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
Vvi19g0570 . . . . . . Aed3g2485 . . . . . . . . . . . . Apr9g1722 . . . . . . . . . . Cca05g01915 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal8g0492 . . . . . . . Mtr5g3261 . . . . . . . . . . . . . . . . . . . . . . . . Ssu6g3438 . . . . Tpr4g3251 . . . Tsu05g03807 . . . . . . . . . . Vra6g0263 .
Vvi19g0571 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car02g02025 . . . . . . . . . . . . . Gma02g02724 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto9g1864 . . . . . . . . . . . . . . . . . . .
Vvi19g0572 . . . . . . . . Aev07g0262 . Ahy17g0437 . Aip07g00366 . . . . . . . . . . . . . Bva12g02764 . . . . . . . Dod08g0317 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g0573 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto9g1865 Sto5g1937 . . . . . . . . . . . . . . . . . .
Vvi19g0574 . . . . . Adu07g00331 Aed3g2486 . Aev07g0261 . Ahy17g0436 . Aip07g00365 . . . . . . Apr9g1723 . Arst7g00503 . Bach3g00834 . . Bva12g02763 . Car02g02026 . Cca05g01916 . . . Dod08g0315 . . . . . . . . Gma14g00215 . . . . Lal18g1556 . . . . . Lan2g1298 . . . . . . . . Lasa2g02208 . . . . . . . . . . . Mal8g0491 . . . Mesa17g04328 . . . Mtr5g3262 . Phac8g03557 . Phco3g00278 . . . Psa2g0353 . Pste8g00490 . . . Pte8g00076 . Pumo9g01915 . Pvu8g2749 . Rops9g00367 . Seca8g00364 . Spst8g00850 Ssu6g3439 . Sto9g1866 . . Tpr4g3248 . Trre9g04912 . Tsu05g03809 . Vian7g01219 . Vifa1g03222 . Vimu1g00461 . Viun8g02783 . Vivi7g02772 Vra6g0262 .
Vvi19g0575 . . . . . Adu07g00305 Aed3g2487 . Aev07g0260 . Ahy17g0412 . Aip07g00327 . . . . . . Apr9g1724 . Arst7g00479 . Bach3g00835 . . Bva12g02762 . Car02g02031 . Cca05g01917 . . . Dod08g0310 . . . . . . . . Gma14g00214 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mepo7g02749 . Mesa17g04335 . . . Mtr5g3266 . Phac8g03587 . Phco3g00277 . . . . . Pste8g00488 . . . . . Pumo9g01914 . Pvu8g2750 . Rops9g00364 . Seca8g00355 . Spst8g00851 Ssu6g3440 . Sto9g1867 . . . . Trre9g04929 . Tsu05g03827 . Vian7g01218 . Vifa1g03224 . Vimu1g00460 . Viun8g02784 . Vivi7g02769 Vra6g0261 .
Vvi19g0576 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto9g1868 . . . . . . . . . . . . . . . . . . .
Vvi19g0577 Acco10g0909 . Accr4g01832 . Adu01g00140 Adu07g00304 Aed3g2488 Aed4g2502 Aev07g0259 . Ahy17g0411 Ahy11g0727 Aip07g00326 Aip01g00714 Alju08g1854 . . . Apr2g0160 Apr9g1725 Arst1g00207 Arst7g00478 . Bach3g00836 Bisa09g0011 . Bva12g02761 . Car02g02032 Car05g00968 Cca05g01918 Cca09g01068 Dere04g2161 . Dod08g0309 Dod05g0877 Enph1g0638 . Glsi08g0046 . Gma08g02955 . Gma02g02725 Gma14g00213 Gso8g2610 . Gso8g2610 Gso8g2610 Lal18g1558 . . . . . Lan2g1301 . . . . . . . Lasa5g00998 Lasa2g02213 Lele01g1438 . Lele03g1440 Lele04g1709 . . . . . . . Mal8g0474 Mepo3g04562 Mepo7g02754 . . Mibi05g1735 . . Mtr5g3269 . . Phco11g02046 Phco3g00276 Prci8g1170 . . . . Pste8g00487 . . . Pte4g00066 . Pumo9g01913 Pvu6g0430 Pvu8g2751 . Rops9g00363 . Seca6g03068 Spst6g02056 Spst8g00852 Ssu6g3441 Ssu9g0912 Sto9g1869 . . Tpr4g0002 Trre5g01393 Trre9g04934 . Tsu05g03830 . Vian7g01217 . Vifa1g03238 Vimu2g02877 Vimu1g00459 . Viun8g02785 . . Vra6g0260 Vra6g0260
Vvi19g0578 . . . . . . . Aed4g2498 . . . . . . . . . . . . . . . . . . . . . . . Cca09g01075 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ssu9g0916 Sto9g1870 . . . . . . . . . . . . . . . . . . .
