chr09 30751474 30754161 +
Gma Gma04g00705 Chr04 6579739 6581590 +
Phco Phco7g00864 Chr7 6873168 6874865 +
Psa Psa6g0763 Chr6 26852080 26854278 -
Pvu Pvu9g1058 Chr9 15609874 15611629 +
Spst Spst9g00898 Chr9 7874399 7881894 +
Vimu Vimu10g02817 Chr10 39514375 39516208 -
Vivi Vivi4g04945 Chr4 179585083 179587474 -
Vvi Vvi4g0275 Chr4 2391465 2394261 +
Aed Aed3g1957 Chr3 23730669 23735520 -
Aev Aev08g1260 Chr08 7890426 7893532 +
Ahy Ahy20g2333 Chr20 126905381 126911420 +
Aip Aip10g02760 Chr10 118994897 119000880 +
Apr Apr5g1165 Chr5 16142255 16145121 +
Bva Bva06g02503 Chr06 15877171 15883595 -
Cca Cca03g01471 Chr03 33192247 33195061 +
Cca Cca05g01364 Chr05 31815316 31817553 -
Dod Dod09g1030 Chr09 30739732 30743082 -
Gma Gma04g00704 Chr04 6573325 6576417 -
Lal Lal21g0388 Chr21 2642008 2644832 -
Lan Lan3g1480 Chr3 26334665 26337118 -
Lja Lja5g2156 Chr5 32729968 32734625 -
Psa Psa6g0764 Chr6 26881243 26883817 +
Ssu Ssu1g3348 Chr1 86531356 86534283 +
Ssu Ssu6g2786 Chr6 64606387 64610256 -
Sto Sto9g3230 Chr9 32575565 32578069 +
Vra Vra5g1098 Chr5 17454110 17456956 +
Vra Vra6g0817 Chr6 8089429 8094234 +
Vvi Vvi4g0276 Chr4 2397246 2398809 +
Acco Acco10g2098 Chr10 33243004 33244435 -
Accr Accr4g00691 Chr4 6676526 6677984 +
Adu Adu10g02122 Chr10 93219084 93226268 +
Aev Aev08g1263 Chr08 7913137 7916760 +
Ahy Ahy20g2337 Chr20 127002240 127006230 +
Aip Aip10g02762 Chr10 119082413 119089964 +
Alju Alju08g0710 Chr08 5295752 5297210 +
Apr Apr5g1167 Chr5 16151482 16154361 +
Arst Arst10g02706 Chr10 92503303 92505885 +
Bach Bach12g00581 Chr12 3961283 3963043 -
Bisa Bisa09g1308 Chr09 18826068 18827715 -
Bva Bva10g00256 Chr10 3600734 3602759 +
Bva Bva06g02502 Chr06 15873897 15875841 -
Cca Cca03g01473 Chr03 33203018 33204912 +
Dere Dere04g0673 Chr04 6674772 6678767 -
Dod Dod09g1028 Chr09 30729331 30730398 -
Glsi Glsi08g1484 Chr08 10803689 10806485 +
Gma Gma04g00703 Chr04 6562235 6572331 -
Gma Gma06g00692 Chr06 6305979 6314966 -
Lal Lal21g0387 Chr21 2630406 2640105 -
Lan Lan3g1479 Chr3 26329035 26331990 -
Lapu Lapu9g01799 Chr9 32815728 32824774 +
Lasa Lasa5g04197 Chr5 639327746 639329186 -
Lele Lele01g0563 Chr01 3334658 3338334 +
Lele Lele03g0566 Chr03 3363784 3367745 +
Lja Lja1g3772 Chr1 47369418 47372895 +
Mepo Mepo3g07541 Chr3 88784990 88787410 -
Mesa Mesa9g05227 Chr9 87006995 87008596 -
Mibi Mibi05g0627 Chr05 6069244 6071390 +
Phco Phco7g00861 Chr7 6823077 6826163 -
Pste Pste2g02036 Chr2 20600259 20607052 -
Pumo Pumo10g00882 Chr10 11564225 11567237 -
Pvu Pvu9g1052 Chr9 15567623 15569635 -
Rops Rops10g01512 Chr10 28438733 28449331 -
Seca Seca4g00805 Chr4 13389760 13400135 +
Spst Spst9g00895 Chr9 7851882 7854069 -
Ssu Ssu1g3350 Chr1 86543881 86545401 +
Sto Sto5g0735 Chr5 4957794 4959709 +
Sto Sto9g3231 Chr9 32580767 32582642 +
Trre Trre5g05365 Chr5 54406128 54408091 -
Vian Vian4g01879 Chr4 35280311 35281982 +
Vifa Vifa2g04144 Chr2 1210226260 1210227642 -
Vimu Vimu10g02820 Chr10 39532419 39534213 +
Viun Viun9g02924 Chr9 37396257 37399425 +
Vivi Vivi3g00022 Chr3 257371 259526 -
Vra Vra5g1100 Chr5 17466285 17468971 +
Vvi Vvi4g0277 Chr4 2400523 2404519 +
Apr Apr5g1168 Chr5 16155489 16161031 +
Apr Apr9g0260 Chr9 3416069 3419984 -
Bva Bva10g00257 Chr10 3603683 3603949 +
Bva Bva06g02501 Chr06 15869124 15873367 -
Cca Cca03g01474 Chr03 33206556 33211692 +
