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
Vvi2g0552 . . . . Adu05g00985 . Aed11g1651 . Aev05g0904 . Ahy15g0962 . Aip05g00992 . . . . . Apr7g0659 . Arst5g01229 . Bach4g00234 . . . Bva08g00275 Bva11g02020 Car08g00278 . Cca06g01725 . . . Dod02g1010 . . . . . Gma01g02128 Gma11g00277 . . Gso1g1799 Gso1g1799 . . Lal15g0275 Lal16g0341 . . . Lal23g1214 Lan18g0893 Lan18g0893 . . . Lan18g0893 Lapu2g00328 . . . . . . . . . . . Lja2g0072 . Mal6g1616 . Mepo5g00441 . Mesa17g00452 . . . Mtr5g0380 . Phac2g00998 . . . . . Psa2g4088 . Pste1g00775 . . . . . Pumo8g02232 . Pvu2g0624 . Rops1g02096 . Seca10g00429 . . . Ssu2g2777 . . Sto11g1988 Tpr2g3801 . Trre9g00469 . Tsu05g00349 . Vian10g00341 . Vifa1g07772 . Vimu7g02528 . Viun2g02477 . Vivi2g03741 . Vra11g0348 .
Vvi2g0553 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0554 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva08g00277 Bva11g02018 . . . . . . . . . . . . . . . . . . . . . . . . Lal16g1273 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto6g3347 . . . . . . . . . . . . . . . . . . .
Vvi2g0555 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0556 . . . . . Adu02g02222 . . Aev05g0903 . Ahy15g0963 . Aip05g00993 . . . . . Apr7g0661 . . Arst2g02878 . Bach6g00828 . . Bva08g00278 Bva11g02017 . . . . . . Dod02g1008 . . . . . Gma01g01421 . . . Gso1g1178 . . . . . . . Lal16g1274 . . . . . . . . Lapu10g01478 . Lasa7g00621 . . . . . . . . Lja2g0073 . Mal6g1613 . . Mepo2g00738 . Mesa13g04668 . . Mtr5g0385 . . . . Phco1g00972 . . Psa2g4086 . . Pste6g02452 . . Pte1g00743 . . Pumo7g01039 . Pvu10g0856 . Rops4g01257 . Seca4g11078 . Spst4g01651 . . . Sto11g1980 Tpr2g3798 . . Trre7g00720 . . . . . Vifa2g05105 . Vimu9g00607 . Viun10g01600 . Vivi5g01080 . .
Vvi2g0557 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0558 . . . . . Adu02g02195 . Aed6g0510 . . . . . . . . . . . Apr10g1571 . Arst2g02834 . Bach6g00850 . . . . . . . Cca11g01642 . . . . . . . . Gma01g01402 . Gma05g00532 Gma17g01282 Gso1g1163 . Gso1g1163 Gso1g1163 . . . . . . . . . . . . . . . Lasa7g00637 . . . . . . . . . . . . . Mepo2g00779 . Mesa13g04606 . . . . . . . Phco1g01004 . . . . . Pste6g02503 . . Pte1g00749 . . . . Pvu10g0828 . Rops4g01203 . Seca4g11044 . Spst4g01626 . Ssu6g1586 . . . . . Trre7g00754 . . . . . Vifa2g05087 . Vimu9g00663 . Viun10g01548 . . . .
