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
Vvi18g0086 . . . . . . Aed11g0004 . . . . Ahy16g0008 . Aip06g00008 . . . . Apr9g0697 . . . . . . . Bva06g01831 . . . Cca05g00434 . . . . Dod08g2332 . . . . . . Gma14g02185 Gma17g02500 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja5g3363 Mal1g6159 . . . . . . . Mtr1g0768 . . . . . . . . . . . . . . . . . . . . . . . . . Ssu5g0007 . Sto5g0035 . Tpr1g3925 . . . Tsu01g00153 . . . . . . . . . . . Vra6g1984 .
Vvi18g0087 . . . . . . . Aed9g0151 Aev08g0130 . Ahy17g2157 . Aip07g02298 . . . Amo17g2001 . . . . . . . . . . Bva10g01011 . Car05g03336 . Cca07g00190 . . . . . . . . Gma04g00153 Gma06g00144 . . Gso4g0147 Gso4g0147 . . . . Lal21g0073 . . . . . . . . . . . . . . . . . . . . . Lja1g2294 . . Mal2g0375 . . . . . . . Mtr3g4354 . . . . . . . . . . . . . . . . Pvu9g0124 . Rops10g02549 . Seca4g00295 . . . . . Sto5g0036 . . Tpr7g0153 . . . Tsu07g00173 Vian4g02467 . . . . . Viun9g03765 . . . . Vra5g1726
Vvi18g0088 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva06g01832 . . Car05g03335 Cca05g00433 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lasa5g04620 . . . . . . . . . . . Mal2g0380 . . . . . . . Mtr3g4353 . . . Phco2g00011 . . . . . . . . . . . . Pvu9g0123 Pvu1g0010 Rops10g02548 Rops9g02536 . . . Spst8g02088 . . . . . Tpr7g0154 . . . Tsu07g00174 Vian4g02466 . Vifa2g04596 . . . Viun9g03764 . . Vivi4g05993 . .
Vvi18g0089 . . . . . . . Aed9g0152 Aev08g0131 . Ahy17g2158 . Aip07g02299 . . . . . Apr9g0696 . . . . . . . . . . . Cca05g00432 Cca07g00191 . . Dod08g2331 . . . . . . . Gma14g02184 . . . . . Lal4g0036 . . . . . Lan14g0981 . . . . . . . . . . . . . . . . . Lja1g2296 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ssu5g0009 . . . . . . . . . . . . . . . . . . . Vra6g1986 Vra5g1725
Vvi18g0090 . . . . . . . Aed9g0153 Aev08g0132 . Ahy17g2159 . Aip07g02300 . . . Amo17g2002 . . . . . . . . . Bva06g01833 Bva10g01010 . Car05g03334 . Cca07g00192 . . . . . . . . Gma04g00154 Gma06g00146 . . Gso4g0148 Gso4g0148 . . Lal4g0037 Lal17g0033 Lal21g0075 . . . Lan14g0980 Lan14g0980 Lan14g0980 . . . . . . . . . . . . . . . Lja1g2297 . . Mal2g0381 . . . . . . . Mtr3g4352 . . . . . . . . . . . Pte1g02714 . . . . Pvu9g0122 . Rops10g02547 . . . . . . . Sto5g0038 . . Tpr7g0155 . . . Tsu07g00175 Vian4g02465 . Vifa2g04595 . . . Viun9g03763 . . . . Vra5g1724
Vvi18g0091 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0092 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0093 . . . . . . . Aed9g0154 . . . . . . . . . . . . . . . . . . . . . Car05g03329 . Cca07g00193 . . . . . . . . Gma04g00155 Gma06g00147 . . Gso4g0149 Gso4g0149 . . . Lal17g0034 . . . . . . . . . . . . . . . . . . . . . . Lja1g2298 . . Mal2g0382 . . . . . . . Mtr3g4351 Phac9g01883 . . . . . . . . . . . . . . . Pvu9g0120 . Rops10g02546 . . . . . . . Sto5g0039 . . Tpr7g0156 . . . Tsu07g00176 Vian4g02464 . Vifa2g04593 . . . Viun9g03762 . . . . Vra5g1721
