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
Vvi2g1122 . . . . Adu05g00249 . Aed11g1057 . Aev05g0261 . Ahy15g0242 . Aip05g00226 . . . . . Apr7g1871 . Arst5g00317 . Bach4g00879 . . . Bva08g01023 . . . Cca06g01110 . . . Dod02g0284 . . . . . Gma01g01561 Gma09g02016 . . Gso1g1294 Gso1g1294 . . . . . . . . . . . . . . Lapu2g00957 . Lasa2g03635 . . . . . . . . . Lja2g0705 . Mal6g0778 . Mepo5g01209 . . . . . Mtr5g1079 . Phac2g01979 . Phco4g00686 . . . Psa2g3274 . Pste1g03611 . . . . . Pumo8g01560 . Pvu2g1276 . Rops1g01374 . . . Spst2g01099 . Ssu2g2087 . . . Tpr2g1324 . Trre9g01580 . Tsu05g01066 . Vian10g00962 . Vifa1g06126 . Vimu7g03283 . Viun2g01632 . Vivi2g02611 . Vra11g0932 .
Vvi2g1123 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g1124 . . . . Adu05g00250 . Aed11g1058 . Aev05g0262 . Ahy15g0243 . Aip05g00227 . . . . . Apr7g1872 Apr3g0467 Arst5g00319 Arst1g01231 Bach4g00878 . . . Bva08g01019 Bva11g01379 . . Cca06g01111 Cca11g01010 . . Dod02g0285 . . . . . . Gma09g02017 . . . . . . Lal15g0335 Lal16g0394 . . Lal16g1783 . Lan18g0838 Lan18g0838 . . Lan18g0838 . . Lapu3g02108 Lasa2g03623 . . . . . . . . . Lja2g0699 Lja4g3005 Mal6g0789 . Mepo5g01199 . . . . . Mtr5g1066 . Phac2g01976 . Phco4g00687 Phco8g00240 . . Psa2g3279 . Pste1g03610 Pste7g00567 . . . . Pumo8g01561 . Pvu2g1275 Pvu3g2859 Rops1g01375 . Seca10g01181 . Spst2g01098 Spst3g03622 Ssu2g2088 . Sto6g4088 . Tpr2g1309 . Trre9g01570 . Tsu05g01049 . Vian10g00961 . Vifa1g06142 . Vimu7g03282 Vimu11g00984 Viun2g01634 . . . Vra11g0931 .
Vvi2g1125 . . . . . . Aed11g1060 . . . . . . . . . . . . . . . . . . . . . . . Cca06g01114 . . . . . . . . . Gma01g01562 . . . Gso1g1295 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco4g00689 . . . . . . . . . . . Pumo8g01562 . Pvu2g1273 . Rops1g01385 . . . . . . . . . . . . . . . Vian10g00958 . . . Vimu7g03279 . Viun2g01640 . . . Vra11g0928 .