Vvi2g0559 . . . . . . . Aed6g0511 . . . Ahy11g1392 . Aip01g01504 . . . . Apr7g0668 . . . . . . . Bva08g00289 Bva11g02009 Car08g00286 Car07g01213 . Cca11g01641 . . . Dod05g1406 . . . . . Gma11g00282 Gma05g00533 Gma17g01283 . . . . Lal15g0271 Lal16g0334 . Lal15g0879 Lal16g0913 . Lan18g0896 Lan18g0896 . Lan18g0896 Lan18g0896 . . . . . . . . . . . . . Lja2g0080 Lja4g2515 Mal6g1604 Mal5g3902 . . . . . . Mtr5g0396 Mtr4g3623 . . . . . . Psa2g4072 Psa4g1619 . . . . . . . . . . . . . . . . . Ssu6g1587 Sto6g3355 . Tpr2g3790 Tpr5g2680 . . Tsu05g00360 Tsu04g02428 . . . . . . . . . . . Vra7g1407
Vvi2g0560 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0561 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi2g0552 Chr2 4762059 4762502 +
Adu Adu05g00985 Chr05 12925470 12925913 +
Aed Aed11g1651 Chr11 20369519 20369962 -
Aev Aev05g0904 Chr05 6381012 6386251 -
Ahy Ahy15g0962 Chr15 14553638 14554487 +
Aip Aip05g00992 Chr05 14072872 14073315 +
Apr Apr7g0659 Chr7 13345121 13346050 +
Arst Arst5g01229 Chr5 12968930 12969944 +
Bach Bach4g00234 Chr4 1520777 1521675 +
Bva Bva08g00275 Chr08 1329130 1330615 +
Bva Bva11g02020 Chr11 17081237 17082329 -
Car Car08g00278 Chr08 2203463 2204908 +
Cca Cca06g01725 Chr06 32552300 32553864 -
Dod Dod02g1010 Chr02 12776063 12776506 -
Gma Gma01g02128 Chr01 56640717 56644088 -
Gma Gma11g00277 Chr11 2201244 2203295 +
Gso Gso1g1799 Chr1 54825871 54826863 -
Gso Gso1g1799 Chr1 54825871 54826863 -
Lal Lal15g0275 Chr15 1863624 1865081 -
Lal Lal16g0341 Chr16 2050658 2053542 -
Lal Lal23g1214 Chr23 13410744 13413363 +
Lan Lan18g0893 Chr18 14212235 14213057 +
Lan Lan18g0893 Chr18 14212235 14213057 +
Lan Lan18g0893 Chr18 14212235 14213057 +
Lapu Lapu2g00328 Chr2 2697478 2697921 +
Lja Lja2g0072 Chr2 540742 541609 +
Mal Mal6g1616 Chr6 30033154 30033597 -
Mepo Mepo5g00441 Chr5 3873517 3874420 +
Mesa Mesa17g00452 Chr17 5246637 5247080 +
Mtr Mtr5g0380 Chr5 3490163 3491091 +
Phac Phac2g00998 Chr2 6461873 6463242 -
Psa Psa2g4088 Chr2 418707010 418710046 -
Pste Pste1g00775 Chr1 2432692 2433135 +
Pumo Pumo8g02232 Chr8 59456431 59457902 -
Pvu Pvu2g0624 Chr2 6500779 6501668 +
Rops Rops1g02096 Chr1 42007322 42008239 -
Seca Seca10g00429 Chr10 3756838 3757281 +
Ssu Ssu2g2777 Chr2 88557616 88558059 -
Sto Sto11g1988 Chr11 18656771 18668447 -
Tpr Tpr2g3801 Chr2 40887616 40888478 -
Trre Trre9g00469 Chr9 3374316 3374759 +
Tsu Tsu05g00349 Chr05 2590101 2591314 +
Vian Vian10g00341 Chr10 3100636 3101079 +
Vifa Vifa1g07772 Chr1 1213234298 1213234741 -
Vimu Vimu7g02528 Chr7 21514212 21515894 +
Viun Viun2g02477 Chr2 31243565 31244468 -
Vivi Vivi2g03741 Chr2 147916022 147916879 -
Vra Vra11g0348 Chr11 2505883 2506940 +
Vvi Vvi2g0553 Chr2 4766746 4768165 -
Vvi Vvi2g0554 Chr2 4768873 4781701 -
Bva Bva08g00277 Chr08 1335191 1338670 -
Bva Bva11g02018 Chr11 17071891 17075800 +
Lal Lal16g1273 Chr16 8963758 8970267 -
Sto Sto6g3347 Chr6 39552213 39557240 -
Vvi Vvi2g0555 Chr2 4784126 4784920 +
Vvi Vvi2g0556 Chr2 4802232 4802906 -
Adu Adu02g02222 Chr02 86731846 86734268 +
Aev Aev05g0903 Chr05 6378094 6379434 +
Ahy Ahy15g0963 Chr15 14570602 14572272 -
Aip Aip05g00993 Chr05 14085418 14088820 -
Apr Apr7g0661 Chr7 13356142 13358405 -
