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
Vvi3g0143 . . . . . . . . Aev04g3552 . Ahy13g0956 . Aip03g01037 . . . Amo13g1101 . . . . . . . . . . . . . . . . . Dod03g3342 . . . . . . . . Gma12g00233 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0144 . . . . . . . . . . . . . . . . . . . . . Arst3g00946 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco9g00316 . . . . . Pste1g01077 . . . . . Pumo11g02035 . Pvu11g0275 . Rops3g00339 . Seca6g00566 . Spst2g02729 . . . . . . . . . . . . . Vifa6g01424 . . . Viun11g02688 . Vivi5g03063 . .
Vvi3g0145 . Acco01g2130 Accr2g00342 Accr1g01840 Adu09g02780 Adu03g00740 . . Aev04g3551 . Ahy13g0955 . Aip03g01036 . Alju01g3558 Alju02g1904 Amo13g1362 . . Apr5g1834 . Arst3g00944 . . Bisa03g2732 Bisa01g4093 Bva13g01591 Bva14g02302 . . . . Dere01g0317 Dere06g0115 Dod03g3341 . . . Glsi12g0788 Glsi01g0108 Gma04g00054 Gma06g00049 . Gma12g00234 Gso4g0048 Gso4g0048 . Gso4g0048 . Lal2g0066 . . . . . . . . . . Lapu7g02446 Lapu11g00923 Lasa6g04705 Lasa7g02393 . Lele06g2622 . Lele08g2561 Lele45g1345 Lele46g1437 Lele47g0072 Lele48g0075 Lja1g2367 . . . Mepo4g04774 Mepo2g02571 Mesa1g05161 Mesa13g02437 Mibi02g3257 Mibi01g1783 . . Phac7g00386 . Phco6g02981 Phco9g00317 Prci1g0297 Prci14g0131 . . Pste4g00584 . . Pte9g00597 . . Pumo3g00252 Pumo11g02034 Pvu7g0251 Pvu11g0276 Rops6g03342 Rops3g00341 Seca8g07923 Seca6g00567 Spst10g01486 Spst2g02728 . . Sto2g0911 Sto10g0091 . . . Trre7g02489 . . Vian3g00235 Vian5g01654 Vifa3g03631 Vifa6g01426 Vimu3g03596 Vimu5g02568 Viun7g03876 Viun11g02686 Vivi1g03523 Vivi5g03062 . .
Vvi3g0146 . . . . . . Aed5g0299 Aed9g0055 . . Ahy13g0076 . Aip03g00081 . . . Amo13g5766 . . . . . . . . . Bva13g01590 Bva14g02303 Car06g02186 . Cca04g00326 Cca07g00064 . . . . . . . . Gma04g00053 Gma06g00048 . Gma12g00284 Gso4g0047 Gso4g0047 . Gso4g0047 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa7g4009 . . . . . . . . . Pvu9g0263 . . . . . . . Ssu3g2974 . Sto2g0912 . . . . . . . . . . . . . Viun9g03938 . . . Vra2g0325 Vra5g1836
Vvi3g0147 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva13g01589 Bva14g02304 Car06g02187 . . . . . . . . . . . . . . Gma12g00285 . . . . Lal1g0140 Lal2g0087 . . . . Lan13g0163 Lan13g0163 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa7g4008 . . . . . . . . . . . . . . . . . . . Sto2g0913 Sto10g0090 . . . . . . . . . . . . . . . . . .
