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
Vvi2g442 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g00349 Chy09g01155 . . . . . . . . . . . . . . . . . . Bhi12g00547 . . . . . . Cla01g00330 . . . . . . Lsi09g00352 . . Cme09g01689
Vvi2g443 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g00351 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g444 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g445 Blo02g01076 . . . Bpe05g00614 . . . . . . . . . . . . Bhi11g00227 Tan01g1959 . . Hepe06g1190 . . Cla10g00317 Cam10g0332 Cec10g0346 Cco10g0338 Clacu10g0329 Cmu10g1169 Cre10g0579 . . . . Lsi07g01366 . . Cme06g02651 . . . . . . Bma05g00794 . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g00340 Chy06g01985 .
Vvi2g446 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g447 Blo02g01075 Blo03g00182 . . Bpe05g00613 Bpe07g00138 . . . . . . . . . . . . . . . . . . Cla10g00316 Cam10g0331 Cec10g0344 Cco10g0336 Clacu10g0327 Cmu10g1167 Cre10g0577 . . Cone6ag0728 . Lsi07g01365 Csa05g00353 Chy09g01154 Cme06g02650 . . . . . . Bma05g00793 Bma12g00114 . . . . . Car06g00661 . . . Bhi12g00349 . . Lac11g2183 Hepe06g1188 . . Cla01g00331 Cam01g0343 Cec01g0339 Cco01g0351 Clacu01g0347 Cmu01g0327 Cre09g2183 Lsi09g00353 Csa03g00339 Chy06g01986 Cme09g01686
Vvi2g448 Blo02g01074 . . . Bpe05g00612 . . . Cmo06g00762 Cmo16g01074 . . . . . Cpe14g00848 . . . . . . . . Cla10g00315 Cam10g0330 Cec10g0343 Cco10g0335 Clacu10g0326 Cmu10g1166 Cre10g0576 . . Cone6ag0727 Cone9ag0733 Lsi07g01364 . . Cme06g02649 . . . . . . Bma05g00792 . . . . Cma06g00740 Cma16g01028 . Car16g00979 Cpe08g00780 . . . . . . . . . . . . . . . . Csa03g00338 Chy06g01987 .
Vvi2g449 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo19g00180 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g450 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g451 Blo02g01073 . . . . . . . . Cmo16g01075 . . . . . Cpe14g00849 . . . . . . . . Cla10g00314 Cam10g0329 Cec10g0342 Cco10g0334 Clacu10g0325 Cmu10g1165 Cre10g0575 . . . . Lsi07g01363 . . Cme06g02648 . . . . . . Bma05g00791 Bma12g00115 . . . . Cma16g01029 . Car16g00980 . . . . . . . . . . . . . . . . . Csa03g00337 Chy06g01988 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 5397142 5399421 - XM_039047996.1 Bhi11g00227 227
12 11145192 11146700 + XM_039020174.1 Bhi12g00349 349
12 17499269 17502270 - XM_039018749.1 Bhi12g00547 547
2 41101062 41111957 + BLOR10803 Blo02g01073 1073
2 41112586 41114568 - BLOR10804 Blo02g01074 1074
2 41115933 41117009 - BLOR10805 Blo02g01075 1075
2 41124286 41127198 + BLOR10806 Blo02g01076 1076
3 4486290 4487366 - BLOR11363 Blo03g00182 182
19 7721288 7726473 - BLOR09523 Blo19g00180 180
