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
Vvi16g0699 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0700 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0701 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0702 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lal2g0784 . . . . . . . . . . . . . . . . . . . . . . Lja2g2464 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0703 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0704 . . . . . . Aed1g2190 . . Aev09g2305 . Ahy19g3496 . Aip09g03951 . . . Amo19g4499 . . . Arst9g03229 . . . . . Bva04g01062 . . Cca02g02331 . . . . Dod06g0689 . . . . Gma10g02294 . . . Gso10g2164 . . . . . . Lal24g0025 . . . . . . . . . Lapu7g02112 . Lasa6g04205 . . . . . . . . . Lja5g0578 Mal1g0802 . . Mepo4g04324 . Mesa1g04737 . . Mtr1g3838 . . . . Phco6g02561 . . . . . . . . . Pte9g00266 . Pumo3g00852 . Pvu7g0645 . Rops6g02840 . Seca8g07488 . Spst10g01060 Ssu7g0698 . . . Tpr1g0669 . . Trre1g05517 Tsu01g04508 . . Vian3g00562 . Vifa3g03045 . Vimu3g03146 . Viun7g03368 . Vivi1g04260 Vra8g2310 .
Vvi16g0705 Acco01g0390 . Accr1g00201 . . Adu05g00963 . Aed11g1669 Aev05g3014 Aev05g0921 Ahy15g3402 Ahy15g0939 Aip05g03712 Aip05g00966 Alju02g3515 . . . . Apr6g0802 Arst5g02614 Arst5g01198 . Bach4g00212 Bisa01g0631 . . Bva04g01063 . . . Cca06g01743 Dere06g1471 . Dod02g3157 Dod02g1029 Enph12g0988 . Glsi01g1679 . Gma16g01659 . . . Gso16g1629 . . . . Lal2g0783 Lal9g0765 . . . . . . . . . . Lapu2g00310 . Lasa2g02833 . . . . . . . . Lja2g2459 Lja2g0046 . Mal6g1646 Mepo7g01090 Mepo5g00419 . . Mibi01g3278 . . Mtr5g0354 . . . Phco4g00377 Prci14g2010 . Psa2g4117 . Pste9g01267 Pste1g00665 . Pte9g00265 Pte14g01225 . Pumo6g02717 . Pvu4g1339 Pvu2g1568 Rops5g00713 . Seca10g04271 . Spst4g03062 Spst2g00365 . Ssu2g2797 Sto10g2586 Sto8g2989 . Tpr2g3820 Trre11g01521 Trre9g00446 . Tsu05g00331 Vian8g01184 . Vifa1g04002 . Vimu8g01918 Vimu7g02505 Viun4g02358 . Vivi2g05639 Vivi2g03908 . .
Vvi16g0706 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0707 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0708 . . . . . . Aed1g2191 . . . . . . . . . . . . Apr6g0799 . . . . . . . . . . Cca02g02330 . . . . . . . . . Gma16g01657 . . . Gso16g1628 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja5g0579 Mal1g0803 . . . . . . . Mtr1g3837 . . . . . . . . . . . . . . . . . . . . . . . . . Ssu7g0699 . . . Tpr1g0670 . . . Tsu01g04507 . . . . . . . . . . . Vra8g2309 .
