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
Vvi4g0994 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva13g03543 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja4g3313 . Mal5g3565 . . . . . . . Mtr8g2602 . . Phco3g02664 . . . . . Pste5g01211 . . Pte8g00602 . . Pumo5g00168 . Pvu8g0560 . Rops8g00985 . Seca2g00878 . Spst1g01152 . . . . . . Tpr4g4071 . . . Tsu04g03285 . . . . Vimu6g00630 . Viun5g00777 . . . . .
Vvi4g0995 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva13g03544 Bva04g03463 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu1g01476 . Lasa3g02049 . . . . . . . . . Lja1g3024 . . Mal1g1247 . . Mesa25g01973 . . . . Mtr1g2773 Phac8g00798 . Phco3g02666 . . . . . Pste5g01206 . . . . . Pumo5g00167 . Pvu8g0557 . . . Seca2g00877 . Spst1g01154 . . . . . . . Trre13g02393 . . Tsu01g03248 Vian2g00534 . Vifa5g01619 . Vimu6g00633 . Viun5g00773 . Vivi6g02952 . . .
Vvi4g0996 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva13g03545 Bva04g03464 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu1g01475 . Lasa3g02051 . . . . . . . . . Lja1g3023 Lja5g1651 . . Mepo3g02245 . Mesa25g01972 . . . . . . . Phco3g02668 . . . . . Pste5g01204 . . . . . Pumo5g00165 . Pvu8g0556 . Rops8g00984 . Seca2g00876 . Spst1g01155 . . . . . . . Trre13g02391 . . . Vian2g00533 . Vifa5g01621 . Vimu6g00636 . Viun5g00770 . Vivi6g02954 . . .
Vvi4g0997 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva04g03466 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu1g01474 . Lasa3g02052 . . . . . . . . . Lja1g3022 . . . . . . . . . . . . . Phco3g02670 . . . . . Pste5g01202 . . . . . Pumo5g00164 . Pvu8g0555 . Rops8g00983 . Seca2g00875 . Spst1g01157 . . . . . . . . . . . Vian2g00532 . Vifa5g01624 . Vimu6g00637 . Viun5g00768 . Vivi6g02955 . . .
Vvi4g0998 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva04g03467 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja1g3021 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g0999 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva13g03546 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu1g01472 . Lasa3g02056 . . . . . . . . . Lja1g3020 . . . Mepo3g02248 . Mesa25g01969 . . . . . . . Phco3g02672 . . . . . Pste5g01200 . . . . . Pumo5g00162 . Pvu8g0553 . Rops8g00981 . . . Spst1g01159 . . . . . . . Trre13g02387 . . . Vian2g00530 . . . Vimu6g00639 . Viun5g00766 . Vivi6g02958 . . .
Vvi4g1000 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva13g03547 Bva04g03468 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu1g01471 . Lasa3g02057 . . . . . . . . . Lja1g3019 . . . Mepo3g02249 . Mesa25g01967 . . . . . . . Phco3g02673 . . . . . Pste5g01199 . . Pte8g00603 . . Pumo5g00161 . Pvu8g0552 . Rops8g00980 . Seca2g00872 . Spst1g01160 . . . . . . . Trre13g02386 . . . Vian2g00529 . . . Vimu6g00640 . Viun5g00765 . Vivi6g02959 . . .
Vvi4g1001 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva13g03548 Bva04g03469 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu1g01470 . Lasa3g02059 . . . . . . . . . Lja1g3018 . . . Mepo3g02250 . Mesa25g01966 . . . . . . . Phco3g02674 . . . . . Pste5g01197 . . . . . Pumo5g00160 . Pvu8g0551 . Rops8g00979 . Seca2g00871 . Spst1g01161 . . . . . . . Trre13g02385 . . . Vian2g00528 . Vifa5g01632 . Vimu6g00641 . Viun5g00764 . Vivi6g02961 . . .
