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
Vvi2g0662 . . . . . . . Aed6g0623 Aev05g0815 . Ahy15g0459 . Aip05g00459 . . . . . Apr7g0751 . . . . . . . Bva08g00402 . Car08g00353 . . Cca11g01516 . . Dod02g0902 . . . . . Gma01g02058 Gma11g00358 . . Gso1g1733 Gso1g1733 . . . Lal16g0297 Lal23g0764 Lal15g0836 . Lal23g1258 . . . . . . . . . . . . . . . . . . Lja2g0165 . Mal6g1492 Mal5g3790 . . . . . . Mtr5g0482 Mtr4g3518 . . . . . . . . . . . . . . . . . . . . . . . . . Ssu6g1697 Sto6g3484 . Tpr2g5582 Tpr4g3870 . . Tsu05g00451 Tsu04g02280 . . . . . . . . . . . Vra7g1312
Vvi2g0663 Acco11g1903 Acco12g1724 Accr9g00550 Accr10g00335 Adu05g00479 Adu01g01287 . . . Aev01g0418 . Ahy11g1205 . Aip01g01274 Alju09g1896 Alju12g0411 . . . Apr10g1675 Arst5g00612 Arst1g01711 Bach4g00348 Bach10g00305 Bisa11g1244 Bisa01g1020 . Bva11g01909 . Car07g01309 . . Dere09g0484 Dere13g0304 . Dod05g1288 Enph13g1199 Enph14g0312 Glsi05g1816 Glsi09g0256 . . Gma05g00642 Gma17g01379 . . . . . . . . Lal16g0863 . . . . . . . Lapu2g00416 Lapu3g01391 Lasa2g02962 Lasa4g02734 Lele49g0442 Lele50g0478 Lele51g0458 Lele52g0473 Lele53g0290 Lele54g0287 Lele55g1198 Lele56g1152 . . . . Mepo5g00544 Mepo1g01697 Mesa17g00569 . Mibi12g1639 Mibi10g0367 . . . . Phco4g01290 Phco8g00853 Prci10g0713 Prci5g0432 . . . Pste7g00678 Pte14g01019 Pte12g00228 Pte14g01019 Pte12g00228 Pumo8g02125 Pumo4g01763 Pvu2g0027 Pvu3g2338 Rops1g01974 Rops2g04350 Seca12g02134 Seca12g02134 Spst3g04208 Spst3g04208 . . . . . . . Trre15g03476 . . Vian10g00433 Vian1g01489 Vifa1g07629 Vifa4g02816 Vimu7g02642 Vimu7g02642 Viun2g02328 Viun3g04056 Vivi2g03624 . . .
Vvi2g0664 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto11g1857 . . . . . . . . . . . . . . . . . .
Vvi2g0665 . . . . Adu05g00482 Adu01g01284 Aed11g1563 Aed6g0624 Aev05g0813 Aev01g0420 Ahy15g0461 Ahy11g1201 Aip05g00461 Aip01g01268 . . . Amo11g1117 Apr7g0753 Apr10g1677 . Arst1g01705 . Bach10g00307 . . Bva08g00404 Bva11g01907 Car08g00355 Car07g01311 Cca06g01627 Cca11g01515 . . Dod02g0900 Dod05g1286 . . . . Gma01g02057 Gma11g00360 Gma05g00644 Gma17g01382 Gso1g1732 Gso1g1732 Gso1g1732 Gso1g1732 . Lal16g0296 . . Lal16g0861 . . . . . . . . . . . . . . . . . . . Lja2g0167 . Mal6g1490 Mal5g3787 . Mepo1g01702 . . . . Mtr5g0484 Mtr4g3516 . . . . . . . Psa4g1812 . Pste7g00690 Pte14g01021 Pte12g00230 . . . Pumo4g01765 Pvu2g0029 Pvu3g2340 . Rops2g04355 . Seca12g02140 Spst3g04203 Spst3g04203 Ssu2g2666 Ssu6g1698 . . Tpr2g5584 Tpr4g3871 . Trre15g03484 Tsu05g00453 Tsu04g02277 . Vian1g01493 . Vifa4g02813 . . . Viun3g04054 Vivi2g03616 . . Vra7g1311
