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
Vvi17g0293 . . . . Adu05g02698 . Aed7g0245 . Aev05g3471 . Ahy15g2719 . Aip05g03031 . . . . . Apr6g1031 . Arst5g03412 . . . . . Bva04g00843 . Car08g01661 . Cca08g00266 . . . Dod02g3686 . . . . . Gma07g00878 . . Gma09g01672 Gso7g0834 . . Gso7g0834 . . . . Lal10g0970 . . . . . . . Lapu4g00223 . Lasa1g03963 . . . . . . . . . Lja2g2135 . . Mal8g3800 Mepo7g00600 . Mesa22g03047 . . . . Mtr6g2134 Phac4g02032 . Phco5g00288 . . . Psa1g0804 . Pste9g01469 . . Pte9g00112 . . . . Pvu4g1623 . Rops5g00291 . Seca10g04843 . Spst4g02794 . . . . . . Tpr5g0293 Trre3g03821 . . Tsu03g03104 Vian8g01439 . Vifa1g07151 . Vimu8g01581 . Viun4g00335 . Vivi4g00294 . Vra1g0646 .
Vvi17g0294 . . . . Adu05g02697 Adu03g04020 Aed7g0244 Aed5g2615 Aev05g3470 . Ahy15g2720 . Aip05g03032 . . . . . Apr6g1032 Apr2g1530 Arst5g03411 Arst3g05293 Bach1g01486 . . . Bva04g00842 Bva03g00697 Car08g01662 Car06g00201 Cca08g00265 Cca09g02780 . . Dod02g3685 . . . . . Gma07g00877 Gma08g00474 Gma05g02345 Gma09g01673 Gso7g0833 Gso7g0833 Gso7g0833 Gso7g0833 Lal15g0936 . Lal23g0678 Lal8g0447 . Lal25g0466 . . . . . . Lapu4g00222 Lapu3g03910 Lasa1g03965 Lasa7g05229 . . . . . . . . Lja2g2134 Lja4g0061 Mal5g0380 Mal8g3801 Mepo7g00599 Mepo2g05050 Mesa22g03048 Mesa13g00086 . . Mtr8g3834 Mtr6g2135 Phac4g02033 . Phco5g00286 . . . Psa1g0805 . Pste9g01470 . . . . . . Pumo6g02973 Pvu4g1624 Pvu2g3346 Rops5g00290 Rops2g00107 Seca10g04846 Seca12g06945 Spst4g02793 . . . . Sto8g2196 Tpr3g0268 Tpr5g0291 Trre3g03823 Trre7g05926 Tsu02g00074 Tsu03g03105 Vian8g01440 Vian1g04175 Vifa1g07149 Vifa6g04089 Vimu8g01580 Vimu11g04875 Viun4g00334 Viun3g00114 Vivi4g00292 Vivi5g06563 Vra1g0645 .
Vvi17g0295 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0296 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0297 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0298 . . . . . . . . . . . . . . . . . . . Apr2g1756 . . . . . . . Bva03g00696 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto8g2191 . . . . . . . . . . . . . . . . . .
Vvi17g0299 . . . . Adu05g02692 . Aed7g0238 . Aev05g3464 . Ahy15g2725 . Aip05g03039 . . . . . Apr6g1035 Apr2g1757 Arst5g03405 . Bach1g01488 . . . Bva04g00839 Bva03g00694 Car08g01667 . Cca08g00261 . . . Dod02g3681 . . . . . Gma07g00871 . . Gma09g01677 Gso7g0830 . . Gso7g0830 . . . Lal8g0444 . . . . . . . . . . Lasa1g03969 . . . . . . . . . . . . . . . . . . . . . Phac4g02037 . . . . . Psa1g0808 . Pste9g01474 . . . . . . . Pvu4g1629 . Rops5g00287 . Seca10g04851 . Spst4g02789 . . . . . . . . . . . Vian8g01443 . Vifa1g07144 . Vimu8g01576 . Viun4g00331 . Vivi4g00289 . Vra1g0641 .
Vvi17g0300 . . . . . . . . . . . . . . . . . . . Apr2g1758 . . . . . . . Bva03g00693 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto8g2189 . . . . . . . . . . . . . . . . . .