5 44916735 44920984 + Bma021893.1 Bma05g00791 791
5 44921691 44923592 - Bma031209 Bma05g00792 792
5 44924973 44926049 - Bma021894.1 Bma05g00793 793
5 44943899 44947026 + Bma021895.1 Bma05g00794 794
12 1761448 1762530 + Bma006988.1 Bma12g00114 114
12 1764413 1768313 - Bma006989.1 Bma12g00115 115
5 20074685 20076641 - Bpe018028.1 Bpe05g00612 612
5 20078052 20079128 - Bpe018029.1 Bpe05g00613 613
5 20081058 20084194 + Bpe018030.1 Bpe05g00614 614
7 976019 977101 + Bpe020949.1 Bpe07g00138 138
1 3831226 3832257 + CaPI482276_01g003430.1 Cam01g0343 343
10 5444830 5449589 + CaPI482276_10g003290.1 Cam10g0329 329
10 5450164 5455368 - CaPI482276_10g003300.1 Cam10g0330 330
10 5461927 5463003 - CaPI482276_10g003310.1 Cam10g0331 331
10 5469318 5472568 - CaPI482276_10g003320.1 Cam10g0332 332
6 3941908 3942981 - Carg21621-RA Car06g00661 661
16 8312375 8315333 + Carg25291-RA Car16g00979 979
16 8315418 8320035 - Carg25290-RA Car16g00980 980
1 3491624 3492655 + CcPI632755_01g003510.1 Cco01g0351 351
10 3928783 3933706 + CcPI632755_10g003340.1 Cco10g0334 334
10 3934284 3939537 - CcPI632755_10g003350.1 Cco10g0335 335
10 3945790 3946866 - CcPI632755_10g003360.1 Cco10g0336 336
10 3953246 3956498 - CcPI632755_10g003380.1 Cco10g0338 338
1 3501589 3502620 + CePI673135_01g003390.1 Cec01g0339 339
10 4103922 4108814 + CePI673135_10g003420.1 Cec10g0342 342
10 4109371 4114575 - CePI673135_10g003430.1 Cec10g0343 343
10 4122475 4123551 - CePI673135_10g003440.1 Cec10g0344 344
10 4129886 4133133 - CePI673135_10g003460.1 Cec10g0346 346
6 23835256 23838558 + Chy6G125130.1 Chy06g01985 1985
6 23844025 23845101 + Chy6G125140.1 Chy06g01986 1986
6 23848617 23852524 + Chy6G125150.1 Chy06g01987 1987
6 23853048 23857861 - Chy6G125160.1 Chy06g01988 1988
9 13785342 13786373 - Chy9G168700.1 Chy09g01154 1154
9 13789129 13791729 + Chy9G168710.1 Chy09g01155 1155
1 3473542 3474573 + ClG42_01g0034700.10 Clacu01g0347 347
10 4208160 4213016 + ClG42_10g0032500.10 Clacu10g0325 325
10 4213520 4218689 - ClG42_10g0032600.10 Clacu10g0326 326
10 4225269 4226345 - ClG42_10g0032700.10 Clacu10g0327 327
10 4232082 4235332 - ClG42_10g0032900.10 Clacu10g0329 329
1 3568732 3573384 - ClCG01G003410.2 Cla01g00330 330
1 3578358 3579389 + ClCG01G003430.1 Cla01g00331 331
10 4152366 4158056 + ClCG10G003340.1 Cla10g00314 314
10 4158575 4163754 - ClCG10G003350.1 Cla10g00315 315
10 4170326 4171402 - ClCG10G003360.1 Cla10g00316 316
10 4175305 4180386 - ClCG10G003370.1 Cla10g00317 317
6 3738863 3741562 - CmaCh06G007400.1 Cma06g00740 740
16 7902238 7905410 + CmaCh16G010280.1 Cma16g01028 1028
16 7905410 7910227 - CmaCh16G010290.1 Cma16g01029 1029
6 33657369 33661318 + MELO3C014003.2.1 Cme06g02648 2648
6 33662432 33667279 - MELO3C014004.2.1 Cme06g02649 2649