Vvi4g1002 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva13g03549 Bva04g03470 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu1g01469 . Lasa3g02060 . . . . . . . . . Lja1g3016 . . . Mepo3g02251 . Mesa25g01965 . . . . . . . Phco3g02675 . . . . . Pste5g01193 . . . . . . . Pvu8g0550 . . . . . Spst1g01162 . . . . . . . Trre13g02382 . . . . . Vifa5g01634 . Vimu6g00642 . Viun5g00762 . . . . .
Vvi4g1003 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cca06g01416 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ssu2g2441 . . . . . . . . . . . . . . . . . . . Vra11g0623 .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi4g0994 Chr4 16545729 16553455 +
Bva Bva13g03543 Chr13 23971583 23974983 +
Lja Lja4g3313 Chr4 62589730 62594378 +
Mal Mal5g3565 Chr5 101648546 101652801 +
Mtr Mtr8g2602 Chr8 36551497 36555937 +
Phco Phco3g02664 Chr3 53203568 53207233 +
Pste Pste5g01211 Chr5 7852587 7856794 -
Pte Pte8g00602 Chr8 28564217 28570313 +
Pumo Pumo5g00168 Chr5 4589264 4594554 -
Pvu Pvu8g0560 Chr8 4927443 4931485 -
Rops Rops8g00985 Chr8 20978234 20984819 -
Seca Seca2g00878 Chr2 13565845 13573697 -
Spst Spst1g01152 Chr1 13866074 13869725 +
Tpr Tpr4g4071 Chr4 47506257 47510480 -
Tsu Tsu04g03285 Chr04 41954040 41958039 -
Vimu Vimu6g00630 Chr6 7468513 7471798 +
Viun Viun5g00777 Chr5 4860332 4864405 -
Vvi Vvi4g0995 Chr4 16561528 16562030 -
Bva Bva13g03544 Chr13 23976405 23979669 -
Bva Bva04g03463 Chr04 27451588 27456489 -
Lapu Lapu1g01476 Chr1 27560801 27563068 +
Lasa Lasa3g02049 Chr3 520701875 520702321 -
Lja Lja1g3024 Chr1 36619521 36620921 +
Mal Mal1g1247 Chr1 15769367 15769754 +
Mesa Mesa25g01973 Chr25 24376969 24377528 +
Mtr Mtr1g2773 Chr1 38919489 38920126 +
Phac Phac8g00798 Chr8 5197780 5200667 +
Phco Phco3g02666 Chr3 53223794 53224303 -
Pste Pste5g01206 Chr5 7804493 7805982 +
Pumo Pumo5g00167 Chr5 4576465 4578039 +
Pvu Pvu8g0557 Chr8 4904293 4905832 +
Seca Seca2g00877 Chr2 13560605 13562567 +
Spst Spst1g01154 Chr1 13886432 13886931 -
Trre Trre13g02393 Chr13 21536864 21537318 +
Tsu Tsu01g03248 Chr01 40259841 40260352 +
Vian Vian2g00534 Chr2 6478901 6479485 +
Vifa Vifa5g01619 Chr5 467553405 467553848 -
Vimu Vimu6g00633 Chr6 7496531 7497052 -
Viun Viun5g00773 Chr5 4838171 4839755 +
Vivi Vivi6g02952 Chr6 116698216 116699220 -
Vvi Vvi4g0996 Chr4 16567940 16579411 -
Bva Bva13g03545 Chr13 23978827 23984519 -
Bva Bva04g03464 Chr04 27458125 27463065 -
Lapu Lapu1g01475 Chr1 27546534 27555447 +
Lasa Lasa3g02051 Chr3 520827649 520832664 -