Vvi2g1126 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g1127 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g1128 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g1129 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g1130 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g1131 Acco11g1404 . . . Adu05g00253 . Aed11g1065 . . . Ahy15g0246 . Aip05g00230 . Alju09g1403 . . . Apr7g0326 . Arst5g00323 . Bach4g00873 . Bisa11g1989 . Bva08g01017 . . . Cca06g01118 . Dere09g1255 . Dod02g0292 . . . Glsi05g1145 . Gma01g01566 Gma09g02023 . . Gso1g1300 Gso1g1300 . . Lal15g0334 Lal16g0393 . . . . Lan18g0839 Lan18g0839 . . . . Lapu2g00963 . Lasa2g03618 . Lele49g0823 Lele50g0860 Lele51g0847 Lele52g0847 . . . . Lja2g0697 . Mal6g0811 . Mepo5g01183 . Mesa17g01259 . Mibi12g1185 . Mtr5g1055 . . . Phco4g00694 . Prci10g1322 . . . Pste1g03583 . . . . . Pumo8g01564 . Pvu2g1269 . Rops1g01388 . Seca10g01168 . Spst2g01077 . Ssu2g2097 . Sto6g4087 . Tpr2g1282 . Trre9g01521 . Tsu05g01031 . Vian10g00952 . Vifa1g06169 . Vimu7g03276 . Viun2g01644 . Vivi2g02636 . Vra11g0925 .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi2g1122 Chr2 17760217 17774420 +
Adu Adu05g00249 Chr05 2582431 2587150 +
Aed Aed11g1057 Chr11 16287254 16292956 +
Aev Aev05g0261 Chr05 1904969 1909247 +
Ahy Ahy15g0242 Chr15 2692172 2696962 +
Aip Aip05g00226 Chr05 2388400 2393136 +
Apr Apr7g1871 Chr7 25973258 25981360 +
Arst Arst5g00317 Chr5 2602077 2606839 +
Bach Bach4g00879 Chr4 5901930 5907182 -
Bva Bva08g01023 Chr08 5238870 5244274 -
Cca Cca06g01110 Chr06 25234702 25241293 +
Dod Dod02g0284 Chr02 3802188 3808430 +
Gma Gma01g01561 Chr01 51098132 51116323 +
Gma Gma09g02016 Chr09 45751652 45757537 +
Gso Gso1g1294 Chr1 49381429 49388362 +
Gso Gso1g1294 Chr1 49381429 49388362 +
Lapu Lapu2g00957 Chr2 8873450 8880951 +
Lasa Lasa2g03635 Chr2 545585607 545591911 -
Lja Lja2g0705 Chr2 6456889 6461813 -
Mal Mal6g0778 Chr6 11419951 11427817 +
Mepo Mepo5g01209 Chr5 12291560 12297998 -
Mtr Mtr5g1079 Chr5 10788795 10795787 -
Phac Phac2g01979 Chr2 21820658 21828311 -
Phco Phco4g00686 Chr4 5184764 5191809 +
Psa Psa2g3274 Chr2 370841124 370847729 +
Pste Pste1g03611 Chr1 17161037 17168431 -
Pumo Pumo8g01560 Chr8 50649501 50655619 +
Pvu Pvu2g1276 Chr2 24975752 24983290 -
Rops Rops1g01374 Chr1 30495982 30503580 +
Spst Spst2g01099 Chr2 9673201 9680685 -
Ssu Ssu2g2087 Chr2 75962221 75969308 +
Tpr Tpr2g1324 Chr2 15496611 15515398 -
Trre Trre9g01580 Chr9 13775223 13781232 -
Tsu Tsu05g01066 Chr05 9360063 9366064 -
Vian Vian10g00962 Chr10 10411036 10416882 -
Vifa Vifa1g06126 Chr1 957020917 957026110 +
Vimu Vimu7g03283 Chr7 27885646 27891439 -
Viun Viun2g01632 Chr2 26045975 26052540 +
