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
Vvi17g1063 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g1064 . . . . . . Aed7g0382 . . . . . . . . . . . Apr6g0903 . Arst5g02828 . Bach1g01359 . . . Bva04g00979 . . . Cca08g00408 . . . . . . . . . . . . Gma09g01549 . . . . Lal8g0509 Lal10g0907 Lal25g0520 . . . Lan10g0494 Lan10g0494 Lan10g0494 . . . Lapu4g00367 . Lasa1g02212 . . . . . . . . . Lja2g2336 . . Mal6g3540 Mepo7g00710 . Mesa22g02924 . . . . Mtr6g2016 . . Phco5g00450 . . . . . Pste9g01347 . . . . . Pumo6g02840 . Pvu4g1470 . Rops5g00540 . Seca10g04523 . Spst4g02950 . . . . . . Tpr2g5151 Trre11g01783 . . Tsu06g03509 Vian8g01294 . Vifa1g03694 . Vimu8g01771 . Viun4g00598 . Vivi2g05840 . Vra1g0792 .
Vvi17g1065 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g1066 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g1067 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g1068 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja2g2335 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g1069 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g1070 . . Accr10g01982 . . . Aed7g0381 . . . . . . . Alju12g2076 . . . Apr6g0904 . . . . . . . Bva04g00978 . . . Cca08g00407 . Dere13g2100 . . . . . . . . . . Gma09g01550 . . . . . . . . . . . . . . . . . . . . Lele53g1449 Lele54g1440 . . . . . . Lja2g2334 . . Mal6g3537 . . . . Mibi10g2025 . . Mtr6g2015 . . Phco8g03357 . Prci5g2477 . . . Pste1g03810 . . . . . . . Pvu3g0068 . . . . . . . . . . Sto10g2719 . Tpr2g5153 . . . Tsu06g03512 . . Vifa1g03684 . Vimu11g00060 . . . . . Vra1g0791 .
Vvi17g1071 Acco12g0014 . . . . . . . . . . . . . . . . . . . . . . . Bisa01g0983 . . . . . . . . . . . Enph14g0621 . . . . . . . . . . . Lal8g0508 . . . . . Lan10g0493 . . . . . . . . . . . Lele55g0018 . . . . . Lja2g2332 . . . . . . . . . . . . . Phco8g03358 . . . . . Pste1g03811 . . . . . . . Pvu3g0067 . . . . . Spst2g02203 . . . . Sto10g2720 . . . . . . . . . . . . . . . . . .
Vvi17g1072 . . . . . . Aed7g0379 . . . . . . . . . . . Apr6g0906 . Arst5g02835 . Bach1g01361 . . . . . . . Cca08g00405 . . . . . . . . . . . . Gma09g01552 . . . . . Lal10g0909 Lal25g0518 . . . . . . . . . Lapu4g00364 . Lasa1g02204 . . . . . . . . . Lja2g2329 . . Mal6g3535 Mepo7g00715 . Mesa22g02919 . . . . Mtr6g2012 . . . . . . . . Pste9g01351 . Pte16g00243 . . . Pumo6g02843 . Pvu4g1474 . Rops5g00516 . Seca10g04527 . Spst4g02947 . . . . . . Tpr2g5159 Trre11g01791 . . Tsu06g03523 Vian8g01297 . Vifa1g03679 . Vimu8g01763 . Viun4g00593 . Vivi2g05845 . Vra1g0789 .
