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
Vvi19g0540 . . . . . . Aed1g0738 . Aev10g2302 . Ahy18g1042 . Aip08g01089 . . . . . . . . . . . . . . . Car01g02150 . Cca10g00965 . . . Dod10g1141 . . . . . . . Gma12g02006 Gma13g02553 . . . . Lal9g0387 . . . Lal1g0492 . Lan8g1535 . . . Lan8g1535 . . . Lasa1g05148 . . . . . . . . . . . . . Mepo6g03280 . Mesa5g01252 . . . Mtr2g2775 . . . . . . . . Psa5g6072 Pste3g02608 . . Pte15g01922 . . . . Pvu5g0964 . . . . . Spst5g00969 . Ssu8g1009 . . . Tpr7g3673 . . . Tsu02g04573 . . . . . . . . . . . . .
Vvi19g0541 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g0542 . Acco08g0901 . Accr13g00884 . Adu03g01578 . Aed5g0992 . . . Ahy13g1702 . Aip03g01913 . Alju10g0919 . . . . . Arst3g02079 . Bach9g00610 . Bisa02g3096 . Bva07g01890 . . . Cca04g01241 . . . Dod03g1976 . . . Glsi04g0956 Gma06g02505 . . . Gso6g2255 . . . . . Lal2g0527 . . . . . . . . . . . . Lasa7g02720 . . . . . . . Lele32g0662 Lja3g3843 . . . . Mepo2g02844 . Mesa13g02196 . Mibi07g0891 . . . . . Phco9g01566 . Prci6g1073 . . . Pste1g03692 . . . . . Pumo11g00924 . Pvu11g1417 . Rops3g01625 . Seca4g04713 . Spst11g00809 . . . . . . . Trre7g02150 . . . Vian5g00631 . Vifa6g01577 . . . Viun11g01118 . Vivi5g03487 . .
Vvi19g0543 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lal5g0801 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g0544 . . . . . . Aed1g0743 . . . . . . . . . . . . . . . . . . . . Bva07g01897 Car01g02162 . Cca10g00953 . . . . . . . . . . . Gma12g01999 Gma13g02561 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal4g0905 . . . . . . . Mtr2g2793 . . . . . . . . . . . . . . . . . . . . . . . . . Ssu8g0987 . . . Tpr7g3687 . . . Tsu02g04593 . . . . . . . . . . . . .
Vvi19g0545 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g0546 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g0547 . . . . Adu04g00364 Adu07g00361 Aed3g2474 Aed4g2533 Aev07g0271 Aev01g1827 Ahy17g0466 Ahy11g0161 Aip07g00405 Aip01g00150 . . . Amo11g0016 Apr2g0129 Apr9g1711 Arst4g00597 Arst7g00538 . Bach3g00819 . Bisa05g2181 Bva12g02779 . Car02g02014 Car05g00944 Cca05g01907 Cca09g01037 . . Dod08g0328 Dod05g0289 . . . Glsi10g2121 Gma08g02935 Gma18g00911 Gma02g02715 Gma14g00224 Gso8g2592 Gso8g2592 Gso8g2592 Gso8g2592 Lal18g1548 Lal22g0090 . . . Lal11g1031 Lan2g1289 Lan2g1289 . . . Lan2g1289 Lapu6g01578 . Lasa1g00962 . . . . . . . . . . Lja6g2393 . . Mepo6g00880 . Mesa5g03781 . . . . . . . Phco11g00787 Phco3g00289 . . . . Pste2g02508 Pste8g00509 Pte9g01095 . . . Pumo2g00385 . Pvu6g1576 Pvu8g2738 Rops11g01017 Rops9g00388 Seca6g04489 Seca6g03089 Spst6g01160 Spst8g00841 Ssu6g3427 Ssu9g0879 Sto9g1851 Sto5g1977 . . Trre3g00949 . . . Vian6g01447 Vian7g01229 Vifa1g09981 . Vimu2g01074 Vimu1g00472 Viun6g02325 Viun8g02768 Vivi5g00045 . Vra6g0271 Vra6g0271
Vvi19g0548 . . . . . . . . . Aev01g1828 . Ahy11g0160 . Aip01g00149 . . . Amo11g0017 Apr2g0130 . . . . . . . Bva12g02778 . . Car05g00945 . . . . . Dod05g0288 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja6g1451 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto9g1852 Sto10g0429 . . . . . . . . . . . . . . . . . .
