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
Vvi17g0223 . . . . . . Aed7g0271 Aed5g2645 . . . . . . . . . . Apr6g0999 Apr2g1575 . . . . . . . Bva03g00742 . Car06g00165 Cca08g00294 Cca09g02823 . . . . . . . . Gma07g00910 Gma08g00511 . . Gso7g0857 Gso7g0857 . . Lal15g0916 . Lal23g0694 Lal8g0464 . Lal25g0476 . . . . . . . Lapu3g03944 Lasa1g04143 . . . . . . . . . Lja2g2181 Lja4g0025 Mal5g0422 Mal6g3614 . Mepo2g05097 . Mesa13g00034 . . Mtr8g3873 Mtr6g2074 Phac4g01981 . . Phco4g03719 . . . Psa7g0052 Pste9g01442 . Pte16g00116 Pte9g00127 . . Pumo6g02954 Pumo6g02954 Pvu4g1604 Pvu2g3388 Rops5g00348 Rops2g00064 . . Spst4g02822 Spst3g00671 Ssu5g3490 Ssu5g3490 . . Tpr3g0237 . . . Tsu02g00033 . Vian8g01411 Vian1g04207 . Vifa1g07317 Vimu8g01629 Vimu11g04917 . . . . Vra1g0668 .
Vvi17g0224 . . . . . Adu03g04050 . . . . . . . . . . . . . Apr2g1574 . Arst3g05338 . Bach1g01453 . . Bva04g00875 Bva03g00741 . Car06g00166 . Cca09g02822 . . . . . . . . . Gma08g00510 . . . . . . Lal15g0917 Lal16g0945 . . . . . . . . . . . Lapu3g03943 . Lasa7g05276 . . . . . . . . . Lja4g0026 Mal5g0421 . . Mepo2g05096 . Mesa13g00035 . . Mtr8g3872 . . . . Phco4g03718 . . . . . . . . . . . Pumo6g00066 . Pvu2g3387 . Rops2g00065 . Seca12g06985 . Spst3g00672 . Ssu5g3489 . . Tpr3g0238 . . Trre7g05963 Tsu02g00034 . . Vian1g04206 . Vifa6g04140 . Vimu11g04916 . Viun3g00070 . Vivi5g06505 . .
Vvi17g0225 . . . . . Adu03g04049 . Aed5g2643 . . . . . . . . . . . Apr2g1571 . Arst3g05337 . . . . Bva04g00874 Bva03g00740 . Car06g00168 . Cca09g02821 . . . . . . . . . Gma08g00507 . . . . . . Lal15g0918 Lal16g0947 . . . . . . . . . . . Lapu3g03942 . Lasa7g05273 . . . . . . . . . Lja4g0027 Mal5g0419 . . Mepo2g05094 . Mesa13g00036 . . Mtr8g3870 . . . . Phco4g03717 . . . . . . . . . . . Pumo6g00069 . Pvu2g3386 . Rops2g00067 . Seca12g06981 . Spst3g00674 . Ssu5g3488 . Sto8g4543 Tpr3g0240 . . Trre7g05960 Tsu02g00037 . . Vian1g04205 . Vifa6g04136 . Vimu11g04914 . Viun3g00071 . Vivi5g06507 . .
Vvi17g0226 . . . . . . . . . . . . . . . . . . . Apr2g1570 . . . . . . Bva04g00873 . . Car06g00169 . . . . . . . . . . . Gma08g00505 Gma05g02374 . . . . . Lal15g0919 . . . . . Lan18g0420 . . . . . . . . . . . . . . . . . . Lja4g0028 Mal5g0418 . . . . . . . Mtr8g3868 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto8g4549 Tpr3g0241 . . . Tsu02g00039 . . . . . . . . . . . . .
Vvi17g0227 . . . . . . . Aed5g2641 Aev05g3503 . Ahy15g2660 . Aip05g02974 . . . . . Apr6g1001 Apr2g1569 . . . . . . Bva04g00872 Bva03g00739 . Car06g00170 . Cca09g02819 . . Dod02g3727 . . . . . . Gma08g00504 . . . . . . . Lal16g0949 Lal23g0693 . . . . . . . . . . . . . . . . . . . . . Lja2g2180 Lja4g0029 Mal5g0417 . . . . . . . Mtr8g3867 . . . . . . . . . . . . . . . . . . . . . . . . . . Ssu5g3485 . . Tpr3g0242 . . . Tsu02g00040 . . . . . . . . . . . . .