Vvi17g0301 . . . . Adu05g02684 . Aed7g0235 . Aev05g3461 . Ahy15g2731 . Aip05g03048 . . . . . Apr6g1037 . Arst5g03401 . Bach1g01490 . . . Bva04g00837 Bva03g00691 Car08g01669 . Cca08g00259 . . . Dod02g3679 . . . . . Gma07g00867 . . Gma09g01679 . . . . . . . Lal8g0443 . . . . . . . . Lapu4g00214 . Lasa1g03973 . . . . . . . . . Lja2g2130 . . Mal8g3809 . . Mesa22g03050 . . . . Mtr6g2139 . . . . . . . . . . . . . . Pumo6g03003 . Pvu4g1631 . . . Seca10g04856 . Spst4g02787 . . . . Sto8g2188 . Tpr5g0287 Trre3g03826 . . . Vian8g01448 . . . . . Viun4g00328 . Vivi4g00276 . Vra1g0638 .
Vvi17g0302 . . . . . . Aed7g0234 . Aev05g3460 . Ahy15g2732 . Aip05g03049 . . . . . Apr6g1038 . . . . . . . Bva04g00836 Bva03g00690 . . Cca08g00258 . . . . . . . . . Gma07g00865 . . Gma09g01680 Gso7g0822 . . Gso7g0822 . . . Lal8g0442 . Lal25g0464 . . . . . . . . . . . . . . . . . . Lja2g2127 . . Mal8g3810 . . . . . . . Mtr6g2140 . . . . . . Psa1g0810 . . . . . . . . . . . . . . . . . . . . Sto8g2187 . Tpr5g0286 . . . Tsu03g03112 . . . . . . . . . . Vra1g0636 .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Pte Pte9g00112 Chr9 1286059 1289135 -
Sto Sto8g2188 Chr8 14414004 14414282 -
Vvi Vvi17g0293 Chr17 3087528 3092399 +
Adu Adu05g02698 Chr05 94347293 94352015 -
Aed Aed7g0245 Chr7 1724044 1728115 -
Aev Aev05g3471 Chr05 34031462 34035356 -
Ahy Ahy15g2719 Chr15 143794388 143799456 +
Aip Aip05g03031 Chr05 132868939 132873729 +
Apr Apr6g1031 Chr6 15043946 15048532 +
Arst Arst5g03412 Chr5 93004877 93010167 -
Bva Bva04g00843 Chr04 5537857 5541287 -
Car Car08g01661 Chr08 26459487 26464261 +
Cca Cca08g00266 Chr08 3742448 3747712 -
Dod Dod02g3686 Chr02 75503756 75509011 -
Gma Gma07g00878 Chr07 9485124 9490343 -
Gma Gma09g01672 Chr09 42270129 42275036 +
Gso Gso7g0834 Chr7 9277121 9282452 -
Gso Gso7g0834 Chr7 9277121 9282452 -
Lal Lal10g0970 Chr10 16978161 16985073 +
Lapu Lapu4g00223 Chr4 2210614 2215476 -
Lasa Lasa1g03963 Chr1 690939007 690941973 +
Lja Lja2g2135 Chr2 23977487 23982425 -
Mal Mal8g3800 Chr8 110216704 110222216 +
Mepo Mepo7g00600 Chr7 9969102 9974811 -
Mesa Mesa22g03047 Chr22 80341453 80347366 +
Mtr Mtr6g2134 Chr6 38172869 38179004 +
Phac Phac4g02032 Chr4 46859594 46864453 +
Phco Phco5g00288 Chr5 2375092 2379386 -
Psa Psa1g0804 Chr1 52042905 52046179 +
Pste Pste9g01469 Chr9 14306270 14311068 +
Pte Pte9g00112 Chr9 1286059 1289135 -
Pvu Pvu4g1623 Chr4 43496227 43500992 +
Rops Rops5g00291 Chr5 4493231 4498280 -
Seca Seca10g04843 Chr10 111754145 111760013 +
Spst Spst4g02794 Chr4 67650697 67655180 -