Vvi19g0549 . . . . . . . . . . . . . . . . . . Apr2g0132 . . . . . . . . . . . . . . . . . . . . . Gma08g02937 . Gma02g02716 Gma14g00223 Gso8g2593 . Gso8g2593 Gso8g2593 Lal18g1549 . . . . . Lan2g1290 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco3g00288 . . . . . . . . . Pte8g00085 . . . Pvu8g2739 . . . . . Spst8g00842 . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Acco Acco08g0901 Chr08 8273104 8282103 -
Accr Accr13g00884 Chr13 10171245 10176209 -
Aed Aed1g0743 Chr1 8474810 8478100 -
Alju Alju10g0919 Chr10 8523573 8528614 -
Bva Bva07g01897 Chr07 16982040 16984708 -
Car Car01g02162 Chr01 47276386 47279973 -
Cca Cca10g00953 Chr10 11052403 11057878 +
Gma Gma12g01999 Chr12 40587964 40592329 +
Gma Gma13g02561 Chr13 40468343 40473010 -
Lele Lele32g0662 Chr32 4162559 4167296 -
Mal Mal4g0905 Chr4 11643711 11648073 +
Mibi Mibi07g0891 Chr07 11556072 11561215 -
Mtr Mtr2g2793 Chr2 41327373 41331817 -
Prci Prci6g1073 Chr6 7472179 7477441 -
Ssu Ssu8g0987 Chr8 16767012 16771401 +
Tpr Tpr7g3687 Chr7 45619696 45623349 -
Tsu Tsu02g04593 Chr02 54867683 54870573 -
Lal Lal9g0387 Chr9 2559705 2566312 -
Lan Lan8g1535 Chr8 22433763 22440151 +
Lan Lan8g1535 Chr8 22433763 22440151 +
Psa Psa5g6072 Chr5 520434252 520440512 -
Sto Sto5g1977 Chr5 14812404 14815682 -
Vvi Vvi19g0540 Chr19 6077196 6084779 +
Aed Aed1g0738 Chr1 8427880 8432811 +
Aev Aev10g2302 Chr10 22987503 22991140 -
Ahy Ahy18g1042 Chr18 15162890 15167518 -
Aip Aip08g01089 Chr08 14357208 14361893 -
Car Car01g02150 Chr01 47126165 47148920 +
Cca Cca10g00965 Chr10 11237434 11242671 -
Dod Dod10g1141 Chr10 30783543 30790848 +
Gma Gma12g02006 Chr12 40648552 40660751 -
Gma Gma13g02553 Chr13 40418599 40422716 +
Lal Lal9g0387 Chr9 2559705 2566312 -
Lal Lal1g0492 Chr1 3113759 3118186 +
Lan Lan8g1535 Chr8 22433763 22440151 +
Lan Lan8g1535 Chr8 22433763 22440151 +
Lasa Lasa1g05148 Chr1 830967657 830970515 +
Mepo Mepo6g03280 Chr6 44763927 44767868 +
Mesa Mesa5g01252 Chr5 17784143 17787777 -
Mtr Mtr2g2775 Chr2 41097510 41101132 +
Psa Psa5g6072 Chr5 520434252 520440512 -
Pste Pste3g02608 Chr3 19030992 19037998 +
Pte Pte15g01922 Chr15 25228915 25245807 -
Pvu Pvu5g0964 Chr5 27672525 27674096 +
Spst Spst5g00969 Chr5 9294958 9296865 -
Ssu Ssu8g1009 Chr8 17178828 17190492 -
Tpr Tpr7g3673 Chr7 45493154 45497883 +
Tsu Tsu02g04573 Chr02 54761894 54766356 +
Vvi Vvi19g0541 Chr19 6093124 6093480 +
Vvi Vvi19g0542 Chr19 6105858 6115641 -
Acco Acco08g0901 Chr08 8273104 8282103 -
Accr Accr13g00884 Chr13 10171245 10176209 -
Adu Adu03g01578 Chr03 24987688 24996053 +
Aed Aed5g0992 Chr5 7816399 7824003 +
Ahy Ahy13g1702 Chr13 26551141 26560672 +
Aip Aip03g01913 Chr03 25532088 25541098 +
Alju Alju10g0919 Chr10 8523573 8528614 -
Arst Arst3g02079 Chr3 25258104 25280473 +
Bach Bach9g00610 Chr9 4228668 4235645 +
Bisa Bisa02g3096 Chr02 78663830 78672993 +
Bva Bva07g01890 Chr07 16947956 16955380 -
