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
Vvi3g0193 . . . . Adu08g00670 . . Aed9g0038 . Aev05g0402 . Ahy15g0386 . Aip05g00375 . . . . . Apr5g1854 Arst8g00878 . . . . . . Bva14g02339 Car06g02222 . . Cca07g00044 . . . Dod02g0424 . . . . Gma04g00037 . . . Gso4g0031 . . . . . Lal9g0125 . . . . . . . . . Lapu9g02494 . Lasa5g04755 . . . . . . . . . Lja1g2385 . . . Mepo3g08036 . Mesa9g05704 . . . . . Phac9g00767 . Phco7g00055 . . . . . . . . . . . Pumo10g01175 . Pvu9g1226 . Rops10g01822 . Seca4g02758 . Spst9g00041 . . . Sto2g0999 . . . Trre5g05958 . . . Vian4g01611 . . . Vimu10g02245 . Viun9g02525 . Vivi3g04449 . . Vra5g1859
Vvi3g0194 . . . . . . . Aed9g0037 . . . . . . . . . . . Apr5g1855 . . . . . . . Bva14g02340 . . . Cca07g00043 . . . . . . . . Gma04g00036 Gma06g00035 . Gma12g00314 Gso4g0030 Gso4g0030 . Gso4g0030 Lal1g0170 Lal2g0102 Lal9g0126 . . . Lan13g0185 Lan13g0185 Lan13g0185 . . . Lapu9g02495 . . . . . . . . . . . Lja1g2386 . . . Mepo3g08037 . Mesa9g05705 . . . . . . . Phco7g00054 . . . . . . . . . . . . . Pvu9g1225 . . . . . Spst9g00039 . . . Sto2g1002 Sto10g0066 . . Trre5g05960 . . . . . . . Vimu10g03734 . . . Vivi3g01083 . . Vra5g1860
Vvi3g0195 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva14g02341 Car06g02225 . . . . . . . . . . . . . . Gma12g00315 . . . . Lal1g0171 Lal2g0103 Lal9g0127 . . . Lan13g0186 Lan13g0186 Lan13g0186 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto10g0065 . . . . . . . . . . . . . . . . . .
Vvi3g0196 . . . . . . . Aed9g0036 . . . . . . . . . . . Apr5g1856 . . . . . . . Bva14g02342 Car06g02226 . . Cca07g00042 . . . . . . . . Gma04g00035 Gma06g00034 . Gma12g00316 Gso4g0029 Gso4g0029 . Gso4g0029 Lal1g0173 Lal2g0104 Lal9g0128 . . . Lan13g0187 Lan13g0187 Lan13g0187 . . . Lapu9g02496 . Lasa5g04749 . . . . . . . . . Lja1g2387 . . . . . . . . . . . . . Phco7g00053 . . . . . . . . . . . . . Pvu9g1224 . . . . . Spst9g00037 . . . Sto2g1003 Sto10g0064 . . . . . . . . . . Vimu10g03735 . . . Vivi3g01084 . . Vra5g1861
Vvi3g0197 . . . . . . . . . Aev05g0399 . Ahy15g0378 . Aip05g00371 . . . . . . . . . . . . . . . . . . . . . Dod02g0420 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa2g3460 . . . . . . . . . . . . . . . . . . Sto2g1007 . . . . . . . . . . . . . . . . . . .
Vvi3g0198 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva14g02343 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0199 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cca02g02735 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ssu7g0237 . . . . . . . . . . . . . . . . . . . . .
Vvi3g0200 . . . . Adu09g02847 . . . Aev09g2697 . Ahy19g3077 . Aip09g03537 . . . . . Apr8g2639 . Arst9g03799 . . . . . . . . . . . . . Dod06g0276 . . . . . . . . . . . . . . . . Lal13g0233 Lal12g0265 . . . . . . . Lapu7g02492 . Lasa6g04758 . . . . . . . . . . . . Mal1g0246 Mepo4g04831 . Mesa1g05234 . . . . Mtr1g4296 Phac7g00314 . Phco6g03034 . . . Psa6g5310 . Pste4g00467 . . Pte9g01587 . . Pumo3g00206 . Pvu7g0195 . Rops6g03397 . Seca8g07988 . Spst10g01542 . . . . Sto10g0063 . Tpr1g0212 Trre1g06145 . . Tsu01g04974 Vian3g00190 . Vifa3g00185 . Vimu3g03644 . Viun7g03949 . Vivi1g03453 . . .
