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
Vvi18g420 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g421 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g422 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g04451 . . . . . . . . . . . . Cmo09g00553 . . . . . . Bhi09g02443 . . . . Mch11g0670 . . . . . . . . . . . .
Vvi18g423 . . . . . . . . . . . Cma09g00564 . . . . . . . . . . . . . . . . . . . . . . . Lsi04g02240 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla11g01388 . . . . . . . . . .
Vvi18g424 . . Bda01g00889 . Bpe02g00113 . . . Cmo05g00530 . . . Car01g01230 Car12g00150 Sed04g0148 . Cpe07g00138 Bhi04g00770 Tan02g2401 Cmetu03g2126 . Hepe10g0490 . Lcy13g1554 Cla08g01116 Cam08g1572 Cec08g1142 Cco08g1269 Clacu08g1273 . Cre08g1054 . . . . Lsi04g02241 Csa03g04452 . . . . Bda11g00770 . Bpe02g01125 Bpe14g00457 . . . Cmo01g01658 . . Cma05g00504 Car05g00453 . Cpe11g00443 . Bhi09g02444 Tan01g3796 . . Hepe01g2133 . . . . . . . . . Lsi08g00972 Csa02g02156 . .
Vvi18g425 . . . . . . . . Cmo05g00531 . . Cma09g00565 . . . Cpe06g00429 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo09g00554 . . Car05g00454 . Cpe11g00444 . . . . . . . . . . . . . . . . . . .
Vvi18g426 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g427 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g428 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy04g00249 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme04g00278
Vvi18g429 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 41877109 41878062 - Bda003026.1 Bda01g00889 889
11 7756593 7757588 + Bda005519.1 Bda11g00770 770
4 18904603 18906960 - XM_039029641.1 Bhi04g00770 770
9 66500321 66503461 - XM_039040951.1 Bhi09g02443 2443
9 66602848 66603960 - XM_039042962.1 Bhi09g02444 2444
2 824393 825391 + Bpe007963.1 Bpe02g00113 113
2 14883861 14884814 - Bpe008983.1 Bpe02g01125 1125
14 4149829 4150809 + Bpe007107.1 Bpe14g00457 457
8 21903946 21905676 - CaPI482276_08g015720.1 Cam08g1572 1572
1 11290104 11291090 + Carg25634-RA Car01g01230 1230
5 2589777 2590721 + Carg08194-RA Car05g00453 453
5 2592086 2599844 + Carg08195-RA Car05g00454 454
12 864000 865586 - Carg20535-RA Car12g00150 150
8 24478760 24480559 - CcPI632755_08g012690.1 Cco08g1269 1269
8 23332416 23334301 - CePI673135_08g011420.1 Cec08g1142 1142
4 2222694 2224498 + Chy4G069670.1 Chy04g00249 249
8 22678057 22679785 - ClG42_08g0127300.10 Clacu08g1273 1273
8 23914129 23915858 - ClCG08G011180.2 Cla08g01116 1116
11 27426974 27429827 - ClCG11G014180.2 Cla11g01388 1388
5 2401008 2404294 + CmaCh05G005040.1 Cma05g00504 504
9 2558665 2561843 - CmaCh09G005640.1 Cma09g00564 564
9 2564998 2568719 + CmaCh09G005650.1 Cma09g00565 565
4 2196303 2198487 + MELO3C003567.2.1 Cme04g00278 278
3 2530561 2532376 - PI0014225.1 Cmetu03g2126 2126
1 12556596 12557582 + CmoCh01G016580.1 Cmo01g01658 1658
5 2559518 2560384 + CmoCh05G005300.1 Cmo05g00530 530
5 2561802 2563043 + CmoCh05G005310.1 Cmo05g00531 531
9 2637554 2640923 - CmoCh09G005530.1 Cmo09g00553 553
9 2643677 2646720 + CmoCh09G005540.1 Cmo09g00554 554
6 2458900 2462547 + Cp4.1LG06g04370.1 Cpe06g00429 429
7 780195 781880 - Cp4.1LG07g01360.1 Cpe07g00138 138
11 2507835 2508779 + Cp4.1LG11g04410.1 Cpe11g00443 443
11 2510022 2516643 + Cp4.1LG11g04580.1 Cpe11g00444 444
8 23677341 23679242 - CrPI670011_08g010540.1 Cre08g1054 1054
2 19478160 19480421 - CsaV3_2G029750.1 Csa02g02156 2156
3 38829253 38831485 - CsaV3_3G047570.1 Csa03g04451 4451
3 38839168 38840584 - CsaV3_3G047580.1 Csa03g04452 4452
1 86002079 86003403 - Hsped.01g21330.1 Hepe01g2133 2133
10 5688423 5690580 + Hsped.10g04900.1 Hepe10g0490 490
13 34401224 34403232 + Maker00033879 Lcy13g1554 1554
4 29449919 29453351 - Lsi04G022400.1 Lsi04g02240 2240
4 29464183 29465109 - Lsi04G022410.1 Lsi04g02241 2241
8 18196425 18198868 - Lsi08G009720.1 Lsi08g00972 972
11 4390979 4393509 - MC11g0561 Mch11g0670 670
4 1011824 1013966 - Sed0013917.1 Sed04g0148 148
1 102887653 102888847 - Tan0014174.1 Tan01g3796 3796
2 92584429 92587150 - Tan0017703.1 Tan02g2401 2401
18 4535172 4537082 + Vvi18g420 Vvi18g420 420
18 4544136 4544831 + Vvi18g421 Vvi18g421 421
18 4550435 4552363 + Vvi18g422 Vvi18g422 422
18 4564026 4586046 - Vvi18g423 Vvi18g423 423
18 4595725 4599044 + Vvi18g424 Vvi18g424 424
18 4600962 4602556 + Vvi18g425 Vvi18g425 425
18 4605339 4607035 - Vvi18g426 Vvi18g426 426
18 4610528 4612093 - Vvi18g427 Vvi18g427 427
18 4612776 4631139 - Vvi18g428 Vvi18g428 428
18 4631191 4631628 + Vvi18g429 Vvi18g429 429
       

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