   
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Select Species Gene Chromosome Start End Strand
Mal Mal6g3537 Chr6 104257201 104262692 -
Mtr Mtr6g2015 Chr6 36596290 36602144 -
Tpr Tpr2g5153 Chr2 57641961 57648265 +
Tsu Tsu06g03512 Chr06 46271218 46277373 +
Aed Aed7g0382 Chr7 2841897 2848739 -
Apr Apr6g0903 Chr6 13455988 13464616 +
Arst Arst5g02828 Chr5 83711215 83716509 +
Bach Bach1g01359 Chr1 27052408 27063027 +
Cca Cca08g00408 Chr08 6203018 6211554 -
Lapu Lapu4g00367 Chr4 3741810 3750520 -
Lasa Lasa1g02212 Chr1 246475026 246480418 -
Mepo Mepo7g00710 Chr7 11474532 11482248 +
Mesa Mesa22g02924 Chr22 77427866 77433097 -
Phco Phco5g00450 Chr5 4135655 4142984 -
Pste Pste9g01347 Chr9 12228681 12236785 +
Pumo Pumo6g02840 Chr6 67906588 67911108 +
Pvu Pvu4g1470 Chr4 41749709 41757514 +
Rops Rops5g00540 Chr5 8904025 8912219 -
Seca Seca10g04523 Chr10 103314687 103321793 +
Spst Spst4g02950 Chr4 69122475 69129577 -
Trre Trre11g01783 Chr11 17383656 17388940 +
Vian Vian8g01294 Chr8 31827330 31834113 +
Vifa Vifa1g03694 Chr1 571428480 571430556 -
Vimu Vimu8g01771 Chr8 23587845 23596127 -
Viun Viun4g00598 Chr4 3915753 3923107 -
Vivi Vivi2g05840 Chr2 188201768 188207567 +
Vra Vra1g0792 Chr1 9408084 9415694 -
Vvi Vvi17g1063 Chr17 14231694 14232077 +
Vvi Vvi17g1064 Chr17 14285204 14293195 -
Aed Aed7g0382 Chr7 2841897 2848739 -
Apr Apr6g0903 Chr6 13455988 13464616 +
Arst Arst5g02828 Chr5 83711215 83716509 +
Bach Bach1g01359 Chr1 27052408 27063027 +
Bva Bva04g00979 Chr04 6420675 6429434 -
Cca Cca08g00408 Chr08 6203018 6211554 -
Gma Gma09g01549 Chr09 40586436 40594535 +
Lal Lal8g0509 Chr8 3492333 3500162 -
Lal Lal10g0907 Chr10 16506457 16513595 +
Lal Lal25g0520 Chr25 3711888 3717632 -
Lan Lan10g0494 Chr10 3848790 3856536 -
Lan Lan10g0494 Chr10 3848790 3856536 -
Lan Lan10g0494 Chr10 3848790 3856536 -
Lapu Lapu4g00367 Chr4 3741810 3750520 -
Lasa Lasa1g02212 Chr1 246475026 246480418 -
Lja Lja2g2336 Chr2 28045943 28055274 -
Mal Mal6g3540 Chr6 104285685 104293013 -
Mepo Mepo7g00710 Chr7 11474532 11482248 +
Mesa Mesa22g02924 Chr22 77427866 77433097 -
Mtr Mtr6g2016 Chr6 36620685 36628667 -
Phco Phco5g00450 Chr5 4135655 4142984 -
Pste Pste9g01347 Chr9 12228681 12236785 +
Pumo Pumo6g02840 Chr6 67906588 67911108 +
Pvu Pvu4g1470 Chr4 41749709 41757514 +
Rops Rops5g00540 Chr5 8904025 8912219 -
Seca Seca10g04523 Chr10 103314687 103321793 +
Spst Spst4g02950 Chr4 69122475 69129577 -
Tpr Tpr2g5151 Chr2 57554614 57562184 +
Trre Trre11g01783 Chr11 17383656 17388940 +
Tsu Tsu06g03509 Chr06 46216296 46223477 +
Vian Vian8g01294 Chr8 31827330 31834113 +
Vifa Vifa1g03694 Chr1 571428480 571430556 -
Vimu Vimu8g01771 Chr8 23587845 23596127 -
Viun Viun4g00598 Chr4 3915753 3923107 -
Vivi Vivi2g05840 Chr2 188201768 188207567 +
Vra Vra1g0792 Chr1 9408084 9415694 -
Vvi Vvi17g1065 Chr17 14375280 14376733 +
Vvi Vvi17g1066 Chr17 14377221 14377898 -
Vvi Vvi17g1067 Chr17 14378171 14378419 +
Vvi Vvi17g1068 Chr17 14425971 14430643 +
