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
Vvi3g506 . . . . . . Bma05g00507 . . . Cma02g00430 Cma20g00883 Car02g00285 Car20g00761 . . . . . . . . . . . . . . . . . Cone12ag1121 Cone8ag1166 Cone3ag1121 . Lsi10g00600 . Chy11g00424 . Blo04g00496 Blo13g00560 . . Bpe15g00884 . Bma03g00530 . Sed01g0327 Cmo02g00432 Cmo20g00891 . . . . . Cpe05g01232 Bhi10g02065 Tan05g1371 Cmetu11g0349 . Hepe08g1052 . . Cla09g01731 Cam09g1826 Cec09g1885 Cco09g1978 . . Cre01g0683 . Csa02g01212 . Cme11g00493
Vvi3g507 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa07g00811 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g508 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g509 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g510 . . Bda06g00949 . . . . Bma12g00550 . . . . . . . . Cpe15g00525 . . . . . . . . . . . . . . . . . . . . . Cme01g01480 . . . . . . . . . . . . . . Car19g00495 . . . . . . . . . . . . . . . . . . Chy01g00828 .
Vvi3g511 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g512 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g513 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g514 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g515 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 26287979 26292779 + Bda022583.1 Bda06g00949 949
10 51647008 51651411 - XM_039046689.1 Bhi10g02065 2065
4 4134274 4136817 + BLOR13408 Blo04g00496 496
13 27599842 27612938 - BLOR19612 Blo13g00560 560
3 4116072 4118682 + Bma016814.2 Bma03g00530 530
5 23314540 23316540 - Bma021439.1 Bma05g00507 507
12 22902641 22906772 + Bma007686.1 Bma12g00550 550
15 18785156 18787723 - Bpe001805.1 Bpe15g00884 884
9 32720133 32723575 + CaPI482276_09g018260.1 Cam09g1826 1826
2 1925584 1934470 - Carg22970-RA Car02g00285 285
19 6543542 6551368 - Carg22028-RA Car19g00495 495
20 4484941 4487088 - Carg23622-RA Car20g00761 761
9 33954592 33958143 + CcPI632755_09g019780.1 Cco09g1978 1978
9 35644869 35648429 + CePI673135_09g018850.1 Cec09g1885 1885
1 6991070 6995410 - Chy1G008280.1 Chy01g00828 828
11 4109658 4117016 - Chy11G190040.1 Chy11g00424 424
9 34626671 34630480 + ClCG09G017680.1 Cla09g01731 1731
2 2178446 2181747 - CmaCh02G004300.1 Cma02g00430 430
20 4245137 4247288 - CmaCh20G008830.1 Cma20g00883 883
1 19297081 19306645 - MELO3C012575.2.1 Cme01g01480 1480
11 4919046 4922819 - MELO3C021929.2.1 Cme11g00493 493
11 26921649 26926713 + PI0014577.1 Cmetu11g0349 349
2 2256945 2260457 - CmoCh02G004320.1 Cmo02g00432 432
20 4516883 4521349 - CmoCh20G008910.1 Cmo20g00891 891
3 29791630 29795480 + Conep03aG0162500.1 Cone3ag1121 1121
8 10086216 10089634 + Conep08aG0119800.1 Cone8ag1166 1166
12 9050836 9053503 + Conep12aG0115700.1 Cone12ag1121 1121
5 8630927 8641843 + Cp4.1LG05g12230.1 Cpe05g01232 1232
15 6156331 6158225 - Cp4.1LG15g05270.1 Cpe15g00525 525
1 6355156 6358709 - CrPI670011_01g006830.1 Cre01g0683 683
2 11910406 11913433 + CsaV3_2G014280.1 Csa02g01212 1212
7 5701200 5708301 + CsaV3_7G010090.1 Csa07g00811 811
8 10161501 10165080 - Hsped.08g10520.1 Hepe08g1052 1052
10 8622330 8624838 + Lsi10G006000.1 Lsi10g00600 600
1 2450488 2454218 - Sed0017286.3 Sed01g0327 327
5 18701653 18705212 - Tan0018531.1 Tan05g1371 1371
3 4879759 4881735 + Vvi3g506 Vvi3g506 506
3 4887974 4921315 + Vvi3g507 Vvi3g507 507
3 4923019 4930341 + Vvi3g508 Vvi3g508 508
3 4940438 4942521 + Vvi3g509 Vvi3g509 509
3 4943034 4950015 - Vvi3g510 Vvi3g510 510
3 4955810 4959737 + Vvi3g511 Vvi3g511 511
3 4959952 4969008 + Vvi3g512 Vvi3g512 512
3 4969556 4976362 + Vvi3g513 Vvi3g513 513
3 4981855 4986948 - Vvi3g514 Vvi3g514 514
3 4986949 4989015 + Vvi3g515 Vvi3g515 515
       

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