Doc-Alignment

  Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Cucurbitales genomes. We used V.vinifera as a reference, and by comparing homologous gene locus maps and Ks values between V.vinifera and other Cucurbitales, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We created a hierarchical lists of homologous genes using V.vinifera as a reference.
  The relevant gene ids can be obtained from the Cucurbitales blast and match under the Tools module. This link is Cucurbitales blast and match.

Orthogroup analysis platform
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Select Vvi1 Blo1 Blo2 Bda1 Bda2 Bpe1 Bpe2 Bma1 Bma2 Cmo1 Cmo2 Cma1 Cma2 Car1 Car2 Sed1 Cpe1 Cpe2 Bhi1 Tan1 Cmetu1 Lac1 Hepe1 Mch1 Lcy1 Cla1 Cam1 Cec1 Cco1 Clacu1 Cmu1 Cre1 Cone1 Cone2 Cone3 Cone4 Lsi1 Csa1 Chy1 Cme1 Blo3 Blo4 Bda3 Bda4 Bpe3 Bpe4 Bma3 Bma4 Sed2 Cmo3 Cmo4 Cma3 Cma4 Car3 Car4 Cpe3 Cpe4 Bhi2 Tan2 Cmetu2 Lac2 Hepe2 Mch2 Lcy2 Cla2 Cam2 Cec2 Cco2 Clacu2 Cmu2 Cre2 Lsi2 Csa2 Chy2 Cme2
Vvi1g961 Blo01g00438 . Bda01g02141 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma01g00109 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g962 . . . . . . . . . Cmo18g01153 . Cma18g01131 . Car18g01044 Sed07g1954 Cpe09g00196 . Bhi07g01532 Tan04g1053 Cmetu10g1096 Lac13g0340 Hepe10g1766 . . Cla05g02421 Cam05g2603 Cec05g2635 Cco05g2674 Clacu05g2604 Cmu05g2457 Cre05g2573 . . . . Lsi04g00395 . Chy10g01027 Cme10g00391 . . Bda07g01518 . . . . . . Cmo04g02908 . . . . Car15g00257 Cpe13g00962 . . . . . . . . . . . . . . . . . Chy09g00229 .
Vvi1g963 Blo01g00440 Blo16g01102 Bda01g02140 Bda11g01200 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g01200 . Bpe02g02328 Bma01g00111 Bma06g00711 . . . . . . . . Cpe07g00642 . . . . . . . . . . . . . . . . . .
Vvi1g964 . . . . . . . . . Cmo18g01150 . Cma18g01128 . Car18g01042 Sed06g1507 . . Bhi07g01530 Tan04g1051 Cmetu06g0752 Lac13g0343 Hepe10g1767 . . Cla05g02420 Cam05g2601 Cec05g2632 Cco05g2672 Clacu05g2602 Cmu05g2456 Cre05g2572 . . . . Lsi04g00392 . Chy10g01029 Cme10g00389 . . . . . . . . . . . . . . Car15g00256 Cpe13g00964 . . . . . . . . . . . . . . . . . Chy09g00228 .
Vvi1g965 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g02480 . . . . . . . . . . . . . . . Car04g01715 . . . . . . . . . . . . . . . . . . . . .
Vvi1g966 . . . . . . . . Cmo04g01756 . . . . . . . Cpe01g01483 . . . . . . . . . . . . . . . . . . . Csa05g02482 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g967 . . . . . . Bma14g01656 . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0939 Cone19ag0933 . . . . . . . . Bda07g01477 . Bpe11g01651 . . . . . . Cma04g01674 . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g968 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g969 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g970 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 57357883 57359151 + Bda004471.1 Bda01g02140 2140
1 57362405 57365496 - Bda004472.2 Bda01g02141 2141
7 27484867 27486294 - Bda028316.1 Bda07g01477 1477
7 28226724 28227291 - Bda028369.1 Bda07g01518 1518
11 12330571 12336818 + Bda007700.1 Bda11g01200 1200
7 44144469 44153594 + XM_039037152.1 Bhi07g01530 1530
7 44192809 44204332 - XM_039036250.1 Bhi07g01532 1532
1 4887213 4889903 + BLOR00438 Blo01g00438 438
1 4893869 4895137 - BLOR00440 Blo01g00440 440
16 39522729 39523997 + BLOR21889 Blo16g01102 1102
1 1127505 1130530 + Bma000273.1 Bma01g00109 109
1 1133855 1135123 - Bma000275.1 Bma01g00111 111
6 37719689 37720957 - Bma023695.1 Bma06g00711 711
14 35160052 35162425 - Bma012387.1 Bma14g01656 1656
