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
Vvi4g1194 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1195 . . . . . . . . . . . . . . . . . . Apr3g0300 . . . . . . . Bva08g00777 . . . . . . . . . . . . . . . . Gma16g01251 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja4g3203 . . . . . . . . . Mtr8g2471 . . . . . . . Psa4g2227 . . . . . . . . . . . . . . . . . . . . . Tpr4g4209 . . . Tsu04g03444 . . . . . . . . . . . .
Vvi4g1196 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1197 . . . . . . . . . . . . . . . . . . . . . . . Bach4g00671 . . . . . . . . . . . . . . . Glsi05g1411 Gma11g00654 Gma01g01750 . . Gso11g0603 Gso11g0603 . . . . . . . . . . . . . . . Lapu2g00704 . Lasa2g03347 . . . . . . . . . . Mal6g1100 . . Mepo5g00923 . Mesa17g00964 . . Mtr5g0818 . . . . Phco4g00932 . . . . . . . . . . . . . Pvu2g0346 . . . . . Spst2g00855 . . Sto6g3863 . Tpr2g1029 . . Trre9g01090 Tsu05g00772 . . . . . . Vimu7g02995 . . . Vivi2g03000 . .
Vvi4g1198 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Gma02g00488 . . . . . . Lal15g1492 . . . . . . . . . . . . Lasa4g02310 . . . . . . . . . . . . . Mepo1g02078 . Mesa29g02246 . . . . . . . Phco8g00460 . . . . Psa4g2228 Pste7g01535 . . Pte12g00470 . . Pumo4g02150 . Pvu3g2640 . Rops2g03333 . Seca12g02763 . Spst3g03865 . . . Sto6g3864 . . . Trre15g04099 . . . Vian1g01789 . Vifa4g02411 . . . Viun3g03651 . . . . .
Vvi4g1199 . . . . . . . . . Aev08g0259 . Ahy17g2370 . Aip07g02544 . . . Amo17g2233 Apr3g0301 . Arst1g00527 . . . . . Bva08g00779 . . . . . . . . . . . . . . . . Gma16g01250 . . . . . Lal15g1470 . . . . . . . . . . . . Lasa4g02309 . . . . . . . . . . Lja4g3198 . Mal5g3408 Mepo1g02079 . Mesa29g02247 . . . . Mtr8g2470 Phac3g04025 . Phco8g00459 . . . . Psa4g2229 Pste7g01537 . Pte14g00897 Pte12g00471 . . Pumo4g02151 . Pvu3g2641 . Rops2g03332 . Seca12g02766 . Spst3g03864 . . . . . . Tpr4g4210 Trre15g04100 . . Tsu04g03445 . . Vifa4g02410 . Vimu11g00664 . Viun3g03650 . . . . .
Vvi4g1200 . . . . . . Aed11g1261 . Aev05g0474 . Ahy15g0834 . Aip05g00849 . . . . . . Apr7g1052 . . . . . . Bva08g00781 . . . Cca06g01312 . . . Dod02g0531 . . . . . Gma11g00655 Gma01g01749 Gma02g00487 Gma16g01249 Gso11g0605 Gso11g0605 Gso11g0605 Gso11g0605 . . Lal23g1430 . . . . . . . . . . . . . . . . . . . . . Lja2g0493 . Mal6g1095 . . . . . . . Mtr5g0819 Mtr8g2469 . . . . . . Psa2g3579 . . . . . . . . . . . . . . . . . . . Sto6g3866 Sto11g1525 Tpr2g1030 Tpr4g4211 . . Tsu05g00773 Tsu04g03446 . . . . . . . . . . Vra11g0727 .
Vvi4g1201 . . . . Adu01g00085 . Aed11g1260 . . . Ahy15g0835 . Aip05g00850 . . . . . Apr3g0302 Apr7g1053 . . Bach10g00567 . Bisa01g1828 . Bva08g00782 . . . Cca06g01311 . Dere13g0683 . Dod02g0530 . . . Glsi09g0588 . Gma11g00656 . . Gma16g01248 Gso11g0607 . . Gso11g0607 . . Lal23g1431 . . . . . . . . . . . Lasa4g02307 . . . . . . . . . Lja2g0495 . . . Mepo1g02080 . . . . . . . Phac3g04026 . Phco8g00458 . . . Psa2g3578 Psa4g2232 Pste7g01539 . Pte14g00896 Pte12g00480 . . Pumo4g02152 . Pvu3g2642 . Rops2g03331 . Seca12g02769 . Spst3g03863 . . . . Sto11g1524 . . . . . . Vian1g01790 . Vifa4g02408 . Vimu7g02997 . Viun3g03648 . Vivi1g03056 . Vra11g0728 .