Vvi2g0666 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0667 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0668 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0669 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0670 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0671 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi2g0662 Chr2 5999840 6000845 -
Aed Aed6g0623 Chr6 5336717 5338593 +
Aev Aev05g0815 Chr05 5719539 5720314 -
Ahy Ahy15g0459 Chr15 5400222 5401500 +
Aip Aip05g00459 Chr05 5164880 5165494 +
Apr Apr7g0751 Chr7 14432526 14433838 +
Bva Bva08g00402 Chr08 2032945 2034095 +
Car Car08g00353 Chr08 2798400 2800218 +
Cca Cca11g01516 Chr11 38204576 38205925 -
Dod Dod02g0902 Chr02 11576680 11578224 -
Gma Gma01g02058 Chr01 55939109 55943379 -
Gma Gma11g00358 Chr11 2896290 2897734 +
Gso Gso1g1733 Chr1 54138744 54140670 -
Gso Gso1g1733 Chr1 54138744 54140670 -
Lal Lal16g0297 Chr16 1794799 1796223 -
Lal Lal23g0764 Chr23 10216514 10218153 +
Lal Lal15g0836 Chr15 6244505 6246260 -
Lal Lal23g1258 Chr23 13700331 13701870 +
Lja Lja2g0165 Chr2 1366298 1367542 +
Mal Mal6g1492 Chr6 27728491 27729108 -
Mal Mal5g3790 Chr5 106402176 106402761 -
Mtr Mtr5g0482 Chr5 4441877 4443056 +
Mtr Mtr4g3518 Chr4 48895287 48896353 -
Ssu Ssu6g1697 Chr6 28630843 28631334 +
Sto Sto6g3484 Chr6 40429948 40430575 +
Tpr Tpr2g5582 Chr2 64581657 64582941 +
Tpr Tpr4g3870 Chr4 44902421 44903468 +
Tsu Tsu05g00451 Chr05 3436944 3438292 +
Tsu Tsu04g02280 Chr04 25434577 25435803 -
Vra Vra7g1312 Chr7 29967297 29968448 -
Vvi Vvi2g0663 Chr2 6021923 6023224 -
Acco Acco11g1903 Chr11 33254541 33255875 +
Acco Acco12g1724 Chr12 28415236 28416495 +
Accr Accr9g00550 Chr9 6297300 6298647 -
Accr Accr10g00335 Chr10 5497079 5498362 -
Adu Adu05g00479 Chr05 5005916 5006967 +
Adu Adu01g01287 Chr01 30262353 30264095 -
Aev Aev01g0418 Chr01 3552946 3554293 +
Ahy Ahy11g1205 Chr11 37827114 37829028 -
Aip Aip01g01274 Chr01 35831093 35832555 -
Alju Alju09g1896 Chr09 42767047 42768407 +
Alju Alju12g0411 Chr12 4992828 4994061 -
Apr Apr10g1675 Chr10 29470510 29479025 +
Arst Arst5g00612 Chr5 5025204 5026250 +
Arst Arst1g01711 Chr1 30663863 30665408 -
Bach Bach4g00348 Chr4 2251050 2252813 +
Bach Bach10g00305 Chr10 2122742 2124102 +
Bisa Bisa11g1244 Chr11 31152171 31153559 +
Bisa Bisa01g1020 Chr01 17270120 17271466 -
Bva Bva11g01909 Chr11 16482930 16485155 -
Car Car07g01309 Chr07 12021527 12022580 +
Dere Dere09g0484 Chr09 7683365 7684752 +
Dere Dere13g0304 Chr13 4218951 4220280 +
Dod Dod05g1288 Chr05 36397004 36399284 -