Vvi17g0228 . . . . . . . Aed5g2640 Aev05g3502 . Ahy15g2664 . Aip05g02975 . . . . . Apr6g1002 Apr2g1566 . Arst5g03470 . Bach1g01455 . . Bva04g00871 Bva03g00738 . Car06g00171 . Cca09g02818 . . Dod02g3726 . . . . . . Gma08g00503 . . . . . . . . . . . . . . . . . . . Lapu3g03938 . Lasa7g05268 . . . . . . . . . Lja4g0030 Mal5g0416 . . Mepo2g05089 . Mesa13g00039 . . Mtr8g3866 . . . . Phco4g03712 . . . Psa7g0071 . . . . . . . Pumo6g00073 . Pvu2g3379 . Rops2g00070 . Seca12g06979 . Spst3g00678 . Ssu5g3483 . Sto8g4551 Tpr3g0243 . . Trre7g05957 Tsu02g00041 . . Vian1g04200 . Vifa1g07281 . Vimu11g04909 . Viun3g00077 . Vivi5g06514 . .
Vvi17g0229 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0230 . . . . . . . Aed5g2639 Aev05g3501 . Ahy15g2665 . Aip05g02976 . . . . . Apr6g1003 Apr2g1564 . . . . . . Bva04g00869 Bva03g00737 . Car06g00172 . Cca09g02817 . . Dod02g3725 . . . . . . Gma08g00502 Gma05g02369 Gma09g01643 . . . . Lal15g0920 Lal16g0951 . . Lal10g0957 Lal25g0475 . . . . . . . . . . . . . . . . . . Lja2g2177 Lja4g0031 Mal5g0415 . . . . . . . Mtr8g3865 . . . . . . . . . . . . . . . . . . . . . . . . . . Ssu5g3482 . Sto8g4556 Tpr3g0244 . . . Tsu02g00042 . . . . . . . . . . . . .
Vvi17g0231 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva03g00736 . . . Cca09g02816 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ssu5g3481 . . . . . . . . . . . . . . . . . . . .
Vvi17g0232 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva03g00733 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja4g0035 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Lal Lal23g0694 Chr23 9641317 9646125 -
Sto Sto8g4543 Chr8 48044775 48047327 +
Vvi Vvi17g0223 Chr17 2282170 2286444 +
Aed Aed7g0271 Chr7 1924686 1927474 +
Aed Aed5g2645 Chr5 27052556 27061174 -
Apr Apr6g0999 Chr6 14652792 14657124 +
Apr Apr2g1575 Chr2 21564526 21567701 -
Bva Bva03g00742 Chr03 4440133 4443448 -
Car Car06g00165 Chr06 1903114 1911894 +
Cca Cca08g00294 Chr08 4252979 4257806 +
Cca Cca09g02823 Chr09 53812852 53815904 -
Gma Gma07g00910 Chr07 9933362 9938751 +
Gma Gma08g00511 Chr08 4214065 4217175 -
Gso Gso7g0857 Chr7 9707817 9712776 +
Gso Gso7g0857 Chr7 9707817 9712776 +
Lal Lal15g0916 Chr15 7013051 7015879 +
Lal Lal23g0694 Chr23 9641317 9646125 -
Lal Lal8g0464 Chr8 3101627 3105480 -
Lal Lal25g0476 Chr25 3283677 3287117 -
Lapu Lapu3g03944 Chr3 62911788 62914731 -
Lasa Lasa1g04143 Chr1 709707301 709709378 -
Lja Lja2g2181 Chr2 24820932 24826429 -
Lja Lja4g0025 Chr4 233262 235824 +
Mal Mal5g0422 Chr5 6264838 6267177 -
Mal Mal6g3614 Chr6 105762803 105767025 +
Mepo Mepo2g05097 Chr2 58854954 58857705 -
Mesa Mesa13g00034 Chr13 422058 424538 +
Mtr Mtr8g3873 Chr8 49366935 49369026 -
Mtr Mtr6g2074 Chr6 37329607 37333445 -
