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
Vvi3g396 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g397 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g398 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g399 . . . . Bpe07g00379 . . Bma12g00451 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme11g00086
Vvi3g400 . . . . . . . . . Cmo11g01367 . . . . . Cpe04g00283 . . . . . . . . Cla02g00604 Cam02g0633 Cec02g0633 Cco02g0652 Clacu02g0637 Cmu02g0633 Cre02g0957 . . . . . . . Cme01g00054 Blo04g00487 . . Bda14g00516 Bpe15g00898 . Bma03g00517 . . . . . . Car11g01093 . . . . . . . . . . . . . . . . . . . Chy01g00058 .
Vvi3g401 . . . . . . . . . . . . . . . . . Bhi05g01068 . . . . . . . . . . . . . . Cone8ag1131 . . . Csa07g00754 . . . . . . . . . Bma08g00800 . . . . . Car11g01094 . . . . . . . . . . . . . . . . . . . . .
Vvi3g402 . . . . . Bpe12g00056 . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag1088 . . . . . . . . Blo13g00575 Bda15g00034 . . . . . . . . Cma11g01744 . Car11g01096 . . . . . . . . . . . . . . . . . . . . .
Vvi3g403 . . . . . . . . Cmo19g00618 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma19g00600 Car11g01097 Car19g00453 . . . . . . . . . . . . . . . . . . . .
Vvi3g404 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g405 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
14 3747571 3747891 + Bda027261.1 Bda14g00516 516
15 1802036 1806059 + Bda011791.1 Bda15g00034 34
5 38522846 38528910 - XM_039032012.1 Bhi05g01068 1068
4 4036919 4039299 + BLOR13399 Blo04g00487 487
13 27879152 27882549 + BLOR19627 Blo13g00575 575
3 4013408 4013728 + Bma016799.1 Bma03g00517 517
8 45614955 45619744 - Bma028188.1 Bma08g00800 800
12 11391396 11392886 + Bma007460.1 Bma12g00451 451
7 3303931 3305460 + Bpe021194.1 Bpe07g00379 379
12 426039 430084 - Bpe005295.1 Bpe12g00056 56
15 18872562 18872849 - Bpe001820.1 Bpe15g00898 898
2 7323978 7326277 - CaPI482276_02g006330.1 Cam02g0633 633
11 8612769 8615591 - Carg26409-RA Car11g01093 1093
11 8617299 8623619 - Carg26408-RA Car11g01094 1094
11 8627046 8627530 + Carg26406-RA Car11g01096 1096
11 8627343 8630739 - Carg26405-RA Car11g01097 1097
19 6249930 6253059 + Carg22071-RA Car19g00453 453
2 6518282 6520585 - CcPI632755_02g006520.1 Cco02g0652 652
2 6409449 6411749 - CePI673135_02g006330.1 Cec02g0633 633
1 433982 436060 - Chy1G000580.1 Chy01g00058 58
2 6333008 6335305 - ClG42_02g0063700.10 Clacu02g0637 637
2 6626552 6629320 - ClCG02G005980.1 Cla02g00604 604
11 11572051 11577585 - CmaCh11G017440.1 Cma11g01744 1744
19 6585446 6589819 + CmaCh19G006000.1 Cma19g00600 600
1 426128 428776 - MELO3C018455.2.1 Cme01g00054 54
11 725357 730345 + MELO3C023273.2.1 Cme11g00086 86
11 9559177 9561917 - CmoCh11G013670.1 Cmo11g01367 1367
19 6778771 6782103 + CmoCh19G006180.1 Cmo19g00618 618
2 6239483 6241777 - CmPI595203_02g006330.1 Cmu02g0633 633
8 9961792 9964150 + Conep08aG0116200.1 Cone8ag1131 1131
12 8903832 8906238 - Conep12aG0112200.1 Cone12ag1088 1088
4 3551273 3554177 - Cp4.1LG04g07990.1 Cpe04g00283 283
2 6860070 6862385 - CrPI670011_02g009570.1 Cre02g0957 957
7 5295800 5301324 + CsaV3_7G008530.1 Csa07g00754 754
3 3833047 3835366 - Vvi3g396 Vvi3g396 396
3 3836733 3850849 - Vvi3g397 Vvi3g397 397
3 3852061 3854362 - Vvi3g398 Vvi3g398 398
3 3854896 3866036 - Vvi3g399 Vvi3g399 399
3 3866769 3872492 - Vvi3g400 Vvi3g400 400
3 3872535 3880620 - Vvi3g401 Vvi3g401 401
3 3882125 3887019 + Vvi3g402 Vvi3g402 402
3 3887066 3889560 - Vvi3g403 Vvi3g403 403
3 3889561 3890478 - Vvi3g404 Vvi3g404 404
3 3890514 3891598 - Vvi3g405 Vvi3g405 405
       

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