Vvi3g0201 . . . . . . . . . . . . . . . . . . . Apr5g1858 . . . . . . . Bva14g02345 . . . Cca07g00039 . . . . . . . . Gma04g00031 Gma06g00032 . . Gso4g0027 Gso4g0027 . . . . . . . . . . . . . . . . Lasa5g04746 . . . . . . . . . Lja1g2389 . . . Mepo3g08039 . . . . . . . . . Phco7g00050 . . . . . . . . . . . . . Pvu9g1222 . . . . . Spst9g00034 . . . Sto2g1014 Sto10g0060 . . . . . . . . . . Vimu10g03738 . . . Vivi3g01088 . . .
Vvi3g0202 . . . . . . Aed1g1779 . . . Ahy19g3076 . Aip09g03536 . . . . . Apr8g2641 . Arst9g03800 . . . . . . Bva14g02346 . . Cca02g02736 . . . Dod06g0278 . . . . . . . . . . . . . . . . Lal13g0235 Lal12g0266 . . . . . . . Lapu7g02494 . Lasa6g04761 . . . . . . . . . . . . Mal1g0235 Mepo4g04841 . Mesa1g05245 . . . . Mtr1g4300 Phac7g00313 . Phco6g03035 . . . . . Pste4g00465 . Pte18g00485 . . . . . Pvu7g0194 . . . . . Spst10g01543 . Ssu7g0236 . . Sto10g0059 . Tpr1g0210 Trre1g06147 . . Tsu01g04976 . . . . Vimu3g03645 . . . Vivi1g03450 . Vra8g2633 .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Adu Adu08g00670 Chr08 12073150 12074377 +
Arst Arst8g00878 Chr8 12043361 12044503 +
Pumo Pumo10g01175 Chr10 15394655 15395535 -
Rops Rops10g01822 Chr10 33894996 33895952 -
Seca Seca4g02758 Chr4 47446854 47447966 +
Vian Vian4g01611 Chr4 31706808 31707368 +
Vimu Vimu10g02245 Chr10 32862497 32863079 +
Viun Viun9g02525 Chr9 34339257 34340271 +
Vivi Vivi3g04449 Chr3 80064144 80064970 -
Vvi Vvi3g0193 Chr3 1691849 1693057 -
Adu Adu08g00670 Chr08 12073150 12074377 +
Aed Aed9g0038 Chr9 259840 260640 +
Aev Aev05g0402 Chr05 2786538 2786846 -
Ahy Ahy15g0386 Chr15 4476563 4477186 -
Aip Aip05g00375 Chr05 4132522 4132992 -
Apr Apr5g1854 Chr5 21658480 21659204 -
Arst Arst8g00878 Chr8 12043361 12044503 +
Bva Bva14g02339 Chr14 20176935 20178071 -
Car Car06g02222 Chr06 22815410 22817350 -
Cca Cca07g00044 Chr07 629488 630446 +
Dod Dod02g0424 Chr02 5663635 5665079 -
Gma Gma04g00037 Chr04 319495 320274 +
Gso Gso4g0031 Chr4 314943 315655 +
Lal Lal9g0125 Chr9 824471 824929 -
Lapu Lapu9g02494 Chr9 39215063 39215700 -
Lasa Lasa5g04755 Chr5 694302752 694303388 +
Lja Lja1g2385 Chr1 27555110 27556070 -
Mepo Mepo3g08036 Chr3 93205110 93206466 -
Mesa Mesa9g05704 Chr9 92733397 92733946 -
Phac Phac9g00767 Chr9 5665652 5666812 -
Phco Phco7g00055 Chr7 356246 356826 +
Pumo Pumo10g01175 Chr10 15394655 15395535 -
Pvu Pvu9g1226 Chr9 17723938 17724991 +
Rops Rops10g01822 Chr10 33894996 33895952 -
Seca Seca4g02758 Chr4 47446854 47447966 +
Spst Spst9g00041 Chr9 338551 339169 +
Sto Sto2g0999 Chr2 8767840 8769089 -
Trre Trre5g05958 Chr5 58980300 58980876 -
Vian Vian4g01611 Chr4 31706808 31707368 +
Vimu Vimu10g02245 Chr10 32862497 32863079 +