Vvi4g1202 . . . . . . . . Aev05g0473 . Ahy15g0836 . Aip05g00851 . . . . . . Apr7g1054 . . . . . . Bva08g00783 . . . . . . . Dod02g0527 . . . . . . Gma01g01748 Gma02g00486 . . . . . . . Lal23g1432 . . . . . . . . . . . . . . . . . . . . . Lja2g0496 . Mal6g1093 . . . . . . . Mtr5g0820 . . . . . . . Psa2g3577 . . . . . . . . . . . . . . . . . . . Sto6g3867 . Tpr2g1032 . . . Tsu05g00775 . . . . . . . . . . . . .
Vvi4g1203 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Seca Seca12g02769 Chr12 49083587 49087024 +
Vvi Vvi4g1194 Chr4 18841990 18842581 +
Vvi Vvi4g1195 Chr4 18846140 18848191 +
Apr Apr3g0300 Chr3 5824495 5831547 +
Bva Bva08g00777 Chr08 3998346 4005070 +
Gma Gma16g01251 Chr16 30635252 30647042 -
Lja Lja4g3203 Chr4 60580320 60584633 -
Mtr Mtr8g2471 Chr8 35125283 35131250 -
Psa Psa4g2227 Chr4 179638521 179648124 +
Tpr Tpr4g4209 Chr4 49208853 49214585 +
Tsu Tsu04g03444 Chr04 43646110 43652990 +
Vvi Vvi4g1196 Chr4 18868963 18869621 +
Vvi Vvi4g1197 Chr4 18876547 18877079 +
Bach Bach4g00671 Chr4 4468567 4469329 +
Glsi Glsi05g1411 Chr05 62978682 62979373 -
Gma Gma11g00654 Chr11 5417398 5418329 +
Gma Gma01g01750 Chr01 53178193 53179226 -
Gso Gso11g0603 Chr11 5374520 5375502 +
Gso Gso11g0603 Chr11 5374520 5375502 +
Lapu Lapu2g00704 Chr2 6193605 6194175 +
Lasa Lasa2g03347 Chr2 531387165 531388117 +
Mal Mal6g1100 Chr6 16744769 16745718 -
Mepo Mepo5g00923 Chr5 8984313 8989636 +
Mesa Mesa17g00964 Chr17 12231852 12234126 +
Mtr Mtr5g0818 Chr5 8056459 8057262 +
Phco Phco4g00932 Chr4 7399696 7400359 -
Pvu Pvu2g0346 Chr2 3406547 3407518 +
Spst Spst2g00855 Chr2 7199843 7200360 +
Sto Sto6g3863 Chr6 43031893 43032400 +
Tpr Tpr2g1029 Chr2 12142602 12143813 +
Trre Trre9g01090 Chr9 8666342 8667440 +
Tsu Tsu05g00772 Chr05 6511444 6512382 +
Vimu Vimu7g02995 Chr7 25222121 25222616 +
Vivi Vivi2g03000 Chr2 128978256 128979945 -
Vvi Vvi4g1198 Chr4 18877642 18887402 +
Gma Gma02g00488 Chr02 4924842 4930395 -
Lal Lal15g1492 Chr15 17072418 17078041 -
Lasa Lasa4g02310 Chr4 457076576 457082300 -
Mepo Mepo1g02078 Chr1 21385327 21391183 +
Mesa Mesa29g02246 Chr29 30786606 30792284 +
Phco Phco8g00460 Chr8 4315257 4321701 -
Psa Psa4g2228 Chr4 179648287 179649604 +
Pste Pste7g01535 Chr7 14092741 14098872 +
Pte Pte12g00470 Chr12 4005075 4009580 +
Pumo Pumo4g02150 Chr4 31187854 31195578 +
Pvu Pvu3g2640 Chr3 48444351 48451397 +
Rops Rops2g03333 Chr2 61200009 61206332 -
Seca Seca12g02763 Chr12 48953376 48957808 +
Spst Spst3g03865 Chr3 88700274 88707506 -
Sto Sto6g3864 Chr6 43033379 43039366 +
Trre Trre15g04099 Chr15 51526306 51531688 +
Vian Vian1g01789 Chr1 21056540 21065229 +
Vifa Vifa4g02411 Chr4 726878212 726885652 -
