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
Vvi2g0512 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0513 . . . . . . . . . . . . . . . . . . . Apr10g1444 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0514 . . . . . . . . Aev05g0923 . Ahy15g0937 Ahy11g1419 Aip05g00963 Aip01g01532 . . . Amo11g1428 Apr7g0640 . . . . . . . Bva08g00244 Bva11g02049 . . . . . . Dod02g1031 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja2g0044 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto6g3315 . . . . . . . . . . . . . . . . . . .
Vvi2g0515 . . . . . . . . . . . Ahy11g1417 . Aip01g01531 . . . Amo11g1427 . . . . . . . . Bva08g00246 . . . . . . . . Dod05g1420 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0516 . . . . . . . . . Aev01g0292 . Ahy11g1415 . Aip01g01529 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lal16g1255 . . . . . . . . . . . . . . . . . . . . . . Mal5g3912 . . . . . . . Mtr4g3632 . . . . . . . . . . . . . . . . . . . . . . . . . . Sto6g3316 . . Tpr5g2687 . . . Tsu04g02438 . . . . . . . . . . . .
Vvi2g0517 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0518 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0519 . . . . Adu05g00962 . Aed11g1670 . Aev05g0922 . Ahy15g0938 Ahy11g1414 Aip05g00964 Aip01g01526 . . . . Apr7g0641 . Arst5g01197 . Bach4g00211 . . . Bva08g00247 Bva11g02048 Car08g00259 . Cca06g01745 . . . Dod02g1030 . . . . . Gma01g02149 Gma11g00257 . . Gso1g1818 Gso1g1818 . . Lal15g0286 . . . Lal16g1256 Lal23g1203 Lan18g0882 . . . Lan18g0882 Lan18g0882 Lapu2g00309 . . . . . . . . . . . Lja2g0045 . Mal6g1647 . Mepo5g00418 . Mesa17g00420 . . . Mtr5g0353 . Phac2g00539 . Phco4g00375 . . . Psa2g4118 . Pste1g00660 . . . . . Pumo8g02255 . Pvu2g1569 . Rops1g02121 . Seca10g00404 . Spst2g00364 . Ssu2g2798 . Sto6g3317 . Tpr2g3823 . Trre9g00443 . Tsu05g00330 . Vian10g00322 . Vifa1g07807 . Vimu7g02504 . Viun2g02502 . Vivi2g03784 . Vra11g0329 .
Vvi2g0520 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0521 . . . . Adu05g00965 . Aed11g1667 . Aev05g0919 . Ahy15g0941 Ahy11g1404 Aip05g00968 Aip01g01517 . . . Amo11g1412 . . Arst5g01200 . Bach4g00214 . . . Bva08g00250 Bva11g02043 Car08g00262 . Cca06g01742 . . . Dod02g1027 . . . . . Gma01g02146 Gma11g00260 . . Gso1g1815 Gso1g1815 . . Lal15g0283 . . . Lal16g1258 Lal23g1206 Lan18g0884 . . . Lan18g0884 Lan18g0884 Lapu2g00312 . Lasa2g02835 . . . . . . . . . Lja2g0048 . Mal6g1644 . Mepo5g00422 . Mesa17g00423 . . . Mtr5g0356 . Phac2g00542 . Phco4g00380 . . . Psa2g4115 . Pste1g00671 . . . . . Pumo8g02252 . Pvu2g1566 . Rops1g02118 . Seca10g00407 . Spst2g00368 . Ssu2g2795 . Sto6g3321 . Tpr2g3818 . Trre9g00448 . Tsu05g00333 . Vian10g00325 . Vifa1g07804 . Vimu7g02508 . Viun2g02496 . Vivi2g03779 . Vra11g0332 .