2 23895408 23896676 + Bpe010144.1 Bpe02g02328 2328
11 12665607 12668092 - Bpe004964.1 Bpe11g01651 1651
5 33640121 33645968 + CaPI482276_05g026010.1 Cam05g2601 2601
5 33650619 33655802 - CaPI482276_05g026030.1 Cam05g2603 2603
4 9825448 9830741 - Carg14390-RA Car04g01715 1715
15 1401596 1405306 + Carg02237-RA Car15g00256 256
15 1406802 1411828 + Carg02238-RA Car15g00257 257
18 10741170 10745217 + Carg17288-RA Car18g01042 1042
18 10748549 10753089 - Carg17286-RA Car18g01044 1044
5 34757863 34763792 + CcPI632755_05g026720.1 Cco05g2672 2672
5 34768376 34773519 - CcPI632755_05g026740.1 Cco05g2674 2674
5 37087113 37093020 + CePI673135_05g026320.1 Cec05g2632 2632
5 37097643 37102795 - CePI673135_05g026350.1 Cec05g2635 2635
9 1878418 1883925 + Chy9G159440.1 Chy09g00228 228
9 1892265 1895946 + Chy9G159450.1 Chy09g00229 229
10 15571648 15576304 + Chy10G182210.1 Chy10g01027 1027
10 15580670 15585557 - Chy10G182230.1 Chy10g01029 1029
5 33850564 33856372 + ClG42_05g0260200.10 Clacu05g2602 2602
5 33861040 33866537 - ClG42_05g0260400.10 Clacu05g2604 2604
5 35726984 35731517 + ClCG05G024030.1 Cla05g02420 2420
5 35733964 35741570 - ClCG05G024040.2 Cla05g02421 2421
4 8413327 8421263 - CmaCh04G016740.1 Cma04g01674 1674
18 9171562 9175800 + CmaCh18G011280.1 Cma18g01128 1128
18 9179371 9183768 - CmaCh18G011310.1 Cma18g01131 1131
10 2508238 2514291 + MELO3C012122.2.1 Cme10g00389 389
10 2519820 2524456 - MELO3C012120.2.1 Cme10g00391 391
6 3228686 3229175 + PI0016390.1 Cmetu06g0752 752
10 19502152 19506845 + PI0006057.1 Cmetu10g1096 1096
4 8859495 8864772 - CmoCh04G017560.1 Cmo04g01756 1756
4 20658145 20663200 - CmoCh04G029080.1 Cmo04g02908 2908
18 11756744 11760818 + CmoCh18G011500.1 Cmo18g01150 1150
18 11763544 11768562 - CmoCh18G011530.1 Cmo18g01153 1153
5 33588277 33594083 + CmPI595203_05g024560.1 Cmu05g2456 2456
5 33594257 33604227 - CmPI595203_05g024570.1 Cmu05g2457 2457
13 8118397 8120246 + Conep13aG0096700.1 Cone13ag0939 939
19 7163228 7163500 + Conep19aG0096100.1 Cone19ag0933 933
1 8847065 8849473 - Cp4.1LG01g12250.1 Cpe01g01483 1483
7 4585726 4588662 + Cp4.1LG07g06500.1 Cpe07g00642 642
9 1127142 1128238 - Cp4.1LG09g01940.1 Cpe09g00196 196
13 8047720 8048600 - Cp4.1LG13g08410.1 Cpe13g00962 962
13 8050573 8054274 - Cp4.1LG13g08400.1 Cpe13g00964 964
5 36944613 36950318 + CrPI670011_05g025720.1 Cre05g2572 2572
5 36951933 36960007 - CrPI670011_05g025730.1 Cre05g2573 2573
5 26522669 26527656 + CsaV3_5G032990.1 Csa05g02480 2480
5 26530988 26536992 - CsaV3_5G033010.1 Csa05g02482 2482
10 54418350 54424696 + Hsped.10g17660.1 Hepe10g1766 1766
10 54430577 54437583 - Hsped.10g17670.1 Hepe10g1767 1767
13 2419196 2424646 + Lag0040136.1 Lac13g0340 340
13 2443677 2449101 - Lag0040139.1 Lac13g0343 343
4 3881727 3887387 + Lsi04G003920.1 Lsi04g00392 392
4 3891777 3897878 - Lsi04G003950.1 Lsi04g00395 395
6 39757228 39764063 + Sed0027706.1 Sed06g1507 1507
7 34058648 34064183 + Sed0027199.1 Sed07g1954 1954
4 9372843 9378368 + Tan0017985.1 Tan04g1051 1051
4 9382878 9388536 - Tan0020363.1 Tan04g1053 1053
1 14007415 14010547 - Vvi1g961 Vvi1g961 961
1 14039773 14044487 + Vvi1g962 Vvi1g962 962
1 14045553 14050837 - Vvi1g963 Vvi1g963 963
1 14162393 14167671 + Vvi1g964 Vvi1g964 964
1 14194101 14198256 + Vvi1g965 Vvi1g965 965
1 14198850 14219965 + Vvi1g966 Vvi1g966 966
1 14246015 14249230 + Vvi1g967 Vvi1g967 967
1 14274406 14275715 + Vvi1g968 Vvi1g968 968
1 14302828 14303488 - Vvi1g969 Vvi1g969 969
1 14353828 14356884 - Vvi1g970 Vvi1g970 970
       

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