Viun Viun9g02525 Chr9 34339257 34340271 +
Vivi Vivi3g04449 Chr3 80064144 80064970 -
Vra Vra5g1859 Chr5 24417087 24417991 -
Vvi Vvi3g0194 Chr3 1707590 1708550 +
Aed Aed9g0037 Chr9 244739 246153 -
Apr Apr5g1855 Chr5 21665690 21666455 +
Bva Bva14g02340 Chr14 20188804 20190234 +
Cca Cca07g00043 Chr07 594388 595654 -
Gma Gma04g00036 Chr04 305947 307301 -
Gma Gma06g00035 Chr06 300064 301432 -
Gma Gma12g00314 Chr12 2540301 2541280 +
Gso Gso4g0030 Chr4 301459 303007 -
Gso Gso4g0030 Chr4 301459 303007 -
Gso Gso4g0030 Chr4 301459 303007 -
Lal Lal1g0170 Chr1 1069680 1073056 -
Lal Lal2g0102 Chr2 644339 645796 +
Lal Lal9g0126 Chr9 833401 834804 +
Lan Lan13g0185 Chr13 1143621 1144790 +
Lan Lan13g0185 Chr13 1143621 1144790 +
Lan Lan13g0185 Chr13 1143621 1144790 +
Lapu Lapu9g02495 Chr9 39226770 39228019 +
Lja Lja1g2386 Chr1 27571086 27572876 +
Mepo Mepo3g08037 Chr3 93211606 93212297 +
Mesa Mesa9g05705 Chr9 92743683 92744355 +
Phco Phco7g00054 Chr7 341120 342294 -
Pvu Pvu9g1225 Chr9 17696702 17698022 -
Spst Spst9g00039 Chr9 328509 334405 -
Sto Sto2g1002 Chr2 8818887 8820651 +
Sto Sto10g0066 Chr10 486725 491025 -
Trre Trre5g05960 Chr5 58990767 58991541 +
Vimu Vimu10g03734 Chr10 46191512 46192972 +
Vivi Vivi3g01083 Chr3 18211767 18213141 +
Vra Vra5g1860 Chr5 24429050 24430541 +
Vvi Vvi3g0195 Chr3 1716009 1720934 +
Bva Bva14g02341 Chr14 20196637 20202245 +
Car Car06g02225 Chr06 22851716 22855147 +
Gma Gma12g00315 Chr12 2550077 2553489 +
Lal Lal1g0171 Chr1 1073981 1078371 +
Lal Lal2g0103 Chr2 646882 651069 +
Lal Lal9g0127 Chr9 838045 842115 +
Lan Lan13g0186 Chr13 1146318 1150822 +
Lan Lan13g0186 Chr13 1146318 1150822 +
Lan Lan13g0186 Chr13 1146318 1150822 +
Sto Sto10g0065 Chr10 482889 486418 -
Vvi Vvi3g0196 Chr3 1722365 1725599 -
Aed Aed9g0036 Chr9 241909 244617 +
Apr Apr5g1856 Chr5 21667499 21670700 -
Bva Bva14g02342 Chr14 20203471 20206493 -
Car Car06g02226 Chr06 22856605 22859011 -
Cca Cca07g00042 Chr07 582800 585496 +
Gma Gma04g00035 Chr04 300153 302286 +
Gma Gma06g00034 Chr06 295576 297585 +
Gma Gma12g00316 Chr12 2555327 2557653 -
Gso Gso4g0029 Chr4 296105 298129 +
Gso Gso4g0029 Chr4 296105 298129 +
Gso Gso4g0029 Chr4 296105 298129 +
Lal Lal1g0173 Chr1 1078720 1082753 -
Lal Lal2g0104 Chr2 651339 654476 -
Lal Lal9g0128 Chr9 842381 844554 -
Lan Lan13g0187 Chr13 1151448 1154090 -
Lan Lan13g0187 Chr13 1151448 1154090 -
Lan Lan13g0187 Chr13 1151448 1154090 -
Lapu Lapu9g02496 Chr9 39245782 39247953 -
Lasa Lasa5g04749 Chr5 693550745 693552589 +
Lja Lja1g2387 Chr1 27582612 27584932 -
Phco Phco7g00053 Chr7 335522 337233 +
Pvu Pvu9g1224 Chr9 17691442 17693538 +
Spst Spst9g00037 Chr9 322570 324390 +