Vivi Vivi2g02611 Chr2 117661277 117666861 +
Vra Vra11g0932 Chr11 8092089 8099711 -
Vvi Vvi2g1123 Chr2 17785702 17785983 -
Vvi Vvi2g1124 Chr2 17792452 17807280 -
Adu Adu05g00250 Chr05 2589509 2591692 -
Aed Aed11g1058 Chr11 16291827 16296310 -
Aev Aev05g0262 Chr05 1909798 1912888 -
Ahy Ahy15g0243 Chr15 2697151 2702368 -
Aip Aip05g00227 Chr05 2395328 2397569 -
Apr Apr7g1872 Chr7 25981629 25985672 -
Apr Apr3g0467 Chr3 9717384 9723052 +
Arst Arst5g00319 Chr5 2607006 2611859 -
Arst Arst1g01231 Chr1 12183744 12189091 +
Bach Bach4g00878 Chr4 5898167 5901399 +
Bva Bva08g01019 Chr08 5218736 5225279 +
Bva Bva11g01379 Chr11 13757964 13764899 -
Cca Cca06g01111 Chr06 25241871 25246098 -
Cca Cca11g01010 Chr11 23123902 23131885 -
Dod Dod02g0285 Chr02 3808669 3812913 -
Gma Gma09g02017 Chr09 45757906 45762653 -
Lal Lal15g0335 Chr15 2265107 2271543 +
Lal Lal16g0394 Chr16 2374601 2388926 +
Lal Lal16g1783 Chr16 16917285 16928527 +
Lan Lan18g0838 Chr18 13721887 13728976 -
Lan Lan18g0838 Chr18 13721887 13728976 -
Lan Lan18g0838 Chr18 13721887 13728976 -
Lapu Lapu3g02108 Chr3 40914532 40921141 +
Lasa Lasa2g03623 Chr2 544875706 544878206 +
Lja Lja2g0699 Chr2 6396183 6402132 -
Lja Lja4g3005 Chr4 55734747 55741643 -
Mal Mal6g0789 Chr6 11595412 11602076 +
Mepo Mepo5g01199 Chr5 12171061 12177055 +
Mtr Mtr5g1066 Chr5 10634054 10642502 -
Phac Phac2g01976 Chr2 21815502 21820561 +
Phco Phco4g00687 Chr4 5192955 5200012 -
Phco Phco8g00240 Chr8 2266163 2271495 +
Psa Psa2g3279 Chr2 371275138 371280580 -
Pste Pste1g03610 Chr1 17155472 17159697 +
Pste Pste7g00567 Chr7 5229694 5235465 -
Pumo Pumo8g01561 Chr8 50656722 50660377 -
Pvu Pvu2g1275 Chr2 24970390 24975564 +
Pvu Pvu3g2859 Chr3 50310992 50316487 -
Rops Rops1g01375 Chr1 30503940 30508622 -
Seca Seca10g01181 Chr10 11585882 11590403 +
Spst Spst2g01098 Chr2 9668002 9672305 +
Spst Spst3g03622 Chr3 86291257 86300468 +
Ssu Ssu2g2088 Chr2 75971156 75975157 -
Sto Sto6g4088 Chr6 44461605 44466910 +
Tpr Tpr2g1309 Chr2 15302840 15310559 -
Trre Trre9g01570 Chr9 13663368 13666686 +
Tsu Tsu05g01049 Chr05 9209542 9216769 -
Vian Vian10g00961 Chr10 10406111 10409635 +
Vifa Vifa1g06142 Chr1 959098462 959101367 -
Vimu Vimu7g03282 Chr7 27880765 27882808 +
Vimu Vimu11g00984 Chr11 10245579 10252048 -
Viun Viun2g01634 Chr2 26052807 26057247 -
Vra Vra11g0931 Chr11 8085119 8090635 +
Vvi Vvi2g1125 Chr2 17855064 17855558 +
Aed Aed11g1060 Chr11 16311860 16313248 +
Cca Cca06g01114 Chr06 25261969 25262277 +
Gma Gma01g01562 Chr01 51128198 51131630 +
Gso Gso1g1295 Chr1 49399581 49403262 +
Phco Phco4g00689 Chr4 5208753 5209055 +
Pumo Pumo8g01562 Chr8 50743740 50747362 +
Pvu Pvu2g1273 Chr2 24927661 24928131 -