Arst Arst2g02878 Chr2 86193434 86195778 +
Bach Bach6g00828 Chr6 6250299 6251594 -
Bva Bva08g00278 Chr08 1340599 1342629 -
Bva Bva11g02017 Chr11 17068568 17070398 +
Dod Dod02g1008 Chr02 12766326 12768860 +
Gma Gma01g01421 Chr01 48928564 48930169 -
Gso Gso1g1178 Chr1 47248372 47250569 -
Lal Lal16g1274 Chr16 8974765 8977253 -
Lapu Lapu10g01478 Chr10 24702561 24704951 +
Lasa Lasa7g00621 Chr7 27597744 27599066 -
Lja Lja2g0073 Chr2 544696 546591 -
Mal Mal6g1613 Chr6 29988015 29990014 +
Mepo Mepo2g00738 Chr2 8904401 8906670 -
Mesa Mesa13g04668 Chr13 74203933 74205255 +
Mtr Mtr5g0385 Chr5 3536362 3538865 -
Phco Phco1g00972 Chr1 10020205 10021503 -
Psa Psa2g4086 Chr2 418676903 418679633 +
Pste Pste6g02452 Chr6 12083635 12084951 -
Pte Pte1g00743 Chr1 10668799 10669821 -
Pumo Pumo7g01039 Chr7 19752039 19754391 -
Pvu Pvu10g0856 Chr10 30539512 30541938 +
Rops Rops4g01257 Chr4 33458069 33460354 +
Seca Seca4g11078 Chr4 249083590 249084906 +
Spst Spst4g01651 Chr4 56168292 56169608 +
Sto Sto11g1980 Chr11 18631500 18632825 +
Tpr Tpr2g3798 Chr2 40871099 40872787 +
Trre Trre7g00720 Chr7 4707013 4708335 -
Vifa Vifa2g05105 Chr2 1526947872 1526949194 +
Vimu Vimu9g00607 Chr9 7420972 7422270 +
Viun Viun10g01600 Chr10 30931019 30933452 +
Vivi Vivi5g01080 Chr5 26741929 26744358 +
Vvi Vvi2g0557 Chr2 4810829 4811634 -
Vvi Vvi2g0558 Chr2 4822703 4823194 -
Adu Adu02g02195 Chr02 86378727 86379200 +
Aed Aed6g0510 Chr6 4361644 4362009 -
Apr Apr10g1571 Chr10 28166241 28166645 -
Arst Arst2g02834 Chr2 85839780 85840907 +
Bach Bach6g00850 Chr6 6381632 6382144 -
Cca Cca11g01642 Chr11 40425910 40426308 +
Gma Gma01g01402 Chr01 48599365 48600584 +
Gma Gma05g00532 Chr05 5076973 5077338 -
Gma Gma17g01282 Chr17 11334427 11334789 -
Gso Gso1g1163 Chr1 46929716 46931037 +
Gso Gso1g1163 Chr1 46929716 46931037 +
Gso Gso1g1163 Chr1 46929716 46931037 +
Lasa Lasa7g00637 Chr7 29730764 29731249 -
Mepo Mepo2g00779 Chr2 9460377 9461692 -
Mesa Mesa13g04606 Chr13 73130312 73130809 +
Phco Phco1g01004 Chr1 10355916 10356401 -
Pste Pste6g02503 Chr6 12361734 12362429 -
Pte Pte1g00749 Chr1 11183364 11184718 -
Pvu Pvu10g0828 Chr10 29678795 29679931 +
Rops Rops4g01203 Chr4 32573380 32573874 +
Seca Seca4g11044 Chr4 248449065 248449559 +
Spst Spst4g01626 Chr4 55898841 55899347 +
Ssu Ssu6g1586 Chr6 26109637 26109942 -
Trre Trre7g00754 Chr7 4937003 4937503 -
Vifa Vifa2g05087 Chr2 1521648172 1521648660 +
Vimu Vimu9g00663 Chr9 8241975 8242472 -
Viun Viun10g01548 Chr10 30541320 30542403 +
Vvi Vvi2g0559 Chr2 4836974 4839409 +
Aed Aed6g0511 Chr6 4377598 4378236 +
Ahy Ahy11g1392 Chr11 53546892 53552193 -
Aip Aip01g01504 Chr01 50522722 50525378 -
Apr Apr7g0668 Chr7 13434893 13439226 +
Bva Bva08g00289 Chr08 1398719 1402690 +
Bva Bva11g02009 Chr11 17027465 17031400 -
Car Car08g00286 Chr08 2247947 2258802 +
Car Car07g01213 Chr07 10920974 10926437 +
Cca Cca11g01641 Chr11 40398455 40404278 -
Dod Dod05g1406 Chr05 38393362 38399123 -
Gma Gma11g00282 Chr11 2240632 2242381 +
Gma Gma05g00533 Chr05 5093059 5096337 +
Gma Gma17g01283 Chr17 11353781 11356902 +
Lal Lal15g0271 Chr15 1846100 1851591 -
Lal Lal16g0334 Chr16 2019732 2025386 -
Lal Lal15g0879 Chr15 6622410 6628717 +