Phac Phac4g01981 Chr4 46486702 46490054 -
Phco Phco4g03719 Chr4 56714127 56716190 -
Psa Psa7g0052 Chr7 2147885 2150062 -
Pste Pste9g01442 Chr9 13861935 13866069 -
Pte Pte16g00116 Chr16 1286404 1287947 -
Pte Pte9g00127 Chr9 1422384 1424567 -
Pumo Pumo6g02954 Chr6 70087174 70096040 -
Pumo Pumo6g02954 Chr6 70087174 70096040 -
Pvu Pvu4g1604 Chr4 43256869 43259741 -
Pvu Pvu2g3388 Chr2 48776072 48779672 -
Rops Rops5g00348 Chr5 5814517 5818679 +
Rops Rops2g00064 Chr2 1094215 1097247 +
Spst Spst4g02822 Chr4 67900010 67902614 +
Spst Spst3g00671 Chr3 10160068 10162173 +
Ssu Ssu5g3490 Chr5 85740931 85743783 -
Ssu Ssu5g3490 Chr5 85740931 85743783 -
Tpr Tpr3g0237 Chr3 2854860 2858064 +
Tsu Tsu02g00033 Chr02 210578 212835 +
Vian Vian8g01411 Chr8 33419839 33423307 -
Vian Vian1g04207 Chr1 65054835 65056822 -
Vifa Vifa1g07317 Chr1 1126420117 1126422283 -
Vimu Vimu8g01629 Chr8 22133332 22136780 +
Vimu Vimu11g04917 Chr11 68750119 68752316 -
Vra Vra1g0668 Chr1 7872002 7875712 +
Vvi Vvi17g0224 Chr17 2288304 2303829 +
Adu Adu03g04050 Chr03 129580929 129586761 -
Apr Apr2g1574 Chr2 21557156 21563825 -
Arst Arst3g05338 Chr3 128345005 128350843 -
Bach Bach1g01453 Chr1 28040822 28047403 +
Bva Bva04g00875 Chr04 5746484 5753078 -
Bva Bva03g00741 Chr03 4432477 4439494 -
Car Car06g00166 Chr06 1912525 1920703 +
Cca Cca09g02822 Chr09 53800510 53811032 -
Gma Gma08g00510 Chr08 4206296 4212264 -
Lal Lal15g0917 Chr15 7017743 7023979 +
Lal Lal16g0945 Chr16 6269224 6274696 +
Lapu Lapu3g03943 Chr3 62905130 62910746 -
Lasa Lasa7g05276 Chr7 719657635 719663852 -
Lja Lja4g0026 Chr4 236713 241710 +
Mal Mal5g0421 Chr5 6255647 6263118 -
Mepo Mepo2g05096 Chr2 58846404 58854069 -
Mesa Mesa13g00035 Chr13 427413 433265 +
Mtr Mtr8g3872 Chr8 49358642 49366080 -
Phco Phco4g03718 Chr4 56705075 56712035 -
Pumo Pumo6g00066 Chr6 743882 750596 +
Pvu Pvu2g3387 Chr2 48768276 48775388 -
Rops Rops2g00065 Chr2 1111951 1117994 +
Seca Seca12g06985 Chr12 161825047 161828266 -
Spst Spst3g00672 Chr3 10163463 10170663 +
Ssu Ssu5g3489 Chr5 85730532 85737863 -
Tpr Tpr3g0238 Chr3 2859622 2867682 +
Trre Trre7g05963 Chr7 63984397 63991132 -
Tsu Tsu02g00034 Chr02 214217 219077 +
Vian Vian1g04206 Chr1 65047939 65053542 -
Vifa Vifa6g04140 Chr6 1362226117 1362232765 -
Vimu Vimu11g04916 Chr11 68743333 68748771 -
Viun Viun3g00070 Chr3 303264 309638 +
Vivi Vivi5g06505 Chr5 171874062 171881159 +
Vvi Vvi17g0225 Chr17 2304660 2316132 -
Adu Adu03g04049 Chr03 129578273 129580775 +
Aed Aed5g2643 Chr5 27045594 27047235 +
Apr Apr2g1571 Chr2 21542129 21551946 +
Arst Arst3g05337 Chr3 128342348 128344874 +
Bva Bva04g00874 Chr04 5743456 5747042 +
Bva Bva03g00740 Chr03 4429704 4432120 +
Car Car06g00168 Chr06 1926046 1929746 -
Cca Cca09g02821 Chr09 53793669 53798214 +