Lja Lja1g3023 Chr1 36603259 36610696 +
Lja Lja5g1651 Chr5 17901868 17907224 -
Mepo Mepo3g02245 Chr3 32173805 32180842 -
Mesa Mesa25g01972 Chr25 24362681 24368969 +
Phco Phco3g02668 Chr3 53232041 53239705 -
Pste Pste5g01204 Chr5 7792489 7798604 +
Pumo Pumo5g00165 Chr5 4563795 4571479 +
Pvu Pvu8g0556 Chr8 4888914 4897088 +
Rops Rops8g00984 Chr8 20956484 20966280 +
Seca Seca2g00876 Chr2 13547783 13558399 +
Spst Spst1g01155 Chr1 13893322 13899504 -
Trre Trre13g02391 Chr13 21519303 21524966 +
Vian Vian2g00533 Chr2 6466788 6474390 +
Vifa Vifa5g01621 Chr5 467575827 467582314 -
Vimu Vimu6g00636 Chr6 7506872 7509993 -
Viun Viun5g00770 Chr5 4826300 4835549 +
Vivi Vivi6g02954 Chr6 116710689 116717146 -
Vvi Vvi4g0997 Chr4 16599678 16607448 +
Bva Bva04g03466 Chr04 27469180 27472842 +
Lapu Lapu1g01474 Chr1 27536610 27540540 -
Lasa Lasa3g02052 Chr3 521139970 521142837 +
Lja Lja1g3022 Chr1 36594954 36599319 -
Phco Phco3g02670 Chr3 53244964 53247967 +
Pste Pste5g01202 Chr5 7764873 7768665 -
Pumo Pumo5g00164 Chr5 4552285 4556146 -
Pvu Pvu8g0555 Chr8 4878321 4882048 -
Rops Rops8g00983 Chr8 20944848 20948604 -
Seca Seca2g00875 Chr2 13523724 13528265 -
Spst Spst1g01157 Chr1 13905582 13908531 +
Vian Vian2g00532 Chr2 6452427 6455339 -
Vifa Vifa5g01624 Chr5 467709880 467712713 +
Vimu Vimu6g00637 Chr6 7524098 7527054 +
Viun Viun5g00768 Chr5 4815626 4819256 -
Vivi Vivi6g02955 Chr6 116728455 116731916 +
Vvi Vvi4g0998 Chr4 16608369 16610633 +
Bva Bva04g03467 Chr04 27473129 27476519 +
Lja Lja1g3021 Chr1 36582545 36585158 -
Vvi Vvi4g0999 Chr4 16612777 16613407 +
Bva Bva13g03546 Chr13 23987475 23988273 +
Lapu Lapu1g01472 Chr1 27527756 27528950 -
Lasa Lasa3g02056 Chr3 521179739 521180465 +
Lja Lja1g3020 Chr1 36577842 36580150 -
Mepo Mepo3g02248 Chr3 32195864 32198001 +
Mesa Mesa25g01969 Chr25 24344279 24346065 -
Phco Phco3g02672 Chr3 53257053 53258247 +
Pste Pste5g01200 Chr5 7751805 7753519 -
Pumo Pumo5g00162 Chr5 4536628 4539003 -
Pvu Pvu8g0553 Chr8 4867544 4869777 -
Rops Rops8g00981 Chr8 20935949 20937490 -
Spst Spst1g01159 Chr1 13921304 13922462 +
Trre Trre13g02387 Chr13 21490657 21492835 -
Vian Vian2g00530 Chr2 6440121 6441250 -
Vimu Vimu6g00639 Chr6 7534958 7536086 +
Viun Viun5g00766 Chr5 4807086 4808541 -
Vivi Vivi6g02958 Chr6 116748677 116749805 +
Vvi Vvi4g1000 Chr4 16613946 16615298 -
Bva Bva13g03547 Chr13 23988530 23989653 -
Bva Bva04g03468 Chr04 27476751 27477658 -
Lapu Lapu1g01471 Chr1 27526359 27527341 +