Gma Gma04g00702 Chr04 6548551 6553733 -
Gma Gma06g00691 Chr06 6299730 6304265 -
Lja Lja1g3773 Chr1 47372592 47378632 -
Lja Lja5g2151 Chr5 30946165 30959813 -
Psa Psa6g0765 Chr6 26903178 26906565 +
Ssu Ssu1g3351 Chr1 86546927 86552811 +
Sto Sto5g0736 Chr5 4962124 4965780 +
Sto Sto9g3232 Chr9 32583967 32587818 +
Vra Vra5g1101 Chr5 17469903 17475495 +
Vvi Vvi4g0278 Chr4 2405101 2406257 -
Vvi Vvi4g0279 Chr4 2408234 2428104 -
Adu Adu08g02397 Chr08 39645878 39653342 -
Apr Apr5g1169 Chr5 16163211 16170248 -
Arst Arst8g03295 Chr8 44010981 44018403 -
Bach Bach12g00579 Chr12 3943700 3953072 +
Bva Bva10g00258 Chr10 3608993 3616812 -
Bva Bva06g02500 Chr06 15861061 15868641 +
Cca Cca03g01475 Chr03 33215480 33222630 -
Gma Gma04g00701 Chr04 6538266 6546238 +
Gma Gma06g00690 Chr06 6288936 6296333 +
Lal Lal21g0386 Chr21 2621159 2628076 +
Lal Lal17g0280 Chr17 1739288 1744939 +
Lan Lan3g1477 Chr3 26312702 26319314 +
Lan Lan3g1477 Chr3 26312702 26319314 +
Lapu Lapu9g01801 Chr9 32827075 32835222 -
Lasa Lasa5g04192 Chr5 639311776 639321338 +
Lja Lja1g3774 Chr1 47390602 47398505 -
Mesa Mesa9g05223 Chr9 86980712 86989055 +
Phac Phac9g00541 Chr9 3525549 3533422 +
Phco Phco7g00859 Chr7 6807126 6814143 +
Psa Psa5g0561 Chr5 45632298 45642720 -
Pste Pste2g02034 Chr2 20582341 20590954 +
Pumo Pumo10g00880 Chr10 11547663 11555538 +
Pvu Pvu9g1050 Chr9 15550849 15558791 +
Rops Rops10g01508 Chr10 28390471 28401521 +
Seca Seca4g00807 Chr4 13422468 13425701 -
Spst Spst9g00892 Chr9 7822502 7829383 +
Ssu Ssu1g3352 Chr1 86558433 86565636 -
Sto Sto5g0737 Chr5 4969441 4975429 -
Trre Trre5g05362 Chr5 54378898 54386207 +
Vian Vian4g01881 Chr4 35297057 35303408 -
Vifa Vifa2g04142 Chr2 1210213567 1210219892 +
Vimu Vimu10g02822 Chr10 39541989 39557041 -
Viun Viun9g02928 Chr9 37408808 37415517 -
Vivi Vivi3g00019 Chr3 244432 252086 +
Vra Vra5g1102 Chr5 17476906 17484010 -
Vvi Vvi4g0280 Chr4 2431570 2463588 -
Bva Bva10g00259 Chr10 3618111 3629535 -
Gma Gma17g01856 Chr17 31788785 31851585 -
Psa Psa6g0767 Chr6 26918093 26940578 -
Sto Sto5g0738 Chr5 4977838 4996965 -
Vvi Vvi4g0281 Chr4 2470501 2472554 +
Vvi Vvi4g0282 Chr4 2476624 2483802 -
Lja Lja5g2122 Chr5 28957133 28963083 -
Vvi Vvi4g0283 Chr4 2484776 2491888 -
Bva Bva06g02503 Chr06 15877171 15883595 -
Adu Adu08g02397 Chr08 39645878 39653342 -
Arst Arst8g03295 Chr8 44010981 44018403 -
Bach Bach12g00579 Chr12 3943700 3953072 +
Lapu Lapu9g01801 Chr9 32827075 32835222 -
Lasa Lasa5g04192 Chr5 639311776 639321338 +
Mesa Mesa9g05223 Chr9 86980712 86989055 +
Phac Phac9g00541 Chr9 3525549 3533422 +
Phco Phco7g00859 Chr7 6807126 6814143 +
Pste Pste2g02034 Chr2 20582341 20590954 +
Pumo Pumo10g00880 Chr10 11547663 11555538 +
Pvu Pvu9g1050 Chr9 15550849 15558791 +
Rops Rops10g01508 Chr10 28390471 28401521 +
Seca Seca4g00807 Chr4 13422468 13425701 -
Spst Spst9g00892 Chr9 7822502 7829383 +
Trre Trre5g05362 Chr5 54378898 54386207 +
Vian Vian4g01881 Chr4 35297057 35303408 -
Vifa Vifa2g04142 Chr2 1210213567 1210219892 +
Vimu Vimu10g02822 Chr10 39541989 39557041 -
Viun Viun9g02928 Chr9 37408808 37415517 -
Vivi Vivi3g00019 Chr3 244432 252086 +
Bva Bva06g02500 Chr06 15861061 15868641 +
Aed Aed3g1957 Chr3 23730669 23735520 -
Cca Cca05g01364 Chr05 31815316 31817553 -
Ssu Ssu6g2786 Chr6 64606387 64610256 -
Vra Vra6g0817 Chr6 8089429 8094234 +
Lja Lja5g2122 Chr5 28957133 28963083 -