   
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Select Species Gene Chromosome Start End Strand
Vivi Vivi2g03908 Chr2 151195178 151197922 -
Adu Adu05g00963 Chr05 12357254 12359904 +
Arst Arst5g01198 Chr5 12400847 12404274 +
Bach Bach4g00212 Chr4 1375246 1378487 +
Lapu Lapu2g00310 Chr2 2548147 2551910 +
Lasa Lasa2g02833 Chr2 512207286 512209241 +
Mepo Mepo5g00419 Chr5 3701273 3703924 +
Phco Phco4g00377 Chr4 2455774 2457978 +
Pste Pste1g00665 Chr1 2101802 2104082 +
Pte Pte14g01225 Chr14 33557613 33560831 -
Pvu Pvu2g1568 Chr2 29319064 29322815 -
Spst Spst2g00365 Chr2 2860039 2862084 +
Trre Trre9g00446 Chr9 3188280 3190955 +
Vimu Vimu7g02505 Chr7 21368570 21370966 +
Vivi Vivi2g03908 Chr2 151195178 151197922 -
Vvi Vvi16g0699 Chr16 14250124 14252140 +
Vvi Vvi16g0700 Chr16 14260709 14262625 -
Vvi Vvi16g0701 Chr16 14269762 14271192 -
Vvi Vvi16g0702 Chr16 14299091 14299549 -
Lal Lal2g0784 Chr2 5028087 5028554 +
Lja Lja2g2464 Chr2 31070854 31071273 +
Vvi Vvi16g0703 Chr16 14301637 14301894 -
Vvi Vvi16g0704 Chr16 14301653 14302916 +
Aed Aed1g2190 Chr1 18289380 18290362 +
Aev Aev09g2305 Chr09 25480578 25481704 -
Ahy Ahy19g3496 Chr19 157668124 157669787 +
Aip Aip09g03951 Chr09 145962524 145963603 +
Amo Amo19g4499 Chr19 162243486 162244550 -
Arst Arst9g03229 Chr9 109812870 109815103 -
Bva Bva04g01062 Chr04 7012872 7015797 +
Cca Cca02g02331 Chr02 44088249 44089865 -
Dod Dod06g0689 Chr06 8318232 8319760 +
Gma Gma10g02294 Chr10 50547856 50549317 -
Gso Gso10g2164 Chr10 48675472 48676947 -
Lal Lal24g0025 Chr24 179008 182287 +
Lapu Lapu7g02112 Chr7 37430777 37432023 -
Lasa Lasa6g04205 Chr6 625653517 625654393 -
Lja Lja5g0578 Chr5 5130518 5131788 +
Mal Mal1g0802 Chr1 9586454 9587550 +
Mepo Mepo4g04324 Chr4 53038159 53039238 -
Mesa Mesa1g04737 Chr1 73574709 73575785 -
Mtr Mtr1g3838 Chr1 49955894 49957142 -
Phco Phco6g02561 Chr6 47160895 47162126 -
Pte Pte9g00266 Chr9 2982005 2983159 +
Pumo Pumo3g00852 Chr3 13344946 13346573 +
Pvu Pvu7g0645 Chr7 5532470 5533783 +
Rops Rops6g02840 Chr6 50961238 50962612 -
Seca Seca8g07488 Chr8 171983200 171984558 -
Spst Spst10g01060 Chr10 11330136 11331437 -
Ssu Ssu7g0698 Chr7 14099202 14100482 +
Tpr Tpr1g0669 Chr1 5625897 5626877 +
Trre Trre1g05517 Chr1 60601664 60602481 -
Tsu Tsu01g04508 Chr01 52689063 52689973 -
Vian Vian3g00562 Chr3 5608151 5608945 +
Vifa Vifa3g03045 Chr3 873208560 873209549 -
Vimu Vimu3g03146 Chr3 45244022 45245176 -
Viun Viun7g03368 Chr7 35545252 35546456 -
Vivi Vivi1g04260 Chr1 90744311 90745669 +
Vra Vra8g2310 Chr8 41351058 41352202 -
Vvi Vvi16g0705 Chr16 14303183 14307067 -
Acco Acco01g0390 Chr01 4653539 4656061 +
Accr Accr1g00201 Chr1 3721587 3724120 +
Adu Adu05g00963 Chr05 12357254 12359904 +
Aed Aed11g1669 Chr11 20477588 20484226 -
Aev Aev05g3014 Chr05 30748465 30750900 +
Aev Aev05g0921 Chr05 6500256 6502453 -
Ahy Ahy15g3402 Chr15 156521648 156524424 -
Ahy Ahy15g0939 Chr15 14001263 14003696 +