Lal Lal16g0913 Chr16 6015043 6018917 -
Lan Lan18g0896 Chr18 14250968 14254839 +
Lan Lan18g0896 Chr18 14250968 14254839 +
Lan Lan18g0896 Chr18 14250968 14254839 +
Lan Lan18g0896 Chr18 14250968 14254839 +
Lja Lja2g0080 Chr2 612602 613854 +
Lja Lja4g2515 Chr4 31072483 31075878 +
Mal Mal6g1604 Chr6 29880534 29882319 -
Mal Mal5g3902 Chr5 108348725 108352606 -
Mtr Mtr5g0396 Chr5 3589359 3593832 +
Mtr Mtr4g3623 Chr4 49992724 49998952 -
Psa Psa2g4072 Chr2 418417175 418420027 -
Psa Psa4g1619 Chr4 113445518 113450081 -
Ssu Ssu6g1587 Chr6 26170701 26173397 +
Sto Sto6g3355 Chr6 39615701 39616944 +
Tpr Tpr2g3790 Chr2 40813734 40818242 -
Tpr Tpr5g2680 Chr5 49028428 49033981 -
Tsu Tsu05g00360 Chr05 2685527 2687380 +
Tsu Tsu04g02428 Chr04 27371134 27375123 -
Vra Vra7g1407 Chr7 31278585 31284517 -
Vvi Vvi2g0560 Chr2 4841365 4841723 -
Vvi Vvi2g0561 Chr2 4846174 4851301 -
Adu Adu02g02222 Chr02 86731846 86734268 +
Arst Arst2g02878 Chr2 86193434 86195778 +
Bach Bach6g00828 Chr6 6250299 6251594 -
Lapu Lapu10g01478 Chr10 24702561 24704951 +
Lasa Lasa7g00621 Chr7 27597744 27599066 -
Mepo Mepo2g00738 Chr2 8904401 8906670 -
Mesa Mesa13g04668 Chr13 74203933 74205255 +
Phco Phco1g00972 Chr1 10020205 10021503 -
Pste Pste6g02452 Chr6 12083635 12084951 -
Pte Pte1g00743 Chr1 10668799 10669821 -
Pumo Pumo7g01039 Chr7 19752039 19754391 -
Pvu Pvu10g0856 Chr10 30539512 30541938 +
Rops Rops4g01257 Chr4 33458069 33460354 +
Seca Seca4g11078 Chr4 249083590 249084906 +
Spst Spst4g01651 Chr4 56168292 56169608 +
Trre Trre7g00720 Chr7 4707013 4708335 -
Vifa Vifa2g05105 Chr2 1526947872 1526949194 +
Vimu Vimu9g00607 Chr9 7420972 7422270 +
Viun Viun10g01600 Chr10 30931019 30933452 +
Vivi Vivi5g01080 Chr5 26741929 26744358 +
Adu Adu02g02195 Chr02 86378727 86379200 +
Arst Arst2g02834 Chr2 85839780 85840907 +
Bach Bach6g00850 Chr6 6381632 6382144 -
Gma Gma17g01282 Chr17 11334427 11334789 -
Gma Gma05g00532 Chr05 5076973 5077338 -
Lasa Lasa7g00637 Chr7 29730764 29731249 -
Mepo Mepo2g00779 Chr2 9460377 9461692 -
Mesa Mesa13g04606 Chr13 73130312 73130809 +
Phco Phco1g01004 Chr1 10355916 10356401 -
Pste Pste6g02503 Chr6 12361734 12362429 -
Pte Pte1g00749 Chr1 11183364 11184718 -
Pvu Pvu10g0828 Chr10 29678795 29679931 +
Rops Rops4g01203 Chr4 32573380 32573874 +
Seca Seca4g11044 Chr4 248449065 248449559 +
Spst Spst4g01626 Chr4 55898841 55899347 +
Trre Trre7g00754 Chr7 4937003 4937503 -
Vifa Vifa2g05087 Chr2 1521648172 1521648660 +
Vimu Vimu9g00663 Chr9 8241975 8242472 -
Viun Viun10g01548 Chr10 30541320 30542403 +
Lja Lja2g0080 Chr2 612602 613854 +
Mal Mal6g1604 Chr6 29880534 29882319 -
Mtr Mtr5g0396 Chr5 3589359 3593832 +
Psa Psa2g4072 Chr2 418417175 418420027 -
Tpr Tpr2g3790 Chr2 40813734 40818242 -
Tsu Tsu05g00360 Chr05 2685527 2687380 +
Aev Aev05g0903 Chr05 6378094 6379434 +
Ahy Ahy15g0963 Chr15 14570602 14572272 -
Aip Aip05g00993 Chr05 14085418 14088820 -
Dod Dod02g1008 Chr02 12766326 12768860 +
Lja Lja2g0073 Chr2 544696 546591 -
Mal Mal6g1613 Chr6 29988015 29990014 +
Mtr Mtr5g0385 Chr5 3536362 3538865 -
Psa Psa2g4086 Chr2 418676903 418679633 +
Tpr Tpr2g3798 Chr2 40871099 40872787 +
Car Car07g01213 Chr07 10920974 10926437 +