Cca Cca04g01241 Chr04 14914269 14922692 +
Dod Dod03g1976 Chr03 44672891 44693608 -
Glsi Glsi04g0956 Chr04 7672205 7682690 -
Gma Gma06g02505 Chr06 47656977 47667299 -
Gso Gso6g2255 Chr6 43604798 43614392 -
Lal Lal2g0527 Chr2 3172179 3177805 +
Lasa Lasa7g02720 Chr7 543282462 543292102 +
Lele Lele32g0662 Chr32 4162559 4167296 -
Lja Lja3g3843 Chr3 75689796 75700259 -
Mepo Mepo2g02844 Chr2 38207944 38217119 +
Mesa Mesa13g02196 Chr13 25750911 25760170 -
Mibi Mibi07g0891 Chr07 11556072 11561215 -
Phco Phco9g01566 Chr9 36515203 36528962 +
Prci Prci6g1073 Chr6 7472179 7477441 -
Pste Pste1g03692 Chr1 17893131 17903943 +
Pumo Pumo11g00924 Chr11 33427368 33432714 -
Pvu Pvu11g1417 Chr11 31597868 31609856 +
Rops Rops3g01625 Chr3 25252176 25263192 +
Seca Seca4g04713 Chr4 87689520 87702346 -
Spst Spst11g00809 Chr11 32114267 32121099 -
Trre Trre7g02150 Chr7 17074524 17082361 +
Vian Vian5g00631 Chr5 22833226 22854886 -
Vifa Vifa6g01577 Chr6 579041361 579043665 -
Viun Viun11g01118 Chr11 24278146 24289024 -
Vivi Vivi5g03487 Chr5 126884742 126892429 +
Vvi Vvi19g0543 Chr19 6129791 6131282 +
Lal Lal5g0801 Chr5 8153156 8156039 -
Vvi Vvi19g0544 Chr19 6133045 6134532 +
Aed Aed1g0743 Chr1 8474810 8478100 -
Bva Bva07g01897 Chr07 16982040 16984708 -
Car Car01g02162 Chr01 47276386 47279973 -
Cca Cca10g00953 Chr10 11052403 11057878 +
Gma Gma12g01999 Chr12 40587964 40592329 +
Gma Gma13g02561 Chr13 40468343 40473010 -
Mal Mal4g0905 Chr4 11643711 11648073 +
Mtr Mtr2g2793 Chr2 41327373 41331817 -
Ssu Ssu8g0987 Chr8 16767012 16771401 +
Tpr Tpr7g3687 Chr7 45619696 45623349 -
Tsu Tsu02g04593 Chr02 54867683 54870573 -
Vvi Vvi19g0545 Chr19 6135227 6137647 -
Vvi Vvi19g0546 Chr19 6147162 6148837 +
Vvi Vvi19g0547 Chr19 6153315 6156621 +
Adu Adu04g00364 Chr04 4225232 4227799 +
Adu Adu07g00361 Chr07 3430884 3434547 -
Aed Aed3g2474 Chr3 27312682 27314936 +
Aed Aed4g2533 Chr4 27260225 27265417 +
Aev Aev07g0271 Chr07 1525846 1529299 -
Aev Aev01g1827 Chr01 23273133 23276892 +
Ahy Ahy17g0466 Chr17 4505648 4509310 -
Ahy Ahy11g0161 Chr11 1646828 1650096 -
Aip Aip07g00405 Chr07 3455263 3459004 -
Aip Aip01g00150 Chr01 1528721 1531942 -
Amo Amo11g0016 Chr11 123361 126880 +
Apr Apr2g0129 Chr2 1899242 1903046 +
Apr Apr9g1711 Chr9 26295509 26299681 -
Arst Arst4g00597 Chr4 4199237 4201878 +
Arst Arst7g00538 Chr7 3581404 3585013 -
Bach Bach3g00819 Chr3 19108129 19111892 +
Bisa Bisa05g2181 Chr05 49220941 49224841 -
Bva Bva12g02779 Chr12 20148469 20152152 -
Car Car02g02014 Chr02 50606484 50607378 +
Car Car05g00944 Chr05 49565565 49570292 +
Cca Cca05g01907 Chr05 38907803 38913015 +
Cca Cca09g01037 Chr09 30922421 30925795 -
Dod Dod08g0328 Chr08 3561907 3565635 -
Dod Dod05g0289 Chr05 3620339 3624862 -
Glsi Glsi10g2121 Chr10 16293000 16296842 -
Gma Gma08g02935 Chr08 45778124 45782790 -
Gma Gma18g00911 Chr18 10748626 10752492 +
Gma Gma02g02715 Chr02 52869275 52873010 +
