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
Vvi16g0769 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0770 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0771 . . . . . . Aed1g2216 . . . . . . . . . . . . . . . . . . . . . . . Cca02g02301 . . . . . . . . . Gma10g02272 . . . Gso10g2141 . . . . . . . Lal12g0030 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ssu7g0730 . Sto10g2516 . . . . . . . . . . . . . . . . . Vra8g2282 .
Vvi16g0772 . . . . Adu05g03282 Adu09g02408 Aed1g2217 Aed11g1686 Aev05g2977 Aev09g2274 Ahy15g3443 . Aip05g03747 Aip09g03977 . . . Amo19g4474 . Apr6g0768 Arst5g04166 Arst9g03182 Bach1g01228 . . . Bva03g01466 Bva04g01092 . . Cca02g02299 Cca06g01761 . . Dod02g3118 Dod06g0730 . . . . Gma10g02271 . . . Gso10g2140 . . . . . . . Lal12g0031 Lal13g0028 . . . . . . . Lapu7g02082 Lasa1g02441 Lasa6g04166 . . . . . . . . Lja2g2416 . Mal1g1980 Mal6g3004 Mepo7g01159 Mepo4g04293 Mesa22g02384 Mesa1g04711 . . Mtr1g3803 Mtr6g1570 . Phac7g00995 Phco5g00607 Phco6g02529 . . Psa6g4605 . Pste9g01235 . . Pte9g00282 . Pte9g00282 Pumo6g02673 Pumo3g00887 Pvu4g1301 Pvu7g0676 Rops5g00789 Rops6g02809 Seca10g04165 Seca8g07449 Spst4g03103 Spst10g01026 Ssu7g0731 Ssu2g2815 . Sto8g3584 Tpr1g0697 Tpr2g4414 Trre11g01417 Trre1g05473 . Tsu06g03191 Vian8g01150 Vian3g00592 Vifa1g04125 Vifa3g03002 Vimu8g01952 Vimu3g03110 Viun4g02305 Viun7g03326 . Vivi1g04305 Vra8g2281 .
Vvi16g0773 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0774 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0775 . . . . . Adu05g01217 . . . . . . . . . . . . . . . Arst5g01550 . . . . . . . . . . . . . . . . . . Gma10g02270 . . . Gso10g2139 . . . . . . . . . . . . . . . . . . Lasa2g02638 . . . . . . . . . . . . . . . . . . . Mtr5g0331 . Phac2g00207 . Phco4g00156 . . Psa2g4135 . . Pste1g01412 . . . . . Pumo8g02489 . Pvu2g0420 . Rops1g02343 . Seca10g00160 . Spst2g00154 . . . . . Tpr2g3839 . . . Tsu05g00312 . Vian10g00124 . Vifa1g08154 . Vimu7g02309 . Viun2g02800 . Vivi2g04077 . .
Vvi16g0776 . . . . . Adu09g02407 Aed1g2218 . . Aev09g2273 . Ahy19g3522 . Aip09g03978 . . . . . . . Arst9g03181 . . . . . Bva04g01093 . . Cca02g02298 . . . . Dod06g0731 . . . . Gma20g01447 . . . Gso20g1240 . . . . . . . Lal12g0032 . . . . . . . . Lapu7g02081 . Lasa6g04163 . . . . . . . . . . Mal1g1982 . . Mepo4g04291 . Mesa1g04710 . . Mtr1g3802 . . Phac7g00997 . Phco6g02528 . . Psa6g4604 . . Pste4g01798 . . . Pte9g00284 . Pumo3g00888 . Pvu7g0677 . Rops6g02807 . Seca8g07447 . Spst10g01024 Ssu7g0733 . Sto10g2519 . Tpr1g0698 . . Trre1g05472 Tsu01g04480 . . Vian3g00593 . Vifa3g02999 . Vimu3g03109 . Viun7g03325 . Vivi1g04306 Vra8g2280 .
Vvi16g0777 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Gma10g02269 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal6g0158 . . . . . . . Mtr5g0330 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tpr2g3843 . . . . . . . . . . . . . . . .