Vvi19g0579 . . . . . . . . . . . . . . . . . . Apr2g0165 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto9g1872 . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Sto Sto9g1865 Chr9 23012783 23017564 -
Aed Aed3g2485 Chr3 27372015 27374907 -
Aev Aev07g0262 Chr07 1477420 1479304 +
Ahy Ahy17g0437 Chr17 4248930 4251472 +
Aip Aip07g00366 Chr07 3210800 3213287 +
Apr Apr9g1722 Chr9 26365249 26367598 -
Cca Cca05g01915 Chr05 38988152 38993167 -
Dod Dod08g0317 Chr08 3309697 3312747 +
Mal Mal8g0492 Chr8 7411109 7413129 +
Mtr Mtr5g3261 Chr5 41431000 41433781 -
Ssu Ssu6g3438 Chr6 77109160 77111289 -
Sto Sto9g1864 Chr9 23005078 23006637 -
Tpr Tpr4g3251 Chr4 38567557 38570036 +
Tsu Tsu05g03807 Chr05 49262837 49265019 -
Vra Vra6g0263 Chr6 1954953 1957358 +
Vvi Vvi19g0570 Chr19 6307747 6309528 -
Aed Aed3g2485 Chr3 27372015 27374907 -
Apr Apr9g1722 Chr9 26365249 26367598 -
Cca Cca05g01915 Chr05 38988152 38993167 -
Mal Mal8g0492 Chr8 7411109 7413129 +
Mtr Mtr5g3261 Chr5 41431000 41433781 -
Ssu Ssu6g3438 Chr6 77109160 77111289 -
Tpr Tpr4g3251 Chr4 38567557 38570036 +
Tsu Tsu05g03807 Chr05 49262837 49265019 -
Vra Vra6g0263 Chr6 1954953 1957358 +
Vvi Vvi19g0571 Chr19 6322312 6322676 -
Car Car02g02025 Chr02 50685908 50688504 -
Gma Gma02g02724 Chr02 52941653 52944261 -
Sto Sto9g1864 Chr9 23005078 23006637 -
Vvi Vvi19g0572 Chr19 6323340 6327058 -
Aev Aev07g0262 Chr07 1477420 1479304 +
Ahy Ahy17g0437 Chr17 4248930 4251472 +
Aip Aip07g00366 Chr07 3210800 3213287 +
Bva Bva12g02764 Chr12 20072587 20074749 +
Dod Dod08g0317 Chr08 3309697 3312747 +
Vvi Vvi19g0573 Chr19 6328075 6329567 -
Sto Sto9g1865 Chr9 23012783 23017564 -
Sto Sto5g1937 Chr5 14452939 14455584 +
Vvi Vvi19g0574 Chr19 6331264 6341180 -
Adu Adu07g00331 Chr07 3098947 3101220 +
Aed Aed3g2486 Chr3 27375849 27378474 -
Aev Aev07g0261 Chr07 1474746 1476627 -
Ahy Ahy17g0436 Chr17 4245051 4247297 +
Aip Aip07g00365 Chr07 3206834 3209034 +
Apr Apr9g1723 Chr9 26370119 26372623 -
Arst Arst7g00503 Chr7 3249420 3251711 +
Bach Bach3g00834 Chr3 19222389 19225253 -
Bva Bva12g02763 Chr12 20069079 20071957 +
Car Car02g02026 Chr02 50691097 50692651 -
Cca Cca05g01916 Chr05 38996685 38999557 -
Dod Dod08g0315 Chr08 3303571 3305941 +
Gma Gma14g00215 Chr14 1834738 1837436 +
Lal Lal18g1556 Chr18 17254353 17258149 -
Lan Lan2g1298 Chr2 23884493 23886853 -
Lasa Lasa2g02208 Chr2 496359472 496361934 -
Mal Mal8g0491 Chr8 7404337 7406123 +
Mesa Mesa17g04328 Chr17 73698544 73700191 -
Mtr Mtr5g3262 Chr5 41434493 41436714 -
Phac Phac8g03557 Chr8 42821790 42824588 -
Phco Phco3g00278 Chr3 1985125 1987504 +
Psa Psa2g0353 Chr2 13595565 13601309 -
Pste Pste8g00490 Chr8 2560262 2562653 +
Pte Pte8g00076 Chr8 1565167 1568112 +
Pumo Pumo9g01915 Chr9 48435767 48438528 +