Vvi18g0094 . . . . . . . Aed9g0155 Aev08g0134 . Ahy17g2163 . Aip07g02306 . . . . . . . . . . . . . . . . Car05g03328 . Cca07g00194 . . . . . . . . Gma04g00156 Gma06g00148 . . . . . . Lal4g0038 . Lal21g0076 . . . Lan14g0979 . Lan14g0979 . . . . . . . . . . . . . . . Lja1g2299 . . Mal2g0383 . . . . . . . Mtr3g4350 Phac9g01884 . . . . . . . . . . . . . . . Pvu9g0119 . Rops10g02545 . . . . . . . . . . Tpr7g0157 . . . Tsu07g00177 Vian4g02463 . Vifa2g04592 . Vimu10g03563 . Viun9g03761 . . . . Vra5g1720
Vvi18g0095 . . . . . . . . . Aev07g2390 . Ahy16g0009 . Aip06g00009 . . . . Apr9g0695 . . . . . . . . Bva10g01009 Car04g03624 Car05g03327 Cca05g00431 Cca07g00195 . . . . . . . . Gma04g00157 Gma06g00149 . Gma17g02499 . . . . . . Lal21g0077 . . . . . . . . . . . . . . . . . . . . . Lja1g3431 . . Mal2g0384 . . . . . . . Mtr3g4348 . . . . . . . . . . . . . . . . . . . . . . . . Ssu5g0010 . Sto5g0040 . . Tpr7g0158 . . . Tsu07g00178 . . . . . . . . . . Vra6g1987 Vra5g1719
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi18g0086 Chr18 767918 779528 +
Aed Aed11g0004 Chr11 27441 28336 -
Ahy Ahy16g0008 Chr16 69650 79648 -
Aip Aip06g00008 Chr06 62393 75845 -
Apr Apr9g0697 Chr9 11582957 11609234 -
Bva Bva06g01831 Chr06 12600182 12611626 +
Cca Cca05g00434 Chr05 9519483 9535967 -
Dod Dod08g2332 Chr08 51401663 51415453 -
Gma Gma14g02185 Chr14 52992345 53007923 -
Gma Gma17g02500 Chr17 43005128 43011643 -
Lja Lja5g3363 Chr5 65739068 65752784 -
Mal Mal1g6159 Chr1 140656009 140669943 -
Mtr Mtr1g0768 Chr1 8633454 8647929 -
Ssu Ssu5g0007 Chr5 112089 128028 +
Sto Sto5g0035 Chr5 216651 227838 +
Tpr Tpr1g3925 Chr1 43376576 43396601 +
Tsu Tsu01g00153 Chr01 1178546 1194394 +
Vra Vra6g1984 Chr6 36554088 36568873 -
Vvi Vvi18g0087 Chr18 781234 784424 -
Aed Aed9g0151 Chr9 1072753 1074880 -
Aev Aev08g0130 Chr08 718017 718898 -
Ahy Ahy17g2157 Chr17 103149642 103151067 -
Aip Aip07g02298 Chr07 95788340 95789657 -
Amo Amo17g2001 Chr17 102510874 102512297 -
Bva Bva10g01011 Chr10 7419820 7420975 +
Car Car05g03336 Chr05 78082844 78084750 +
Cca Cca07g00190 Chr07 2391643 2393461 -
Gma Gma04g00153 Chr04 1289528 1291635 -
Gma Gma06g00144 Chr06 1260927 1262510 -
Gso Gso4g0147 Chr4 1268262 1270304 -
Gso Gso4g0147 Chr4 1268262 1270304 -
Lal Lal21g0073 Chr21 517886 520886 -
Lja Lja1g2294 Chr1 26667638 26669105 -
Mal Mal2g0375 Chr2 4155921 4157168 -
Mtr Mtr3g4354 Chr3 57516220 57518777 +
Pvu Pvu9g0124 Chr9 1939877 1941301 +
Rops Rops10g02549 Chr10 44390086 44391739 +
Seca Seca4g00295 Chr4 4688219 4690106 -
Sto Sto5g0036 Chr5 229076 229453 -
Tpr Tpr7g0153 Chr7 1232987 1234595 -
Tsu Tsu07g00173 Chr07 1298793 1299944 -
Vian Vian4g02467 Chr4 41300868 41301952 +
Viun Viun9g03765 Chr9 42635523 42636878 +