Aip Aip05g03712 Chr05 145099598 145102199 -
Aip Aip05g00966 Chr05 13520770 13523786 +
Alju Alju02g3515 Chr02 53611079 53613587 -
Apr Apr6g0802 Chr6 12488887 12492804 +
Arst Arst5g02614 Chr5 80388839 80391581 +
Arst Arst5g01198 Chr5 12400847 12404274 +
Bach Bach4g00212 Chr4 1375246 1378487 +
Bisa Bisa01g0631 Chr01 9721210 9723184 -
Bva Bva04g01063 Chr04 7013200 7017482 -
Cca Cca06g01743 Chr06 32718007 32731069 -
Dere Dere06g1471 Chr06 27649512 27652730 +
Dod Dod02g3157 Chr02 66556347 66558917 +
Dod Dod02g1029 Chr02 12954007 12957551 -
Enph Enph12g0988 Chr12 16434727 16437478 +
Glsi Glsi01g1679 Chr01 77863972 77867652 +
Gma Gma16g01659 Chr16 37618166 37621595 +
Gso Gso16g1629 Chr16 36950972 36954669 +
Lal Lal2g0783 Chr2 5022196 5025583 +
Lal Lal9g0765 Chr9 5365299 5368621 -
Lapu Lapu2g00310 Chr2 2548147 2551910 +
Lasa Lasa2g02833 Chr2 512207286 512209241 +
Lja Lja2g2459 Chr2 30965123 30968411 +
Lja Lja2g0046 Chr2 371636 374761 +
Mal Mal6g1646 Chr6 30463147 30465848 -
Mepo Mepo7g01090 Chr7 16819249 16824990 -
Mepo Mepo5g00419 Chr5 3701273 3703924 +
Mibi Mibi01g3278 Chr01 57875253 57877928 -
Mtr Mtr5g0354 Chr5 3279739 3282937 +
Phco Phco4g00377 Chr4 2455774 2457978 +
Prci Prci14g2010 Chr14 27554479 27557253 -
Psa Psa2g4117 Chr2 419560693 419561975 -
Pste Pste9g01267 Chr9 11080571 11084057 +
Pste Pste1g00665 Chr1 2101802 2104082 +
Pte Pte9g00265 Chr9 2981168 2986054 -
Pte Pte14g01225 Chr14 33557613 33560831 -
Pumo Pumo6g02717 Chr6 65133998 65138025 +
Pvu Pvu4g1339 Chr4 40180852 40184964 +
Pvu Pvu2g1568 Chr2 29319064 29322815 -
Rops Rops5g00713 Chr5 12539961 12542953 +
Seca Seca10g04271 Chr10 96488632 96492566 +
Spst Spst4g03062 Chr4 69972662 69976409 -
Spst Spst2g00365 Chr2 2860039 2862084 +
Ssu Ssu2g2797 Chr2 88865244 88867105 -
Sto Sto10g2586 Chr10 36150952 36154404 +
Sto Sto8g2989 Chr8 22229728 22232063 -
Tpr Tpr2g3820 Chr2 41034436 41038132 -
Trre Trre11g01521 Chr11 14768382 14772256 +
Trre Trre9g00446 Chr9 3188280 3190955 +
Tsu Tsu05g00331 Chr05 2443624 2446614 +
Vian Vian8g01184 Chr8 30438500 30441405 +
Vifa Vifa1g04002 Chr1 615578705 615582003 -
Vimu Vimu8g01918 Chr8 24828214 24831797 -
Vimu Vimu7g02505 Chr7 21368570 21370966 +
Viun Viun4g02358 Chr4 39067142 39071448 +
Vivi Vivi2g05639 Chr2 184316311 184320288 +
Vivi Vivi2g03908 Chr2 151195178 151197922 -
Vvi Vvi16g0706 Chr16 14333890 14335165 +
Vvi Vvi16g0707 Chr16 14336650 14338025 +
Vvi Vvi16g0708 Chr16 14344649 14351507 -
Aed Aed1g2191 Chr1 18290964 18298615 -
Apr Apr6g0799 Chr6 12461106 12468117 +
Cca Cca02g02330 Chr02 44079121 44086174 +
Gma Gma16g01657 Chr16 37597877 37611672 +
Gso Gso16g1628 Chr16 36942387 36944762 +
Lja Lja5g0579 Chr5 5132106 5138773 -
Mal Mal1g0803 Chr1 9589611 9596948 -
Mtr Mtr1g3837 Chr1 49946545 49954896 +
Ssu Ssu7g0699 Chr7 14109222 14116398 -
Tpr Tpr1g0670 Chr1 5628158 5636605 -
Tsu Tsu01g04507 Chr01 52679199 52687236 +
Vra Vra8g2309 Chr8 41341917 41349454 +