Rops Rops1g01385 Chr1 30824927 30828616 +
Vian Vian10g00958 Chr10 10372951 10379399 -
Vimu Vimu7g03279 Chr7 27850970 27860234 -
Viun Viun2g01640 Chr2 26077629 26081444 +
Vra Vra11g0928 Chr11 8059613 8060632 -
Vvi Vvi2g1126 Chr2 17864675 17865514 +
Vvi Vvi2g1127 Chr2 17868123 17868566 -
Vvi Vvi2g1128 Chr2 17891521 17900419 +
Vvi Vvi2g1129 Chr2 17912353 17912851 -
Vvi Vvi2g1130 Chr2 17913253 17913975 -
Vvi Vvi2g1131 Chr2 17957867 17974533 -
Acco Acco11g1404 Chr11 28406877 28409558 -
Adu Adu05g00253 Chr05 2670117 2671905 -
Aed Aed11g1065 Chr11 16338284 16342574 -
Ahy Ahy15g0246 Chr15 2805435 2807979 -
Aip Aip05g00230 Chr05 2459360 2460687 -
Alju Alju09g1403 Chr09 37922393 37925823 -
Apr Apr7g0326 Chr7 8654196 8656545 +
Arst Arst5g00323 Chr5 2689886 2691580 -
Bach Bach4g00873 Chr4 5863179 5867765 +
Bisa Bisa11g1989 Chr11 42646227 42649005 +
Bva Bva08g01017 Chr08 5206260 5208643 +
Cca Cca06g01118 Chr06 25373676 25377075 -
Dere Dere09g1255 Chr09 16490041 16492637 +
Dod Dod02g0292 Chr02 3969430 3973194 -
Glsi Glsi05g1145 Chr05 61136222 61138909 -
Gma Gma01g01566 Chr01 51195530 51199016 -
Gma Gma09g02023 Chr09 45813517 45818058 -
Gso Gso1g1300 Chr1 49474614 49480187 -
Gso Gso1g1300 Chr1 49474614 49480187 -
Lal Lal15g0334 Chr15 2250969 2256725 +
Lal Lal16g0393 Chr16 2368490 2370546 +
Lan Lan18g0839 Chr18 13742454 13745920 -
Lan Lan18g0839 Chr18 13742454 13745920 -
Lapu Lapu2g00963 Chr2 8944571 8947257 -
Lasa Lasa2g03618 Chr2 544500829 544502359 +
Lele Lele49g0823 Chr49 5064973 5067506 +
Lele Lele50g0860 Chr50 5376395 5378661 +
Lele Lele51g0847 Chr51 5169507 5171577 +
Lele Lele52g0847 Chr52 5431666 5434223 +
Lja Lja2g0697 Chr2 6356231 6359603 +
Mal Mal6g0811 Chr6 12108252 12110767 -
Mepo Mepo5g01183 Chr5 12001594 12004476 +
Mesa Mesa17g01259 Chr17 16196703 16198773 +
Mibi Mibi12g1185 Chr12 27184296 27187600 -
Mtr Mtr5g1055 Chr5 10536805 10539819 +
Phco Phco4g00694 Chr4 5247707 5257901 -
Prci Prci10g1322 Chr10 8825854 8830037 +
Pste Pste1g03583 Chr1 17028284 17031195 +
Pumo Pumo8g01564 Chr8 50870544 50875257 -
Pvu Pvu2g1269 Chr2 24866250 24868765 +
Rops Rops1g01388 Chr1 30929188 30933741 -
Seca Seca10g01168 Chr10 11379946 11383154 +
Spst Spst2g01077 Chr2 9505985 9508631 +
Ssu Ssu2g2097 Chr2 76341883 76345174 -
Sto Sto6g4087 Chr6 44441719 44443501 +
Tpr Tpr2g1282 Chr2 15002889 15006099 +
Trre Trre9g01521 Chr9 13197767 13199859 +
Tsu Tsu05g01031 Chr05 8987721 8990683 +
Vian Vian10g00952 Chr10 10039137 10042810 +
Vifa Vifa1g06169 Chr1 964357575 964358955 -
Vimu Vimu7g03276 Chr7 27799673 27802065 +
Viun Viun2g01644 Chr2 26119118 26122232 -
Vivi Vivi2g02636 Chr2 118659035 118661261 -
Vra Vra11g0925 Chr11 8012999 8015869 +