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
Vvi2g0802 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0803 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0804 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0805 Acco11g1281 . . . Adu05g00122 . Aed6g0163 . Aev05g0151 . Ahy15g0112 . Aip05g00109 . Alju09g1299 . . . Apr7g1768 . Arst5g00150 . Bach4g00981 . Bisa11g2092 . Bva08g01138 Bva11g01300 . . Cca06g00978 . Dere09g1368 . Dod02g0166 . Enph13g1654 . Glsi05g1046 . Gma01g00142 Gma09g01918 . . Gso1g0142 Gso1g0142 . . Lal15g0396 . . . . . Lan18g0773 . . . . . Lapu2g00847 . Lasa2g03753 . . . . . . . . . Lja2g0824 . Mal6g0686 . Mepo5g01367 . Mesa17g01495 . Mibi12g1083 . Mtr5g1222 . Phac2g02198 . Phco4g00523 Phco8g00177 Prci10g1466 . Psa2g3124 . Pste1g00883 Pste7g02253 Pte14g00700 Pte12g00656 . . Pumo8g01391 . Pvu2g1427 Pvu3g2915 Rops1g01259 . . . Spst2g01224 Spst3g03545 Ssu2g1960 . Sto6g4171 Sto11g1303 Tpr2g1475 . . . Tsu05g01241 . Vian10g01089 Vian1g02058 Vifa1g05858 . Vimu7g03487 Vimu11g01070 Viun2g01440 Viun3g03076 Vivi2g02409 . Vra11g1056 .
Vvi2g0806 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0807 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0808 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0809 . . . . . . . . . . . . . . . . . . . Apr3g0634 . . . . . . . Bva11g01302 . . . Cca11g00823 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa4g2848 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0810 Acco11g1283 . . . Adu05g00126 . Aed6g0160 . Aev05g0154 . Ahy15g0115 . Aip05g00113 . Alju09g1300 . . . . Apr3g0633 Arst5g00158 . Bach4g00978 . Bisa11g2090 . Bva08g01135 Bva11g01303 . . Cca06g00981 . Dere09g1367 . Dod02g0168 . Enph13g1653 . Glsi05g1048 . Gma01g00139 Gma09g01920 . . Gso1g0139 Gso1g0139 . . Lal15g0393 . . . . Lal23g1124 Lan18g0775 . . . . Lan18g0775 Lapu2g00850 . Lasa2g03750 . Lele49g0900 Lele50g0947 Lele51g0916 Lele52g0927 . . . . Lja2g0821 Lja4g2789 Mal6g0682 . Mepo5g01364 . Mesa17g01488 . Mibi12g1084 . Mtr5g1219 . . . Phco4g00526 . Prci10g1465 . . Psa4g2851 . . Pte14g00703 . . . Pumo8g01394 . Pvu2g1424 . Rops1g01261 . Seca10g01297 . Spst2g01221 . Ssu2g1963 . Sto6g4170 Sto11g1300 Tpr2g1471 . . . Tsu05g01237 . Vian10g01086 . Vifa1g05860 . Vimu7g03484 . Viun2g01443 . Vivi2g02414 . Vra11g1053 .
Vvi2g0811 Acco11g1284 . . . Adu05g00128 . . . Aev05g0155 . Ahy15g0116 . Aip05g00114 . Alju09g1301 . . . . . Arst5g00159 . Bach4g00977 . Bisa11g2089 . Bva08g01134 Bva11g01304 . . Cca06g00983 . Dere09g1366 . Dod02g0169 . Enph13g1652 . Glsi05g1050 . Gma01g00138 Gma09g01921 . . Gso1g0138 Gso1g0138 . . . Lal16g0444 . . . Lal23g1125 . . . . . . Lapu2g00851 . Lasa2g03749 . Lele49g0898 Lele50g0946 Lele51g0915 Lele52g0926 . . . . Lja2g0820 . Mal6g0681 . Mepo5g01363 . Mesa17g01484 . Mibi12g1085 . Mtr5g1218 . . . Phco4g00527 . Prci10g1464 . . Psa4g2854 Pste1g00857 . Pte14g00704 Pte12g00651 . . Pumo8g00268 . Pvu2g1423 . Rops1g01262 . . . Spst2g01220 . Ssu2g1965 . Sto6g4168 Sto11g1299 Tpr2g1470 . . . Tsu05g01236 . . . . . Vimu7g03481 . Viun2g01445 . Vivi2g02416 . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Pumo Pumo8g00268 Chr8 7637721 7641447 +