Lasa Lasa3g02057 Chr3 521198191 521198934 -
Lja Lja1g3019 Chr1 36569967 36572315 +
Mepo Mepo3g02249 Chr3 32216322 32217815 -
Mesa Mesa25g01967 Chr25 24332703 24333922 +
Phco Phco3g02673 Chr3 53258746 53259838 -
Pste Pste5g01199 Chr5 7749204 7751096 +
Pte Pte8g00603 Chr8 28568097 28570313 -
Pumo Pumo5g00161 Chr5 4534062 4536001 +
Pvu Pvu8g0552 Chr8 4866191 4867432 +
Rops Rops8g00980 Chr8 20932388 20934037 +
Seca Seca2g00872 Chr2 13511630 13513075 +
Spst Spst1g01160 Chr1 13922896 13923793 -
Trre Trre13g02386 Chr13 21485835 21487184 +
Vian Vian2g00529 Chr2 6438918 6439630 +
Vimu Vimu6g00640 Chr6 7536551 7543518 -
Viun Viun5g00765 Chr5 4805679 4806728 +
Vivi Vivi6g02959 Chr6 116757179 116758146 -
Vvi Vvi4g1001 Chr4 16630135 16632757 +
Bva Bva13g03548 Chr13 23992129 23994628 +
Bva Bva04g03469 Chr04 27477860 27480599 +
Lapu Lapu1g01470 Chr1 27517851 27521230 -
Lasa Lasa3g02059 Chr3 521692594 521694018 +
Lja Lja1g3018 Chr1 36561817 36564202 -
Mepo Mepo3g02250 Chr3 32230292 32232200 +
Mesa Mesa25g01966 Chr25 24326035 24327655 -
Phco Phco3g02674 Chr3 53274442 53276446 +
Pste Pste5g01197 Chr5 7720940 7723268 -
Pumo Pumo5g00160 Chr5 4523913 4526266 -
Pvu Pvu8g0551 Chr8 4851086 4853304 -
Rops Rops8g00979 Chr8 20917574 20919846 -
Seca Seca2g00871 Chr2 13469936 13472593 -
Spst Spst1g01161 Chr1 13931940 13933887 +
Trre Trre13g02385 Chr13 21459348 21460985 -
Vian Vian2g00528 Chr2 6422774 6424642 -
Vifa Vifa5g01632 Chr5 480358034 480359559 +
Vimu Vimu6g00641 Chr6 7568623 7570526 +
Viun Viun5g00764 Chr5 4793191 4795928 -
Vivi Vivi6g02961 Chr6 116879384 116881372 +
Vvi Vvi4g1002 Chr4 16642240 16645489 +
Bva Bva13g03549 Chr13 23994987 23995608 +
Bva Bva04g03470 Chr04 27481031 27481803 +
Lapu Lapu1g01469 Chr1 27509082 27509941 -
Lasa Lasa3g02060 Chr3 521928327 521928647 +
Lja Lja1g3016 Chr1 36545030 36546461 -
Mepo Mepo3g02251 Chr3 32238464 32239485 +
Mesa Mesa25g01965 Chr25 24322951 24323271 -
Phco Phco3g02675 Chr3 53278998 53279792 +
Pste Pste5g01193 Chr5 7702409 7704902 -
Pvu Pvu8g0550 Chr8 4846843 4848175 -
Spst Spst1g01162 Chr1 13959709 13960023 +
Trre Trre13g02382 Chr13 21432970 21433284 -
Vifa Vifa5g01634 Chr5 481271904 481272224 +
Vimu Vimu6g00642 Chr6 7579827 7580141 +
Viun Viun5g00762 Chr5 4788786 4789663 -
Vvi Vvi4g1003 Chr4 16649310 16652943 -
Cca Cca06g01416 Chr06 29027332 29029572 +
Ssu Ssu2g2441 Chr2 82711995 82713371 +
Vra Vra11g0623 Chr11 4936695 4938512 -
Bva Bva13g03545 Chr13 23978827 23984519 -
Bva Bva04g03464 Chr04 27458125 27463065 -