   
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Select Species Gene Chromosome Start End Strand
Car Car08g00262 Chr08 2100624 2102996 -
Vvi Vvi2g0512 Chr2 4414166 4417327 -
Vvi Vvi2g0513 Chr2 4421651 4422503 +
Apr Apr10g1444 Chr10 26824510 26827803 -
Vvi Vvi2g0514 Chr2 4424613 4425671 +
Aev Aev05g0923 Chr05 6515845 6516921 -
Ahy Ahy15g0937 Chr15 13983829 13985632 +
Ahy Ahy11g1419 Chr11 55692205 55694040 -
Aip Aip05g00963 Chr05 13502051 13507928 +
Aip Aip01g01532 Chr01 52425738 52427540 -
Amo Amo11g1428 Chr11 52613925 52615747 -
Apr Apr7g0640 Chr7 13127184 13128620 +
Bva Bva08g00244 Chr08 1177548 1179165 +
Bva Bva11g02049 Chr11 17220265 17221678 -
Dod Dod02g1031 Chr02 12972224 12975516 -
Lja Lja2g0044 Chr2 360943 361998 +
Sto Sto6g3315 Chr6 39348333 39349406 +
Vvi Vvi2g0515 Chr2 4428884 4429428 -
Ahy Ahy11g1417 Chr11 55592350 55593206 +
Aip Aip01g01531 Chr01 52339137 52340178 +
Amo Amo11g1427 Chr11 52486156 52487012 +
Bva Bva08g00246 Chr08 1180160 1180747 -
Dod Dod05g1420 Chr05 38543006 38544207 -
Vvi Vvi2g0516 Chr2 4431533 4434153 +
Aev Aev01g0292 Chr01 2396361 2399714 -
Ahy Ahy11g1415 Chr11 55261060 55263960 -
Aip Aip01g01529 Chr01 52033884 52036677 -
Lal Lal16g1255 Chr16 8790832 8800026 +
Mal Mal5g3912 Chr5 108484198 108486732 +
Mtr Mtr4g3632 Chr4 50090672 50093711 +
Sto Sto6g3316 Chr6 39352861 39355711 +
Tpr Tpr5g2687 Chr5 49100241 49102557 +
Tsu Tsu04g02438 Chr04 27481060 27483284 +
Vvi Vvi2g0517 Chr2 4434338 4436260 -
Vvi Vvi2g0518 Chr2 4439115 4439825 +
Vvi Vvi2g0519 Chr2 4445309 4451539 -
Adu Adu05g00962 Chr05 12348441 12353284 -
Aed Aed11g1670 Chr11 20486939 20491771 +
Aev Aev05g0922 Chr05 6508360 6512812 +
Ahy Ahy15g0938 Chr15 13991337 13996412 -
Ahy Ahy11g1414 Chr11 55184981 55190039 +
Aip Aip05g00964 Chr05 13509576 13515448 -
Aip Aip01g01526 Chr01 51959035 51964551 +
Apr Apr7g0641 Chr7 13132546 13138213 -
Arst Arst5g01197 Chr5 12392131 12396975 -
Bach Bach4g00211 Chr4 1364588 1369994 -
Bva Bva08g00247 Chr08 1184122 1189214 -
Bva Bva11g02048 Chr11 17213244 17219292 +
Car Car08g00259 Chr08 2079089 2085785 -
Cca Cca06g01745 Chr06 32744001 32751509 +
Dod Dod02g1030 Chr02 12964854 12970988 +
Gma Gma01g02149 Chr01 56805832 56811460 +
Gma Gma11g00257 Chr11 2034145 2040174 -
Gso Gso1g1818 Chr1 54981661 54987854 +
Gso Gso1g1818 Chr1 54981661 54987854 +
Lal Lal15g0286 Chr15 1929730 1934571 +
Lal Lal16g1256 Chr16 8800188 8806828 -
Lal Lal23g1203 Chr23 13335493 13340958 -
Lan Lan18g0882 Chr18 14130402 14135747 -
Lan Lan18g0882 Chr18 14130402 14135747 -
Lan Lan18g0882 Chr18 14130402 14135747 -
Lapu Lapu2g00309 Chr2 2538876 2545946 -
Lja Lja2g0045 Chr2 363142 368778 -
Mal Mal6g1647 Chr6 30474634 30480635 +
Mepo Mepo5g00418 Chr5 3684545 3689918 -
Mesa Mesa17g00420 Chr17 4833506 4838389 -
Mtr Mtr5g0353 Chr5 3268269 3273993 -
Phac Phac2g00539 Chr2 2689539 2696232 -
Phco Phco4g00375 Chr4 2445413 2451462 -
Psa Psa2g4118 Chr2 419577111 419583923 +