Vvi3g0148 . . . . . . . Aed9g0054 . . . . . . . . . . . Apr5g1835 . . . . . . Bva13g01588 . . . . Cca07g00063 . . . . . . . . Gma04g00052 Gma06g00047 . . Gso4g0046 Gso4g0046 . . . . . . . . . . . . . . . . . . . . . . . . . . Lja1g2368 . . . . . . . . . . . . . . . . . . . . . . . . . . . Pvu9g0262 . Rops10g02677 . . . . . . . Sto2g0914 . . . . . . . . . . . . . Viun9g03939 . . . . Vra5g1837
Vvi3g0149 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0150 . . . . . . . . . . . . Aip03g00920 . . . . . . . . . . . . . . Bva14g02305 Car06g02188 . . . . . . . . . . . . . . Gma12g00286 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0151 . . . . . . . . Aev04g3496 . . . Aip03g00921 . . . Amo13g0863 . . . . . . . . . . . . . . . . . Dod03g3270 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0152 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa7g4007 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi3g0143 Chr3 1309921 1320293 +
Aev Aev04g3552 Chr04 33535006 33555183 -
Ahy Ahy13g0956 Chr13 10341227 10358972 -
Aip Aip03g01037 Chr03 10030523 10047995 -
Amo Amo13g1101 Chr13 13943716 13958061 -
Dod Dod03g3342 Chr03 66033154 66063451 -
Gma Gma12g00233 Chr12 1808494 1830303 +
Vvi Vvi3g0144 Chr3 1333168 1346901 +
Arst Arst3g00946 Chr3 6896591 6914137 -
Phco Phco9g00316 Chr9 2134591 2154254 +
Pste Pste1g01077 Chr1 3477095 3513995 +
Pumo Pumo11g02035 Chr11 52413008 52419184 -
Pvu Pvu11g0275 Chr11 2187234 2195107 +
Rops Rops3g00339 Chr3 4226468 4245941 +
Seca Seca6g00566 Chr6 16744181 16746733 +
Spst Spst2g02729 Chr2 27078948 27102662 -
Vifa Vifa6g01424 Chr6 518946163 518986586 +
Viun Viun11g02688 Chr11 39626352 39644211 -
Vivi Vivi5g03063 Chr5 119044214 119076458 -
Vvi Vvi3g0145 Chr3 1347939 1348457 +
Acco Acco01g2130 Chr01 37206610 37207319 +
Accr Accr2g00342 Chr2 8068651 8069487 -
Accr Accr1g01840 Chr1 48795259 48795774 +
Adu Adu09g02780 Chr09 115537973 115539067 +
Adu Adu03g00740 Chr03 6888158 6889130 -
Aev Aev04g3551 Chr04 33532854 33533372 -
Ahy Ahy13g0955 Chr13 10338088 10338994 -
Aip Aip03g01036 Chr03 10026693 10027668 -
Alju Alju01g3558 Chr01 64513504 64515441 -
Alju Alju02g1904 Chr02 18312095 18314036 -
Amo Amo13g1362 Chr13 18145701 18147752 -
Apr Apr5g1834 Chr5 21539054 21539671 +
Arst Arst3g00944 Chr3 6893819 6894703 -
Bisa Bisa03g2732 Chr03 42939199 42941483 -
Bisa Bisa01g4093 Chr01 98452889 98453407 +
Bva Bva13g01591 Chr13 9534493 9535537 -
Bva Bva14g02302 Chr14 19901506 19902318 +
Dere Dere01g0317 Chr01 7687821 7689596 -
Dere Dere06g0115 Chr06 1292168 1292686 -
Dod Dod03g3341 Chr03 66026444 66027879 -
Glsi Glsi12g0788 Chr12 25198849 25200630 +
Glsi Glsi01g0108 Chr01 902260 902781 -
Gma Gma04g00054 Chr04 452026 452726 -
Gma Gma06g00049 Chr06 432203 433027 -
Gma Gma12g00234 Chr12 1834298 1835414 +
Gso Gso4g0048 Chr4 445927 446705 -
Gso Gso4g0048 Chr4 445927 446705 -
Gso Gso4g0048 Chr4 445927 446705 -