Gma Gma14g00224 Chr14 1905267 1908952 -
Gso Gso8g2592 Chr8 43507183 43511803 -
Gso Gso8g2592 Chr8 43507183 43511803 -
Gso Gso8g2592 Chr8 43507183 43511803 -
Gso Gso8g2592 Chr8 43507183 43511803 -
Lal Lal18g1548 Chr18 17215962 17220464 +
Lal Lal22g0090 Chr22 558598 563198 -
Lal Lal11g1031 Chr11 13905485 13913352 -
Lan Lan2g1289 Chr2 23829605 23833015 +
Lan Lan2g1289 Chr2 23829605 23833015 +
Lan Lan2g1289 Chr2 23829605 23833015 +
Lapu Lapu6g01578 Chr6 15617604 15620542 +
Lasa Lasa1g00962 Chr1 77709362 77711098 +
Lja Lja6g2393 Chr6 52828876 52853561 +
Mepo Mepo6g00880 Chr6 9075781 9078139 +
Mesa Mesa5g03781 Chr5 65584994 65586165 -
Phco Phco11g00787 Chr11 5702340 5704428 +
Phco Phco3g00289 Chr3 2066764 2070474 -
Pste Pste2g02508 Chr2 25368319 25377236 +
Pste Pste8g00509 Chr8 2640673 2644089 -
Pte Pte9g01095 Chr9 32576296 32581227 +
Pumo Pumo2g00385 Chr2 6714192 6717094 -
Pvu Pvu6g1576 Chr6 26470971 26473964 -
Pvu Pvu8g2738 Chr8 57654293 57658813 +
Rops Rops11g01017 Chr11 14732829 14735803 +
Rops Rops9g00388 Chr9 5225106 5229306 -
Seca Seca6g04489 Chr6 112386864 112390833 -
Seca Seca6g03089 Chr6 97012262 97016669 -
Spst Spst6g01160 Chr6 10670453 10672351 +
Spst Spst8g00841 Chr8 7544694 7551679 +
Ssu Ssu6g3427 Chr6 76910154 76915128 +
Ssu Ssu9g0879 Chr9 38021834 38025269 -
Sto Sto9g1851 Chr9 22918906 22921413 +
Sto Sto5g1977 Chr5 14812404 14815682 -
Trre Trre3g00949 Chr3 6786625 6787745 +
Vian Vian6g01447 Chr6 32028801 32030605 -
Vian Vian7g01229 Chr7 20492557 20495858 -
Vifa Vifa1g09981 Chr1 1638127193 1638128926 -
Vimu Vimu2g01074 Chr2 7031579 7032166 +
Vimu Vimu1g00472 Chr1 2859344 2861461 -
Viun Viun6g02325 Chr6 28614360 28616639 -
Viun Viun8g02768 Chr8 36235641 36238575 +
Vivi Vivi5g00045 Chr5 426694 429025 -
Vra Vra6g0271 Chr6 2004774 2008068 -
Vra Vra6g0271 Chr6 2004774 2008068 -
Vvi Vvi19g0548 Chr19 6158588 6161928 -
Aev Aev01g1828 Chr01 23280521 23284098 -
Ahy Ahy11g0160 Chr11 1640571 1644748 +
Aip Aip01g00149 Chr01 1522470 1526660 +
Amo Amo11g0017 Chr11 128726 132876 -
Apr Apr2g0130 Chr2 1907463 1912368 -
Bva Bva12g02778 Chr12 20143406 20147025 +
Car Car05g00945 Chr05 49573019 49577410 -
Dod Dod05g0288 Chr05 3612084 3617096 +
Lja Lja6g1451 Chr6 40247815 40251280 +
Sto Sto9g1852 Chr9 22924399 22928234 -
Sto Sto10g0429 Chr10 3456778 3457092 +
Vvi Vvi19g0549 Chr19 6167525 6169106 +
Apr Apr2g0132 Chr2 1947448 1950209 +
Gma Gma08g02937 Chr08 45809096 45812484 +
Gma Gma02g02716 Chr02 52876192 52877965 +
Gma Gma14g00223 Chr14 1895057 1896797 -
Gso Gso8g2593 Chr8 43538044 43541598 +
Gso Gso8g2593 Chr8 43538044 43541598 +
Gso Gso8g2593 Chr8 43538044 43541598 +
Lal Lal18g1549 Chr18 17225446 17227328 +
Lan Lan2g1290 Chr2 23836165 23838968 +
Phco Phco3g00288 Chr3 2056774 2058438 -
Pte Pte8g00085 Chr8 1739022 1741205 -
Pvu Pvu8g2739 Chr8 57665957 57667856 +
Spst Spst8g00842 Chr8 7551843 7557129 +