6 33670153 33671692 - MELO3C014005.2.1 Cme06g02650 2650
6 33675483 33680820 - MELO3C014006.2.1 Cme06g02651 2651
9 21540286 21541620 - MELO3C005600.2.1 Cme09g01686 1686
9 21554909 21557719 + MELO3C005602.2.1 Cme09g01689 1689
6 3957413 3960030 - CmoCh06G007620.1 Cmo06g00762 762
16 7589230 7592346 + CmoCh16G010740.1 Cmo16g01074 1074
16 7593430 7598111 - CmoCh16G010750.1 Cmo16g01075 1075
1 3419229 3420260 + CmPI595203_01g003270.1 Cmu01g0327 327
10 4350655 4355440 + CmPI595203_10g011650.1 Cmu10g1165 1165
10 4356021 4361194 - CmPI595203_10g011660.1 Cmu10g1166 1166
10 4367775 4368851 - CmPI595203_10g011670.1 Cmu10g1167 1167
10 4374591 4377841 - CmPI595203_10g011690.1 Cmu10g1169 1169
6 3669355 3671817 - Conep06aG0074900.1 Cone6ag0727 727
6 3672437 3673276 - Conep06aG0075000.1 Cone6ag0728 728
9 3489544 3491070 - Conep09aG0075000.1 Cone9ag0733 733
8 6216872 6220243 + Cp4.1LG08g07810.1 Cpe08g00780 780
14 7012586 7015663 + Cp4.1LG14g08430.1 Cpe14g00848 848
14 7016073 7021689 - Cp4.1LG14g08480.1 Cpe14g00849 849
9 40887498 40888529 - CrPI670011_09g021830.1 Cre09g2183 2183
10 5277345 5282182 + CrPI670011_10g005750.1 Cre10g0575 575
10 5282761 5288000 - CrPI670011_10g005760.1 Cre10g0576 576
10 5294329 5295405 - CrPI670011_10g005770.1 Cre10g0577 577
10 5301753 5305005 - CrPI670011_10g005790.1 Cre10g0579 579
3 2809525 2815467 + CsaV3_3G003370.1 Csa03g00337 337
3 2814812 2818508 - CsaV3_3G003380.1 Csa03g00338 338
3 2820935 2822976 - CsaV3_3G003390.1 Csa03g00339 339
3 2825151 2830780 - CsaV3_3G003400.1 Csa03g00340 340
5 2234239 2237777 - CsaV3_5G003490.1 Csa05g00349 349
5 2242558 2246789 + CsaV3_5G003510.1 Csa05g00351 351
5 2250983 2253170 + CsaV3_5G003530.1 Csa05g00353 353
6 61389184 61390260 - Hsped.06g11880.1 Hepe06g1188 1188
6 61417577 61422025 - Hsped.06g11900.1 Hepe06g1190 1190
11 37962485 37963510 + Lag0032821.1 Lac11g2183 2183
7 19832382 19837687 + Lsi07G013630.1 Lsi07g01363 1363
7 19837934 19851552 - Lsi07G013640.1 Lsi07g01364 1364
7 19852343 19853419 - Lsi07G013650.1 Lsi07g01365 1365
7 19856844 19862647 - Lsi07G013660.1 Lsi07g01366 1366
9 3673185 3681224 - Lsi09G003520.1 Lsi09g00352 352
9 3684551 3685582 + Lsi09G003530.1 Lsi09g00353 353
1 21717828 21725718 + Tan0014823.1 Tan01g1959 1959
2 4399411 4401227 + Vvi2g442 Vvi2g442 442
2 4402597 4404744 + Vvi2g443 Vvi2g443 443
2 4404762 4411169 + Vvi2g444 Vvi2g444 444
2 4413956 4418111 - Vvi2g445 Vvi2g445 445
2 4421517 4424601 + Vvi2g446 Vvi2g446 446
2 4424612 4427223 + Vvi2g447 Vvi2g447 447
2 4431619 4434153 + Vvi2g448 Vvi2g448 448
2 4434337 4436260 - Vvi2g449 Vvi2g449 449
2 4438965 4440027 + Vvi2g450 Vvi2g450 450
2 4445124 4451530 - Vvi2g451 Vvi2g451 451
       

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