Gma Gma08g00507 Chr08 4192916 4198829 +
Lal Lal15g0918 Chr15 7025039 7029054 -
Lal Lal16g0947 Chr16 6280571 6283674 -
Lapu Lapu3g03942 Chr3 62899413 62904325 +
Lasa Lasa7g05273 Chr7 719618773 719620997 +
Lja Lja4g0027 Chr4 241287 244490 -
Mal Mal5g0419 Chr5 6236708 6239320 +
Mepo Mepo2g05094 Chr2 58836833 58840366 +
Mesa Mesa13g00036 Chr13 441839 444712 -
Mtr Mtr8g3870 Chr8 49347183 49349653 +
Phco Phco4g03717 Chr4 56699567 56703626 +
Pumo Pumo6g00069 Chr6 756408 761606 -
Pvu Pvu2g3386 Chr2 48763587 48767890 +
Rops Rops2g00067 Chr2 1124375 1128349 -
Seca Seca12g06981 Chr12 161812879 161817586 +
Spst Spst3g00674 Chr3 10182076 10185145 -
Ssu Ssu5g3488 Chr5 85718682 85723942 +
Sto Sto8g4543 Chr8 48044775 48047327 +
Tpr Tpr3g0240 Chr3 2874421 2877410 -
Trre Trre7g05960 Chr7 63976407 63978675 +
Tsu Tsu02g00037 Chr02 232140 234918 -
Vian Vian1g04205 Chr1 65022847 65026506 +
Vifa Vifa6g04136 Chr6 1361733067 1361735677 +
Vimu Vimu11g04914 Chr11 68731646 68734851 +
Viun Viun3g00071 Chr3 311143 314388 -
Vivi Vivi5g06507 Chr5 171889384 171894112 -
Vvi Vvi17g0226 Chr17 2319991 2321254 -
Apr Apr2g1570 Chr2 21542025 21543960 +
Bva Bva04g00873 Chr04 5741018 5742820 +
Car Car06g00169 Chr06 1931650 1933139 -
Gma Gma08g00505 Chr08 4183420 4185246 +
Gma Gma05g02374 Chr05 44591741 44599744 -
Lal Lal15g0919 Chr15 7032075 7034372 -
Lan Lan18g0420 Chr18 8146062 8147643 +
Lja Lja4g0028 Chr4 245702 247025 -
Mal Mal5g0418 Chr5 6233438 6234433 +
Mtr Mtr8g3868 Chr8 49341716 49342826 +
Sto Sto8g4549 Chr8 48072821 48075132 -
Tpr Tpr3g0241 Chr3 2879124 2880474 -
Tsu Tsu02g00039 Chr02 238712 240661 -
Vvi Vvi17g0227 Chr17 2322153 2341697 -
Aed Aed5g2641 Chr5 27025728 27034915 +
Aev Aev05g3503 Chr05 34263459 34271768 +
Ahy Ahy15g2660 Chr15 142554869 142563834 -
Aip Aip05g02974 Chr05 131683117 131692023 -
Apr Apr6g1001 Chr6 14667709 14688672 -
Apr Apr2g1569 Chr2 21531676 21541089 +
Bva Bva04g00872 Chr04 5732304 5740487 +
Bva Bva03g00739 Chr03 4420464 4429112 +
Car Car06g00170 Chr06 1933988 1941750 -
Cca Cca09g02819 Chr09 53773379 53781889 +
Dod Dod02g3727 Chr02 76058192 76062038 +
Gma Gma08g00504 Chr08 4175170 4182243 +
Lal Lal16g0949 Chr16 6287444 6295900 -
Lal Lal23g0693 Chr23 9631496 9640796 +
Lja Lja2g2180 Chr2 24794205 24805795 +
Lja Lja4g0029 Chr4 247814 257180 -
Mal Mal5g0417 Chr5 6225716 6231998 +
Mtr Mtr8g3867 Chr8 49333360 49340785 +
Ssu Ssu5g3485 Chr5 85697236 85703114 +
Tpr Tpr3g0242 Chr3 2880807 2889565 -
Tsu Tsu02g00040 Chr02 241334 249113 -
Vvi Vvi17g0228 Chr17 2350968 2352022 -
Aed Aed5g2640 Chr5 27017802 27021011 +
Aev Aev05g3502 Chr05 34247997 34253032 +
Ahy Ahy15g2664 Chr15 142735906 142743989 -
Aip Aip05g02975 Chr05 131857867 131867342 -
Apr Apr6g1002 Chr6 14700421 14704077 -
