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
Vvi2g0222 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0223 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0224 . . Accr9g00967 . . . . . . Aev03g3170 . Ahy13g2665 . Aip03g03007 Alju09g1473 . . . . Apr2g1300 . . . . Bisa11g0806 . . Bva11g02242 . Car06g00417 . . Dere09g0056 . . Dod04g2856 Enph13g1517 . Glsi05g2220 . . . . Gma08g00239 . . . . . . Lal23g0500 Lal15g1460 . . . . . . . . Lapu3g03686 . Lasa7g04911 . . . . . . . . . Lja4g0311 Lja4g0311 . Mal7g5073 Mepo2g04757 . . . Mibi12g1250 . . Mtr8g3579 Phac2g04517 . Phco4g03414 . Prci10g1244 . . Psa7g0544 Pste3g00754 . . . . . . . Pvu2g3096 . . . . . Spst3g00980 . . . Sto6g3083 . . Tpr3g0532 Trre7g05596 . . Tsu02g00342 . . . . Vimu11g04553 . . . Vivi5g06093 . . .
Vvi2g0225 Acco11g1472 . Accr9g00968 . . . . . . Aev03g3171 . Ahy13g2660 . Aip03g03006 Alju09g1470 . . Amo13g3230 . Apr2g1301 . . Bach4g00024 . Bisa11g0805 . Bva08g00029 Bva11g02243 . Car06g00416 . . Dere09g0054 . . Dod04g2858 Enph13g1518 . Glsi05g2221 . . . Gma05g02133 Gma08g00240 . . . . . . Lal23g0507 . . . . . . . . . Lapu3g03687 . Lasa7g04913 . Lele49g0768 Lele50g0810 Lele51g0792 Lele52g0794 . . . . Lja4g0310 Lja4g0310 . Mal7g5074 Mepo2g04758 . Mesa13g00358 . Mibi12g1249 . . Mtr8g3580 Phac2g04518 . Phco4g03415 . Prci10g1245 . . Psa7g0541 Pste3g00752 . Pte14g01325 Pte12g00012 . . Pumo6g00383 . Pvu2g3097 . Rops2g00425 . Seca12g06618 . Spst3g00979 . . . Sto6g3082 . . Tpr3g0531 Trre7g05597 . . Tsu02g00341 Vian1g03932 . Vifa6g03728 . Vimu11g04555 . Viun3g00428 . Vivi5g06094 . . .
Vvi2g0226 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0227 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0228 Acco11g1471 . Accr9g00969 . . . . . . Aev03g3173 . Ahy13g2657 . Aip03g03002 Alju09g1469 . . Amo13g3226 . Apr2g1302 . . Bach4g00023 . Bisa11g0802 . Bva08g00028 . . Car06g00414 . . Dere09g0052 . . Dod04g2860 Enph13g1519 . Glsi05g2222 . . . Gma05g02135 Gma08g00242 . . . . . . Lal23g0509 . . . . . . . . . Lapu3g03688 . Lasa7g04917 . Lele49g0770 Lele50g0811 Lele51g0793 Lele52g0795 . . . . Lja4g0308 Lja4g0308 . Mal7g5076 Mepo2g04760 . Mesa13g00357 . Mibi12g1248 . . Mtr8g3582 Phac2g04520 . Phco4g03418 . Prci10g1247 . . Psa7g0538 Pste3g00747 . . . . . Pumo6g00381 . Pvu2g3099 . Rops2g00421 . Seca12g06621 . Spst3g00977 . . . Sto6g3081 . . Tpr3g0529 Trre7g05599 . . Tsu02g00339 Vian1g03934 . Vifa6g03729 . Vimu11g04556 . Viun3g00427 . Vivi5g06095 . . .
Vvi2g0229 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0230 . . . . . . . . . Aev03g3177 . Ahy13g2653 . Aip03g02991 . . . Amo13g3222 . Apr2g1304 Arst3g03432 . . . . . . Bva11g02246 . Car06g00411 . . . . . Dod04g2862 . . . . . . Gma05g02137 Gma08g00244 . . . . . . Lal23g0512 Lal15g1462 Lal16g1134 . . . . . . . Lapu3g03691 . . . . . . . . . . . Lja4g0306 Lja4g0306 . Mal7g5078 . . . . . . . Mtr8g3584 Phac2g04525 . Phco4g03420 . . . . . Pste3g00733 . . . . . Pumo6g00377 . Pvu2g3101 . Rops2g00419 . Seca12g06624 . Spst3g00973 . . . . . . Tpr3g0527 . . . Tsu02g00337 Vian1g03936 . . . Vimu11g04560 . Viun3g00425 . . . . .
