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
Vvi3g0913 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0914 . . . . Adu10g00438 . . . . . Ahy20g0640 . Aip10g00646 . . . Amo20g0715 . Apr3g1922 . Arst10g00563 . . . . . Bva13g00986 Bva14g01161 Car06g01463 Car01g00208 . . . . Dod03g0272 . . . . . . Gma13g02248 . . . . . . . . . . Lal5g1784 Lal11g0111 . . . . . . . . Lasa1g05176 . . . . . . . . . Lja6g3199 . Mal7g3729 . . . . . . . Mtr4g3101 . Phac6g02843 . . . . . Psa7g2410 Psa1g4850 . . . . . . Pumo2g00972 . Pvu6g2047 . Rops11g00382 . Seca6g05041 . . . . . . . Tpr3g1750 . Trre3g00311 . . . Vian6g01890 . Vifa1g10661 . . . . . Vivi1g08490 . . .
Vvi3g0915 . . . . . Adu03g03293 Aed10g2009 . . . . . . . . . . . Apr3g1925 . . . . Bach11g00811 . . Bva13g00984 . . . Cca09g01378 . . . . . . . . . . . . . . . . . . Lal23g0994 . . . . . . . . . . . Lapu3g02923 . . . . . . . . . . . Lja4g3952 . . . . . . . . . . . . . Phco4g02485 . . . . . Pste3g03536 . . . . . Pumo6g01740 . Pvu2g2235 . Rops2g01904 . Seca12g05060 . Spst3g00463 Ssu5g1832 . Sto2g2834 . . . . . . . . Vian1g03080 . . . Vimu11g03431 . Viun3g01636 . . Vra7g1577 .
Vvi3g0916 . . . . Adu10g00440 . . . Aev04g0721 . Ahy20g0643 . Aip10g00647 . . . Amo20g0713 . . Apr1g1301 Arst10g00569 . Bach7g00790 . . . Bva13g00983 Bva14g01158 . Car01g00207 . . . . Dod03g0271 . . . . . Gma15g00589 Gma13g02249 . . Gso15g0534 Gso15g0534 . . . . . Lal3g0053 Lal5g1785 . . . . . . . Lapu6g01146 . Lasa1g00283 . . . . . . . . . Lja6g3200 . . . Mepo6g00281 . Mesa5g04378 . . . . . . . Phco11g00276 . . . . . Pste2g01825 . Pte19g00862 Pte2g00740 . . Pumo2g00974 . Pvu6g2048 . Rops11g00380 . Seca6g05043 . Spst6g00645 . . . Sto2g2833 . . . Trre3g00309 . . . Vian6g01891 . Vifa1g10662 . Vimu2g00517 . Viun6g02953 . Vivi1g08498 . . .
Vvi3g0917 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0918 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0919 . . . . . Adu03g03291 Aed10g2011 . . . . . . . . . . . Apr3g1926 Apr1g1300 . Arst3g04274 Bach7g00791 Bach11g00809 . . Bva13g00982 Bva14g01157 Car06g01459 Car01g00206 Cca09g01380 . . . . . . . . . Gma15g00588 Gma13g02250 . . Gso15g0533 Gso15g0533 . . Lal15g0567 . . . . . Lan18g0608 . . . . . Lapu6g01145 Lapu3g02922 Lasa1g00282 Lasa7g03433 . . . . . . . . Lja6g3201 Lja4g3953 Mal7g3735 . Mepo6g00279 Mepo2g03418 Mesa5g04380 Mesa13g01731 . . Mtr4g3106 . Phac6g02846 Phac2g03281 Phco11g00275 Phco4g02483 . . Psa7g2406 Psa1g4852 . Pste3g03532 Pte19g00860 Pte2g00739 Pte2g00739 Pte19g00860 Pumo2g00981 Pumo6g01739 Pvu6g2049 Pvu2g2234 . Rops2g01903 Seca6g05044 Seca12g05061 Spst6g00644 Spst3g00462 Ssu5g1833 . . . Tpr3g1740 . Trre3g00307 Trre7g03850 Tsu02g01722 . Vian6g01893 Vian1g03079 Vifa1g10663 Vifa1g10663 Vimu2g00516 Vimu11g03428 Viun6g02956 Viun3g01638 Vivi5g04331 Vivi5g04331 Vra7g1575 .
