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
Vvi18g1216 . Acco05g2969 . Accr3g00088 . Adu06g01275 Aed11g0054 . . Aev07g0692 . Ahy16g0066 . Aip06g00057 . Alju07g2928 . . Apr9g0627 . . Arst6g01678 . Bach3g02405 . Bisa05g0624 Bva06g01915 Bva10g00913 Car04g03583 . Cca05g00360 . . Dere05g2795 . Dod08g2274 . Enph7g1474 . Glsi10g0138 . . Gma14g02130 Gma17g02459 . . . . . . . Lal8g0540 . . . . . . . . . Lapu8g01017 . Lasa6g00275 . . . . Lele25g0074 Lele26g0086 . Lele28g0085 . Lja5g3317 Mal1g6058 . . Mepo4g01875 . Mesa1g00056 . Mibi08g2599 Mtr1g0709 . . Phac1g00067 . Phco2g00081 . Prci2g0110 . . . Pste8g01389 . . Pte3g01417 Pte2g00201 . Pumo9g00072 . Pvu1g0074 . Rops9g02617 . Seca8g04020 . Spst8g02011 Ssu5g0068 . Sto5g0142 . Tpr1g3871 . . Trre1g00078 Tsu01g00202 . . Vian7g00903 . Vifa3g05189 . . . Viun8g00114 . Vivi4g05909 Vra6g2038 .
Vvi18g1217 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1218 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1219 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1220 . . . . . . . . . . . Ahy16g2956 . Aip06g03160 . . . Amo16g3580 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa5g1998 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1221 . . . . . . . Aed10g0356 Aev08g0902 . Ahy17g2763 . Aip07g03014 . . . Amo17g2669 . . . . . . . . . . . . . . Cca03g01085 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja1g4989 . Mal1g5081 . . . . . . . Mtr1g0899 . . . . . . . Psa6g0934 . . . . . . . . . . . . . . . . . . Ssu1g2952 Sto5g0360 . Tpr1g3068 . . . Tsu01g01020 . . . . . . . . . . . . Vra5g0744
Vvi18g1222 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Gma04g02343 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1223 . . . . . . . Aed9g0227 . . . . . . . . . . . . . . . . . . . . . . . Cca07g00272 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco7g00291 . . . . . Pste2g00668 . . Pte1g02689 . . . . Pvu9g0169 . . . Seca4g00424 . Spst9g00290 . . . . . . . . . . . Vian4g02387 . . . Vimu10g03481 . Viun9g03670 . Vivi4g05910 . . Vra5g1648
Vvi18g1224 . . . . Adu08g00154 . . Aed9g0226 Aev08g0202 Aev07g0690 Ahy17g2273 Ahy16g0064 Aip07g02420 Aip06g00055 . . . . . Apr5g1653 Arst8g00179 . Bach12g00096 . . . Bva06g01913 Bva10g00915 . Car05g03264 . Cca07g00271 . . Dod08g2276 Dod08g2276 . . . . Gma04g00232 Gma06g00214 . . Gso4g0217 Gso4g0217 . . . . . Lal8g0538 . . . . . . . . Lapu9g02291 . Lasa5g04525 . . . . . . . . . Lja1g3503 . . Mal2g0485 Mepo3g07858 . Mesa9g05487 . . . . Mtr3g4263 Phac9g00079 . Phco7g00290 . . . . Psa5g0312 . . . Pte1g02688 . . . . Pvu9g0170 . Rops10g02466 . Seca4g00423 . Spst9g00289 . . . Sto5g0140 . . Tpr7g0234 Trre5g05673 . . Tsu07g00265 Vian4g02388 . Vifa2g04494 . Vimu10g03483 . Viun9g03671 . Vivi3g00591 . . Vra5g1649