Vra Vra5g1726 Chr5 23504549 23505821 +
Vvi Vvi18g0088 Chr18 792239 794919 +
Bva Bva06g01832 Chr06 12612257 12613720 +
Car Car05g03335 Chr05 78075567 78079210 -
Cca Cca05g00433 Chr05 9505073 9506175 -
Lasa Lasa5g04620 Chr5 680813842 680815220 -
Mal Mal2g0380 Chr2 4213691 4215958 +
Mtr Mtr3g4353 Chr3 57504760 57508382 -
Phco Phco2g00011 Chr2 146307 149886 +
Pvu Pvu9g0123 Chr9 1927124 1929074 -
Pvu Pvu1g0010 Chr1 169087 171622 +
Rops Rops10g02548 Chr10 44361575 44366618 -
Rops Rops9g02536 Chr9 47595738 47603692 +
Spst Spst8g02088 Chr8 29015294 29021412 -
Tpr Tpr7g0154 Chr7 1237102 1240810 +
Tsu Tsu07g00174 Chr07 1303508 1305460 +
Vian Vian4g02466 Chr4 41290672 41292550 -
Vifa Vifa2g04596 Chr2 1355169958 1355171648 -
Viun Viun9g03764 Chr9 42618873 42621092 -
Vivi Vivi4g05993 Chr4 197182224 197185330 -
Vvi Vvi18g0089 Chr18 803487 805930 +
Aed Aed9g0152 Chr9 1077318 1078554 +
Aev Aev08g0131 Chr08 723537 725540 +
Ahy Ahy17g2158 Chr17 103203985 103210197 +
Aip Aip07g02299 Chr07 95829186 95834855 +
Apr Apr9g0696 Chr9 11571389 11576668 -
Cca Cca05g00432 Chr05 9497127 9499480 -
Cca Cca07g00191 Chr07 2409708 2413314 +
Dod Dod08g2331 Chr08 51385230 51388770 -
Gma Gma14g02184 Chr14 52981181 52983872 -
Lal Lal4g0036 Chr4 211273 212841 +
Lan Lan14g0981 Chr14 16089522 16091364 -
Lja Lja1g2296 Chr1 26695275 26697685 +
Ssu Ssu5g0009 Chr5 138331 144897 +
Vra Vra6g1986 Chr6 36574337 36576590 +
Vra Vra5g1725 Chr5 23496307 23498281 -
Vvi Vvi18g0090 Chr18 807953 809293 -
Aed Aed9g0153 Chr9 1080599 1082862 -
Aev Aev08g0132 Chr08 726766 728345 -
Ahy Ahy17g2159 Chr17 103209927 103211971 -
Aip Aip07g02300 Chr07 95835231 95837487 -
Amo Amo17g2002 Chr17 102563210 102564963 -
Bva Bva06g01833 Chr06 12614533 12616413 -
Bva Bva10g01010 Chr10 7414243 7418359 +
Car Car05g03334 Chr05 78073136 78075243 +
Cca Cca07g00192 Chr07 2449089 2451692 -
Gma Gma04g00154 Chr04 1298467 1303479 -
Gma Gma06g00146 Chr06 1281869 1285598 -
Gso Gso4g0148 Chr4 1276938 1279001 -
Gso Gso4g0148 Chr4 1276938 1279001 -
Lal Lal4g0037 Chr4 213791 215689 -
Lal Lal17g0033 Chr17 186588 188590 -
Lal Lal21g0075 Chr21 523558 525910 -
Lan Lan14g0980 Chr14 16086649 16088271 +
Lan Lan14g0980 Chr14 16086649 16088271 +
Lan Lan14g0980 Chr14 16086649 16088271 +
Lja Lja1g2297 Chr1 26698166 26700146 -
Mal Mal2g0381 Chr2 4218610 4219950 -
Mtr Mtr3g4352 Chr3 57499153 57501188 +
Pte Pte1g02714 Chr1 47159122 47161193 +
Pvu Pvu9g0122 Chr9 1920774 1922843 +
Rops Rops10g02547 Chr10 44354738 44356744 +
Sto Sto5g0038 Chr5 235990 237303 -
Tpr Tpr7g0155 Chr7 1241802 1243717 -
Tsu Tsu07g00175 Chr07 1305628 1309436 -
Vian Vian4g02465 Chr4 41285907 41287303 +
Vifa Vifa2g04595 Chr2 1355160234 1355161594 +
Viun Viun9g03763 Chr9 42612444 42614594 +
Vra Vra5g1724 Chr5 23491664 23493624 +
Vvi Vvi18g0091 Chr18 813776 815605 +
Vvi Vvi18g0092 Chr18 817919 819390 -