Pvu Pvu8g2749 Chr8 57726821 57729678 -
Rops Rops9g00367 Chr9 4671104 4672891 +
Seca Seca8g00364 Chr8 4213660 4216274 +
Spst Spst8g00850 Chr8 7620648 7623090 -
Ssu Ssu6g3439 Chr6 77118892 77121770 -
Sto Sto9g1866 Chr9 23022916 23025652 -
Tpr Tpr4g3248 Chr4 38552640 38555081 +
Trre Trre9g04912 Chr9 55426013 55427877 -
Tsu Tsu05g03809 Chr05 49273203 49275772 -
Vian Vian7g01219 Chr7 20426716 20429149 +
Vifa Vifa1g03222 Chr1 503888433 503890211 -
Vimu Vimu1g00461 Chr1 2801884 2804269 +
Viun Viun8g02783 Chr8 36307772 36310634 -
Vivi Vivi7g02772 Chr7 91894220 91897042 +
Vra Vra6g0262 Chr6 1950803 1953704 +
Vvi Vvi19g0575 Chr19 6343440 6344705 +
Adu Adu07g00305 Chr07 2821818 2823296 -
Aed Aed3g2487 Chr3 27378910 27380163 +
Aev Aev07g0260 Chr07 1472867 1473964 -
Ahy Ahy17g0412 Chr17 4008457 4010189 -
Aip Aip07g00327 Chr07 2979842 2981334 -
Apr Apr9g1724 Chr9 26374454 26386874 +
Arst Arst7g00479 Chr7 2972181 2973910 -
Bach Bach3g00835 Chr3 19225551 19226858 +
Bva Bva12g02762 Chr12 20067216 20068953 -
Car Car02g02031 Chr02 50775272 50776883 +
Cca Cca05g01917 Chr05 39005124 39007322 +
Dod Dod08g0310 Chr08 3273270 3274951 -
Gma Gma14g00214 Chr14 1832360 1833631 -
Mepo Mepo7g02749 Chr7 38543684 38545252 +
Mesa Mesa17g04335 Chr17 73845771 73846151 +
Mtr Mtr5g3266 Chr5 41488667 41493028 +
Phac Phac8g03587 Chr8 42951118 42952780 +
Phco Phco3g00277 Chr3 1981305 1982570 -
Pste Pste8g00488 Chr8 2557476 2559094 -
Pumo Pumo9g01914 Chr9 48431377 48433199 -
Pvu Pvu8g2750 Chr8 57732477 57734337 +
Rops Rops9g00364 Chr9 4645028 4647089 -
Seca Seca8g00355 Chr8 4140769 4141917 -
Spst Spst8g00851 Chr8 7626332 7627594 +
Ssu Ssu6g3440 Chr6 77130685 77131947 +
Sto Sto9g1867 Chr9 23026569 23028252 +
Trre Trre9g04929 Chr9 55503381 55504586 +
Tsu Tsu05g03827 Chr05 49407198 49408304 +
Vian Vian7g01218 Chr7 20420806 20422071 -
Vifa Vifa1g03224 Chr1 504236139 504237254 -
Vimu Vimu1g00460 Chr1 2797281 2798546 -
Viun Viun8g02784 Chr8 36313174 36315223 +
Vivi Vivi7g02769 Chr7 91841341 91842881 -
Vra Vra6g0261 Chr6 1946260 1948166 -
Vvi Vvi19g0576 Chr19 6347194 6349234 +
Sto Sto9g1868 Chr9 23030194 23033206 +
Vvi Vvi19g0577 Chr19 6350202 6356089 -
Acco Acco10g0909 Chr10 22884761 22888425 -
Accr Accr4g01832 Chr4 19926985 19930624 +
Adu Adu01g00140 Chr01 1916789 1922311 +
Adu Adu07g00304 Chr07 2818835 2821591 +
Aed Aed3g2488 Chr3 27378991 27383686 -
Aed Aed4g2502 Chr4 27078126 27082026 +
Aev Aev07g0259 Chr07 1469822 1472143 +
Ahy Ahy17g0411 Chr17 4005514 4008341 +
Ahy Ahy11g0727 Chr11 12484299 12489469 -
Aip Aip07g00326 Chr07 2976820 2979615 +
Aip Aip01g00714 Chr01 11808685 11813954 -
Alju Alju08g1854 Chr08 16028749 16032714 +
Apr Apr2g0160 Chr2 2158580 2161857 -