Vvi18g1225 . . . . . Adu06g01278 Aed11g0053 . . Aev07g0689 . Ahy16g0063 . Aip06g00054 . . . . Apr9g0629 . . Arst6g01682 . Bach3g02408 . . Bva06g01912 Bva10g00916 Car04g03586 . Cca05g00361 . . . . . . . . . . . Gma14g02131 Gma17g02460 . . . . . . . . . . . . . . . . . Lapu8g01018 . Lasa6g00277 . . . . . . . . . Lja5g3320 Mal1g6062 . . Mepo4g01878 . Mesa1g00048 . . Mtr1g0713 . . Phac1g00066 . Phco2g00080 . . . . . Pste8g01391 . . . . . Pumo9g00071 . Pvu1g0073 . Rops9g02616 . Seca8g04025 . Spst8g02012 Ssu5g0067 . . . Tpr1g3874 . . Trre1g00076 Tsu01g00200 . . Vian7g00904 . . . . . Viun8g00113 . Vivi4g05912 Vra6g2037 .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Aev Aev08g0202 Chr08 1121845 1127614 +
Ahy Ahy17g2273 Chr17 109678680 109681030 +
Aip Aip07g02420 Chr07 101848670 101852946 +
Dod Dod08g2276 Chr08 50756100 50759009 -
Aed Aed10g0356 Chr10 2878139 2881415 -
Aev Aev08g0902 Chr08 5324762 5326450 +
Ahy Ahy17g2763 Chr17 125971276 125973738 +
Aip Aip07g03014 Chr07 117052075 117053617 +
Amo Amo17g2669 Chr17 126946180 126948747 +
Cca Cca03g01085 Chr03 26444182 26447432 +
Gma Gma04g02343 Chr04 53853822 53854196 +
Lja Lja1g4989 Chr1 69840094 69842936 +
Ssu Ssu1g2952 Chr1 77628973 77630057 +
Sto Sto5g0360 Chr5 2194306 2195445 +
Vra Vra5g0744 Chr5 12691192 12694340 +
Psa Psa5g1998 Chr5 154883318 154885905 -
Vvi Vvi18g1216 Chr18 12179640 12181575 +
Acco Acco05g2969 Chr05 44348365 44350581 +
Accr Accr3g00088 Chr3 1093664 1095884 -
Adu Adu06g01275 Chr06 17339199 17342499 +
Aed Aed11g0054 Chr11 363195 367465 -
Aev Aev07g0692 Chr07 4404686 4409921 -
Ahy Ahy16g0066 Chr16 583189 586906 -
Aip Aip06g00057 Chr06 513625 518793 -
Alju Alju07g2928 Chr07 54363755 54366377 +
Apr Apr9g0627 Chr9 10069545 10072662 +
Arst Arst6g01678 Chr6 17372484 17375849 +
Bach Bach3g02405 Chr3 30382802 30385369 +
Bisa Bisa05g0624 Chr05 10235653 10237932 -
Bva Bva06g01915 Chr06 13015139 13017581 -
Bva Bva10g00913 Chr10 6911387 6913683 +
Car Car04g03583 Chr04 65013928 65019087 +
Cca Cca05g00360 Chr05 7910974 7914506 +
Dere Dere05g2795 Chr05 38642931 38645263 +
Dod Dod08g2274 Chr08 50742021 50746786 +
Enph Enph7g1474 Chr7 19961118 19963797 +
Glsi Glsi10g0138 Chr10 1005829 1008083 -
Gma Gma14g02130 Chr14 52475750 52479216 +
Gma Gma17g02459 Chr17 42622505 42626373 +
Lal Lal8g0540 Chr8 3685266 3689528 -
Lapu Lapu8g01017 Chr8 28288823 28292129 +
Lasa Lasa6g00275 Chr6 8364947 8367440 +
Lele Lele25g0074 Chr25 432841 435072 -
Lele Lele26g0086 Chr26 465776 467922 -
Lele Lele28g0085 Chr28 466923 469091 -
Lja Lja5g3317 Chr5 64343397 64346912 +
Mal Mal1g6058 Chr1 138862464 138866386 +
Mepo Mepo4g01875 Chr4 24042660 24047019 +
Mesa Mesa1g00056 Chr1 708976 713388 -
Mibi Mibi08g2599 Chr08 43761217 43763667 +
Mtr Mtr1g0709 Chr1 8027902 8031501 +
Phac Phac1g00067 Chr1 489085 492657 -
Phco Phco2g00081 Chr2 732112 736455 -
Prci Prci2g0110 Chr2 870833 873401 -
Pste Pste8g01389 Chr8 7523353 7527147 +
Pte Pte3g01417 Chr3 12406904 12409367 +