Vvi Vvi2g0802 Chr2 8176139 8185141 -
Vvi Vvi2g0803 Chr2 8205082 8210369 +
Vvi Vvi2g0804 Chr2 8212643 8220279 -
Vvi Vvi2g0805 Chr2 8223134 8234512 +
Acco Acco11g1281 Chr11 26890127 26893736 +
Adu Adu05g00122 Chr05 1343309 1346393 -
Aed Aed6g0163 Chr6 1444367 1447057 -
Aev Aev05g0151 Chr05 1178925 1181907 -
Ahy Ahy15g0112 Chr15 1329998 1333534 -
Aip Aip05g00109 Chr05 1265377 1268488 -
Alju Alju09g1299 Chr09 36665493 36669130 +
Apr Apr7g1768 Chr7 25008671 25015567 +
Arst Arst5g00150 Chr5 1357682 1361876 +
Bach Bach4g00981 Chr4 6593126 6596442 -
Bisa Bisa11g2092 Chr11 44022215 44025548 -
Bva Bva08g01138 Chr08 5837160 5842698 -
Bva Bva11g01300 Chr11 13370059 13373223 +
Cca Cca06g00978 Chr06 23539509 23544388 +
Dere Dere09g1368 Chr09 17742758 17746115 -
Dod Dod02g0166 Chr02 2365257 2369970 -
Enph Enph13g1654 Chr13 22546996 22549999 -
Glsi Glsi05g1046 Chr05 60344330 60347659 +
Gma Gma01g00142 Chr01 1562018 1565711 -
Gma Gma09g01918 Chr09 44805205 44808321 +
Gso Gso1g0142 Chr1 1577833 1581532 -
Gso Gso1g0142 Chr1 1577833 1581532 -
Lal Lal15g0396 Chr15 2687623 2691611 -
Lan Lan18g0773 Chr18 13176517 13180176 +
Lapu Lapu2g00847 Chr2 7732701 7736651 +
Lasa Lasa2g03753 Chr2 553056591 553060242 -
Lja Lja2g0824 Chr2 7674854 7679028 -
Mal Mal6g0686 Chr6 9722895 9726474 -
Mepo Mepo5g01367 Chr5 14170969 14175461 -
Mesa Mesa17g01495 Chr17 20290213 20292421 -
Mibi Mibi12g1083 Chr12 25964550 25975419 +
Mtr Mtr5g1222 Chr5 12522084 12526883 -
Phac Phac2g02198 Chr2 23644509 23648369 -
Phco Phco4g00523 Chr4 3769253 3772784 +
Phco Phco8g00177 Chr8 1557712 1562534 +
Prci Prci10g1466 Chr10 9871383 9874754 -
Psa Psa2g3124 Chr2 357740324 357744759 +
Pste Pste1g00883 Chr1 2721269 2725505 -
Pste Pste7g02253 Chr7 20864078 20874108 -
Pte Pte14g00700 Chr14 28058446 28062564 +
Pte Pte12g00656 Chr12 6491330 6493746 +
Pumo Pumo8g01391 Chr8 46490186 46494057 +
Pvu Pvu2g1427 Chr2 27124383 27128271 -
Pvu Pvu3g2915 Chr3 50951530 50955595 -
Rops Rops1g01259 Chr1 28848061 28857150 +
Spst Spst2g01224 Chr2 10819790 10823224 -
Spst Spst3g03545 Chr3 85453109 85458184 +
Ssu Ssu2g1960 Chr2 72213924 72217397 +
Sto Sto6g4171 Chr6 45003471 45005546 -
Sto Sto11g1303 Chr11 12683261 12687293 -
Tpr Tpr2g1475 Chr2 17358059 17362569 -
Tsu Tsu05g01241 Chr05 11157297 11161719 -
Vian Vian10g01089 Chr10 12537196 12540675 -
Vian Vian1g02058 Chr1 24820424 24825269 -
Vifa Vifa1g05858 Chr1 917960865 917964925 +
Vimu Vimu7g03487 Chr7 29531700 29535195 -
Vimu Vimu11g01070 Chr11 11357143 11361879 -
Viun Viun2g01440 Chr2 24853258 24857078 +
Viun Viun3g03076 Chr3 37074880 37079840 -
Vivi Vivi2g02409 Chr2 111033157 111038263 +
Vra Vra11g1056 Chr11 9734848 9738892 -
Vvi Vvi2g0806 Chr2 8259453 8259656 -
Vvi Vvi2g0807 Chr2 8260076 8260480 -
Vvi Vvi2g0808 Chr2 8272022 8272510 -
Vvi Vvi2g0809 Chr2 8280834 8285271 +
Apr Apr3g0634 Chr3 16006043 16016474 -