Vvi Vvi18g0093 Chr18 821694 826998 +
Aed Aed9g0154 Chr9 1085163 1093476 +
Car Car05g03329 Chr05 78023831 78028324 -
Cca Cca07g00193 Chr07 2467123 2471604 +
Gma Gma04g00155 Chr04 1304320 1308999 +
Gma Gma06g00147 Chr06 1292241 1296748 +
Gso Gso4g0149 Chr4 1282012 1286647 +
Gso Gso4g0149 Chr4 1282012 1286647 +
Lal Lal17g0034 Chr17 189227 193188 +
Lja Lja1g2298 Chr1 26704580 26708910 +
Mal Mal2g0382 Chr2 4228252 4232268 +
Mtr Mtr3g4351 Chr3 57484327 57488906 -
Phac Phac9g01883 Chr9 17807447 17812212 +
Pvu Pvu9g0120 Chr9 1909335 1913892 -
Rops Rops10g02546 Chr10 44332556 44337096 -
Sto Sto5g0039 Chr5 243557 247676 +
Tpr Tpr7g0156 Chr7 1249747 1254530 +
Tsu Tsu07g00176 Chr07 1314021 1318804 +
Vian Vian4g02464 Chr4 41275021 41279207 -
Vifa Vifa2g04593 Chr2 1354067479 1354071770 -
Viun Viun9g03762 Chr9 42591058 42595531 -
Vra Vra5g1721 Chr5 23477225 23481732 -
Vvi Vvi18g0094 Chr18 827872 829569 -
Aed Aed9g0155 Chr9 1091061 1092767 -
Aev Aev08g0134 Chr08 734717 736501 -
Ahy Ahy17g2163 Chr17 103366268 103368551 +
Aip Aip07g02306 Chr07 95992770 95994882 +
Car Car05g03328 Chr05 78018296 78020598 +
Cca Cca07g00194 Chr07 2474392 2476699 -
Gma Gma04g00156 Chr04 1314236 1315075 -
Gma Gma06g00148 Chr06 1299521 1301278 -
Lal Lal4g0038 Chr4 217379 219106 -
Lal Lal21g0076 Chr21 531124 532869 -
Lan Lan14g0979 Chr14 16082774 16084857 +
Lan Lan14g0979 Chr14 16082774 16084857 +
Lja Lja1g2299 Chr1 26710471 26712186 -
Mal Mal2g0383 Chr2 4235808 4237733 -
Mtr Mtr3g4350 Chr3 57476780 57479108 +
Phac Phac9g01884 Chr9 17816604 17818682 -
Pvu Pvu9g0119 Chr9 1903269 1905349 +
Rops Rops10g02545 Chr10 44327021 44328826 +
Tpr Tpr7g0157 Chr7 1256958 1259339 -
Tsu Tsu07g00177 Chr07 1320160 1321974 -
Vian Vian4g02463 Chr4 41268361 41270307 +
Vifa Vifa2g04592 Chr2 1353675393 1353677237 -
Vimu Vimu10g03563 Chr10 45166329 45168390 +
Viun Viun9g03761 Chr9 42585515 42587524 +
Vra Vra5g1720 Chr5 23471802 23474381 +
Vvi Vvi18g0095 Chr18 836855 838752 +
Aev Aev07g2390 Chr07 24589186 24590692 +
Ahy Ahy16g0009 Chr16 87878 89051 +
Aip Aip06g00009 Chr06 79818 81399 +
Apr Apr9g0695 Chr9 11551172 11553144 -
Bva Bva10g01009 Chr10 7409540 7413223 -
Car Car04g03624 Chr04 65691694 65693582 +
Car Car05g03327 Chr05 78004764 78008660 -
Cca Cca05g00431 Chr05 9464137 9465909 -
Cca Cca07g00195 Chr07 2479872 2483758 +
Gma Gma04g00157 Chr04 1319967 1324172 +
Gma Gma06g00149 Chr06 1305395 1309229 +
Gma Gma17g02499 Chr17 43001068 43002380 -
Lal Lal21g0077 Chr21 535533 538765 +
Lja Lja1g3431 Chr1 42798182 42802216 +
Mal Mal2g0384 Chr2 4245502 4248392 +
Mtr Mtr3g4348 Chr3 57453355 57457038 -
Ssu Ssu5g0010 Chr5 158681 162953 +
Sto Sto5g0040 Chr5 249591 254238 +
Tpr Tpr7g0158 Chr7 1274561 1278295 +
Tsu Tsu07g00178 Chr07 1332451 1336229 +
Vra Vra6g1987 Chr6 36576762 36578665 +
Vra Vra5g1719 Chr5 23464166 23468487 -