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
Vvi4g262 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g263 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g264 . . . . . . . . . . Cma01g01558 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo01g01605 . . . . . . Cpe02g00409 . . . . . . . . . . . . . . . . . .
Vvi4g265 . . . . . . . . Cmo05g00668 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car05g00585 Cpe11g00563 . . . . . . . . Cla08g01279 Cam08g1737 Cec08g1319 Cco08g1440 Clacu08g1434 . Cre08g1221 . Csa02g02337 . .
Vvi4g266 . . . . . . . . Cmo05g00667 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car05g00583 Cpe11g00561 . . . . . . . . . . . . . . . . . . .
Vvi4g267 . . . . . . . . . . Cma01g01557 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo01g01604 . . . . . . Cpe02g00410 . . . . . . . . . . . . . . . . . .
Vvi4g268 . . . . . . . . . . Cma01g01554 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo01g01603 . . . . . . Cpe02g00411 . . . . . . . . . . . . . . . . . .
Vvi4g269 . . . Bda03g00459 . . . . Cmo05g00665 . . . . . Sed01g1313 . . Bhi04g01060 Tan02g2655 Cmetu03g1138 . . . . . . . . . . . . . . . Lsi04g02276 . . Cme03g01678 . . . Bda13g01355 . Bpe04g00420 . . . . . . . . Car05g00581 Cpe11g00560 . . . . . . . . Cla08g01169 Cam08g1632 Cec08g1206 Cco08g1329 Clacu08g1330 . Cre08g1114 . . Chy03g01302 .
Vvi4g270 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g271 . . . . . . . . Cmo05g00644 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car05g00559 Cpe11g00541 . . . . . . . . . . . . . . . . Csa02g02308 . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 3963791 3969259 - Bda016427.2 Bda03g00459 459
13 35919912 35925046 + Bda000171.1 Bda13g01355 1355
4 26271809 26282905 - XM_039028947.1 Bhi04g01060 1060
4 2709267 2714765 - Bpe015105.1 Bpe04g00420 420
8 22537546 22544103 - CaPI482276_08g016320.1 Cam08g1632 1632
8 23645851 23650212 - CaPI482276_08g017370.1 Cam08g1737 1737
5 3283345 3287757 + Carg08302-RA Car05g00559 559
5 3404093 3416177 + Carg08324-RA Car05g00581 581
5 3419162 3422717 + Carg08326-RA Car05g00583 583
5 3425160 3427396 - Carg08328-RA Car05g00585 585
8 25169370 25175936 - CcPI632755_08g013290.1 Cco08g1329 1329
8 26285831 26290309 - CcPI632755_08g014400.1 Cco08g1440 1440
8 23992510 24000300 - CePI673135_08g012060.1 Cec08g1206 1206
8 25147205 25151616 - CePI673135_08g013190.1 Cec08g1319 1319
3 16001883 16008322 + Chy3G062820.1 Chy03g01302 1302
8 23310267 23316834 - ClG42_08g0133000.10 Clacu08g1330 1330
8 24396087 24400511 - ClG42_08g0143400.10 Clacu08g1434 1434
8 24568424 24575614 - ClCG08G011730.2 Cla08g01169 1169
8 25698222 25706961 - ClCG08G012810.2 Cla08g01279 1279
1 10817246 10818513 - CmaCh01G015540.1 Cma01g01554 1554
1 10819003 10824002 + CmaCh01G015570.1 Cma01g01557 1557
1 10823214 10829522 - CmaCh01G015580.1 Cma01g01558 1558
3 25524043 25541603 - MELO3C011203.2.1 Cme03g01678 1678
3 3902909 3916472 + PI0026992.3 Cmetu03g1138 1138
1 12271908 12273177 - CmoCh01G016030.1 Cmo01g01603 1603
1 12272747 12278817 + CmoCh01G016040.1 Cmo01g01604 1604
1 12277943 12284244 - CmoCh01G016050.1 Cmo01g01605 1605
5 3254539 3258864 + CmoCh05G006440.1 Cmo05g00644 644
5 3373013 3384247 + CmoCh05G006650.1 Cmo05g00665 665
5 3385487 3390691 + CmoCh05G006670.1 Cmo05g00667 667
5 3390937 3395021 - CmoCh05G006680.1 Cmo05g00668 668
2 2284334 2291026 + Cp4.1LG02g04730.1 Cpe02g00409 409
2 2290013 2294653 - Cp4.1LG02g04580.1 Cpe02g00410 410
2 2295257 2296574 + Cp4.1LG02g04680.1 Cpe02g00411 411
11 3208658 3213108 + Cp4.1LG11g05440.1 Cpe11g00541 541
11 3324704 3339487 + Cp4.1LG11g05590.1 Cpe11g00560 560
11 3340815 3347316 + Cp4.1LG11g05570.1 Cpe11g00561 561
11 3344778 3348869 - Cp4.1LG11g05680.1 Cpe11g00563 563
8 24334761 24342276 - CrPI670011_08g011140.1 Cre08g1114 1114
8 25439090 25443588 - CrPI670011_08g012210.1 Cre08g1221 1221
2 20586294 20591378 + CsaV3_2G031270.1 Csa02g02308 2308
2 20774567 20779116 - CsaV3_2G031560.1 Csa02g02337 2337
4 29785323 29791808 + Lsi04G022760.1 Lsi04g02276 2276
1 9833148 9845145 + Sed0011780.1 Sed01g1313 1313
2 94907428 94920313 + Tan0022012.3 Tan02g2655 2655
4 2572121 2577860 - Vvi4g262 Vvi4g262 262
4 2577915 2581211 - Vvi4g263 Vvi4g263 263
4 2582426 2595604 + Vvi4g264 Vvi4g264 264
4 2596950 2601892 + Vvi4g265 Vvi4g265 265
4 2604512 2611059 - Vvi4g266 Vvi4g266 266
4 2611676 2616490 - Vvi4g267 Vvi4g267 267
4 2617384 2618366 + Vvi4g268 Vvi4g268 268
4 2624576 2635776 - Vvi4g269 Vvi4g269 269
4 2635805 2635892 + Vvi4g270 Vvi4g270 270
4 2639714 2646512 - Vvi4g271 Vvi4g271 271
       

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