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
Vvi4g422 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g423 . . . . Bpe02g01231 . . . Cmo05g00687 Cmo12g00265 . Cma05g00655 . Car12g00294 . . . . . . . . . . . . . . . . . . . . . . . . Cme03g01659 . . . . . . . . . . . . Cma12g00313 . . Cpe11g00582 . . . . . . . . . . . . . . . Lsi08g01158 . . .
Vvi4g424 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g425 . . . . . . . . . . . . . . . Cpe07g00268 . Bhi04g01023 . . . . . . . . . . . . . . . . . . . . . . . . Bda13g01277 . . . Bma02g00036 . . . . . . . . . . . . . . . . Cla08g01295 Cam08g1754 Cec08g1334 Cco08g1458 Clacu08g1451 . Cre08g1238 . . . .
Vvi4g426 . . . . . . . . Cmo05g00686 . . Cma05g00654 . . Sed01g1339 Cpe07g00273 . Bhi04g01022 Tan02g2682 Cmetu03g2197 . Hepe10g0285 . Lcy13g1301 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car05g00598 Cpe11g00581 . . . . . . . . . . . . . . . . . . .
Vvi4g427 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g428 . . . . . . . . . . . . . . . . . Bhi04g01021 Tan02g2683 . . . . . . . . . . . . . . . . . . . . . . Bda01g00984 . Bpe14g00568 . . . . . . . . . Car05g00599 . . . . . . . . . . . . . . . . . . . .
Vvi4g429 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g430 . . . . . . . . Cmo05g00685 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe11g00580 . . . . . . . . . . . . . . . . . . .
Vvi4g431 . . . . . . . . Cmo05g00680 . . Cma05g00649 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma01g01291 . . . . . . . . Cpe11g00573 . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 43453870 43464753 - Bda003144.1 Bda01g00984 984
13 35120063 35125833 + Bda000082.1 Bda13g01277 1277
4 25701157 25709517 + XM_039028895.1 Bhi04g01021 1021
4 25701359 25709804 + XM_039028897.1 Bhi04g01022 1022
4 25701643 25709804 + XM_039028896.1 Bhi04g01023 1023
1 17572579 17574495 - Bma001607.1 Bma01g01291 1291
2 363492 369334 + Bma014492.2 Bma02g00036 36
2 15940868 15942415 - Bpe009090.1 Bpe02g01231 1231
14 4834158 4848135 - Bpe007218.5 Bpe14g00568 568
8 23773606 23791152 - CaPI482276_08g017540.1 Cam08g1754 1754
5 3538585 3539953 - Carg08341-RA Car05g00598 598
5 3540076 3545067 - Carg08342-RA Car05g00599 599
12 1933366 1935139 - Carg03901-RA Car12g00294 294
8 26428740 26436633 - CcPI632755_08g014580.1 Cco08g1458 1458
8 25275591 25293838 - CePI673135_08g013340.1 Cec08g1334 1334
8 24524031 24541595 - ClG42_08g0145100.10 Clacu08g1451 1451
8 25832447 25851688 - ClCG08G012970.2 Cla08g01295 1295
5 3293066 3294672 + CmaCh05G006490.1 Cma05g00649 649
5 3329369 3340842 - CmaCh05G006540.1 Cma05g00654 654
5 3341907 3348936 - CmaCh05G006550.1 Cma05g00655 655
12 1602036 1603929 - CmaCh12G003130.1 Cma12g00313 313
3 25357178 25359789 + MELO3C011221.2.1 Cme03g01659 1659
3 4033494 4041968 - PI0005170.2 Cmetu03g2197 2197
5 3450069 3455678 + CmoCh05G006800.1 Cmo05g00680 680
5 3489853 3496767 - CmoCh05G006850.1 Cmo05g00685 685
5 3497525 3503601 - CmoCh05G006860.1 Cmo05g00686 686
5 3503641 3509890 - CmoCh05G006870.1 Cmo05g00687 687
12 1703640 1705386 - CmoCh12G002650.1 Cmo12g00265 265
7 1739884 1746932 - Cp4.1LG07g01850.1 Cpe07g00268 268
7 1796599 1804900 - Cp4.1LG07g02770.1 Cpe07g00273 273
11 3403146 3404329 + Cp4.1LG11g05740.1 Cpe11g00573 573
11 3445310 3451976 - Cp4.1LG11g05810.1 Cpe11g00580 580
11 3452582 3459303 - Cp4.1LG11g05840.1 Cpe11g00581 581
11 3464004 3465534 - Cp4.1LG11g05820.1 Cpe11g00582 582
8 25581254 25589272 - CrPI670011_08g012380.1 Cre08g1238 1238
10 2996307 3003868 + Hsped.10g02850.1 Hepe10g0285 285
13 30493718 30502480 + Maker00025508 Lcy13g1301 1301
8 20208723 20230984 - Lsi08G011580.1 Lsi08g01158 1158
1 9968764 9979517 - Sed0005148.2 Sed01g1339 1339
2 95121253 95130244 - Tan0011570.2 Tan02g2682 2682
2 95121253 95130071 - Tan0011570.3 Tan02g2683 2683
4 4318171 4319763 + Vvi4g422 Vvi4g422 422
4 4330632 4333507 + Vvi4g423 Vvi4g423 423
4 4352128 4353580 + Vvi4g424 Vvi4g424 424
4 4366916 4370044 + Vvi4g425 Vvi4g425 425
4 4370043 4384297 + Vvi4g426 Vvi4g426 426
4 4388552 4388836 + Vvi4g427 Vvi4g427 427
4 4389208 4409630 + Vvi4g428 Vvi4g428 428
4 4415689 4418065 + Vvi4g429 Vvi4g429 429
4 4419326 4428625 + Vvi4g430 Vvi4g430 430
4 4431412 4432859 - Vvi4g431 Vvi4g431 431
       

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