Tpr Tpr5g0293 Chr5 4367832 4373940 -
Trre Trre3g03821 Chr3 49300417 49305471 +
Tsu Tsu03g03104 Chr03 42813594 42819596 +
Vian Vian8g01439 Chr8 33759333 33761819 +
Vifa Vifa1g07151 Chr1 1103746404 1103750098 -
Vimu Vimu8g01581 Chr8 21714180 21718483 -
Viun Viun4g00335 Chr4 2061763 2066289 -
Vivi Vivi4g00294 Chr4 6590662 6594911 -
Vra Vra1g0646 Chr1 7523822 7528576 -
Vvi Vvi17g0294 Chr17 3094361 3100262 -
Adu Adu05g02697 Chr05 94342907 94346451 +
Adu Adu03g04020 Chr03 129275958 129278498 +
Aed Aed7g0244 Chr7 1705114 1710300 +
Aed Aed5g2615 Chr5 26862114 26866229 +
Aev Aev05g3470 Chr05 34027668 34030525 +
Ahy Ahy15g2720 Chr15 143799894 143803734 -
Aip Aip05g03032 Chr05 132874542 132880441 -
Apr Apr6g1032 Chr6 15049561 15053852 -
Apr Apr2g1530 Chr2 21207027 21211102 +
Arst Arst5g03411 Chr5 93001002 93004724 +
Arst Arst3g05293 Chr3 128040467 128042565 +
Bach Bach1g01486 Chr1 28331665 28335319 -
Bva Bva04g00842 Chr04 5533644 5537439 +
Bva Bva03g00697 Chr03 4164071 4168059 +
Car Car08g01662 Chr08 26465122 26468717 -
Car Car06g00201 Chr06 2184451 2188100 -
Cca Cca08g00265 Chr08 3734428 3741019 +
Cca Cca09g02780 Chr09 53441259 53445220 -
Dod Dod02g3685 Chr02 75499714 75503207 +
Gma Gma07g00877 Chr07 9477839 9484656 +
Gma Gma08g00474 Chr08 3938955 3943497 +
Gma Gma05g02345 Chr05 44372411 44375818 +
Gma Gma09g01673 Chr09 42277459 42282981 -
Gso Gso7g0833 Chr7 9269681 9275246 +
Gso Gso7g0833 Chr7 9269681 9275246 +
Gso Gso7g0833 Chr7 9269681 9275246 +
Gso Gso7g0833 Chr7 9269681 9275246 +
Lal Lal15g0936 Chr15 7196694 7200856 -
Lal Lal23g0678 Chr23 9434197 9438836 +
Lal Lal8g0447 Chr8 2978437 2983738 +
Lal Lal25g0466 Chr25 3224309 3228232 +
Lapu Lapu4g00222 Chr4 2202991 2209332 +
Lapu Lapu3g03910 Chr3 62628868 62633008 +
Lasa Lasa1g03965 Chr1 690942241 690944787 -
Lasa Lasa7g05229 Chr7 716864204 716866550 +
Lja Lja2g2134 Chr2 23970835 23975187 +
Lja Lja4g0061 Chr4 491592 496447 -
Mal Mal5g0380 Chr5 5847469 5850736 +
Mal Mal8g3801 Chr8 110224836 110229524 -
Mepo Mepo7g00599 Chr7 9963777 9968361 +
Mepo Mepo2g05050 Chr2 58444244 58447579 +
Mesa Mesa22g03048 Chr22 80348495 80352531 -
Mesa Mesa13g00086 Chr13 1126927 1127966 -
Mtr Mtr8g3834 Chr8 49009758 49013303 +
Mtr Mtr6g2135 Chr6 38179459 38184481 -
Phac Phac4g02033 Chr4 46866149 46873047 -
Phco Phco5g00286 Chr5 2367990 2373087 +
Psa Psa1g0805 Chr1 52046909 52048803 -
Pste Pste9g01470 Chr9 14317354 14323580 -
Pumo Pumo6g02973 Chr6 71278814 71284702 +
Pvu Pvu4g1624 Chr4 43503036 43506578 -
Pvu Pvu2g3346 Chr2 48389044 48393168 +
Rops Rops5g00290 Chr5 4484747 4489027 +