Pte Pte2g00201 Chr2 1661428 1663557 +
Pumo Pumo9g00072 Chr9 1087578 1090880 -
Pvu Pvu1g0074 Chr1 566703 569916 -
Rops Rops9g02617 Chr9 48992529 48995480 -
Seca Seca8g04020 Chr8 115312545 115315557 +
Spst Spst8g02011 Chr8 27660055 27662840 +
Ssu Ssu5g0068 Chr5 1294288 1297299 -
Sto Sto5g0142 Chr5 816847 819498 -
Tpr Tpr1g3871 Chr1 42837521 42842752 +
Trre Trre1g00078 Chr1 547026 551757 -
Tsu Tsu01g00202 Chr01 1563651 1573147 -
Vian Vian7g00903 Chr7 17320897 17323654 +
Vifa Vifa3g05189 Chr3 1515596612 1515599380 +
Viun Viun8g00114 Chr8 652969 656168 -
Vivi Vivi4g05909 Chr4 196009462 196012793 +
Vra Vra6g2038 Chr6 36943390 36946657 -
Vvi Vvi18g1217 Chr18 12191395 12193357 +
Vvi Vvi18g1218 Chr18 12197073 12197669 -
Vvi Vvi18g1219 Chr18 12205116 12205631 +
Vvi Vvi18g1220 Chr18 12212398 12214785 -
Ahy Ahy16g2956 Chr16 144268211 144272170 +
Aip Aip06g03160 Chr06 127374743 127376899 +
Amo Amo16g3580 Chr16 146102252 146106068 +
Psa Psa5g1998 Chr5 154883318 154885905 -
Vvi Vvi18g1221 Chr18 12216225 12219253 -
Aed Aed10g0356 Chr10 2878139 2881415 -
Aev Aev08g0902 Chr08 5324762 5326450 +
Ahy Ahy17g2763 Chr17 125971276 125973738 +
Aip Aip07g03014 Chr07 117052075 117053617 +
Amo Amo17g2669 Chr17 126946180 126948747 +
Cca Cca03g01085 Chr03 26444182 26447432 +
Lja Lja1g4989 Chr1 69840094 69842936 +
Mal Mal1g5081 Chr1 122358287 122362177 -
Mtr Mtr1g0899 Chr1 10358970 10363565 +
Psa Psa6g0934 Chr6 35201820 35203916 +
Ssu Ssu1g2952 Chr1 77628973 77630057 +
Sto Sto5g0360 Chr5 2194306 2195445 +
Tpr Tpr1g3068 Chr1 35159049 35162680 -
Tsu Tsu01g01020 Chr01 9336608 9340273 +
Vra Vra5g0744 Chr5 12691192 12694340 +
Vvi Vvi18g1222 Chr18 12225492 12227949 +
Gma Gma04g02343 Chr04 53853822 53854196 +
Vvi Vvi18g1223 Chr18 12229450 12229851 +
Aed Aed9g0227 Chr9 1601368 1601763 -
Cca Cca07g00272 Chr07 3500210 3500602 -
Phco Phco7g00291 Chr7 2022358 2022717 -
Pste Pste2g00668 Chr2 6962349 6962726 -
Pte Pte1g02689 Chr1 46999426 46999956 -
Pvu Pvu9g0169 Chr9 2864766 2865128 +
Seca Seca4g00424 Chr4 6946298 6946946 -
Spst Spst9g00290 Chr9 2718070 2718432 -
Vian Vian4g02387 Chr4 40577822 40578187 +
Vimu Vimu10g03481 Chr10 44544255 44544620 +
Viun Viun9g03670 Chr9 42007095 42007760 +
Vivi Vivi4g05910 Chr4 196037733 196037981 +
Vra Vra5g1648 Chr5 22906096 22906607 +
Vvi Vvi18g1224 Chr18 12230581 12231893 -
Adu Adu08g00154 Chr08 2376006 2378087 -
Aed Aed9g0226 Chr9 1598974 1600105 +
Aev Aev08g0202 Chr08 1121845 1127614 +
Aev Aev07g0690 Chr07 4394785 4397324 +
Ahy Ahy17g2273 Chr17 109678680 109681030 +
Ahy Ahy16g0064 Chr16 564907 567409 +
Aip Aip07g02420 Chr07 101848670 101852946 +
Aip Aip06g00055 Chr06 497519 499684 +
Apr Apr5g1653 Chr5 20153158 20154688 -
Arst Arst8g00179 Chr8 2388099 2390322 -
Bach Bach12g00096 Chr12 692531 694013 +
Bva Bva06g01913 Chr06 13009946 13011709 +
Bva Bva10g00915 Chr10 6917783 6919818 -
Car Car05g03264 Chr05 77400019 77401618 -