Lal Lal2g0066 Chr2 369744 370262 +
Lapu Lapu7g02446 Chr7 40856880 40858803 +
Lapu Lapu11g00923 Chr11 11748987 11750447 -
Lasa Lasa6g04705 Chr6 663536110 663537885 -
Lasa Lasa7g02393 Chr7 519871436 519871954 -
Lele Lele06g2622 Chr06 34101710 34103497 -
Lele Lele08g2561 Chr08 31373456 31375234 -
Lele Lele45g1345 Chr45 23101486 23102004 +
Lele Lele46g1437 Chr46 21178225 21178743 +
Lele Lele47g0072 Chr47 495374 495892 -
Lele Lele48g0075 Chr48 1200290 1200808 -
Lja Lja1g2367 Chr1 27367957 27368690 +
Mepo Mepo4g04774 Chr4 57170385 57172478 +
Mepo Mepo2g02571 Chr2 35372957 35373910 -
Mesa Mesa1g05161 Chr1 78710151 78711935 +
Mesa Mesa13g02437 Chr13 28533161 28533679 +
Mibi Mibi02g3257 Chr02 57996211 57997544 +
Mibi Mibi01g1783 Chr01 26105841 26106452 -
Phac Phac7g00386 Chr7 1953969 1956192 -
Phco Phco6g02981 Chr6 50967161 50968960 +
Phco Phco9g00317 Chr9 2157298 2157816 +
Prci Prci1g0297 Chr1 2886515 2888631 +
Prci Prci14g0131 Chr14 1114404 1115232 -
Pste Pste4g00584 Chr4 4460069 4461799 -
Pte Pte9g00597 Chr9 9074166 9075917 +
Pumo Pumo3g00252 Chr3 3235754 3237981 -
Pumo Pumo11g02034 Chr11 52402953 52404176 -
Pvu Pvu7g0251 Chr7 1800944 1803088 -
Pvu Pvu11g0276 Chr11 2197477 2199019 +
Rops Rops6g03342 Chr6 57907161 57909067 +
Rops Rops3g00341 Chr3 4247413 4248258 +
Seca Seca8g07923 Chr8 176887413 176889272 +
Seca Seca6g00567 Chr6 16748407 16748925 +
Spst Spst10g01486 Chr10 15501496 15503304 +
Spst Spst2g02728 Chr2 27075423 27076010 -
Sto Sto2g0911 Chr2 7884438 7886389 +
Sto Sto10g0091 Chr10 681444 681962 -
Trre Trre7g02489 Chr7 20496997 20497515 +
Vian Vian3g00235 Chr3 2068084 2069895 -
Vian Vian5g01654 Chr5 38992327 38992845 -
Vifa Vifa3g03631 Chr3 1058652572 1058654335 -
Vifa Vifa6g01426 Chr6 519859864 519860379 +
Vimu Vimu3g03596 Chr3 48703057 48704868 +
Vimu Vimu5g02568 Chr5 36006643 36008299 -
Viun Viun7g03876 Chr7 38825002 38827081 +
Viun Viun11g02686 Chr11 39622316 39623208 -
Vivi Vivi1g03523 Chr1 75236867 75238926 +
Vivi Vivi5g03062 Chr5 119000420 119001327 -
Vvi Vvi3g0146 Chr3 1350250 1356150 +
Aed Aed5g0299 Chr5 2065519 2069163 +
Aed Aed9g0055 Chr9 390913 393489 -
Ahy Ahy13g0076 Chr13 760938 765092 -
Aip Aip03g00081 Chr03 739652 743871 -
Amo Amo13g5766 Chr13 159721028 159725181 -
Bva Bva13g01590 Chr13 9526286 9531006 -
Bva Bva14g02303 Chr14 19906090 19906713 +
Car Car06g02186 Chr06 22327278 22331446 +
Cca Cca04g00326 Chr04 3172875 3176602 +
Cca Cca07g00064 Chr07 878310 881729 -
Gma Gma04g00053 Chr04 446258 448677 -
Gma Gma06g00048 Chr06 425412 428433 -
Gma Gma12g00284 Chr12 2275563 2278815 +
Gso Gso4g0047 Chr4 440148 443018 -
Gso Gso4g0047 Chr4 440148 443018 -
Gso Gso4g0047 Chr4 440148 443018 -
Psa Psa7g4009 Chr7 330875062 330879358 -
Pvu Pvu9g0263 Chr9 5899933 5902972 -
Ssu Ssu3g2974 Chr3 84872529 84875218 -
Sto Sto2g0912 Chr2 7892320 7895494 +
Viun Viun9g03938 Chr9 43422809 43425676 +
