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
Vvi17g976 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g00037 Csa01g00513 Chy12g01571 Cme12g02029 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g977 . . Bda06g00836 . . . . Bma12g01254 Cmo13g01002 Cmo18g00069 . . . . . Cpe20g00045 . . . . . . . . . . . . . . . . . . . Lsi02g00262 Csa01g00514 Chy12g01570 Cme12g02028 . Blo15g00047 . . Bpe07g01061 . . . . . . Cma13g01108 Cma18g00092 Car13g00801 Car18g00082 Cpe09g01098 . Bhi08g01334 Tan05g2153 . Lac10g0316 Hepe07g2327 . . Cla01g01469 . Cec01g1577 Cco01g1625 . . Cre01g1374 . . . .
Vvi17g978 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g979 . . . . Bpe12g00626 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo13g00095 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g980 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g981 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g982 . . Bda06g00848 . . . . . Cmo13g01159 . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0363 . . . . . . . . . Bpe07g01069 . . . . . . Cma13g01111 . Car13g00944 . . . . . . . . . . . . . . . . . . . . .
Vvi17g983 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g984 . . . . . . . . Cmo13g01158 . . . . . . Cpe20g00043 . . . . . . . . . . . . . . . . . Cone13ag0362 . Lsi02g00041 Csa01g00517 Chy12g01568 Cme12g02024 . . . . . . . Bma08g00121 . . . . . Car13g00943 . . . . . . . . . . . . . . . . . . . . .
Vvi17g985 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0361 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 11589235 11590651 - Bda024169.1 Bda06g00836 836
6 11735586 11741394 - Bda024185.1 Bda06g00848 848
8 40540292 40544330 + XM_039039226.1 Bhi08g01334 1334
13 1666316 1671288 + BLOR05376 Blo13g00095 95
15 359462 363204 + BLOR06441 Blo15g00047 47
8 1491941 1493610 + Bma027125.1 Bma08g00121 121
12 45561292 45563224 - Bma008618.1 Bma12g01254 1254
7 16063878 16065258 - Bpe021904.1 Bpe07g01061 1061
7 16095725 16101494 - Bpe021912.1 Bpe07g01069 1069
12 11912430 11917271 + Bpe005886.1 Bpe12g00626 626
13 8834563 8838778 - Carg04871-RA Car13g00801 801
13 9608632 9612407 - Carg04728-RA Car13g00943 943
13 9613301 9620624 - Carg04727-RA Car13g00944 944
18 437730 441269 + Carg06647-RA Car18g00082 82
1 28934797 28938204 - CcPI632755_01g016250.1 Cco01g1625 1625
1 30352451 30366984 - CePI673135_01g015770.1 Cec01g1577 1577
12 19242467 19246299 + Chy12G221680.1 Chy12g01568 1568
12 19253698 19260044 + Chy12G221700.1 Chy12g01570 1570
12 19260439 19261791 - Chy12G221710.1 Chy12g01571 1571
1 29230299 29245262 - ClCG01G014900.2 Cla01g01469 1469
13 8300321 8303918 - CmaCh13G011080.1 Cma13g01108 1108
13 8310637 8318329 - CmaCh13G011110.1 Cma13g01111 1111
18 427312 430754 + CmaCh18G000920.1 Cma18g00092 92
12 25794492 25798808 + MELO3C001956.2.1 Cme12g02024 2024
12 25810731 25813481 + MELO3C001952.2.1 Cme12g02028 2028
12 25813539 25814945 - MELO3C001951.2.1 Cme12g02029 2029
13 8530762 8534840 - CmoCh13G010020.1 Cmo13g01002 1002
13 9325582 9329716 - CmoCh13G011580.1 Cmo13g01158 1158
13 9330678 9336812 - CmoCh13G011590.1 Cmo13g01159 1159
18 472938 476122 + CmoCh18G000690.1 Cmo18g00069 69
13 3270739 3275257 - Conep13aG0038100.1 Cone13ag0361 361
13 3279189 3284614 - Conep13aG0038200.1 Cone13ag0362 362
13 3287540 3295101 + Conep13aG0038300.1 Cone13ag0363 363
9 9477625 9482068 - Cp4.1LG09g11010.1 Cpe09g01098 1098
20 196724 200776 + Cp4.1LG20g00480.1 Cpe20g00043 43
20 201943 206230 + Cp4.1LG20g00510.1 Cpe20g00045 45
1 26923138 26937655 - CrPI670011_01g013740.1 Cre01g1374 1374
1 3415666 3416784 + CsaV3_1G005130.1 Csa01g00513 513
1 3417418 3420676 - CsaV3_1G005140.1 Csa01g00514 514
1 3431491 3436573 - CsaV3_1G005170.1 Csa01g00517 517
7 67598879 67602023 - Hsped.07g23270.1 Hepe07g2327 2327
10 2463769 2466607 + Lag0024361.1 Lac10g0316 316
2 387156 388206 + Lsi02G000370.1 Lsi02g00037 37
2 406421 411103 - Lsi02G000410.1 Lsi02g00041 41
2 2248508 2251978 + Lsi02G002620.1 Lsi02g00262 262
5 72259158 72263699 - Tan0004971.1 Tan05g2153 2153
17 15631826 15634248 - Vvi17g976 Vvi17g976 976
17 15635142 15638604 - Vvi17g977 Vvi17g977 977
17 15675900 15676431 + Vvi17g978 Vvi17g978 978
17 15684396 15698230 + Vvi17g979 Vvi17g979 979
17 15811508 15812357 - Vvi17g980 Vvi17g980 980
17 15915384 15917742 - Vvi17g981 Vvi17g981 981
17 15920268 15928175 + Vvi17g982 Vvi17g982 982
17 15973975 15974229 - Vvi17g983 Vvi17g983 983
17 15994778 15999389 + Vvi17g984 Vvi17g984 984
17 16030702 16074072 + Vvi17g985 Vvi17g985 985
       

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