Vvi16g0778 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Mal Mal6g0158 Chr6 2266526 2270407 -
Mtr Mtr5g0330 Chr5 3095784 3101694 +
Psa Psa2g4135 Chr2 420362924 420366186 -
Tpr Tpr2g3843 Chr2 41218436 41221927 -
Aed Aed11g1686 Chr11 20574574 20576301 -
Cca Cca06g01761 Chr06 32896337 32898067 -
Ssu Ssu2g2815 Chr2 89098239 89100029 -
Adu Adu05g01217 Chr05 17553510 17557535 +
Arst Arst5g01550 Chr5 17603373 17607872 +
Lasa Lasa2g02638 Chr2 506884746 506885308 -
Phac Phac2g00207 Chr2 1078915 1083601 -
Phco Phco4g00156 Chr4 933787 937764 -
Pste Pste1g01412 Chr1 4470416 4480198 -
Pumo Pumo8g02489 Chr8 62048156 62053119 +
Pvu Pvu2g0420 Chr2 3873770 3879113 +
Rops Rops1g02343 Chr1 45734655 45738171 +
Seca Seca10g00160 Chr10 1494461 1498858 -
Spst Spst2g00154 Chr2 1203710 1207415 -
Vian Vian10g00124 Chr10 1055449 1058939 -
Vifa Vifa1g08154 Chr1 1273136348 1273143702 +
Vimu Vimu7g02309 Chr7 19928773 19932491 -
Viun Viun2g02800 Chr2 32808663 32811772 +
Vivi Vivi2g04077 Chr2 153773587 153776749 +
Vvi Vvi16g0769 Chr16 15489819 15491820 +
Vvi Vvi16g0770 Chr16 15560187 15560393 -
Vvi Vvi16g0771 Chr16 15604719 15610731 +
Aed Aed1g2216 Chr1 18469767 18471554 +
Cca Cca02g02301 Chr02 43671815 43673666 -
Gma Gma10g02272 Chr10 50312021 50313808 -
Gso Gso10g2141 Chr10 48444362 48446805 -
Lal Lal12g0030 Chr12 236917 238704 +
Ssu Ssu7g0730 Chr7 14715495 14717282 +
Sto Sto10g2516 Chr10 35423509 35433414 +
Vra Vra8g2282 Chr8 41090457 41096611 -
Vvi Vvi16g0772 Chr16 15611865 15613829 -
Adu Adu05g03282 Chr05 105147424 105149392 -
Adu Adu09g02408 Chr09 111470659 111473076 +
Aed Aed1g2217 Chr1 18473790 18475745 -
Aed Aed11g1686 Chr11 20574574 20576301 -
Aev Aev05g2977 Chr05 30449881 30451818 +
Aev Aev09g2274 Chr09 25301648 25303618 +
Ahy Ahy15g3443 Chr15 157007103 157009436 -
Aip Aip05g03747 Chr05 145566436 145568412 -
Aip Aip09g03977 Chr09 146182034 146184441 -
Amo Amo19g4474 Chr19 161793316 161795946 +
Apr Apr6g0768 Chr6 11996520 11998751 +
Arst Arst5g04166 Chr5 103822942 103825196 -
Arst Arst9g03182 Chr9 109367704 109370327 +
Bach Bach1g01228 Chr1 25652276 25654237 +
Bva Bva03g01466 Chr03 13911509 13913691 +
Bva Bva04g01092 Chr04 7258076 7260484 -
Cca Cca02g02299 Chr02 43656860 43659449 +
Cca Cca06g01761 Chr06 32896337 32898067 -
Dod Dod02g3118 Chr02 65974093 65976320 +
Dod Dod06g0730 Chr06 8818324 8820294 -
Gma Gma10g02271 Chr10 50307033 50308982 +
Gso Gso10g2140 Chr10 48439762 48442120 +
Lal Lal12g0031 Chr12 240826 242769 -