Rops Rops2g00107 Chr2 1673949 1679833 -
Seca Seca10g04846 Chr10 111763386 111765573 -
Seca Seca12g06945 Chr12 161431389 161435498 +
Spst Spst4g02793 Chr4 67643231 67648408 +
Sto Sto8g2196 Chr8 14506902 14514263 +
Tpr Tpr3g0268 Chr3 3076955 3079969 -
Tpr Tpr5g0291 Chr5 4350465 4355684 +
Trre Trre3g03823 Chr3 49306579 49312179 -
Trre Trre7g05926 Chr7 63770075 63773359 +
Tsu Tsu02g00074 Chr02 460644 464071 -
Tsu Tsu03g03105 Chr03 42820407 42825681 -
Vian Vian8g01440 Chr8 33764381 33768915 -
Vian Vian1g04175 Chr1 64778476 64781645 +
Vifa Vifa1g07149 Chr1 1103736570 1103744542 +
Vifa Vifa6g04089 Chr6 1347806429 1347808573 +
Vimu Vimu8g01580 Chr8 21707044 21711633 +
Vimu Vimu11g04875 Chr11 68494347 68498235 +
Viun Viun4g00334 Chr4 2053557 2059772 +
Viun Viun3g00114 Chr3 536845 540367 -
Vivi Vivi4g00292 Chr4 6587040 6590180 +
Vivi Vivi5g06563 Chr5 172535674 172538283 -
Vra Vra1g0645 Chr1 7516729 7521903 +
Vvi Vvi17g0295 Chr17 3107222 3108900 -
Vvi Vvi17g0296 Chr17 3111086 3118604 -
Vvi Vvi17g0297 Chr17 3128739 3129656 +
Vvi Vvi17g0298 Chr17 3130936 3135651 +
Apr Apr2g1756 Chr2 23214251 23216299 +
Bva Bva03g00696 Chr03 4153289 4157986 -
Sto Sto8g2191 Chr8 14434522 14440918 -
Vvi Vvi17g0299 Chr17 3141621 3143565 -
Adu Adu05g02692 Chr05 94060806 94062627 +
Aed Aed7g0238 Chr7 1684553 1686534 +
Aev Aev05g3464 Chr05 33995034 33995974 +
Ahy Ahy15g2725 Chr15 144098906 144100912 -
Aip Aip05g03039 Chr05 133149080 133150948 -
Apr Apr6g1035 Chr6 15077407 15079046 -
Apr Apr2g1757 Chr2 23224018 23226114 -
Arst Arst5g03405 Chr5 92718921 92720800 +
Bach Bach1g01488 Chr1 28348788 28350254 -
Bva Bva04g00839 Chr04 5522451 5524047 +
Bva Bva03g00694 Chr03 4148295 4149858 +
Car Car08g01667 Chr08 26515532 26517593 -
Cca Cca08g00261 Chr08 3708897 3711808 +
Dod Dod02g3681 Chr02 75469999 75471673 +
Gma Gma07g00871 Chr07 9419771 9421904 +
Gma Gma09g01677 Chr09 42316935 42320741 -
Gso Gso7g0830 Chr7 9206706 9209161 +
Gso Gso7g0830 Chr7 9206706 9209161 +
Lal Lal8g0444 Chr8 2969624 2971546 +
Lasa Lasa1g03969 Chr1 691151496 691152645 -
Phac Phac4g02037 Chr4 46903692 46906210 -
Psa Psa1g0808 Chr1 52075795 52078624 -
Pste Pste9g01474 Chr9 14347747 14349863 -
Pvu Pvu4g1629 Chr4 43576099 43578414 -
Rops Rops5g00287 Chr5 4439109 4443941 +
Seca Seca10g04851 Chr10 111880237 111883119 -
Spst Spst4g02789 Chr4 67627297 67628993 +
Vian Vian8g01443 Chr8 33798385 33799690 -
Vifa Vifa1g07144 Chr1 1102924912 1102927505 +
Vimu Vimu8g01576 Chr8 21541046 21542628 +
Viun Viun4g00331 Chr4 2022047 2023968 +
Vivi Vivi4g00289 Chr4 6570344 6571489 +
