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
Vvi2g1082 . . . . . . Aed11g1036 . Aev05g0235 . Ahy15g0215 . Aip05g00201 . . . . . Apr7g0345 . . . . . . . Bva08g01049 . . . Cca06g01090 . . . Dod02g0249 . . . . . . . . . . . . . Lal15g0348 . . . . . Lan18g0824 . . . . . . . . . . . . . . . . . Lja2g0728 . Mal6g0560 . . . . . . . Mtr5g1106 . . . . . . . Psa2g3234 . . . . . . . . . . . . . . . . . Ssu2g2065 . . . Tpr2g1356 . . . Tsu05g01101 . . . . . . . . . . . . .
Vvi2g1083 . . . . . . . . . . . . . . . . . . . . . . Bach4g00902 . . . . . . . . . . . . . . . . . . Gma09g01998 . . . . . . . . . . . . . . . . . . Lapu2g00938 . Lasa2g03657 . . . . . . . . . . . . . Mepo5g01237 . Mesa17g01325 . . . . . Phac2g03774 . Phco4g00665 . . . . . Pste1g00113 . . . . . . . Pvu2g1309 . . . . . . . . . . . . . Trre9g01623 . . . . . . . Vimu7g03314 . . . Vivi2g02578 . . .
Vvi2g1084 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g1085 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g1086 . . . . . . Aed11g1038 . Aev05g0236 . Ahy15g0216 . Aip05g00202 . . . . . Apr7g1852 . . . . . . . . . . . Cca06g01091 . . . Dod02g0250 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa2g3236 . . . . . . . . . . . . . . . . . Ssu2g2067 . . . . . . . . . . . . . . . . . . . . .
Vvi2g1087 . . . . Adu05g00224 . . . . . . . . . . . . . . . Arst5g00272 . . . . . Bva08g01048 . . . . . . . . . . . . . . . . . . . . . Lal15g0347 . . . . . Lan18g0825 . . . . . . . . . . . . . . . . . Lja2g0726 . Mal6g0559 . . . . . . . Mtr5g1105 . . . Phco4g00666 . . . Psa2g3240 . Pste1g00094 . . . . . . . Pvu2g1308 . Rops1g01358 . Seca10g01201 . Spst2g01121 . . . . . Tpr2g1355 . . . Tsu05g01100 . Vian10g00979 . Vifa1g06080 . Vimu7g03313 . Viun2g01603 . . . . .
Vvi2g1088 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lal23g1159 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g1089 . . . . Adu05g00225 . Aed11g1039 . Aev05g0237 . Ahy15g0217 . Aip05g00203 . . . . . Apr7g1853 . Arst5g00273 . Bach4g00900 . . . Bva08g01047 . . . Cca06g01092 . . . Dod02g0252 . . . . . . Gma09g01999 . . . . . . Lal15g0346 . . . . . Lan18g0826 . . . . . Lapu2g00939 . Lasa2g03656 . . . . . . . . . Lja2g0725 . Mal6g0558 . Mepo5g01236 . Mesa17g01322 . . . Mtr5g1104 . . . Phco4g00667 . . . Psa2g3244 . Pste1g00087 . . Pte12g00606 . . . . Pvu2g1307 . Rops1g01359 . Seca10g01200 . . . Ssu2g2069 . . Sto11g1211 Tpr2g1354 . Trre9g01611 . Tsu05g01098 . Vian10g00977 . Vifa1g06081 . Vimu7g03312 . Viun2g01606 . Vivi2g02583 . . .
