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
Vvi2g1152 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g1153 Acco11g1419 . . . Adu05g00270 . Aed11g1080 . . . . . Aip05g00379 . Alju09g1418 . . . Apr7g0310 . Arst5g00340 . . . Bisa11g1973 . Bva08g01002 Bva11g01395 . . Cca06g01133 . Dere09g1242 . . . Enph13g1555 . Glsi05g1163 . Gma01g01583 Gma11g00827 . . Gso1g1314 Gso1g1314 . . Lal15g0324 Lal16g0381 . . . . . . . . . . Lapu2g00979 . Lasa2g03599 . Lele49g0811 Lele50g0847 Lele51g0833 Lele52g0834 . . . . Lja2g0681 . Mal6g0829 . Mepo5g01164 . Mesa17g01245 . Mibi12g1197 . Mtr5g1039 . . . Phco4g00709 . Prci10g1306 . . . Pste1g03529 . . . . . . . Pvu2g1253 . Rops1g01400 . Seca10g01151 . Spst2g01055 . Ssu2g2115 . Sto6g4073 . Tpr2g1261 . Trre9g01504 . Tsu05g01011 . Vian10g00939 . Vifa1g06203 . Vimu7g03263 . Viun2g01662 . Vivi2g02662 . Vra11g0910 .
Vvi2g1154 . . . . Adu05g00271 . Aed11g1081 . . . . . Aip05g00378 . . . . . Apr7g0309 . Arst5g00341 . Bach4g00860 . . . Bva08g01001 . . . Cca06g01134 . . . . . . . . . Gma01g01584 Gma11g00826 . . Gso1g1315 Gso1g1315 . . Lal15g0323 . . . . . . . . . . . Lapu2g00980 . . . . . . . . . . . Lja2g0680 . . . . . . . . . . . . . Phco4g00710 . . . . . Pste1g03527 . Pte14g00785 . . . Pumo8g01587 . Pvu2g1252 . Rops1g01401 . Seca10g01150 . . . Ssu2g2116 . . . . . . . . . Vian10g00938 . . . Vimu7g03260 . Viun2g01663 . . . Vra11g0909 .
Vvi2g1155 . . . . . . Aed11g1082 Aed7g1337 . . . . Aip05g00377 . . . . . Apr7g0308 Apr3g0454 . . . . . . Bva08g01000 Bva11g01396 . . Cca06g01135 Cca11g00999 . . . . . . . . Gma01g01585 Gma11g00825 . . Gso1g1316 Gso1g1316 . . Lal15g0322 Lal16g0380 . . . Lal23g1174 . . . . . . . . . . . . . . . . . . Lja2g0679 . Mal6g0832 . . . . . . . Mtr5g1036 . . . . . . . Psa2g3315 . . . . . . . . . . . . . . . . . Ssu2g2117 Ssu5g0861 Sto6g4069 . Tpr2g1258 . . . Tsu05g01008 . . . . . . . . . . . Vra11g0908 .
Vvi2g1156 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g1157 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g1158 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g1159 . . . . Adu05g00275 . Aed11g1085 Aed7g1335 . . Ahy15g0267 . Aip05g00253 . . . . . Apr7g0306 Apr3g0452 Arst5g00348 Arst1g01212 . . . . Bva08g00998 Bva11g01398 . . Cca06g01137 Cca11g00995 . . Dod02g0321 . . . . . . Gma11g00823 . . . . . . . . . . . Lal23g1177 . . . . . . Lapu3g02096 Lapu3g02096 Lasa2g03590 Lasa4g01947 . . . . . . . . Lja2g0675 Lja4g3018 Mal6g0840 Mal5g3195 Mepo5g01160 Mepo1g02291 . . . . Mtr5g1032 Mtr8g2275 . . Phco4g00715 Phco8g00227 . . Psa2g3323 Psa4g2498 . Pste7g00607 . . . . . . Pvu2g1249 Pvu3g2870 . . . . Spst2g01051 Spst3g03605 Ssu2g2119 Ssu5g0860 . . . Tpr4g4418 . . Tsu05g01001 Tsu04g02727 . . . . Vimu7g03254 Vimu11g01001 . . Vivi2g02681 . Vra11g0906 .