Enph Enph13g1199 Chr13 17832583 17835093 -
Enph Enph14g0312 Chr14 5246802 5249841 +
Glsi Glsi05g1816 Chr05 65875739 65877109 -
Glsi Glsi09g0256 Chr09 1838134 1839441 +
Gma Gma05g00642 Chr05 7013230 7014680 +
Gma Gma17g01379 Chr17 12742775 12744646 +
Lal Lal16g0863 Chr16 5661378 5663826 -
Lapu Lapu2g00416 Chr2 3397800 3400489 +
Lapu Lapu3g01391 Chr3 15568958 15572082 +
Lasa Lasa2g02962 Chr2 515443372 515444557 +
Lasa Lasa4g02734 Chr4 518768227 518769602 -
Lele Lele49g0442 Chr49 2638756 2640089 -
Lele Lele50g0478 Chr50 2819154 2820985 -
Lele Lele51g0458 Chr51 2684912 2686247 -
Lele Lele52g0473 Chr52 2889278 2890561 -
Lele Lele53g0290 Chr53 2404176 2405537 -
Lele Lele54g0287 Chr54 2430624 2431965 -
Lele Lele55g1198 Chr55 18612342 18613710 +
Lele Lele56g1152 Chr56 14975361 14976701 +
Mepo Mepo5g00544 Chr5 4777636 4779835 +
Mepo Mepo1g01697 Chr1 16742053 16744299 +
Mesa Mesa17g00569 Chr17 6622578 6623855 +
Mibi Mibi12g1639 Chr12 32317027 32318371 +
Mibi Mibi10g0367 Chr10 5880930 5881664 -
Phco Phco4g01290 Chr4 11054340 11055645 -
Phco Phco8g00853 Chr8 8671685 8673015 +
Prci Prci10g0713 Chr10 4883157 4885717 -
Prci Prci5g0432 Chr5 5679995 5681681 -
Pste Pste7g00678 Chr7 6193360 6195111 +
Pte Pte14g01019 Chr14 31849948 31852486 -
Pte Pte12g00228 Chr12 1818214 1820140 -
Pte Pte14g01019 Chr14 31849948 31852486 -
Pte Pte12g00228 Chr12 1818214 1820140 -
Pumo Pumo8g02125 Chr8 58262989 58265626 -
Pumo Pumo4g01763 Chr4 23179176 23179586 +
Pvu Pvu2g0027 Chr2 270280 271875 +
Pvu Pvu3g2338 Chr3 44699656 44701692 +
Rops Rops1g01974 Chr1 39966996 39969182 -
Rops Rops2g04350 Chr2 79319067 79320599 +
Seca Seca12g02134 Chr12 26971680 26973404 +
Seca Seca12g02134 Chr12 26971680 26973404 +
Spst Spst3g04208 Chr3 93546899 93554025 -
Spst Spst3g04208 Chr3 93546899 93554025 -
Trre Trre15g03476 Chr15 41424194 41425556 +
Vian Vian10g00433 Chr10 3898282 3899520 +
Vian Vian1g01489 Chr1 16475314 16476662 +
Vifa Vifa1g07629 Chr1 1184342621 1184343786 -
Vifa Vifa4g02816 Chr4 898134913 898136235 -
Vimu Vimu7g02642 Chr7 22238613 22239797 +
Vimu Vimu7g02642 Chr7 22238613 22239797 +
Viun Viun2g02328 Chr2 30571838 30573937 -
Viun Viun3g04056 Chr3 48233207 48235724 -
Vivi Vivi2g03624 Chr2 145320794 145322575 -
Vvi Vvi2g0664 Chr2 6039133 6077694 -
Sto Sto11g1857 Chr11 17341042 17344872 -
Vvi Vvi2g0665 Chr2 6092856 6111433 +
Adu Adu05g00482 Chr05 5102440 5105759 +
Adu Adu01g01284 Chr01 29810912 29818457 -
Aed Aed11g1563 Chr11 19764199 19771749 -
Aed Aed6g0624 Chr6 5344277 5354891 +
Aev Aev05g0813 Chr05 5671087 5678034 -