Sto Sto2g1003 Chr2 8830376 8833233 -
Sto Sto10g0064 Chr10 479596 481816 +
Vimu Vimu10g03735 Chr10 46195581 46197374 -
Vivi Vivi3g01084 Chr3 18224651 18226874 -
Vra Vra5g1861 Chr5 24432153 24434222 -
Vvi Vvi3g0197 Chr3 1727221 1732864 -
Aev Aev05g0399 Chr05 2769561 2770588 -
Ahy Ahy15g0378 Chr15 4405501 4407216 -
Aip Aip05g00371 Chr05 4106809 4108872 -
Dod Dod02g0420 Chr02 5616667 5618526 -
Psa Psa2g3460 Chr2 382678250 382680572 +
Sto Sto2g1007 Chr2 8870716 8871293 +
Vvi Vvi3g0198 Chr3 1740965 1742446 -
Bva Bva14g02343 Chr14 20210397 20212064 +
Vvi Vvi3g0199 Chr3 1746786 1748003 -
Cca Cca02g02735 Chr02 48780381 48781808 +
Ssu Ssu7g0237 Chr7 3850877 3852379 -
Vvi Vvi3g0200 Chr3 1749910 1752847 -
Adu Adu09g02847 Chr09 116143466 116146447 +
Aev Aev09g2697 Chr09 27856632 27859568 +
Ahy Ahy19g3077 Chr19 153546906 153549869 -
Aip Aip09g03537 Chr09 142068186 142071171 -
Apr Apr8g2639 Chr8 36211419 36214791 +
Arst Arst9g03799 Chr9 114039874 114042817 +
Dod Dod06g0276 Chr06 3766997 3770942 +
Lal Lal13g0233 Chr13 1487426 1490694 +
Lal Lal12g0265 Chr12 1895584 1899052 +
Lapu Lapu7g02492 Chr7 41334708 41336666 +
Lasa Lasa6g04758 Chr6 667678471 667681391 -
Mal Mal1g0246 Chr1 2671446 2674849 +
Mepo Mepo4g04831 Chr4 57708592 57712776 -
Mesa Mesa1g05234 Chr1 79552914 79556364 -
Mtr Mtr1g4296 Chr1 54638761 54642478 -
Phac Phac7g00314 Chr7 1457471 1461308 -
Phco Phco6g03034 Chr6 51417793 51420698 +
Psa Psa6g5310 Chr6 465912032 465915648 -
Pste Pste4g00467 Chr4 3542582 3544337 -
Pte Pte9g01587 Chr9 36924625 36927701 +
Pumo Pumo3g00206 Chr3 2636428 2640452 -
Pvu Pvu7g0195 Chr7 1327081 1330442 -
Rops Rops6g03397 Chr6 58580400 58584045 +
Seca Seca8g07988 Chr8 177491106 177495092 +
Spst Spst10g01542 Chr10 16042805 16045808 +
Sto Sto10g0063 Chr10 474119 477169 -
Tpr Tpr1g0212 Chr1 1723191 1732112 +
Trre Trre1g06145 Chr1 65379411 65382543 -
Tsu Tsu01g04974 Chr01 56575739 56579761 -
Vian Vian3g00190 Chr3 1611059 1614004 -
Vifa Vifa3g00185 Chr3 14127901 14131002 +
Vimu Vimu3g03644 Chr3 49135996 49140744 +
Viun Viun7g03949 Chr7 39270461 39273732 +
Vivi Vivi1g03453 Chr1 74095681 74099018 +
Vvi Vvi3g0201 Chr3 1761077 1762217 +
Apr Apr5g1858 Chr5 21674405 21682139 +
Bva Bva14g02345 Chr14 20224246 20225770 +
Cca Cca07g00039 Chr07 540072 541502 -
Gma Gma04g00031 Chr04 276247 277514 -
Gma Gma06g00032 Chr06 272405 283730 -
Gso Gso4g0027 Chr4 273713 275067 -
Gso Gso4g0027 Chr4 273713 275067 -
Lasa Lasa5g04746 Chr5 693319071 693320014 -
Lja Lja1g2389 Chr1 27594785 27595953 +
Mepo Mepo3g08039 Chr3 93226139 93227475 +
Phco Phco7g00050 Chr7 319882 320990 -
Pvu Pvu9g1222 Chr9 17670440 17671959 -
Spst Spst9g00034 Chr9 308135 309295 -