Cca Cca07g00271 Chr07 3494354 3496932 +
Dod Dod08g2276 Chr08 50756100 50759009 -
Dod Dod08g2276 Chr08 50756100 50759009 -
Gma Gma04g00232 Chr04 1986976 1989290 +
Gma Gma06g00214 Chr06 1881093 1882947 +
Gso Gso4g0217 Chr4 1952214 1955100 +
Gso Gso4g0217 Chr4 1952214 1955100 +
Lal Lal8g0538 Chr8 3676794 3679320 +
Lapu Lapu9g02291 Chr9 37520393 37522413 -
Lasa Lasa5g04525 Chr5 670113404 670114221 -
Lja Lja1g3503 Chr1 43632095 43634781 +
Mal Mal2g0485 Chr2 5591629 5593162 +
Mepo Mepo3g07858 Chr3 91621727 91623766 +
Mesa Mesa9g05487 Chr9 90209567 90211087 -
Mtr Mtr3g4263 Chr3 56508800 56510873 -
Phac Phac9g00079 Chr9 625801 627827 +
Phco Phco7g00290 Chr7 2018139 2019730 +
Psa Psa5g0312 Chr5 22493135 22493951 +
Pte Pte1g02688 Chr1 46997583 46998744 +
Pvu Pvu9g0170 Chr9 2869361 2871420 -
Rops Rops10g02466 Chr10 43095768 43097608 -
Seca Seca4g00423 Chr4 6941184 6944554 +
Spst Spst9g00289 Chr9 2715328 2716731 +
Sto Sto5g0140 Chr5 810807 811742 +
Tpr Tpr7g0234 Chr7 1934694 1936253 +
Trre Trre5g05673 Chr5 56786723 56787808 -
Tsu Tsu07g00265 Chr07 2028832 2030261 +
Vian Vian4g02388 Chr4 40584656 40585925 -
Vifa Vifa2g04494 Chr2 1323317820 1323318686 -
Vimu Vimu10g03483 Chr10 44547153 44548400 -
Viun Viun9g03671 Chr9 42010381 42011959 -
Vivi Vivi3g00591 Chr3 9842462 9843700 -
Vra Vra5g1649 Chr5 22909464 22911103 -
Vvi Vvi18g1225 Chr18 12252612 12256877 +
Adu Adu06g01278 Chr06 17404484 17407760 +
Aed Aed11g0053 Chr11 353643 359637 -
Aev Aev07g0689 Chr07 4389248 4392808 -
Ahy Ahy16g0063 Chr16 560820 564411 -
Aip Aip06g00054 Chr06 493698 496855 -
Apr Apr9g0629 Chr9 10142035 10146167 +
Arst Arst6g01682 Chr6 17437655 17441212 +
Bach Bach3g02408 Chr3 30393015 30395956 +
Bva Bva06g01912 Chr06 13005923 13009516 -
Bva Bva10g00916 Chr10 6920545 6924006 +
Car Car04g03586 Chr04 65081722 65085452 +
Cca Cca05g00361 Chr05 7946159 7951345 +
Gma Gma14g02131 Chr14 52485381 52489282 +
Gma Gma17g02460 Chr17 42632204 42635902 +
Lapu Lapu8g01018 Chr8 28294979 28298613 +
Lasa Lasa6g00277 Chr6 8426067 8428477 -
Lja Lja5g3320 Chr5 64378281 64382060 +
Mal Mal1g6062 Chr1 138975259 138978922 -
Mepo Mepo4g01878 Chr4 24077150 24080084 -
Mesa Mesa1g00048 Chr1 636706 639407 +
Mtr Mtr1g0713 Chr1 8080945 8083874 -
Phac Phac1g00066 Chr1 480787 484634 -
Phco Phco2g00080 Chr2 724599 727879 -
Pste Pste8g01391 Chr8 7537629 7541291 +
Pumo Pumo9g00071 Chr9 1074078 1077967 -
Pvu Pvu1g0073 Chr1 558249 561987 -
Rops Rops9g02616 Chr9 48950346 48953859 -
Seca Seca8g04025 Chr8 115441584 115445095 +
Spst Spst8g02012 Chr8 27689098 27692309 +
Ssu Ssu5g0067 Chr5 1273745 1276880 -
Tpr Tpr1g3874 Chr1 42865403 42868503 -
Trre Trre1g00076 Chr1 530928 533981 +
Tsu Tsu01g00200 Chr01 1548272 1551511 +
Vian Vian7g00904 Chr7 17328741 17330682 +
Viun Viun8g00113 Chr8 646104 649932 -
Vivi Vivi4g05912 Chr4 196042856 196045254 -
Vra Vra6g2037 Chr6 36933546 36936824 -