Lal Lal13g0028 Chr13 177011 178948 -
Lapu Lapu7g02082 Chr7 37113972 37115924 +
Lasa Lasa1g02441 Chr1 290505840 290507702 -
Lasa Lasa6g04166 Chr6 621900055 621902028 +
Lja Lja2g2416 Chr2 29762628 29764658 +
Mal Mal1g1980 Chr1 26003777 26006573 -
Mal Mal6g3004 Chr6 83687145 83689028 +
Mepo Mepo7g01159 Chr7 18141392 18143001 -
Mepo Mepo4g04293 Chr4 52708368 52710684 +
Mesa Mesa22g02384 Chr22 61104031 61105479 +
Mesa Mesa1g04711 Chr1 73226155 73228092 +
Mtr Mtr1g3803 Chr1 49602565 49605799 +
Mtr Mtr6g1570 Chr6 28007694 28009900 +
Phac Phac7g00995 Chr7 6133042 6135540 -
Phco Phco5g00607 Chr5 5916874 5918814 -
Phco Phco6g02529 Chr6 46804673 46806625 +
Psa Psa6g4605 Chr6 400248512 400253389 +
Pste Pste9g01235 Chr9 10499221 10501161 +
Pte Pte9g00282 Chr9 3148788 3151396 -
Pte Pte9g00282 Chr9 3148788 3151396 -
Pumo Pumo6g02673 Chr6 63963331 63965540 +
Pumo Pumo3g00887 Chr3 13768874 13771192 -
Pvu Pvu4g1301 Chr4 39472263 39474545 +
Pvu Pvu7g0676 Chr7 5875927 5877882 -
Rops Rops5g00789 Chr5 14945543 14947908 -
Rops Rops6g02809 Chr6 50405341 50407563 +
Seca Seca10g04165 Chr10 93052790 93054754 +
Seca Seca8g07449 Chr8 171521969 171523933 +
Spst Spst4g03103 Chr4 70425298 70427238 -
Spst Spst10g01026 Chr10 10966116 10968041 +
Ssu Ssu7g0731 Chr7 14720391 14722340 -
Ssu Ssu2g2815 Chr2 89098239 89100029 -
Sto Sto8g3584 Chr8 33084067 33086007 -
Tpr Tpr1g0697 Chr1 5913655 5915983 -
Tpr Tpr2g4414 Chr2 48276624 48278785 +
Trre Trre11g01417 Chr11 13851621 13853543 +
Trre Trre1g05473 Chr1 60239959 60241926 +
Tsu Tsu06g03191 Chr06 42338557 42340497 +
Vian Vian8g01150 Chr8 29907417 29909333 +
Vian Vian3g00592 Chr3 5909705 5911657 -
Vifa Vifa1g04125 Chr1 636083067 636084965 -
Vifa Vifa3g03002 Chr3 852682365 852684332 +
Vimu Vimu8g01952 Chr8 25278061 25279310 -
Vimu Vimu3g03110 Chr3 44878815 44881826 +
Viun Viun4g02305 Chr4 38667726 38670170 +
Viun Viun7g03326 Chr7 35241716 35244034 +
Vivi Vivi1g04305 Chr1 91691732 91695390 -
Vra Vra8g2281 Chr8 41086705 41089100 +
Vvi Vvi16g0773 Chr16 15614058 15614501 +
Vvi Vvi16g0774 Chr16 15621143 15621307 +
Vvi Vvi16g0775 Chr16 15621736 15623941 -
Adu Adu05g01217 Chr05 17553510 17557535 +
Arst Arst5g01550 Chr5 17603373 17607872 +
Gma Gma10g02270 Chr10 50293197 50295897 +
Gso Gso10g2139 Chr10 48420005 48424253 +
Lasa Lasa2g02638 Chr2 506884746 506885308 -
Mtr Mtr5g0331 Chr5 3105534 3110536 +
Phac Phac2g00207 Chr2 1078915 1083601 -
Phco Phco4g00156 Chr4 933787 937764 -