Vvi2g0231 . . . . . . . . . . . . . . . . . . . Apr2g1305 . . . . . . . . . Car06g00410 . . . . . . . . . . . . Gma05g02138 Gma08g00245 . . . . . . . Lal15g1463 . . . . . . . . . . . . . . . . . . . . Lja4g0305 Lja4g0305 . Mal7g5081 . . . . . . . Mtr8g3587 . . . . . . . Psa7g0536 . . . . . . . . . . . . . . . . . . Sto6g3078 . . Tpr3g0526 . . . Tsu02g00335 . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi2g0222 Chr2 1842611 1843381 +
Vvi Vvi2g0223 Chr2 1850689 1857255 +
Vvi Vvi2g0224 Chr2 1858353 1860290 -
Accr Accr9g00967 Chr9 11310749 11313188 -
Aev Aev03g3170 Chr03 30121991 30129658 -
Ahy Ahy13g2665 Chr13 96673125 96675314 +
Aip Aip03g03007 Chr03 89273286 89275730 +
Alju Alju09g1473 Chr09 38784644 38788260 +
Apr Apr2g1300 Chr2 19183547 19185870 -
Bisa Bisa11g0806 Chr11 23267961 23271738 +
Bva Bva11g02242 Chr11 18103954 18105588 -
Car Car06g00417 Chr06 4346969 4350800 +
Dere Dere09g0056 Chr09 3498001 3514504 +
Dod Dod04g2856 Chr04 52435001 52438238 -
Enph Enph13g1517 Chr13 20609438 20612002 -
Glsi Glsi05g2220 Chr05 68379108 68385987 -
Gma Gma08g00239 Chr08 2020313 2023116 -
Lal Lal23g0500 Chr23 7738954 7743061 -
Lal Lal15g1460 Chr15 16819049 16821709 -
Lapu Lapu3g03686 Chr3 60285448 60289262 -
Lasa Lasa7g04911 Chr7 694443826 694447006 -
Lja Lja4g0311 Chr4 2532927 2536627 +
Lja Lja4g0311 Chr4 2532927 2536627 +
Mal Mal7g5073 Chr7 119853809 119858636 -
Mepo Mepo2g04757 Chr2 55809015 55812981 -
Mibi Mibi12g1250 Chr12 28095915 28105087 +
Mtr Mtr8g3579 Chr8 46356498 46359450 -
Phac Phac2g04517 Chr2 42933466 42936814 -
Phco Phco4g03414 Chr4 54397679 54400490 -
Prci Prci10g1244 Chr10 8168890 8173411 -
Psa Psa7g0544 Chr7 37000604 37004143 +
Pste Pste3g00754 Chr3 4721785 4725469 +
Pvu Pvu2g3096 Chr2 46311623 46315210 -
Spst Spst3g00980 Chr3 13283943 13284970 +
Sto Sto6g3083 Chr6 37827503 37829032 +
Tpr Tpr3g0532 Chr3 5365454 5370236 +
Trre Trre7g05596 Chr7 61456810 61457617 -
Tsu Tsu02g00342 Chr02 2908539 2911757 +
Vimu Vimu11g04553 Chr11 66287995 66292731 -
Vivi Vivi5g06093 Chr5 166014594 166018888 -
Vvi Vvi2g0225 Chr2 1865523 1872460 -
Acco Acco11g1472 Chr11 29271451 29274293 +
Accr Accr9g00968 Chr9 11325407 11328297 -
Aev Aev03g3171 Chr03 30136026 30138556 -
Ahy Ahy13g2660 Chr13 95857256 95860511 +
Aip Aip03g03006 Chr03 88533688 88536982 +
Alju Alju09g1470 Chr09 38717891 38720738 +
Amo Amo13g3230 Chr13 100111782 100115173 +
Apr Apr2g1301 Chr2 19195367 19198898 -
Bach Bach4g00024 Chr4 208495 212070 +
Bisa Bisa11g0805 Chr11 23196546 23199673 +
Bva Bva08g00029 Chr08 158936 162494 +
Bva Bva11g02243 Chr11 18107021 18110510 -
Car Car06g00416 Chr06 4336956 4339706 +
Dere Dere09g0054 Chr09 3471794 3475310 +
Dod Dod04g2858 Chr04 52460087 52462631 -
Enph Enph13g1518 Chr13 20624235 20628044 -
Glsi Glsi05g2221 Chr05 68386129 68391649 -
Gma Gma05g02133 Chr05 42496870 42500256 -
Gma Gma08g00240 Chr08 2040794 2044608 -
Lal Lal23g0507 Chr23 7833952 7838329 -