Viun Viun3g03651 Chr3 43340602 43347381 -
Vvi Vvi4g1199 Chr4 18887977 18891508 -
Aev Aev08g0259 Chr08 1469500 1474345 +
Ahy Ahy17g2370 Chr17 114183307 114185752 +
Aip Aip07g02544 Chr07 105974134 105976454 +
Amo Amo17g2233 Chr17 114779707 114781990 +
Apr Apr3g0301 Chr3 5831851 5835201 -
Arst Arst1g00527 Chr1 4985485 4991672 -
Bva Bva08g00779 Chr08 4009890 4012960 -
Gma Gma16g01250 Chr16 30629870 30634577 +
Lal Lal15g1470 Chr15 16888919 16895858 +
Lasa Lasa4g02309 Chr4 457070740 457073764 +
Lja Lja4g3198 Chr4 60461265 60473313 -
Mal Mal5g3408 Chr5 98756379 98760240 -
Mepo Mepo1g02079 Chr1 21391634 21396664 -
Mesa Mesa29g02247 Chr29 30793053 30795398 -
Mtr Mtr8g2470 Chr8 35120678 35125007 +
Phac Phac3g04025 Chr3 39781082 39789943 -
Phco Phco8g00459 Chr8 4310337 4314293 +
Psa Psa4g2229 Chr4 179651528 179657084 -
Pste Pste7g01537 Chr7 14099202 14105809 -
Pte Pte14g00897 Chr14 30688291 30691108 +
Pte Pte12g00471 Chr12 4011629 4014417 -
Pumo Pumo4g02151 Chr4 31196172 31200705 -
Pvu Pvu3g2641 Chr3 48451560 48455867 -
Rops Rops2g03332 Chr2 61194003 61197652 +
Seca Seca12g02766 Chr12 48961015 48963848 -
Spst Spst3g03864 Chr3 88695391 88699298 +
Tpr Tpr4g4210 Chr4 49215521 49222459 -
Trre Trre15g04100 Chr15 51532823 51536314 -
Tsu Tsu04g03445 Chr04 43653135 43658017 -
Vifa Vifa4g02410 Chr4 726874063 726877204 +
Vimu Vimu11g00664 Chr11 7104528 7108958 -
Viun Viun3g03650 Chr3 43335649 43340310 +
Vvi Vvi4g1200 Chr4 18902110 18904497 +
Aed Aed11g1261 Chr11 17744489 17747981 -
Aev Aev05g0474 Chr05 3312017 3315390 -
Ahy Ahy15g0834 Chr15 11951672 11955778 +
Aip Aip05g00849 Chr05 11527193 11531490 +
Apr Apr7g1052 Chr7 17492494 17495457 +
Bva Bva08g00781 Chr08 4021962 4024426 +
Cca Cca06g01312 Chr06 27910131 27934227 -
Dod Dod02g0531 Chr02 6921893 6926941 -
Gma Gma11g00655 Chr11 5423826 5429853 +
Gma Gma01g01749 Chr01 53163339 53167064 -
Gma Gma02g00487 Chr02 4917100 4919646 -
Gma Gma16g01249 Chr16 30604396 30607476 -
Gso Gso11g0605 Chr11 5394238 5396370 +
Gso Gso11g0605 Chr11 5394238 5396370 +
Gso Gso11g0605 Chr11 5394238 5396370 +
Gso Gso11g0605 Chr11 5394238 5396370 +
Lal Lal23g1430 Chr23 14760358 14763304 +
Lja Lja2g0493 Chr2 4479393 4484311 +
Mal Mal6g1095 Chr6 16630344 16634657 -
Mtr Mtr5g0819 Chr5 8063137 8066960 +
Mtr Mtr8g2469 Chr8 35109493 35112456 -
Psa Psa2g3579 Chr2 389334881 389336781 +
Sto Sto6g3866 Chr6 43049522 43051469 +
Sto Sto11g1525 Chr11 14441076 14442672 -
Tpr Tpr2g1030 Chr2 12163112 12167724 +
Tpr Tpr4g4211 Chr4 49232508 49235561 +
Tsu Tsu05g00773 Chr05 6516392 6520585 +
Tsu Tsu04g03446 Chr04 43664594 43673798 +
Vra Vra11g0727 Chr11 5857285 5858819 -