Vvi3g0920 . . . . . . . . . . . . . . . . . . . Apr1g1298 . . Bach7g00792 . . . Bva13g00981 Bva14g01156 . . . . . . . . . . . . . Gma13g02252 . . . . . . . . . . Lal5g1786 . . . . . . . . . Lasa1g00281 . . . . . . . . . Lja6g3202 . . . Mepo6g00277 . Mesa5g04381 . . . . . Phac6g02849 . Phco11g00273 . . . . Psa1g4853 Pste2g01821 . . . . . Pumo2g00982 . Pvu6g2050 . Rops11g00376 . . . Spst6g00642 . . . Sto2g2832 . . . Trre3g00306 . . . Vian6g01894 . Vifa1g10664 . . . Viun6g02957 . Vivi1g08500 . . .
Vvi3g0921 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0922 . . . . . . . . . . . . . . . . . . Apr3g1927 . . . . . . . . . Car06g01458 . . . . . . . . . . . . . . . . . . . Lal15g0566 . . . . . . . . . . . . . . . . . . . . . . . . Lja4g3954 Mal7g3736 . . . . . . . Mtr4g3107 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tpr3g1736 . . . Tsu02g01721 . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Lal Lal3g0053 Chr3 311305 314843 +
Vvi Vvi3g0913 Chr3 9146222 9147403 -
Vvi Vvi3g0914 Chr3 9150089 9150574 -
Adu Adu10g00438 Chr10 5093706 5097487 -
Ahy Ahy20g0640 Chr20 6962197 6963207 -
Aip Aip10g00646 Chr10 6745347 6746254 -
Amo Amo20g0715 Chr20 10444098 10445022 +
Apr Apr3g1922 Chr3 35240446 35240934 -
Arst Arst10g00563 Chr10 4702806 4703303 +
Bva Bva13g00986 Chr13 4742203 4742478 +
Bva Bva14g01161 Chr14 5656818 5657434 +
Car Car06g01463 Chr06 14141682 14142173 +
Car Car01g00208 Chr01 1592952 1593531 +
Dod Dod03g0272 Chr03 2897020 2897869 +
Gma Gma13g02248 Chr13 37355588 37356294 -
Lal Lal5g1784 Chr5 19784272 19784745 -
Lal Lal11g0111 Chr11 743431 743904 +
Lasa Lasa1g05176 Chr1 833967171 833967674 +
Lja Lja6g3199 Chr6 60417200 60418079 -
Mal Mal7g3729 Chr7 102927392 102927832 -
Mtr Mtr4g3101 Chr4 44601940 44602536 -
Phac Phac6g02843 Chr6 25303441 25304156 -
Psa Psa7g2410 Chr7 170495269 170495972 +
Psa Psa1g4850 Chr1 362061325 362062055 +
Pumo Pumo2g00972 Chr2 14555836 14556360 +
Pvu Pvu6g2047 Chr6 30296708 30297398 -
Rops Rops11g00382 Chr11 5216392 5216889 +
Seca Seca6g05041 Chr6 117643800 117681846 -
Tpr Tpr3g1750 Chr3 15494265 15494741 +
Trre Trre3g00311 Chr3 2043922 2044398 +
Vian Vian6g01890 Chr6 36183790 36188802 -
Vifa Vifa1g10661 Chr1 1791959493 1791959981 -
Vivi Vivi1g08490 Chr1 243079865 243080694 -
Vvi Vvi3g0915 Chr3 9153387 9162396 -
Adu Adu03g03293 Chr03 119367588 119370691 +
Aed Aed10g2009 Chr10 24099947 24103297 -
Apr Apr3g1925 Chr3 35260400 35263892 -
Bach Bach11g00811 Chr11 6798757 6801492 +
Bva Bva13g00984 Chr13 4734259 4737098 +
Cca Cca09g01378 Chr09 37012950 37016909 -
Lal Lal23g0994 Chr23 11857447 11861459 -