Lapu Lapu3g03687 Chr3 60300079 60303738 -
Lasa Lasa7g04913 Chr7 694595821 694598092 -
Lele Lele49g0768 Chr49 4665676 4668769 -
Lele Lele50g0810 Chr50 4982454 4985610 -
Lele Lele51g0792 Chr51 4787586 4790691 -
Lele Lele52g0794 Chr52 5036760 5039878 -
Lja Lja4g0310 Chr4 2502591 2505661 +
Lja Lja4g0310 Chr4 2502591 2505661 +
Mal Mal7g5074 Chr7 119879799 119881946 -
Mepo Mepo2g04758 Chr2 55829871 55832604 -
Mesa Mesa13g00358 Chr13 4230343 4232551 +
Mibi Mibi12g1249 Chr12 28082366 28085309 +
Mtr Mtr8g3580 Chr8 46369984 46372758 -
Phac Phac2g04518 Chr2 42948798 42952455 -
Phco Phco4g03415 Chr4 54411097 54413925 -
Prci Prci10g1245 Chr10 8187962 8192052 -
Psa Psa7g0541 Chr7 36549338 36552349 +
Pste Pste3g00752 Chr3 4704668 4708560 +
Pte Pte14g01325 Chr14 34453164 34456557 -
Pte Pte12g00012 Chr12 238006 241310 +
Pumo Pumo6g00383 Chr6 4975129 4979401 +
Pvu Pvu2g3097 Chr2 46326735 46330009 -
Rops Rops2g00425 Chr2 6201750 6203300 +
Seca Seca12g06618 Chr12 158255063 158259160 -
Spst Spst3g00979 Chr3 13271994 13273546 +
Sto Sto6g3082 Chr6 37813911 37816791 +
Tpr Tpr3g0531 Chr3 5354420 5357717 +
Trre Trre7g05597 Chr7 61474762 61476891 -
Tsu Tsu02g00341 Chr02 2892385 2895280 +
Vian Vian1g03932 Chr1 62365903 62368856 -
Vifa Vifa6g03728 Chr6 1224979661 1224981989 -
Vimu Vimu11g04555 Chr11 66302530 66305483 -
Viun Viun3g00428 Chr3 2592915 2596342 +
Vivi Vivi5g06094 Chr5 166061203 166063965 -
Vvi Vvi2g0226 Chr2 1877529 1878322 -
Vvi Vvi2g0227 Chr2 1882314 1882942 -
Vvi Vvi2g0228 Chr2 1885570 1889062 -
Acco Acco11g1471 Chr11 29260832 29263778 +
Accr Accr9g00969 Chr9 11335092 11338029 -
Aev Aev03g3173 Chr03 30145889 30148492 -
Ahy Ahy13g2657 Chr13 94612441 94615903 +
Aip Aip03g03002 Chr03 87467982 87474325 +
Alju Alju09g1469 Chr09 38710474 38713392 +
Amo Amo13g3226 Chr13 99018713 99021932 +
Apr Apr2g1302 Chr2 19208463 19211524 -
Bach Bach4g00023 Chr4 204823 207810 +
Bisa Bisa11g0802 Chr11 23133373 23136258 +
Bva Bva08g00028 Chr08 154686 157882 +
Car Car06g00414 Chr06 4322501 4325768 +
Dere Dere09g0052 Chr09 3455860 3458785 +
Dod Dod04g2860 Chr04 52473665 52476938 -
Enph Enph13g1519 Chr13 20630263 20634044 -
Glsi Glsi05g2222 Chr05 68391872 68394720 -
Gma Gma05g02135 Chr05 42512054 42514847 -
Gma Gma08g00242 Chr08 2065383 2068464 -
Lal Lal23g0509 Chr23 7887890 7892560 -
Lapu Lapu3g03688 Chr3 60316755 60320523 -
Lasa Lasa7g04917 Chr7 694848345 694851381 -
Lele Lele49g0770 Chr49 4671487 4674364 -
Lele Lele50g0811 Chr50 4988503 4991371 -
Lele Lele51g0793 Chr51 4794347 4797232 -
Lele Lele52g0795 Chr52 5040161 5046397 -
Lja Lja4g0308 Chr4 2493117 2496244 +
Lja Lja4g0308 Chr4 2493117 2496244 +
Mal Mal7g5076 Chr7 119897179 119900289 -
Mepo Mepo2g04760 Chr2 55845663 55849355 -
Mesa Mesa13g00357 Chr13 4193373 4196430 +
Mibi Mibi12g1248 Chr12 28075366 28078313 +
Mtr Mtr8g3582 Chr8 46383451 46387016 -
Phac Phac2g04520 Chr2 42964036 42967098 -
Phco Phco4g03418 Chr4 54424979 54427458 -