Psa Psa2g4135 Chr2 420362924 420366186 -
Pste Pste1g01412 Chr1 4470416 4480198 -
Pumo Pumo8g02489 Chr8 62048156 62053119 +
Pvu Pvu2g0420 Chr2 3873770 3879113 +
Rops Rops1g02343 Chr1 45734655 45738171 +
Seca Seca10g00160 Chr10 1494461 1498858 -
Spst Spst2g00154 Chr2 1203710 1207415 -
Tpr Tpr2g3839 Chr2 41158284 41161995 -
Tsu Tsu05g00312 Chr05 2328256 2332437 +
Vian Vian10g00124 Chr10 1055449 1058939 -
Vifa Vifa1g08154 Chr1 1273136348 1273143702 +
Vimu Vimu7g02309 Chr7 19928773 19932491 -
Viun Viun2g02800 Chr2 32808663 32811772 +
Vivi Vivi2g04077 Chr2 153773587 153776749 +
Vvi Vvi16g0776 Chr16 15627876 15628494 -
Adu Adu09g02407 Chr09 111431613 111433847 +
Aed Aed1g2218 Chr1 18482789 18485144 -
Aev Aev09g2273 Chr09 25287414 25289942 +
Ahy Ahy19g3522 Chr19 157953852 157956551 +
Aip Aip09g03978 Chr09 146214230 146216436 -
Arst Arst9g03181 Chr9 109328505 109331131 +
Bva Bva04g01093 Chr04 7272038 7274470 -
Cca Cca02g02298 Chr02 43633436 43635964 +
Dod Dod06g0731 Chr06 8844110 8847538 -
Gma Gma20g01447 Chr20 41605200 41608954 -
Gso Gso20g1240 Chr20 42429634 42432648 -
Lal Lal12g0032 Chr12 244057 246845 -
Lapu Lapu7g02081 Chr7 37100881 37104351 +
Lasa Lasa6g04163 Chr6 621688353 621691099 +
Mal Mal1g1982 Chr1 26027075 26030062 -
Mepo Mepo4g04291 Chr4 52694788 52696958 +
Mesa Mesa1g04710 Chr1 73211504 73213570 +
Mtr Mtr1g3802 Chr1 49589692 49593209 +
Phac Phac7g00997 Chr7 6141943 6145346 -
Phco Phco6g02528 Chr6 46793994 46796874 +
Psa Psa6g4604 Chr6 400223336 400225795 +
Pste Pste4g01798 Chr4 13425121 13428592 -
Pte Pte9g00284 Chr9 3197587 3199581 -
Pumo Pumo3g00888 Chr3 13791651 13794781 -
Pvu Pvu7g0677 Chr7 5884696 5887976 -
Rops Rops6g02807 Chr6 50370438 50373037 +
Seca Seca8g07447 Chr8 171489584 171492329 +
Spst Spst10g01024 Chr10 10939214 10950052 +
Ssu Ssu7g0733 Chr7 14750784 14754921 -
Sto Sto10g2519 Chr10 35466911 35475814 -
Tpr Tpr1g0698 Chr1 5924543 5927692 -
Trre Trre1g05472 Chr1 60225865 60229259 +
Tsu Tsu01g04480 Chr01 52455350 52458431 +
Vian Vian3g00593 Chr3 5918411 5920641 -
Vifa Vifa3g02999 Chr3 849943653 849945814 +
Vimu Vimu3g03109 Chr3 44871023 44875340 +
Viun Viun7g03325 Chr7 35233580 35236049 +
Vivi Vivi1g04306 Chr1 91712428 91715014 -
Vra Vra8g2280 Chr8 41079250 41081807 +
Vvi Vvi16g0777 Chr16 15628685 15630144 -
Gma Gma10g02269 Chr10 50287461 50291231 +
Mal Mal6g0158 Chr6 2266526 2270407 -
Mtr Mtr5g0330 Chr5 3095784 3101694 +
Tpr Tpr2g3843 Chr2 41218436 41221927 -
Vvi Vvi16g0778 Chr16 15638748 15639528 +