Lapu Lapu3g02923 Chr3 52297907 52301979 +
Lja Lja4g3952 Chr4 72519039 72522668 -
Phco Phco4g02485 Chr4 46039475 46043208 +
Pste Pste3g03536 Chr3 27775848 27779834 +
Pumo Pumo6g01740 Chr6 26230317 26234421 +
Pvu Pvu2g2235 Chr2 38001050 38004803 +
Rops Rops2g01904 Chr2 29911329 29915559 +
Seca Seca12g05060 Chr12 137576567 137580373 -
Spst Spst3g00463 Chr3 7769276 7772440 +
Ssu Ssu5g1832 Chr5 54562759 54566576 -
Sto Sto2g2834 Chr2 41841478 41845923 +
Vian Vian1g03080 Chr1 51361904 51364977 +
Vimu Vimu11g03431 Chr11 55518477 55521552 +
Viun Viun3g01636 Chr3 11294081 11296958 -
Vra Vra7g1577 Chr7 34109771 34114191 +
Vvi Vvi3g0916 Chr3 9168720 9181229 -
Adu Adu10g00440 Chr10 5107587 5111316 -
Aev Aev04g0721 Chr04 4443939 4446499 -
Ahy Ahy20g0643 Chr20 6996318 7000020 -
Aip Aip10g00647 Chr10 6778542 6782363 -
Amo Amo20g0713 Chr20 10393093 10396812 +
Apr Apr1g1301 Chr1 21933851 21939445 +
Arst Arst10g00569 Chr10 4757319 4760887 -
Bach Bach7g00790 Chr7 19160219 19163348 -
Bva Bva13g00983 Chr13 4729066 4733642 +
Bva Bva14g01158 Chr14 5631672 5635338 +
Car Car01g00207 Chr01 1584322 1587976 +
Dod Dod03g0271 Chr03 2886877 2890158 +
Gma Gma15g00589 Chr15 4868016 4873316 +
Gma Gma13g02249 Chr13 37362315 37366833 -
Gso Gso15g0534 Chr15 4785313 4790677 +
Gso Gso15g0534 Chr15 4785313 4790677 +
Lal Lal3g0053 Chr3 311305 314843 +
Lal Lal5g1785 Chr5 19786435 19790774 -
Lapu Lapu6g01146 Chr6 11396807 11402621 +
Lasa Lasa1g00283 Chr1 18640824 18643389 +
Lja Lja6g3200 Chr6 60421087 60425890 -
Mepo Mepo6g00281 Chr6 2724757 2729984 +
Mesa Mesa5g04378 Chr5 72984272 72986947 -
Phco Phco11g00276 Chr11 1813954 1817987 +
Pste Pste2g01825 Chr2 18598350 18605138 +
Pte Pte19g00862 Chr19 7129118 7131141 +
Pte Pte2g00740 Chr2 6091645 6098024 +
Pumo Pumo2g00974 Chr2 14661463 14662857 -
Pvu Pvu6g2048 Chr6 30301799 30307518 -
Rops Rops11g00380 Chr11 5180375 5186530 +
Seca Seca6g05043 Chr6 117692835 117698286 -
Spst Spst6g00645 Chr6 5843071 5847879 +
Sto Sto2g2833 Chr2 41835227 41838925 +
Trre Trre3g00309 Chr3 2027184 2029866 +
Vian Vian6g01891 Chr6 36192266 36196191 -
Vifa Vifa1g10662 Chr1 1792095092 1792097701 -
Vimu Vimu2g00517 Chr2 2983064 2987666 +
Viun Viun6g02953 Chr6 32527443 32532459 -
Vivi Vivi1g08498 Chr1 243326081 243330321 -
Vvi Vvi3g0917 Chr3 9190121 9193027 -
Vvi Vvi3g0918 Chr3 9205881 9213548 -
Vvi Vvi3g0919 Chr3 9216205 9223052 +
Adu Adu03g03291 Chr03 119305972 119309939 -
Aed Aed10g2011 Chr10 24111242 24117623 +
Apr Apr3g1926 Chr3 35272044 35278404 +
Apr Apr1g1300 Chr1 21922549 21926171 -
Arst Arst3g04274 Chr3 118029165 118033086 -