Vra Vra1g0641 Chr1 7408734 7410358 +
Vvi Vvi17g0300 Chr17 3148899 3152741 +
Apr Apr2g1758 Chr2 23230000 23234941 +
Bva Bva03g00693 Chr03 4144284 4146728 -
Sto Sto8g2189 Chr8 14423277 14423612 -
Vvi Vvi17g0301 Chr17 3158510 3158788 +
Adu Adu05g02684 Chr05 93934789 93935587 -
Aed Aed7g0235 Chr7 1674117 1675468 -
Aev Aev05g3461 Chr05 33980188 33980466 -
Ahy Ahy15g2731 Chr15 144257745 144258426 +
Aip Aip05g03048 Chr05 133298031 133298823 +
Apr Apr6g1037 Chr6 15089839 15090257 +
Arst Arst5g03401 Chr5 92593006 92593690 -
Bach Bach1g01490 Chr1 28366701 28366979 +
Bva Bva04g00837 Chr04 5510004 5510282 -
Bva Bva03g00691 Chr03 4135085 4135363 -
Car Car08g01669 Chr08 26527734 26528557 +
Cca Cca08g00259 Chr08 3665825 3666590 -
Dod Dod02g3679 Chr02 75458279 75459077 -
Gma Gma07g00867 Chr07 9361837 9363402 -
Gma Gma09g01679 Chr09 42347267 42348226 +
Lal Lal8g0443 Chr8 2962607 2962885 +
Lapu Lapu4g00214 Chr4 2139039 2139317 -
Lasa Lasa1g03973 Chr1 691305670 691305948 +
Lja Lja2g2130 Chr2 23878075 23878706 -
Mal Mal8g3809 Chr8 110533252 110533530 +
Mesa Mesa22g03050 Chr22 80438100 80438378 +
Mtr Mtr6g2139 Chr6 38251638 38252435 +
Pumo Pumo6g03003 Chr6 71852167 71852853 +
Pvu Pvu4g1631 Chr4 43591141 43591790 +
Seca Seca10g04856 Chr10 111934692 111934970 +
Spst Spst4g02787 Chr4 67617140 67621852 -
Sto Sto8g2188 Chr8 14414004 14414282 -
Tpr Tpr5g0287 Chr5 4230488 4231023 -
Trre Trre3g03826 Chr3 49349752 49350030 +
Vian Vian8g01448 Chr8 33837574 33838208 +
Viun Viun4g00328 Chr4 1993476 1994172 -
Vivi Vivi4g00276 Chr4 6163280 6164044 -
Vra Vra1g0638 Chr1 7393156 7393839 -
Vvi Vvi17g0302 Chr17 3160676 3165198 -
Aed Aed7g0234 Chr7 1668882 1674187 +
Aev Aev05g3460 Chr05 33974224 33978836 +
Ahy Ahy15g2732 Chr15 144259044 144264502 -
Aip Aip05g03049 Chr05 133299233 133304889 -
Apr Apr6g1038 Chr6 15095498 15099926 -
Bva Bva04g00836 Chr04 5503828 5509198 +
Bva Bva03g00690 Chr03 4128875 4134131 +
Cca Cca08g00258 Chr08 3658399 3663582 +
Gma Gma07g00865 Chr07 9344794 9349937 +
Gma Gma09g01680 Chr09 42356889 42361384 -
Gso Gso7g0822 Chr7 9131572 9136857 +
Gso Gso7g0822 Chr7 9131572 9136857 +
Lal Lal8g0442 Chr8 2962540 2968982 -
Lal Lal25g0464 Chr25 3182480 3192385 -
Lja Lja2g2127 Chr2 23755383 23760344 +
Mal Mal8g3810 Chr8 110534648 110539081 -
Mtr Mtr6g2140 Chr6 38253357 38258930 -
Psa Psa1g0810 Chr1 52139506 52146389 -
Sto Sto8g2187 Chr8 14408436 14412995 +
Tpr Tpr5g0286 Chr5 4224272 4229744 +
Tsu Tsu03g03112 Chr03 42889569 42895063 -
Vra Vra1g0636 Chr1 7383751 7389190 +
Vifa Vifa1g07149 Chr1 1103736570 1103744542 +