Bva Bva11g01302 Chr11 13375272 13377471 +
Cca Cca11g00823 Chr11 15836038 15838469 +
Psa Psa4g2848 Chr4 227687920 227691141 +
Vvi Vvi2g0810 Chr2 8287614 8297867 -
Acco Acco11g1283 Chr11 26895018 26897956 -
Adu Adu05g00126 Chr05 1363992 1367649 -
Aed Aed6g0160 Chr6 1432579 1437533 +
Aev Aev05g0154 Chr05 1192142 1194654 -
Ahy Ahy15g0115 Chr15 1349105 1355074 -
Aip Aip05g00113 Chr05 1288860 1291522 -
Alju Alju09g1300 Chr09 36670694 36673610 -
Apr Apr3g0633 Chr3 16001353 16004984 +
Arst Arst5g00158 Chr5 1385022 1387678 -
Bach Bach4g00978 Chr4 6582006 6585220 +
Bisa Bisa11g2090 Chr11 44016389 44019898 +
Bva Bva08g01135 Chr08 5827766 5831177 +
Bva Bva11g01303 Chr11 13378432 13381791 -
Cca Cca06g00981 Chr06 23563879 23568664 -
Dere Dere09g1367 Chr09 17737417 17740763 +
Dod Dod02g0168 Chr02 2387005 2390631 -
Enph Enph13g1653 Chr13 22542346 22546232 +
Glsi Glsi05g1048 Chr05 60348754 60351803 -
Gma Gma01g00139 Chr01 1546798 1552068 +
Gma Gma09g01920 Chr09 44817849 44822437 -
Gso Gso1g0139 Chr1 1563274 1568390 +
Gso Gso1g0139 Chr1 1563274 1568390 +
Lal Lal15g0393 Chr15 2678178 2681671 +
Lal Lal23g1124 Chr23 12784264 12788527 -
Lan Lan18g0775 Chr18 13184765 13188152 -
Lan Lan18g0775 Chr18 13184765 13188152 -
Lapu Lapu2g00850 Chr2 7748022 7751637 -
Lasa Lasa2g03750 Chr2 552965002 552968140 +
Lele Lele49g0900 Chr49 5617023 5619857 +
Lele Lele50g0947 Chr50 5994370 5997266 +
Lele Lele51g0916 Chr51 5697318 5700115 +
Lele Lele52g0927 Chr52 6041725 6044633 +
Lja Lja2g0821 Chr2 7658169 7666493 +
Lja Lja4g2789 Chr4 46029865 46034173 +
Mal Mal6g0682 Chr6 9689134 9692434 +
Mepo Mepo5g01364 Chr5 14158751 14162806 +
Mesa Mesa17g01488 Chr17 20250582 20254023 +
Mibi Mibi12g1084 Chr12 25976939 25979855 -
Mtr Mtr5g1219 Chr5 12506428 12510416 +
Phco Phco4g00526 Chr4 3785264 3788065 -
Prci Prci10g1465 Chr10 9866508 9870132 +
Psa Psa4g2851 Chr4 227798615 227803502 -
Pte Pte14g00703 Chr14 28070540 28074160 -
Pumo Pumo8g01394 Chr8 46505393 46508353 -
Pvu Pvu2g1424 Chr2 27105821 27109316 +
Rops Rops1g01261 Chr1 28872515 28875364 -
Seca Seca10g01297 Chr10 12989703 12993830 +
Spst Spst2g01221 Chr2 10806473 10809253 +
Ssu Ssu2g1963 Chr2 72228012 72231585 -
Sto Sto6g4170 Chr6 44999373 45001992 +
Sto Sto11g1300 Chr11 12667912 12671016 +
Tpr Tpr2g1471 Chr2 17332327 17336369 +
Tsu Tsu05g01237 Chr05 11135381 11138861 +
Vian Vian10g01086 Chr10 12443690 12446504 +
Vifa Vifa1g05860 Chr1 917991779 917994519 -
Vimu Vimu7g03484 Chr7 29514157 29517395 +
Viun Viun2g01443 Chr2 24870529 24873925 -
Vivi Vivi2g02414 Chr2 111056928 111059081 -
Vra Vra11g1053 Chr11 9709062 9712526 +
Vvi Vvi2g0811 Chr2 8319729 8329958 +
Acco Acco11g1284 Chr11 26907562 26910736 +
Adu Adu05g00128 Chr05 1374345 1378362 +
Aev Aev05g0155 Chr05 1199913 1202862 +
Ahy Ahy15g0116 Chr15 1359721 1363724 +
Aip Aip05g00114 Chr05 1296592 1299515 +
Alju Alju09g1301 Chr09 36679363 36682714 +
Arst Arst5g00159 Chr5 1394159 1397435 +
Bach Bach4g00977 Chr4 6575589 6582004 -
Bisa Bisa11g2089 Chr11 43989668 43994649 -