Bach Bach7g00791 Chr7 19168809 19173572 +
Bach Bach11g00809 Chr11 6784581 6789011 -
Bva Bva13g00982 Chr13 4722022 4726325 -
Bva Bva14g01157 Chr14 5624812 5629241 -
Car Car06g01459 Chr06 14087266 14092622 -
Car Car01g00206 Chr01 1580691 1582501 -
Cca Cca09g01380 Chr09 37031898 37038646 +
Gma Gma15g00588 Chr15 4861226 4864990 -
Gma Gma13g02250 Chr13 37370386 37375089 +
Gso Gso15g0533 Chr15 4776962 4782514 -
Gso Gso15g0533 Chr15 4776962 4782514 -
Lal Lal15g0567 Chr15 3928947 3933753 -
Lan Lan18g0608 Chr18 11147381 11152196 +
Lapu Lapu6g01145 Chr6 11388399 11392301 -
Lapu Lapu3g02922 Chr3 52281765 52287908 -
Lasa Lasa1g00282 Chr1 18436774 18439856 -
Lasa Lasa7g03433 Chr7 596268610 596273423 +
Lja Lja6g3201 Chr6 60426813 60429638 +
Lja Lja4g3953 Chr4 72539887 72543984 +
Mal Mal7g3735 Chr7 103020417 103024747 +
Mepo Mepo6g00279 Chr6 2686024 2688148 -
Mepo Mepo2g03418 Chr2 43897784 43902829 +
Mesa Mesa5g04380 Chr5 73000809 73003491 +
Mesa Mesa13g01731 Chr13 20556523 20558434 -
Mtr Mtr4g3106 Chr4 44643268 44648560 +
Phac Phac6g02846 Chr6 25327697 25331381 +
Phac Phac2g03281 Chr2 34358463 34364257 -
Phco Phco11g00275 Chr11 1805986 1809004 -
Phco Phco4g02483 Chr4 46016314 46021430 -
Psa Psa7g2406 Chr7 170385842 170392261 -
Psa Psa1g4852 Chr1 362089965 362094392 +
Pste Pste3g03532 Chr3 27745891 27750794 -
Pte Pte19g00860 Chr19 7099169 7103845 -
Pte Pte2g00739 Chr2 6075814 6079728 -
Pte Pte2g00739 Chr2 6075814 6079728 -
Pte Pte19g00860 Chr19 7099169 7103845 -
Pumo Pumo2g00981 Chr2 14904248 14907456 +
Pumo Pumo6g01739 Chr6 26195340 26200860 -
Pvu Pvu6g2049 Chr6 30311179 30314938 +
Pvu Pvu2g2234 Chr2 37976948 37982698 -
Rops Rops2g01903 Chr2 29898174 29904058 -
Seca Seca6g05044 Chr6 117701438 117705642 +
Seca Seca12g05061 Chr12 137606911 137612577 +
Spst Spst6g00644 Chr6 5834199 5837813 -
Spst Spst3g00462 Chr3 7737247 7742374 -
Ssu Ssu5g1833 Chr5 54575604 54581712 +
Tpr Tpr3g1740 Chr3 15402647 15411827 -
Trre Trre3g00307 Chr3 2015687 2018584 -
Trre Trre7g03850 Chr7 46798331 46804744 +
Tsu Tsu02g01722 Chr02 15148264 15153409 -
Vian Vian6g01893 Chr6 36207955 36210694 +
Vian Vian1g03079 Chr1 51315988 51320827 -
Vifa Vifa1g10663 Chr1 1792338202 1792340723 +
Vifa Vifa1g10663 Chr1 1792338202 1792340723 +
Vimu Vimu2g00516 Chr2 2972248 2977056 -
Vimu Vimu11g03428 Chr11 55479567 55485759 -
Viun Viun6g02956 Chr6 32541919 32544668 +
Viun Viun3g01638 Chr3 11326789 11331710 +
Vivi Vivi5g04331 Chr5 140784464 140789940 +
Vivi Vivi5g04331 Chr5 140784464 140789940 +
Vra Vra7g1575 Chr7 34053351 34058870 -
Vvi Vvi3g0920 Chr3 9224027 9231652 -
Apr Apr1g1298 Chr1 21916202 21919021 +