Vvi2g1090 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g1091 . . . . Adu05g00226 . Aed11g1040 . Aev05g0240 . Ahy15g0218 . Aip05g00204 . . . . . Apr7g1854 . Arst5g00274 . Bach4g00899 . . . Bva08g01046 Bva11g01362 . . Cca06g01093 . . . Dod02g0254 . . . . . Gma01g01546 Gma09g02000 . . Gso1g1281 Gso1g1281 . . Lal15g0344 . . . . . Lan18g0828 . . . . . Lapu2g00941 . Lasa2g03655 . . . . . . . . . Lja2g0724 . Mal6g0556 . Mepo5g01234 . Mesa17g01321 . . . Mtr5g1103 . Phac2g02026 . Phco4g00668 . . . Psa2g3246 . Pste1g00078 . . . . . . . Pvu2g1306 . Rops1g01360 . Seca10g01199 . Spst2g01118 . Ssu2g2071 . . . Tpr2g1353 . Trre9g01609 . Tsu05g01097 . Vian10g00976 . Vifa1g06082 . Vimu7g03310 . Viun2g01608 . Vivi2g02584 . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Sto Sto11g1211 Chr11 12028498 12033795 +
Vvi Vvi2g1082 Chr2 16903963 16905207 -
Aed Aed11g1036 Chr11 16173064 16174401 +
Aev Aev05g0235 Chr05 1746174 1748408 +
Ahy Ahy15g0215 Chr15 2471201 2473371 +
Aip Aip05g00201 Chr05 2156654 2165566 +
Apr Apr7g0345 Chr7 9182633 9186103 -
Bva Bva08g01049 Chr08 5370926 5372747 -
Cca Cca06g01090 Chr06 24981461 24984425 +
Dod Dod02g0249 Chr02 3345680 3346905 +
Lal Lal15g0348 Chr15 2355742 2358001 -
Lan Lan18g0824 Chr18 13618181 13620635 +
Lja Lja2g0728 Chr2 6617030 6619500 -
Mal Mal6g0560 Chr6 7432527 7434837 -
Mtr Mtr5g1106 Chr5 11003007 11006223 -
Psa Psa2g3234 Chr2 368299752 368301028 +
Ssu Ssu2g2065 Chr2 75351114 75357493 +
Tpr Tpr2g1356 Chr2 15841769 15844118 -
Tsu Tsu05g01101 Chr05 9635243 9637832 -
Vvi Vvi2g1083 Chr2 16907409 16934203 -
Bach Bach4g00902 Chr4 6041214 6054449 +
Gma Gma09g01998 Chr09 45584378 45598406 -
Lapu Lapu2g00938 Chr2 8697584 8714127 -
Lasa Lasa2g03657 Chr2 546524736 546539496 +
Mepo Mepo5g01237 Chr5 12578146 12590085 +
Mesa Mesa17g01325 Chr17 17309013 17324548 +
Phac Phac2g03774 Chr2 38219170 38225145 +
Phco Phco4g00665 Chr4 5009515 5023248 -
Pste Pste1g00113 Chr1 438588 449946 +
Pvu Pvu2g1309 Chr2 25616145 25630562 +
Trre Trre9g01623 Chr9 14164998 14173553 +
Vimu Vimu7g03314 Chr7 28105242 28118387 +
Vivi Vivi2g02578 Chr2 116945417 116980677 -
Vvi Vvi2g1084 Chr2 17046955 17049219 -
Vvi Vvi2g1085 Chr2 17064914 17065384 -
Vvi Vvi2g1086 Chr2 17073807 17102360 -
Aed Aed11g1038 Chr11 16185510 16197961 -
Aev Aev05g0236 Chr05 1749362 1759204 -
Ahy Ahy15g0216 Chr15 2473765 2482955 -
Aip Aip05g00202 Chr05 2166186 2175007 -
Apr Apr7g1852 Chr7 25808832 25820312 -
Cca Cca06g01091 Chr06 24985700 24998709 -
Dod Dod02g0250 Chr02 3347470 3356247 -
Psa Psa2g3236 Chr2 368323885 368341954 -
Ssu Ssu2g2067 Chr2 75411052 75428004 -
Vvi Vvi2g1087 Chr2 17126803 17131472 -
Adu Adu05g00224 Chr05 2352086 2361172 -
Arst Arst5g00272 Chr5 2371923 2380784 -
Bva Bva08g01048 Chr08 5359644 5370320 +
Lal Lal15g0347 Chr15 2345237 2355616 +
Lan Lan18g0825 Chr18 13621264 13631246 -
Lja Lja2g0726 Chr2 6600251 6612286 +
Mal Mal6g0559 Chr6 7417665 7430221 +
Mtr Mtr5g1105 Chr5 10989159 11001576 +
Phco Phco4g00666 Chr4 5026874 5039167 -
Psa Psa2g3240 Chr2 368392501 368402124 -
Pste Pste1g00094 Chr1 401086 410956 +
Pvu Pvu2g1308 Chr2 25583455 25598632 +
Rops Rops1g01358 Chr1 30271284 30289223 -
Seca Seca10g01201 Chr10 11792209 11812428 +
Spst Spst2g01121 Chr2 9886145 9901647 +
Tpr Tpr2g1355 Chr2 15818450 15830587 +
Tsu Tsu05g01100 Chr05 9623055 9633436 +
Vian Vian10g00979 Chr10 10662324 10677501 +
Vifa Vifa1g06080 Chr1 949498888 949507582 -
Vimu Vimu7g03313 Chr7 28075335 28091660 +
Viun Viun2g01603 Chr2 25866035 25878194 -