Apr Apr2g1566 Chr2 21506182 21510076 +
Arst Arst5g03470 Chr5 93624141 93631740 +
Bach Bach1g01455 Chr1 28067006 28070888 -
Bva Bva04g00871 Chr04 5719630 5723368 +
Bva Bva03g00738 Chr03 4410777 4414540 +
Car Car06g00171 Chr06 1950970 1953745 -
Cca Cca09g02818 Chr09 53756854 53760543 +
Dod Dod02g3726 Chr02 76039044 76044250 +
Gma Gma08g00503 Chr08 4160826 4163867 +
Lapu Lapu3g03938 Chr3 62863825 62867628 +
Lasa Lasa7g05268 Chr7 719518533 719520635 +
Lja Lja4g0030 Chr4 259219 261530 -
Mal Mal5g0416 Chr5 6207887 6209771 +
Mepo Mepo2g05089 Chr2 58805597 58807112 +
Mesa Mesa13g00039 Chr13 470493 472436 -
Mtr Mtr8g3866 Chr8 49320742 49323694 +
Phco Phco4g03712 Chr4 56671823 56674588 +
Psa Psa7g0071 Chr7 4910463 4913020 -
Pumo Pumo6g00073 Chr6 814376 817858 -
Pvu Pvu2g3379 Chr2 48616976 48620229 +
Rops Rops2g00070 Chr2 1183150 1184897 -
Seca Seca12g06979 Chr12 161784220 161787356 +
Spst Spst3g00678 Chr3 10210824 10213443 -
Ssu Ssu5g3483 Chr5 85678396 85679462 +
Sto Sto8g4551 Chr8 48099896 48105601 -
Tpr Tpr3g0243 Chr3 2907386 2910175 -
Trre Trre7g05957 Chr7 63945112 63947537 +
Tsu Tsu02g00041 Chr02 256799 259617 -
Vian Vian1g04200 Chr1 64991991 64994641 +
Vifa Vifa1g07281 Chr1 1124229678 1124240540 +
Vimu Vimu11g04909 Chr11 68701603 68704324 +
Viun Viun3g00077 Chr3 344538 347672 -
Vivi Vivi5g06514 Chr5 171945665 171948175 -
Vvi Vvi17g0229 Chr17 2360667 2363479 +
Vvi Vvi17g0230 Chr17 2368322 2377336 +
Aed Aed5g2639 Chr5 27004119 27009337 -
Aev Aev05g3501 Chr05 34239061 34242859 -
Ahy Ahy15g2665 Chr15 142779306 142784629 +
Aip Aip05g02976 Chr05 131892123 131897361 +
Apr Apr6g1003 Chr6 14721243 14726691 +
Apr Apr2g1564 Chr2 21489096 21494633 -
Bva Bva04g00869 Chr04 5708850 5713307 -
Bva Bva03g00737 Chr03 4401935 4406963 -
Car Car06g00172 Chr06 1957396 1963033 +
Cca Cca09g02817 Chr09 53742068 53746768 -
Dod Dod02g3725 Chr02 76009246 76014339 -
Gma Gma08g00502 Chr08 4150058 4154119 -
Gma Gma05g02369 Chr05 44559205 44564027 -
Gma Gma09g01643 Chr09 41904567 41910999 -
Lal Lal15g0920 Chr15 7038152 7043546 +
Lal Lal16g0951 Chr16 6312829 6317938 +
Lal Lal10g0957 Chr10 16885839 16891625 -
Lal Lal25g0475 Chr25 3273340 3278936 +
Lja Lja2g2177 Chr2 24762276 24770378 -
Lja Lja4g0031 Chr4 266227 270678 +
Mal Mal5g0415 Chr5 6201609 6205484 -
Mtr Mtr8g3865 Chr8 49306150 49311172 -
Ssu Ssu5g3482 Chr5 85660225 85664589 -
Sto Sto8g4556 Chr8 48142409 48148555 +
Tpr Tpr3g0244 Chr3 2913508 2919225 +
Tsu Tsu02g00042 Chr02 266295 271612 +
Vvi Vvi17g0231 Chr17 2379238 2381888 -
Bva Bva03g00736 Chr03 4397618 4401061 +
Cca Cca09g02816 Chr09 53737040 53740038 +
Ssu Ssu5g3481 Chr5 85653806 85655872 +
Vvi Vvi17g0232 Chr17 2388650 2392759 +
Bva Bva03g00733 Chr03 4391822 4394171 -
Lja Lja4g0035 Chr4 285730 288613 +