Prci Prci10g1247 Chr10 8197914 8201548 -
Psa Psa7g0538 Chr7 36468193 36471386 +
Pste Pste3g00747 Chr3 4676824 4680084 +
Pumo Pumo6g00381 Chr6 4946267 4946659 +
Pvu Pvu2g3099 Chr2 46340499 46343469 -
Rops Rops2g00421 Chr2 6190350 6193861 +
Seca Seca12g06621 Chr12 158265273 158269018 -
Spst Spst3g00977 Chr3 13242888 13245407 +
Sto Sto6g3081 Chr6 37803887 37809503 +
Tpr Tpr3g0529 Chr3 5342048 5345642 +
Trre Trre7g05599 Chr7 61484935 61488452 -
Tsu Tsu02g00339 Chr02 2883941 2887649 +
Vian Vian1g03934 Chr1 62387080 62389575 -
Vifa Vifa6g03729 Chr6 1225255586 1225259127 -
Vimu Vimu11g04556 Chr11 66326255 66329084 -
Viun Viun3g00427 Chr3 2579973 2582875 +
Vivi Vivi5g06095 Chr5 166086375 166090340 -
Vvi Vvi2g0229 Chr2 1895553 1899925 +
Vvi Vvi2g0230 Chr2 1900899 1904576 +
Aev Aev03g3177 Chr03 30165137 30168476 +
Ahy Ahy13g2653 Chr13 94251466 94255005 -
Aip Aip03g02991 Chr03 87154013 87161208 -
Amo Amo13g3222 Chr13 98703899 98707732 -
Apr Apr2g1304 Chr2 19226688 19231486 +
Arst Arst3g03432 Chr3 85422266 85425433 +
Bva Bva11g02246 Chr11 18121018 18125112 +
Car Car06g00411 Chr06 4284946 4288968 -
Dod Dod04g2862 Chr04 52496854 52500914 +
Gma Gma05g02137 Chr05 42528829 42532967 +
Gma Gma08g00244 Chr08 2081392 2084946 +
Lal Lal23g0512 Chr23 7912995 7916977 +
Lal Lal15g1462 Chr15 16834293 16838474 +
Lal Lal16g1134 Chr16 7692502 7696449 -
Lapu Lapu3g03691 Chr3 60338005 60342117 +
Lja Lja4g0306 Chr4 2478710 2482215 -
Lja Lja4g0306 Chr4 2478710 2482215 -
Mal Mal7g5078 Chr7 119929964 119933224 +
Mtr Mtr8g3584 Chr8 46404105 46407553 +
Phac Phac2g04525 Chr2 42998280 43002209 +
Phco Phco4g03420 Chr4 54438468 54441837 +
Pste Pste3g00733 Chr3 4620505 4623939 -
Pumo Pumo6g00377 Chr6 4920752 4924842 -
Pvu Pvu2g3101 Chr2 46357082 46360857 +
Rops Rops2g00419 Chr2 6145480 6159371 -
Seca Seca12g06624 Chr12 158302547 158306781 +
Spst Spst3g00973 Chr3 13204132 13207574 -
Tpr Tpr3g0527 Chr3 5327625 5331444 -
Tsu Tsu02g00337 Chr02 2871296 2874708 -
Vian Vian1g03936 Chr1 62401040 62404362 +
Vimu Vimu11g04560 Chr11 66342494 66345919 +
Viun Viun3g00425 Chr3 2563288 2567656 -
Vvi Vvi2g0231 Chr2 1905770 1913702 -
Apr Apr2g1305 Chr2 19231503 19238843 -
Car Car06g00410 Chr06 4275755 4283610 +
Gma Gma05g02138 Chr05 42534303 42540436 -
Gma Gma08g00245 Chr08 2086639 2092657 -
Lal Lal15g1463 Chr15 16842599 16851755 -
Lja Lja4g0305 Chr4 2470839 2477435 +
Lja Lja4g0305 Chr4 2470839 2477435 +
Mal Mal7g5081 Chr7 119942312 119948976 -
Mtr Mtr8g3587 Chr8 46430177 46437682 -
Psa Psa7g0536 Chr7 36255095 36265235 +
Sto Sto6g3078 Chr6 37784755 37793729 +
Tpr Tpr3g0526 Chr3 5317239 5326603 +
Tsu Tsu02g00335 Chr02 2837762 2844575 +
Aev Aev03g3177 Chr03 30165137 30168476 +
Ahy Ahy13g2653 Chr13 94251466 94255005 -
Aip Aip03g02991 Chr03 87154013 87161208 -
Amo Amo13g3222 Chr13 98703899 98707732 -
Dod Dod04g2862 Chr04 52496854 52500914 +
Vivi Vivi5g06094 Chr5 166061203 166063965 -