Lja Lja2g2335 Chr2 28029221 28034598 -
Vvi Vvi17g1069 Chr17 14461861 14465916 -
Vvi Vvi17g1070 Chr17 14475366 14480298 +
Accr Accr10g01982 Chr10 44450265 44453934 +
Aed Aed7g0381 Chr7 2833468 2838644 -
Alju Alju12g2076 Chr12 41616354 41620061 +
Apr Apr6g0904 Chr6 13469308 13474223 +
Bva Bva04g00978 Chr04 6414090 6418088 -
Cca Cca08g00407 Chr08 6169897 6175527 -
Dere Dere13g2100 Chr13 28304205 28304792 +
Gma Gma09g01550 Chr09 40602677 40607227 +
Lele Lele53g1449 Chr53 22321666 22325137 +
Lele Lele54g1440 Chr54 19024818 19030571 +
Lja Lja2g2334 Chr2 27978734 27983787 -
Mal Mal6g3537 Chr6 104257201 104262692 -
Mibi Mibi10g2025 Chr10 43420503 43424524 +
Mtr Mtr6g2015 Chr6 36596290 36602144 -
Phco Phco8g03357 Chr8 48175962 48179602 -
Prci Prci5g2477 Chr5 41243399 41247075 +
Pste Pste1g03810 Chr1 18892163 18895967 -
Pvu Pvu3g0068 Chr3 631300 635614 +
Sto Sto10g2719 Chr10 37405795 37410834 +
Tpr Tpr2g5153 Chr2 57641961 57648265 +
Tsu Tsu06g03512 Chr06 46271218 46277373 +
Vifa Vifa1g03684 Chr1 569430000 569458640 +
Vimu Vimu11g00060 Chr11 534079 537196 +
Vra Vra1g0791 Chr1 9375476 9380047 -
Vvi Vvi17g1071 Chr17 14485402 14485884 +
Acco Acco12g0014 Chr12 211896 215554 -
Bisa Bisa01g0983 Chr01 16564290 16568427 -
Enph Enph14g0621 Chr14 8257968 8260644 -
Lal Lal8g0508 Chr8 3485509 3490092 -
Lan Lan10g0493 Chr10 3819522 3824207 -
Lele Lele55g0018 Chr55 150767 154220 -
Lja Lja2g2332 Chr2 27959715 27964702 -
Phco Phco8g03358 Chr8 48180990 48184783 -
Pste Pste1g03811 Chr1 18907425 18912350 -
Pvu Pvu3g0067 Chr3 626299 630130 +
Spst Spst2g02203 Chr2 21190854 21193920 -
Sto Sto10g2720 Chr10 37420560 37425388 +
Vvi Vvi17g1072 Chr17 14509292 14517801 -
Aed Aed7g0379 Chr7 2820622 2826384 -
Apr Apr6g0906 Chr6 13484819 13490670 +
Arst Arst5g02835 Chr5 83770024 83775865 +
Bach Bach1g01361 Chr1 27074446 27080692 +
Cca Cca08g00405 Chr08 6148679 6153504 -
Gma Gma09g01552 Chr09 40619642 40625172 +
Lal Lal10g0909 Chr10 16521205 16532692 +
Lal Lal25g0518 Chr25 3695011 3702960 -
Lapu Lapu4g00364 Chr4 3700647 3706728 -
Lasa Lasa1g02204 Chr1 245372705 245380430 -
Lja Lja2g2329 Chr2 27916903 27922746 -
Mal Mal6g3535 Chr6 104229007 104237196 -
Mepo Mepo7g00715 Chr7 11541772 11548908 +
Mesa Mesa22g02919 Chr22 77373996 77380493 -
Mtr Mtr6g2012 Chr6 36573269 36580440 -
Pste Pste9g01351 Chr9 12261420 12267969 +
Pte Pte16g00243 Chr16 2972737 2979197 +
Pumo Pumo6g02843 Chr6 67944039 67950264 +
Pvu Pvu4g1474 Chr4 41795376 41801185 +
Rops Rops5g00516 Chr5 8658214 8665289 -
Seca Seca10g04527 Chr10 103407346 103413900 +
Spst Spst4g02947 Chr4 69089746 69094984 -
Tpr Tpr2g5159 Chr2 57685994 57692637 +
Trre Trre11g01791 Chr11 17469127 17475195 +
Tsu Tsu06g03523 Chr06 46352642 46359568 +
Vian Vian8g01297 Chr8 31903651 31908975 +
Vifa Vifa1g03679 Chr1 568422765 568433862 -
Vimu Vimu8g01763 Chr8 23528291 23533580 -
Viun Viun4g00593 Chr4 3862033 3868059 -
Vivi Vivi2g05845 Chr2 188290769 188298236 +
Vra Vra1g0789 Chr1 9340805 9346762 -