Vvi Vvi4g1201 Chr4 18915668 18918534 +
Adu Adu01g00085 Chr01 1249002 1251901 -
Aed Aed11g1260 Chr11 17735318 17737783 -
Ahy Ahy15g0835 Chr15 11994764 11996623 +
Aip Aip05g00850 Chr05 11569766 11571483 +
Apr Apr3g0302 Chr3 5864483 5866907 +
Apr Apr7g1053 Chr7 17500047 17501869 +
Bach Bach10g00567 Chr10 4040153 4042443 +
Bisa Bisa01g1828 Chr01 31760909 31763232 -
Bva Bva08g00782 Chr08 4026738 4028406 +
Cca Cca06g01311 Chr06 27898134 27900102 -
Dere Dere13g0683 Chr13 8628583 8632608 +
Dod Dod02g0530 Chr02 6914983 6917004 -
Glsi Glsi09g0588 Chr09 4079830 4082202 +
Gma Gma11g00656 Chr11 5437131 5451832 +
Gma Gma16g01248 Chr16 30580738 30583417 -
Gso Gso11g0607 Chr11 5403608 5409311 +
Gso Gso11g0607 Chr11 5403608 5409311 +
Lal Lal23g1431 Chr23 14768712 14770631 +
Lasa Lasa4g02307 Chr4 456734237 456735689 -
Lja Lja2g0495 Chr2 4502336 4504027 +
Mepo Mepo1g02080 Chr1 21407931 21411220 +
Phac Phac3g04026 Chr3 39797805 39800529 +
Phco Phco8g00458 Chr8 4287012 4295446 -
Psa Psa2g3578 Chr2 389292002 389293610 +
Psa Psa4g2232 Chr4 179868783 179871287 +
Pste Pste7g01539 Chr7 14157070 14159739 -
Pte Pte14g00896 Chr14 30680233 30683373 -
Pte Pte12g00480 Chr12 4277363 4319630 -
Pumo Pumo4g02152 Chr4 31230597 31250587 +
Pvu Pvu3g2642 Chr3 48465374 48468034 +
Rops Rops2g03331 Chr2 61170707 61172718 -
Seca Seca12g02769 Chr12 49083587 49087024 +
Spst Spst3g03863 Chr3 88680785 88683122 -
Sto Sto11g1524 Chr11 14435733 14437203 +
Vian Vian1g01790 Chr1 21090805 21093059 +
Vifa Vifa4g02408 Chr4 726233326 726234923 -
Vimu Vimu7g02997 Chr7 25243087 25244602 -
Viun Viun3g03648 Chr3 43319518 43321893 -
Vivi Vivi1g03056 Chr1 67535369 67537227 -
Vra Vra11g0728 Chr11 5866065 5867573 +
Vvi Vvi4g1202 Chr4 18932987 18934303 +
Aev Aev05g0473 Chr05 3299730 3308687 -
Ahy Ahy15g0836 Chr15 12010515 12012163 +
Aip Aip05g00851 Chr05 11584284 11585989 +
Apr Apr7g1054 Chr7 17503921 17505602 +
Bva Bva08g00783 Chr08 4028919 4030737 +
Dod Dod02g0527 Chr02 6872657 6874336 -
Gma Gma01g01748 Chr01 53156684 53158242 -
Gma Gma02g00486 Chr02 4910795 4913112 -
Lal Lal23g1432 Chr23 14772303 14778214 +
Lja Lja2g0496 Chr2 4518709 4520409 +
Mal Mal6g1093 Chr6 16579201 16582425 -
Mtr Mtr5g0820 Chr5 8071517 8074189 +
Psa Psa2g3577 Chr2 389254124 389257538 +
Sto Sto6g3867 Chr6 43057832 43065012 +
Tpr Tpr2g1032 Chr2 12182872 12184868 +
Tsu Tsu05g00775 Chr05 6533050 6535242 +
Vvi Vvi4g1203 Chr4 18940831 18943383 +
Aev Aev08g0259 Chr08 1469500 1474345 +
Ahy Ahy17g2370 Chr17 114183307 114185752 +
Aip Aip07g02544 Chr07 105974134 105976454 +
Amo Amo17g2233 Chr17 114779707 114781990 +
Gma Gma16g01251 Chr16 30635252 30647042 -