Pste Pste1g00660 Chr1 2080939 2087383 -
Pumo Pumo8g02255 Chr8 59692475 59698157 +
Pvu Pvu2g1569 Chr2 29327680 29334136 +
Rops Rops1g02121 Chr1 42461808 42467970 +
Seca Seca10g00404 Chr10 3519103 3525651 -
Spst Spst2g00364 Chr2 2850734 2856607 -
Ssu Ssu2g2798 Chr2 88876956 88883281 +
Sto Sto6g3317 Chr6 39356618 39362171 -
Tpr Tpr2g3823 Chr2 41046740 41052395 +
Trre Trre9g00443 Chr9 3178731 3184790 -
Tsu Tsu05g00330 Chr05 2434427 2440011 -
Vian Vian10g00322 Chr10 2925818 2931820 -
Vifa Vifa1g07807 Chr1 1219237634 1219241410 -
Vimu Vimu7g02504 Chr7 21359073 21365197 -
Viun Viun2g02502 Chr2 31401003 31407366 +
Vivi Vivi2g03784 Chr2 149050617 149054603 +
Vra Vra11g0329 Chr11 2362163 2368597 -
Vvi Vvi2g0520 Chr2 4454773 4455858 -
Vvi Vvi2g0521 Chr2 4470392 4474788 -
Adu Adu05g00965 Chr05 12365754 12368273 -
Aed Aed11g1667 Chr11 20472910 20474711 +
Aev Aev05g0919 Chr05 6488541 6490835 +
Ahy Ahy15g0941 Chr15 14010091 14013310 -
Ahy Ahy11g1404 Chr11 54387635 54391061 +
Aip Aip05g00968 Chr05 13529176 13532385 -
Aip Aip01g01517 Chr01 51275711 51279165 +
Amo Amo11g1412 Chr11 51611397 51614902 +
Arst Arst5g01200 Chr5 12409554 12411950 -
Bach Bach4g00214 Chr4 1384401 1387797 -
Bva Bva08g00250 Chr08 1203363 1206795 -
Bva Bva11g02043 Chr11 17197600 17201061 +
Car Car08g00262 Chr08 2100624 2102996 -
Cca Cca06g01742 Chr06 32711424 32714257 +
Dod Dod02g1027 Chr02 12942537 12944355 +
Gma Gma01g02146 Chr01 56785065 56788745 +
Gma Gma11g00260 Chr11 2053824 2057454 -
Gso Gso1g1815 Chr1 54961332 54965070 +
Gso Gso1g1815 Chr1 54961332 54965070 +
Lal Lal15g0283 Chr15 1916346 1920094 +
Lal Lal16g1258 Chr16 8825561 8829610 -
Lal Lal23g1206 Chr23 13353002 13360367 -
Lan Lan18g0884 Chr18 14144057 14147623 -
Lan Lan18g0884 Chr18 14144057 14147623 -
Lan Lan18g0884 Chr18 14144057 14147623 -
Lapu Lapu2g00312 Chr2 2560280 2562833 -
Lasa Lasa2g02835 Chr2 512224223 512226552 -
Lja Lja2g0048 Chr2 383213 386065 -
Mal Mal6g1644 Chr6 30405392 30406463 +
Mepo Mepo5g00422 Chr5 3711334 3712835 -
Mesa Mesa17g00423 Chr17 4857184 4858822 -
Mtr Mtr5g0356 Chr5 3289799 3291711 -
Phac Phac2g00542 Chr2 2711834 2714697 -
Phco Phco4g00380 Chr4 2467682 2471662 -
Psa Psa2g4115 Chr2 419529757 419532800 +
Pste Pste1g00671 Chr1 2115490 2119171 -
Pumo Pumo8g02252 Chr8 59661413 59665160 +
Pvu Pvu2g1566 Chr2 29306400 29309666 +
Rops Rops1g02118 Chr1 42415043 42418733 +
Seca Seca10g00407 Chr10 3542975 3546431 -
Spst Spst2g00368 Chr2 2870320 2873143 -
Ssu Ssu2g2795 Chr2 88849859 88853624 +
Sto Sto6g3321 Chr6 39378469 39381986 -
Tpr Tpr2g3818 Chr2 41021694 41023318 +
Trre Trre9g00448 Chr9 3198752 3200471 -
Tsu Tsu05g00333 Chr05 2452977 2454906 -
Vian Vian10g00325 Chr10 2948808 2951334 -
Vifa Vifa1g07804 Chr1 1218912641 1218915431 +
Vimu Vimu7g02508 Chr7 21380202 21382667 -
Viun Viun2g02496 Chr2 31374283 31377112 +
Vivi Vivi2g03779 Chr2 149026728 149029549 +
Vra Vra11g0332 Chr11 2382825 2385941 -
Apr Apr10g1444 Chr10 26824510 26827803 -