Vvi Vvi2g1088 Chr2 17133923 17139180 -
Lal Lal23g1159 Chr23 13017502 13030300 -
Vvi Vvi2g1089 Chr2 17148473 17187066 -
Adu Adu05g00225 Chr05 2363033 2370402 +
Aed Aed11g1039 Chr11 16197501 16205834 +
Aev Aev05g0237 Chr05 1760093 1767458 +
Ahy Ahy15g0217 Chr15 2484840 2492307 +
Aip Aip05g00203 Chr05 2177919 2185330 +
Apr Apr7g1853 Chr7 25821616 25832794 +
Arst Arst5g00273 Chr5 2382712 2390080 +
Bach Bach4g00900 Chr4 6016884 6026752 -
Bva Bva08g01047 Chr08 5349639 5358731 -
Cca Cca06g01092 Chr06 25003420 25016669 +
Dod Dod02g0252 Chr02 3369451 3378928 +
Gma Gma09g01999 Chr09 45607963 45618182 +
Lal Lal15g0346 Chr15 2333299 2343292 -
Lan Lan18g0826 Chr18 13636438 13646041 +
Lapu Lapu2g00939 Chr2 8717566 8728127 +
Lasa Lasa2g03656 Chr2 546493701 546507632 -
Lja Lja2g0725 Chr2 6587169 6597092 -
Mal Mal6g0558 Chr6 7405026 7411549 -
Mepo Mepo5g01236 Chr5 12554013 12555528 -
Mesa Mesa17g01322 Chr17 17216990 17217575 -
Mtr Mtr5g1104 Chr5 10967815 10981908 -
Phco Phco4g00667 Chr4 5042331 5052411 +
Psa Psa2g3244 Chr2 368573848 368578702 +
Pste Pste1g00087 Chr1 363330 382634 -
Pte Pte12g00606 Chr12 5493039 5502051 -
Pvu Pvu2g1307 Chr2 25570729 25581289 -
Rops Rops1g01359 Chr1 30295603 30305716 +
Seca Seca10g01200 Chr10 11775235 11786492 -
Ssu Ssu2g2069 Chr2 75474007 75489318 +
Sto Sto11g1211 Chr11 12028498 12033795 +
Tpr Tpr2g1354 Chr2 15804918 15816518 -
Trre Trre9g01611 Chr9 14084121 14095696 -
Tsu Tsu05g01098 Chr05 9585125 9596439 -
Vian Vian10g00977 Chr10 10601318 10613044 -
Vifa Vifa1g06081 Chr1 949603644 949632564 +
Vimu Vimu7g03312 Chr7 28062133 28071462 -
Viun Viun2g01606 Chr2 25908131 25919336 +
Vivi Vivi2g02583 Chr2 117019528 117033753 +
Vvi Vvi2g1090 Chr2 17193880 17198277 -
Vvi Vvi2g1091 Chr2 17219851 17220414 +
Adu Adu05g00226 Chr05 2394020 2394993 +
Aed Aed11g1040 Chr11 16208130 16209215 +
Aev Aev05g0240 Chr05 1775239 1776755 +
Ahy Ahy15g0218 Chr15 2516795 2518169 +
Aip Aip05g00204 Chr05 2202818 2204436 +
Apr Apr7g1854 Chr7 25840453 25842296 +
Arst Arst5g00274 Chr5 2413568 2414880 +
Bach Bach4g00899 Chr4 6010583 6011797 -
Bva Bva08g01046 Chr08 5343762 5345599 -
Bva Bva11g01362 Chr11 13692524 13694151 +
Cca Cca06g01093 Chr06 25020550 25021660 +
Dod Dod02g0254 Chr02 3401399 3403456 +
Gma Gma01g01546 Chr01 50968295 50969875 +
Gma Gma09g02000 Chr09 45623388 45624892 +
Gso Gso1g1281 Chr1 49249633 49251057 +
Gso Gso1g1281 Chr1 49249633 49251057 +
Lal Lal15g0344 Chr15 2327591 2329130 -
Lan Lan18g0828 Chr18 13652629 13653983 +
Lapu Lapu2g00941 Chr2 8738707 8740139 +
Lasa Lasa2g03655 Chr2 546475225 546476367 -
Lja Lja2g0724 Chr2 6581612 6583267 -
Mal Mal6g0556 Chr6 7380540 7381706 -
Mepo Mepo5g01234 Chr5 12535789 12537443 -
Mesa Mesa17g01321 Chr17 17208045 17209211 -
Mtr Mtr5g1103 Chr5 10962009 10963799 -
Phac Phac2g02026 Chr2 22206532 22208107 -
Phco Phco4g00668 Chr4 5056153 5057328 +
Psa Psa2g3246 Chr2 368815368 368818061 +
Pste Pste1g00078 Chr1 330703 331782 -
Pvu Pvu2g1306 Chr2 25547769 25548947 -
Rops Rops1g01360 Chr1 30324999 30327338 +
Seca Seca10g01199 Chr10 11757795 11758997 -
Spst Spst2g01118 Chr2 9828000 9829139 -
Ssu Ssu2g2071 Chr2 75529673 75529996 +
Tpr Tpr2g1353 Chr2 15801269 15803130 -
Trre Trre9g01609 Chr9 14078710 14079909 -
Tsu Tsu05g01097 Chr05 9581801 9583081 -
Vian Vian10g00976 Chr10 10582741 10583886 -
Vifa Vifa1g06082 Chr1 949652320 949653459 +
Vimu Vimu7g03310 Chr7 28047514 28049624 -
Viun Viun2g01608 Chr2 25930847 25932321 +
Vivi Vivi2g02584 Chr2 117048959 117050382 +