Bach Bach7g00792 Chr7 19174928 19176491 -
Bva Bva13g00981 Chr13 4718908 4721616 +
Bva Bva14g01156 Chr14 5621986 5624579 +
Gma Gma13g02252 Chr13 37380633 37388257 -
Lal Lal5g1786 Chr5 19791880 19799857 -
Lasa Lasa1g00281 Chr1 18413237 18414540 +
Lja Lja6g3202 Chr6 60446448 60449295 +
Mepo Mepo6g00277 Chr6 2671639 2677317 +
Mesa Mesa5g04381 Chr5 73011836 73016649 -
Phac Phac6g02849 Chr6 25336525 25341081 -
Phco Phco11g00273 Chr11 1794371 1797711 +
Psa Psa1g4853 Chr1 362110342 362111670 -
Pste Pste2g01821 Chr2 18580666 18590587 +
Pumo Pumo2g00982 Chr2 14909246 14913726 -
Pvu Pvu6g2050 Chr6 30316538 30320356 -
Rops Rops11g00376 Chr11 5148835 5157165 +
Spst Spst6g00642 Chr6 5824073 5826783 +
Sto Sto2g2832 Chr2 41831543 41832865 +
Trre Trre3g00306 Chr3 2012088 2014212 +
Vian Vian6g01894 Chr6 36211677 36214437 -
Vifa Vifa1g10664 Chr1 1792363541 1792364785 -
Viun Viun6g02957 Chr6 32545246 32548922 -
Vivi Vivi1g08500 Chr1 243354367 243356399 -
Vvi Vvi3g0921 Chr3 9249737 9251605 -
Vvi Vvi3g0922 Chr3 9270978 9285279 +
Apr Apr3g1927 Chr3 35281520 35289260 +
Car Car06g01458 Chr06 14074993 14081482 -
Lal Lal15g0566 Chr15 3921055 3926945 +
Lja Lja4g3954 Chr4 72545961 72558432 +
Mal Mal7g3736 Chr7 103026495 103031661 +
Mtr Mtr4g3107 Chr4 44652437 44657709 +
Tpr Tpr3g1736 Chr3 15383527 15387087 -
Tsu Tsu02g01721 Chr02 15140910 15146433 -
Adu Adu10g00438 Chr10 5093706 5097487 -
Ahy Ahy20g0640 Chr20 6962197 6963207 -
Aip Aip10g00646 Chr10 6745347 6746254 -
Amo Amo20g0715 Chr20 10444098 10445022 +
Arst Arst10g00563 Chr10 4702806 4703303 +
Dod Dod03g0272 Chr03 2897020 2897869 +
Lasa Lasa1g05176 Chr1 833967171 833967674 +
Phac Phac6g02843 Chr6 25303441 25304156 -
Pumo Pumo2g00972 Chr2 14555836 14556360 +
Pvu Pvu6g2047 Chr6 30296708 30297398 -
Rops Rops11g00382 Chr11 5216392 5216889 +
Seca Seca6g05041 Chr6 117643800 117681846 -
Trre Trre3g00311 Chr3 2043922 2044398 +
Vian Vian6g01890 Chr6 36183790 36188802 -
Vifa Vifa1g10661 Chr1 1791959493 1791959981 -
Vivi Vivi1g08490 Chr1 243079865 243080694 -
Adu Adu03g03293 Chr03 119367588 119370691 +
Bach Bach11g00811 Chr11 6798757 6801492 +
Lapu Lapu3g02923 Chr3 52297907 52301979 +
Phco Phco4g02485 Chr4 46039475 46043208 +
Pste Pste3g03536 Chr3 27775848 27779834 +
Pumo Pumo6g01740 Chr6 26230317 26234421 +
Pvu Pvu2g2235 Chr2 38001050 38004803 +
Rops Rops2g01904 Chr2 29911329 29915559 +
Seca Seca12g05060 Chr12 137576567 137580373 -
Spst Spst3g00463 Chr3 7769276 7772440 +
Vian Vian1g03080 Chr1 51361904 51364977 +
Vimu Vimu11g03431 Chr11 55518477 55521552 +
Viun Viun3g01636 Chr3 11294081 11296958 -