Aev Aev01g0420 Chr01 3589598 3599789 +
Ahy Ahy15g0461 Chr15 5450330 5458866 +
Ahy Ahy11g1201 Chr11 37367979 37388497 -
Aip Aip05g00461 Chr05 5221229 5228959 +
Aip Aip01g01268 Chr01 35391464 35411283 -
Amo Amo11g1117 Chr11 34760660 34780513 -
Apr Apr7g0753 Chr7 14504399 14518813 +
Apr Apr10g1677 Chr10 29519942 29530290 +
Arst Arst1g01705 Chr1 30207636 30226836 -
Bach Bach10g00307 Chr10 2139576 2147499 +
Bva Bva08g00404 Chr08 2081020 2090100 +
Bva Bva11g01907 Chr11 16461831 16470037 -
Car Car08g00355 Chr08 2882169 2891183 +
Car Car07g01311 Chr07 12060527 12074238 +
Cca Cca06g01627 Chr06 31413922 31424106 -
Cca Cca11g01515 Chr11 38154178 38166844 -
Dod Dod02g0900 Chr02 11470603 11484971 -
Dod Dod05g1286 Chr05 36292457 36302802 -
Gma Gma01g02057 Chr01 55919035 55935702 -
Gma Gma11g00360 Chr11 2956427 2958296 +
Gma Gma05g00644 Chr05 7101778 7112142 +
Gma Gma17g01382 Chr17 12804130 12813894 +
Gso Gso1g1732 Chr1 54116967 54133623 -
Gso Gso1g1732 Chr1 54116967 54133623 -
Gso Gso1g1732 Chr1 54116967 54133623 -
Gso Gso1g1732 Chr1 54116967 54133623 -
Lal Lal16g0296 Chr16 1781745 1792614 -
Lal Lal16g0861 Chr16 5626399 5642642 -
Lja Lja2g0167 Chr2 1423793 1432818 +
Mal Mal6g1490 Chr6 27594781 27596235 -
Mal Mal5g3787 Chr5 106343986 106356160 -
Mepo Mepo1g01702 Chr1 16788358 16802055 +
Mtr Mtr5g0484 Chr5 4506667 4516351 +
Mtr Mtr4g3516 Chr4 48856041 48869141 -
Psa Psa4g1812 Chr4 128037663 128051022 +
Pste Pste7g00690 Chr7 6320308 6337876 +
Pte Pte14g01021 Chr14 31886329 31893517 +
Pte Pte12g00230 Chr12 1847143 1863535 +
Pumo Pumo4g01765 Chr4 23242005 23253188 +
Pvu Pvu2g0029 Chr2 303573 312728 -
Pvu Pvu3g2340 Chr3 44761239 44766367 +
Rops Rops2g04355 Chr2 79382345 79393059 +
Seca Seca12g02140 Chr12 27194771 27204948 +
Spst Spst3g04203 Chr3 93452959 93467093 -
Spst Spst3g04203 Chr3 93452959 93467093 -
Ssu Ssu2g2666 Chr2 86641572 86653534 -
Ssu Ssu6g1698 Chr6 28669285 28683416 +
Tpr Tpr2g5584 Chr2 64648273 64658970 +
Tpr Tpr4g3871 Chr4 44911799 44924827 +
Trre Trre15g03484 Chr15 41646709 41658592 +
Tsu Tsu05g00453 Chr05 3503052 3512228 +
Tsu Tsu04g02277 Chr04 25391415 25405054 -
Vian Vian1g01493 Chr1 16551797 16563090 +
Vifa Vifa4g02813 Chr4 894579814 894589447 -
Viun Viun3g04054 Chr3 48141281 48152903 -
Vivi Vivi2g03616 Chr2 144941596 144958266 -
Vra Vra7g1311 Chr7 29937203 29948863 -
Vvi Vvi2g0666 Chr2 6113176 6119879 +
Vvi Vvi2g0667 Chr2 6126914 6130224 +
Vvi Vvi2g0668 Chr2 6130888 6146577 +
Vvi Vvi2g0669 Chr2 6161364 6173803 +
Vvi Vvi2g0670 Chr2 6174349 6176342 +
Vvi Vvi2g0671 Chr2 6184237 6187378 +