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
Vvi18g1370 Blo01g01730 . . Bda03g00393 Bpe02g00211 Bpe04g00355 Bma04g00371 Bma01g02509 Cmo04g02568 Cmo15g00598 . . Car01g00864 . . . . . . . . . . . . . . . . . . Cone4ag1498 Cone7ag1450 . . . . . . . . Bda11g00872 . . . . . . . . . . Car04g02360 Car15g00550 Cpe01g02120 . . . . . . . . . . . . . . . . . Chy03g00502 .
Vvi18g1371 . . . . . . . . . . . . . . . . Cpe13g00686 . . . . . . . . . . . . . . . . . Cone20ag0376 . . . Cme03g00308 Blo17g00145 . . Bda13g01431 . Bpe14g00429 . Bma02g00167 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1372 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1500 Cone7ag1449 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla09g00948 Cam09g0999 Cec09g1000 Cco09g1012 . . Cre09g0962 . . . .
Vvi18g1373 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1374 Blo01g01729 Blo12g00785 . Bda03g00392 Bpe02g00212 Bpe04g00354 Bma04g00370 Bma01g02508 . . . . . . . Cpe06g00909 . . . . . . . . . . . . . . . . . Cone17ag0783 . . . . . . . Bda11g00873 . . . . . . . . . . . . . . Bhi09g01534 . . . . Mch11g1487 . . . . . . . . . . . Cme01g00793
Vvi18g1375 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1376 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma01g01448 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1377 Blo01g01728 Blo12g00786 . Bda03g00391 Bpe02g00213 Bpe04g00353 Bma04g00369 Bma01g02507 Cmo04g02565 Cmo15g00602 . . . . . . Cpe13g00683 Bhi04g01774 Tan11g1139 . . . . . Cla08g00355 Cam08g0782 Cec08g0347 Cco08g0447 Clacu08g0497 . Cre08g0325 . . . . . . . Cme03g00315 . . Bda11g00874 . . . . . . . . . . Car04g02358 Car15g00552 Cpe01g02118 . . . . . . . . . . . . . . . Lsi08g00555 . Chy03g00507 .
Vvi18g1378 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1379 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 3234059 3237298 + Bda016354.1 Bda03g00391 391
3 3238759 3239904 + Bda016355.1 Bda03g00392 392
3 3243371 3245883 - Bda016356.1 Bda03g00393 393
11 8586249 8588311 + Bda005625.1 Bda11g00872 872
11 8590541 8591695 - Bda005626.1 Bda11g00873 873
11 8595125 8598560 - Bda005627.3 Bda11g00874 874
13 37007159 37008296 - Bda000257.1 Bda13g01431 1431
4 43071404 43075526 - XM_039029608.1 Bhi04g01774 1774
9 41239668 41244045 - XM_039041683.1 Bhi09g01534 1534
1 57017987 57021257 + BLOR01728 Blo01g01728 1728
1 57023266 57024420 + BLOR01729 Blo01g01729 1729
1 57027097 57029185 - BLOR01730 Blo01g01730 1730
12 26249875 26251020 - BLOR04804 Blo12g00785 785
12 26257209 26259917 - BLOR04805 Blo12g00786 786
17 1343171 1344100 - BLOR15966 Blo17g00145 145
1 25334657 25336423 + Bma001825.1 Bma01g01448 1448
1 82764747 82768121 + Bma003386.1 Bma01g02507 2507
1 82771294 82772448 + Bma003387.1 Bma01g02508 2508
1 82779991 82782049 - Bma003389.1 Bma01g02509 2509
2 1467948 1468828 - Bma014622.1 Bma02g00167 167
4 2965742 2969068 + Bma018827.1 Bma04g00369 369
4 2973219 2974367 + Bma018828.1 Bma04g00370 370
4 2978451 2980962 - Bma018829.1 Bma04g00371 371