Vvi2g1160 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g1161 . . . . . . . . . . . . Aip05g00286 . . . . . Apr7g0304 . . . . . . . Bva08g00997 Bva11g01402 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja2g0673 . Mal6g0844 . . . . . . . Mtr5g1028 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto11g1356 . . . . Tsu05g00996 . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Sto Sto11g1356 Chr11 13112605 13127386 -
Vvi Vvi2g1152 Chr2 18395627 18399417 -
Vvi Vvi2g1153 Chr2 18405789 18408726 -
Acco Acco11g1419 Chr11 28689737 28691342 +
Adu Adu05g00270 Chr05 2880243 2881307 +
Aed Aed11g1080 Chr11 16461826 16464108 +
Aip Aip05g00379 Chr05 4244857 4250637 -
Alju Alju09g1418 Chr09 38238930 38240562 +
Apr Apr7g0310 Chr7 8454042 8455757 -
Arst Arst5g00340 Chr5 2899526 2900817 +
Bisa Bisa11g1973 Chr11 42319077 42320718 -
Bva Bva08g01002 Chr08 5117949 5119741 -
Bva Bva11g01395 Chr11 13856729 13858584 +
Cca Cca06g01133 Chr06 25583577 25585305 +
Dere Dere09g1242 Chr09 16294235 16295895 -
Enph Enph13g1555 Chr13 21061900 21064141 -
Glsi Glsi05g1163 Chr05 61267582 61269282 +
Gma Gma01g01583 Chr01 51398687 51400577 +
Gma Gma11g00827 Chr11 6961928 6963823 -
Gso Gso1g1314 Chr1 49673224 49675088 +
Gso Gso1g1314 Chr1 49673224 49675088 +
Lal Lal15g0324 Chr15 2174598 2175944 -
Lal Lal16g0381 Chr16 2303379 2304670 -
Lapu Lapu2g00979 Chr2 9122045 9123000 +
Lasa Lasa2g03599 Chr2 543240362 543241779 -
Lele Lele49g0811 Chr49 4947394 4949017 -
Lele Lele50g0847 Chr50 5262839 5264330 -
Lele Lele51g0833 Chr51 5042819 5044887 -
Lele Lele52g0834 Chr52 5327716 5329223 -
Lja Lja2g0681 Chr2 6176436 6178173 -
Mal Mal6g0829 Chr6 12507060 12508546 +
Mepo Mepo5g01164 Chr5 11827004 11828844 -
Mesa Mesa17g01245 Chr17 15899242 15900804 -
Mibi Mibi12g1197 Chr12 27457026 27458830 +
Mtr Mtr5g1039 Chr5 10377491 10379216 -
Phco Phco4g00709 Chr4 5422423 5423990 +
Prci Prci10g1306 Chr10 8635894 8637710 -
Pste Pste1g03529 Chr1 16641809 16644558 -
Pvu Pvu2g1253 Chr2 24591833 24593819 -
Rops Rops1g01400 Chr1 31202458 31203819 +
Seca Seca10g01151 Chr10 11128800 11130430 -
Spst Spst2g01055 Chr2 9269725 9271088 -
Ssu Ssu2g2115 Chr2 76714354 76716261 +
Sto Sto6g4073 Chr6 44327907 44329214 -
Tpr Tpr2g1261 Chr2 14718673 14720586 -
Trre Trre9g01504 Chr9 12881049 12882162 -
Tsu Tsu05g01011 Chr05 8754423 8757130 -
Vian Vian10g00939 Chr10 9756897 9758456 -
Vifa Vifa1g06203 Chr1 969712353 969713758 +
Vimu Vimu7g03263 Chr7 27605994 27607539 -
Viun Viun2g01662 Chr2 26274940 26276816 +
Vivi Vivi2g02662 Chr2 119717840 119719589 +
Vra Vra11g0910 Chr11 7811789 7813669 -