Vra Vra2g0325 Chr2 2487146 2490754 +
Vra Vra5g1836 Chr5 24277930 24281279 +
Vvi Vvi3g0147 Chr3 1357958 1360211 +
Bva Bva13g01589 Chr13 9522260 9525297 -
Bva Bva14g02304 Chr14 19908588 19911029 +
Car Car06g02187 Chr06 22338114 22341056 +
Gma Gma12g00285 Chr12 2280153 2282703 +
Lal Lal1g0140 Chr1 926869 929548 +
Lal Lal2g0087 Chr2 537099 546436 +
Lan Lan13g0163 Chr13 992080 994770 +
Lan Lan13g0163 Chr13 992080 994770 +
Psa Psa7g4008 Chr7 330856199 330858931 -
Sto Sto2g0913 Chr2 7898092 7900207 +
Sto Sto10g0090 Chr10 675099 676903 -
Vvi Vvi3g0148 Chr3 1362271 1363572 +
Aed Aed9g0054 Chr9 386631 388713 -
Apr Apr5g1835 Chr5 21543611 21546096 +
Bva Bva13g01588 Chr13 9518428 9520935 -
Cca Cca07g00063 Chr07 859422 861651 -
Gma Gma04g00052 Chr04 441227 443556 -
Gma Gma06g00047 Chr06 419869 422054 -
Gso Gso4g0046 Chr4 435464 437937 -
Gso Gso4g0046 Chr4 435464 437937 -
Lja Lja1g2368 Chr1 27377172 27379865 +
Pvu Pvu9g0262 Chr9 5893981 5896213 -
Rops Rops10g02677 Chr10 46408839 46410695 +
Sto Sto2g0914 Chr2 7908646 7911914 +
Viun Viun9g03939 Chr9 43427077 43429004 +
Vra Vra5g1837 Chr5 24282189 24284595 +
Vvi Vvi3g0149 Chr3 1367364 1369340 +
Vvi Vvi3g0150 Chr3 1374043 1381233 +
Aip Aip03g00920 Chr03 8808040 8808585 -
Bva Bva14g02305 Chr14 19914435 19916689 +
Car Car06g02188 Chr06 22360090 22362681 +
Gma Gma12g00286 Chr12 2283754 2288240 +
Vvi Vvi3g0151 Chr3 1384164 1391096 +
Aev Aev04g3496 Chr04 33159372 33162233 -
Aip Aip03g00921 Chr03 8813906 8814778 -
Amo Amo13g0863 Chr13 10725143 10725850 -
Dod Dod03g3270 Chr03 65401978 65405835 -
Vvi Vvi3g0152 Chr3 1393183 1395922 +
Psa Psa7g4007 Chr7 330823757 330826673 -
Gma Gma12g00234 Chr12 1834298 1835414 +
Lal Lal2g0066 Chr2 369744 370262 +
Accr Accr2g00342 Chr2 8068651 8069487 -
Adu Adu09g02780 Chr09 115537973 115539067 +
Alju Alju01g3558 Chr01 64513504 64515441 -
Bisa Bisa03g2732 Chr03 42939199 42941483 -
Dere Dere01g0317 Chr01 7687821 7689596 -
Glsi Glsi12g0788 Chr12 25198849 25200630 +
Lapu Lapu7g02446 Chr7 40856880 40858803 +
Lasa Lasa6g04705 Chr6 663536110 663537885 -
Lele Lele06g2622 Chr06 34101710 34103497 -
Lele Lele08g2561 Chr08 31373456 31375234 -
Mepo Mepo4g04774 Chr4 57170385 57172478 +
Mesa Mesa1g05161 Chr1 78710151 78711935 +
Mibi Mibi02g3257 Chr02 57996211 57997544 +
Phac Phac7g00386 Chr7 1953969 1956192 -
Phco Phco6g02981 Chr6 50967161 50968960 +
Prci Prci1g0297 Chr1 2886515 2888631 +
Pste Pste4g00584 Chr4 4460069 4461799 -
Pte Pte9g00597 Chr9 9074166 9075917 +
Pumo Pumo3g00252 Chr3 3235754 3237981 -
Pvu Pvu7g0251 Chr7 1800944 1803088 -
Rops Rops6g03342 Chr6 57907161 57909067 +
Seca Seca8g07923 Chr8 176887413 176889272 +
Spst Spst10g01486 Chr10 15501496 15503304 +
Vian Vian3g00235 Chr3 2068084 2069895 -
Vifa Vifa3g03631 Chr3 1058652572 1058654335 -
Vimu Vimu3g03596 Chr3 48703057 48704868 +
Viun Viun7g03876 Chr7 38825002 38827081 +
Vivi Vivi1g03523 Chr1 75236867 75238926 +