2 1470144 1472158 + Bpe008060.1 Bpe02g00211 211
2 1474421 1475575 - Bpe008061.1 Bpe02g00212 212
2 1479145 1482527 - Bpe025063 Bpe02g00213 213
4 2239597 2242949 + Bpe015045.1 Bpe04g00353 353
4 2245064 2246200 + Bpe015046.1 Bpe04g00354 354
4 2249520 2252057 - Bpe025613 Bpe04g00355 355
14 3942566 3943506 + Bpe007080.1 Bpe14g00429 429
8 8903032 8905691 - CaPI482276_08g007820.1 Cam08g0782 782
9 10371803 10380006 + CaPI482276_09g009990.1 Cam09g0999 999
1 7437296 7439116 - Carg28260-RA Car01g00864 864
4 18952185 18956505 + Carg15792-RA Car04g02358 2358
4 18962141 18963257 + Carg15794-RA Car04g02360 2360
15 3026222 3029444 - Carg01606-RA Car15g00550 550
15 3044590 3049335 - Carg01603-RA Car15g00552 552
8 10908332 10910943 - CcPI632755_08g004470.1 Cco08g0447 447
9 9660446 9668763 + CcPI632755_09g010120.1 Cco09g1012 1012
8 8778268 8780902 - CePI673135_08g003470.1 Cec08g0347 347
9 9675679 9683896 + CePI673135_09g010000.1 Cec09g1000 1000
3 6948342 6951798 - Chy3G054820.1 Chy03g00502 502
3 6981256 6983665 - Chy3G054870.1 Chy03g00507 507
8 8779629 8782288 - ClG42_08g0049700.10 Clacu08g0497 497
8 8941658 8946068 - ClCG08G003430.1 Cla08g00355 355
9 9934546 9936842 + ClCG09G010170.1 Cla09g00948 948
1 8313771 8316016 + MELO3C024075.2.1 Cme01g00793 793
3 3930173 3932295 - MELO3C008336.2.1 Cme03g00308 308
3 3994795 3998980 - MELO3C008341.2.1 Cme03g00315 315
4 18784932 18789376 + CmoCh04G025650.1 Cmo04g02565 2565
4 18794775 18798877 + CmoCh04G025680.1 Cmo04g02568 2568
15 2909179 2913201 - CmoCh15G005980.1 Cmo15g00598 598
15 2928155 2931478 - CmoCh15G006020.1 Cmo15g00602 602
4 11671434 11672859 + Conep04aG0155000.1 Cone4ag1498 1498
4 11673567 11674569 + Conep04aG0155200.1 Cone4ag1500 1500
7 10257905 10258836 - Conep07aG0149100.1 Cone7ag1449 1449
7 10259165 10261185 - Conep07aG0149200.1 Cone7ag1450 1450
17 6031754 6037688 - Conep17aG0080100.1 Cone17ag0783 783
20 1738907 1740358 + Conep20aG0039000.1 Cone20ag0376 376
1 17906672 17911314 + Cp4.1LG01g21180.1 Cpe01g02118 2118
1 17916960 17921338 + Cp4.1LG01g21190.1 Cpe01g02120 2120
6 6266709 6267887 - Cp4.1LG06g07460.1 Cpe06g00909 909
13 6388206 6393078 + Cp4.1LG13g04040.1 Cpe13g00683 683
13 6413434 6417153 + Cp4.1LG13g04010.1 Cpe13g00686 686
8 10012404 10015047 - CrPI670011_08g003250.1 Cre08g0325 325
9 9868043 9874040 + CrPI670011_09g009620.1 Cre09g0962 962
8 13741039 13743853 + Lsi08G005550.1 Lsi08g00555 555
11 11751336 11752517 - MC11g1205 Mch11g1487 1487
11 8989235 8993567 - Tan0021409.2 Tan11g1139 1139
18 19680341 19687518 + Vvi18g1370 Vvi18g1370 1370
18 19689524 19691184 + Vvi18g1371 Vvi18g1371 1371
18 19691813 19692987 + Vvi18g1372 Vvi18g1372 1372
18 19698452 19699507 + Vvi18g1373 Vvi18g1373 1373
18 19720788 19740328 - Vvi18g1374 Vvi18g1374 1374
18 19750075 19751858 + Vvi18g1375 Vvi18g1375 1375
18 19797742 19801223 - Vvi18g1376 Vvi18g1376 1376
18 19866885 19871844 - Vvi18g1377 Vvi18g1377 1377
18 19871853 19873289 - Vvi18g1378 Vvi18g1378 1378
18 19881477 19881979 + Vvi18g1379 Vvi18g1379 1379
       

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