Vvi Vvi2g1154 Chr2 18421197 18426718 -
Adu Adu05g00271 Chr05 2882063 2885834 -
Aed Aed11g1081 Chr11 16464426 16468077 -
Aip Aip05g00378 Chr05 4240338 4243655 +
Apr Apr7g0309 Chr7 8448958 8453421 +
Arst Arst5g00341 Chr5 2901346 2905130 -
Bach Bach4g00860 Chr4 5744821 5748586 +
Bva Bva08g01001 Chr08 5113371 5117571 +
Cca Cca06g01134 Chr06 25587293 25591185 -
Gma Gma01g01584 Chr01 51401908 51406083 -
Gma Gma11g00826 Chr11 6954518 6961028 +
Gso Gso1g1315 Chr1 49676447 49680634 -
Gso Gso1g1315 Chr1 49676447 49680634 -
Lal Lal15g0323 Chr15 2169415 2173802 +
Lapu Lapu2g00980 Chr2 9124370 9128866 -
Lja Lja2g0680 Chr2 6170871 6175322 +
Phco Phco4g00710 Chr4 5425515 5429613 -
Pste Pste1g03527 Chr1 16633852 16637705 +
Pte Pte14g00785 Chr14 29375941 29380890 -
Pumo Pumo8g01587 Chr8 51128078 51133649 -
Pvu Pvu2g1252 Chr2 24586496 24590945 +
Rops Rops1g01401 Chr1 31204999 31209864 -
Seca Seca10g01150 Chr10 11122135 11127653 +
Ssu Ssu2g2116 Chr2 76718685 76723874 -
Vian Vian10g00938 Chr10 9750089 9754536 +
Vimu Vimu7g03260 Chr7 27594595 27600272 +
Viun Viun2g01663 Chr2 26278172 26285530 -
Vra Vra11g0909 Chr11 7805349 7810142 +
Vvi Vvi2g1155 Chr2 18431736 18434852 -
Aed Aed11g1082 Chr11 16471658 16474786 -
Aed Aed7g1337 Chr7 11237873 11241954 +
Aip Aip05g00377 Chr05 4214145 4222053 +
Apr Apr7g0308 Chr7 8440632 8443570 +
Apr Apr3g0454 Chr3 9273763 9276965 +
Bva Bva08g01000 Chr08 5107810 5110803 +
Bva Bva11g01396 Chr11 13860979 13864013 -
Cca Cca06g01135 Chr06 25595403 25598840 -
Cca Cca11g00999 Chr11 22180689 22184335 +
Gma Gma01g01585 Chr01 51411160 51414018 -
Gma Gma11g00825 Chr11 6946803 6950343 +
Gso Gso1g1316 Chr1 49685494 49688700 -
Gso Gso1g1316 Chr1 49685494 49688700 -
Lal Lal15g0322 Chr15 2165013 2168050 +
Lal Lal16g0380 Chr16 2299106 2302225 +
Lal Lal23g1174 Chr23 13125679 13128510 -
Lja Lja2g0679 Chr2 6162877 6166719 +
Mal Mal6g0832 Chr6 12530366 12532893 -
Mtr Mtr5g1036 Chr5 10357525 10360283 +
Psa Psa2g3315 Chr2 374542911 374545712 -
Ssu Ssu2g2117 Chr2 76730388 76733264 -
Ssu Ssu5g0861 Chr5 22791968 22795207 +
Sto Sto6g4069 Chr6 44317316 44319968 +
Tpr Tpr2g1258 Chr2 14691038 14694253 +
Tsu Tsu05g01008 Chr05 8733583 8736358 +
Vra Vra11g0908 Chr11 7796681 7799786 +
Vvi Vvi2g1156 Chr2 18437675 18461078 -
Vvi Vvi2g1157 Chr2 18476519 18476674 -
Vvi Vvi2g1158 Chr2 18512183 18512554 +
Vvi Vvi2g1159 Chr2 18516563 18524738 +
Adu Adu05g00275 Chr05 2935895 2939767 +
Aed Aed11g1085 Chr11 16509221 16511866 +
Aed Aed7g1335 Chr7 11193397 11201189 -
Ahy Ahy15g0267 Chr15 3102134 3104791 +
Aip Aip05g00253 Chr05 2734268 2738115 +
Apr Apr7g0306 Chr7 8400897 8405153 -