Sto Sto2g1014 Chr2 8940297 8942149 +
Sto Sto10g0060 Chr10 468515 469617 -
Vimu Vimu10g03738 Chr10 46208197 46210250 +
Vivi Vivi3g01088 Chr3 18289831 18294215 +
Vvi Vvi3g0202 Chr3 1764839 1767159 -
Aed Aed1g1779 Chr1 15265769 15274054 +
Ahy Ahy19g3076 Chr19 153535724 153538296 +
Aip Aip09g03536 Chr09 142057030 142059678 +
Apr Apr8g2641 Chr8 36218219 36220815 -
Arst Arst9g03800 Chr9 114048743 114051316 -
Bva Bva14g02346 Chr14 20227894 20230410 -
Cca Cca02g02736 Chr02 48783330 48791541 -
Dod Dod06g0278 Chr06 3776149 3778911 -
Lal Lal13g0235 Chr13 1494584 1497071 -
Lal Lal12g0266 Chr12 1900176 1902778 -
Lapu Lapu7g02494 Chr7 41342263 41345300 -
Lasa Lasa6g04761 Chr6 667733296 667735484 -
Mal Mal1g0235 Chr1 2611050 2613052 +
Mepo Mepo4g04841 Chr4 57763189 57766618 -
Mesa Mesa1g05245 Chr1 79705540 79708436 -
Mtr Mtr1g4300 Chr1 54693123 54697317 -
Phac Phac7g00313 Chr7 1453514 1456433 +
Phco Phco6g03035 Chr6 51422229 51425986 -
Pste Pste4g00465 Chr4 3533359 3537205 +
Pte Pte18g00485 Chr18 10538898 10539202 -
Pvu Pvu7g0194 Chr7 1321621 1324218 +
Spst Spst10g01543 Chr10 16047355 16050298 -
Ssu Ssu7g0236 Chr7 3846113 3848777 +
Sto Sto10g0059 Chr10 464365 466826 +
Tpr Tpr1g0210 Chr1 1713983 1717057 +
Trre Trre1g06147 Chr1 65387065 65389340 -
Tsu Tsu01g04976 Chr01 56585325 56590229 -
Vimu Vimu3g03645 Chr3 49141157 49142698 -
Vivi Vivi1g03450 Chr1 74082428 74085515 +
Vra Vra8g2633 Chr8 44215517 44219636 -
Aev Aev05g0402 Chr05 2786538 2786846 -
Ahy Ahy15g0386 Chr15 4476563 4477186 -
Aip Aip05g00375 Chr05 4132522 4132992 -
Dod Dod02g0424 Chr02 5663635 5665079 -
Adu Adu08g00670 Chr08 12073150 12074377 +
Arst Arst8g00878 Chr8 12043361 12044503 +
Lapu Lapu9g02494 Chr9 39215063 39215700 -
Lasa Lasa5g04755 Chr5 694302752 694303388 +
Mepo Mepo3g08036 Chr3 93205110 93206466 -
Mesa Mesa9g05704 Chr9 92733397 92733946 -
Phac Phac9g00767 Chr9 5665652 5666812 -
Phco Phco7g00055 Chr7 356246 356826 +
Pumo Pumo10g01175 Chr10 15394655 15395535 -
Pvu Pvu9g1226 Chr9 17723938 17724991 +
Rops Rops10g01822 Chr10 33894996 33895952 -
Seca Seca4g02758 Chr4 47446854 47447966 +
Spst Spst9g00041 Chr9 338551 339169 +
Trre Trre5g05958 Chr5 58980300 58980876 -
Vian Vian4g01611 Chr4 31706808 31707368 +
Vimu Vimu10g02245 Chr10 32862497 32863079 +
Viun Viun9g02525 Chr9 34339257 34340271 +
Vivi Vivi3g04449 Chr3 80064144 80064970 -
Vivi Vivi3g04449 Chr3 80064144 80064970 -
Lapu Lapu9g02496 Chr9 39245782 39247953 -
Lasa Lasa5g04749 Chr5 693550745 693552589 +
Phco Phco7g00053 Chr7 335522 337233 +
Pvu Pvu9g1224 Chr9 17691442 17693538 +
Spst Spst9g00037 Chr9 322570 324390 +
Vimu Vimu10g03735 Chr10 46195581 46197374 -
Vivi Vivi3g01084 Chr3 18224651 18226874 -