Bva Bva08g01134 Chr08 5819798 5824321 -
Bva Bva11g01304 Chr11 13384598 13389231 +
Cca Cca06g00983 Chr06 23593944 23597526 +
Dere Dere09g1366 Chr09 17721364 17725687 -
Dod Dod02g0169 Chr02 2398279 2402887 +
Enph Enph13g1652 Chr13 22508972 22511769 -
Glsi Glsi05g1050 Chr05 60354942 60358233 +
Gma Gma01g00138 Chr01 1541194 1544707 -
Gma Gma09g01921 Chr09 44827530 44831427 +
Gso Gso1g0138 Chr1 1555288 1558623 -
Gso Gso1g0138 Chr1 1555288 1558623 -
Lal Lal16g0444 Chr16 2736869 2740011 -
Lal Lal23g1125 Chr23 12791373 12794193 +
Lapu Lapu2g00851 Chr2 7759754 7763223 +
Lasa Lasa2g03749 Chr2 552912881 552916646 -
Lele Lele49g0898 Chr49 5607959 5611755 -
Lele Lele50g0946 Chr50 5987665 5991162 -
Lele Lele51g0915 Chr51 5687222 5691034 -
Lele Lele52g0926 Chr52 6034720 6037680 -
Lja Lja2g0820 Chr2 7652778 7656659 -
Mal Mal6g0681 Chr6 9683157 9686791 -
Mepo Mepo5g01363 Chr5 14147664 14152819 -
Mesa Mesa17g01484 Chr17 20215908 20218584 -
Mibi Mibi12g1085 Chr12 25990012 25997147 +
Mtr Mtr5g1218 Chr5 12499830 12504269 -
Phco Phco4g00527 Chr4 3791651 3794765 +
Prci Prci10g1464 Chr10 9852496 9856292 -
Psa Psa4g2854 Chr4 227995292 228001566 +
Pste Pste1g00857 Chr1 2647108 2652105 -
Pte Pte14g00704 Chr14 28076362 28078621 +
Pte Pte12g00651 Chr12 6376703 6380604 -
Pumo Pumo8g00268 Chr8 7637721 7641447 +
Pvu Pvu2g1423 Chr2 27097911 27101200 -
Rops Rops1g01262 Chr1 28881370 28885095 +
Spst Spst2g01220 Chr2 10800139 10803517 -
Ssu Ssu2g1965 Chr2 72245657 72248991 +
Sto Sto6g4168 Chr6 44990150 44996553 -
Sto Sto11g1299 Chr11 12659626 12662322 -
Tpr Tpr2g1470 Chr2 17326068 17329976 -
Tsu Tsu05g01236 Chr05 11130396 11134460 -
Vimu Vimu7g03481 Chr7 29477383 29477781 -
Viun Viun2g01445 Chr2 24881213 24884702 +
Vivi Vivi2g02416 Chr2 111098753 111103278 +
Acco Acco11g1281 Chr11 26890127 26893736 +
Adu Adu05g00122 Chr05 1343309 1346393 -
Alju Alju09g1299 Chr09 36665493 36669130 +
Arst Arst5g00150 Chr5 1357682 1361876 +
Bach Bach4g00981 Chr4 6593126 6596442 -
Bisa Bisa11g2092 Chr11 44022215 44025548 -
Dere Dere09g1368 Chr09 17742758 17746115 -
Enph Enph13g1654 Chr13 22546996 22549999 -
Glsi Glsi05g1046 Chr05 60344330 60347659 +
Lapu Lapu2g00847 Chr2 7732701 7736651 +
Lasa Lasa2g03753 Chr2 553056591 553060242 -
Mepo Mepo5g01367 Chr5 14170969 14175461 -
Mesa Mesa17g01495 Chr17 20290213 20292421 -
Mibi Mibi12g1083 Chr12 25964550 25975419 +
Phac Phac2g02198 Chr2 23644509 23648369 -
Phco Phco4g00523 Chr4 3769253 3772784 +
Prci Prci10g1466 Chr10 9871383 9874754 -
Pste Pste1g00883 Chr1 2721269 2725505 -
Pte Pte14g00700 Chr14 28058446 28062564 +
Pte Pte12g00656 Chr12 6491330 6493746 +
Pumo Pumo8g01391 Chr8 46490186 46494057 +
Pvu Pvu2g1427 Chr2 27124383 27128271 -
Rops Rops1g01259 Chr1 28848061 28857150 +
Spst Spst2g01224 Chr2 10819790 10823224 -
Vian Vian10g01089 Chr10 12537196 12540675 -
Vifa Vifa1g05858 Chr1 917960865 917964925 +
Vimu Vimu7g03487 Chr7 29531700 29535195 -
Viun Viun2g01440 Chr2 24853258 24857078 +
Vivi Vivi2g02409 Chr2 111033157 111038263 +