Apr Apr3g0452 Chr3 9170189 9175498 -
Arst Arst5g00348 Chr5 2955239 2959008 +
Arst Arst1g01212 Chr1 11973250 11975847 -
Bva Bva08g00998 Chr08 5082407 5091159 -
Bva Bva11g01398 Chr11 13881799 13885923 +
Cca Cca06g01137 Chr06 25633181 25647953 +
Cca Cca11g00995 Chr11 21903850 21924404 -
Dod Dod02g0321 Chr02 4401706 4406751 +
Gma Gma11g00823 Chr11 6904701 6908727 -
Lal Lal23g1177 Chr23 13153943 13161820 +
Lapu Lapu3g02096 Chr3 40603728 40617153 -
Lapu Lapu3g02096 Chr3 40603728 40617153 -
Lasa Lasa2g03590 Chr2 542825052 542827968 -
Lasa Lasa4g01947 Chr4 394169434 394174177 -
Lja Lja2g0675 Chr2 6099625 6129613 -
Lja Lja4g3018 Chr4 56403373 56409589 +
Mal Mal6g0840 Chr6 12616025 12618191 +
Mal Mal5g3195 Chr5 93835487 93841514 +
Mepo Mepo5g01160 Chr5 11752352 11758889 +
Mepo Mepo1g02291 Chr1 23573220 23579068 -
Mtr Mtr5g1032 Chr5 10304706 10308969 +
Mtr Mtr8g2275 Chr8 33040607 33045168 +
Phco Phco4g00715 Chr4 5473402 5478022 +
Phco Phco8g00227 Chr8 2112904 2128543 -
Psa Psa2g3323 Chr2 374944366 374948531 -
Psa Psa4g2498 Chr4 201088599 201094662 -
Pste Pste7g00607 Chr7 5666440 5683330 +
Pvu Pvu2g1249 Chr2 24464953 24470016 -
Pvu Pvu3g2870 Chr3 50446885 50456149 +
Spst Spst2g01051 Chr2 9209359 9213367 -
Spst Spst3g03605 Chr3 86105771 86113038 -
Ssu Ssu2g2119 Chr2 76786100 76791689 +
Ssu Ssu5g0860 Chr5 22700077 22709467 -
Tpr Tpr4g4418 Chr4 51621008 51626195 -
Tsu Tsu05g01001 Chr05 8654892 8674809 -
Tsu Tsu04g02727 Chr04 31225972 31231268 -
Vimu Vimu7g03254 Chr7 27514148 27524512 -
Vimu Vimu11g01001 Chr11 10502353 10508740 +
Vivi Vivi2g02681 Chr2 120256375 120261223 +
Vra Vra11g0906 Chr11 7758528 7762468 -
Vvi Vvi2g1160 Chr2 18524902 18525066 -
Vvi Vvi2g1161 Chr2 18560792 18562591 -
Aip Aip05g00286 Chr05 3104178 3107077 +
Apr Apr7g0304 Chr7 8391940 8394044 +
Bva Bva08g00997 Chr08 5079365 5081522 +
Bva Bva11g01402 Chr11 13902126 13904094 -
Lja Lja2g0673 Chr2 6084713 6086995 +
Mal Mal6g0844 Chr6 12642262 12644013 -
Mtr Mtr5g1028 Chr5 10274583 10276747 +
Sto Sto11g1356 Chr11 13112605 13127386 -
Tsu Tsu05g00996 Chr05 8638182 8638865 +
Adu Adu05g00275 Chr05 2935895 2939767 +
Arst Arst5g00348 Chr5 2955239 2959008 +
Lapu Lapu3g02096 Chr3 40603728 40617153 -
Lasa Lasa2g03590 Chr2 542825052 542827968 -
Mepo Mepo5g01160 Chr5 11752352 11758889 +
Phco Phco4g00715 Chr4 5473402 5478022 +
Pvu Pvu2g1249 Chr2 24464953 24470016 -
Spst Spst2g01051 Chr2 9209359 9213367 -
Vimu Vimu7g03254 Chr7 27514148 27524512 -
Vivi Vivi2g02681 Chr2 120256375 120261223 +
Aed Aed7g1337 Chr7 11237873 11241954 +
Cca Cca11g00999 Chr11 22180689 22184335 +
Ssu Ssu5g0861 Chr5 22791968 22795207 +