Apr Apr9g1725 Chr9 26387226 26389741 -
Arst Arst1g00207 Chr1 1916841 1922247 +
Arst Arst7g00478 Chr7 2969323 2972056 +
Bach Bach3g00836 Chr3 19229626 19232618 -
Bisa Bisa09g0011 Chr09 146857 152899 -
Bva Bva12g02761 Chr12 20064129 20066860 +
Car Car02g02032 Chr02 50777027 50781990 -
Car Car05g00968 Chr05 50199454 50203661 -
Cca Cca05g01918 Chr05 39007514 39010195 -
Cca Cca09g01068 Chr09 31423595 31428250 -
Dere Dere04g2161 Chr04 24770726 24780250 +
Dod Dod08g0309 Chr08 3269857 3273044 +
Dod Dod05g0877 Chr05 15653054 15656688 -
Enph Enph1g0638 Chr1 32305428 32310542 -
Glsi Glsi08g0046 Chr08 459835 469511 -
Gma Gma08g02955 Chr08 46035277 46039435 -
Gma Gma02g02725 Chr02 52945996 52948866 -
Gma Gma14g00213 Chr14 1828346 1831205 +
Gso Gso8g2610 Chr8 43741335 43745557 -
Gso Gso8g2610 Chr8 43741335 43745557 -
Gso Gso8g2610 Chr8 43741335 43745557 -
Lal Lal18g1558 Chr18 17265237 17267817 -
Lan Lan2g1301 Chr2 23896185 23901986 -
Lasa Lasa5g00998 Chr5 278361454 278363881 -
Lasa Lasa2g02213 Chr2 496568308 496570282 +
Lele Lele01g1438 Chr01 8876449 8880295 +
Lele Lele03g1440 Chr03 8768905 8772833 +
Lele Lele04g1709 Chr04 21691553 21695254 +
Mal Mal8g0474 Chr8 7126615 7129378 +
Mepo Mepo3g04562 Chr3 56521620 56525354 -
Mepo Mepo7g02754 Chr7 38575295 38578422 -
Mibi Mibi05g1735 Chr05 20978956 20982686 +
Mtr Mtr5g3269 Chr5 41523319 41526440 -
Phco Phco11g02046 Chr11 16955462 16960552 +
Phco Phco3g00276 Chr3 1976867 1979566 +
Prci Prci8g1170 Chr8 7847436 7852507 +
Pste Pste8g00487 Chr8 2554001 2556884 +
Pte Pte4g00066 Chr4 1107134 1110500 +
Pumo Pumo9g01913 Chr9 48428274 48431194 +
Pvu Pvu6g0430 Chr6 15191461 15196112 -
Pvu Pvu8g2751 Chr8 57734357 57737318 -
Rops Rops9g00363 Chr9 4641494 4644721 +
Seca Seca6g03068 Chr6 96804965 96809383 +
Spst Spst6g02056 Chr6 20997545 21001356 +
Spst Spst8g00852 Chr8 7628975 7631513 -
Ssu Ssu6g3441 Chr6 77133764 77136526 -
Ssu Ssu9g0912 Chr9 38701991 38706124 -
Sto Sto9g1869 Chr9 23034833 23039969 -
Tpr Tpr4g0002 Chr4 14135 18946 -
Trre Trre5g01393 Chr5 9812728 9815624 +
Trre Trre9g04934 Chr9 55514839 55517604 -
Tsu Tsu05g03830 Chr05 49413540 49416803 -
Vian Vian7g01217 Chr7 20415146 20419488 +
Vifa Vifa1g03238 Chr1 506320513 506323901 +
Vimu Vimu2g02877 Chr2 27151039 27155152 +
Vimu Vimu1g00459 Chr1 2793639 2795929 +
Viun Viun8g02785 Chr8 36315486 36318309 -
Vra Vra6g0260 Chr6 1943171 1945867 +
Vra Vra6g0260 Chr6 1943171 1945867 +
Vvi Vvi19g0578 Chr19 6359412 6362990 -
Aed Aed4g2498 Chr4 27047259 27051020 -
Cca Cca09g01075 Chr09 31644514 31648599 +
Ssu Ssu9g0916 Chr9 38791655 38795047 +
Sto Sto9g1870 Chr9 23045173 23051367 +
Vvi Vvi19g0579 Chr19 6368730 6371752 -
Apr Apr2g0165 Chr2 2216711 2225969 +
Sto Sto9g1872 Chr9 23058394 23063064 +