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
Vvi19g494 . . Bda07g00357 Bda09g00396 . . . . . . . Cma09g00945 . Car09g00859 Sed10g2110 Cpe06g00761 . Bhi09g01887 Tan01g3346 Cmetu01g0289 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo09g00944 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g495 . . Bda07g00358 Bda09g00397 . Bpe08g01127 . . . . Cma01g01135 . . . . . Cpe02g00766 . . . . . . . . . . . . . . . . . . Lsi04g01207 . . . Blo07g00910 . Bda05g00726 . Bpe11g00543 . Bma07g01301 Bma14g00343 . Cmo01g01186 . . . . Car16g00546 . . . . . . . . . Cla05g01494 Cam05g1610 . Cco05g1639 Clacu05g1590 Cmu05g1493 . . . . .
Vvi19g496 Blo03g00565 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe11g00544 . . Bma14g00342 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g497 . Blo03g01448 . Bda09g00398 . Bpe08g01126 . . . . . Cma09g00946 . Car09g00860 . Cpe06g00762 . . . . . . . . . . . . . . . . . . . Lsi04g01206 . . . . . . . . . Bma07g01300 . . . Cmo09g00945 . . . . . . . . . . . . . Cla05g01493 Cam05g1609 . Cco05g1638 Clacu05g1589 Cmu05g1492 . . . . .
Vvi19g498 Blo03g00564 . . . . . . . . . Cma01g01134 Cma09g00948 . Car09g00861 . Cpe06g00763 Cpe02g00767 . . . . . . . . . . . . . . . . . . Lsi04g01205 . . . . . . . Bpe11g00545 . . Bma14g00341 . Cmo01g01185 Cmo09g00946 . . . Car16g00545 . . . . . . . . . Cla05g01492 Cam05g1608 . Cco05g1637 Clacu05g1588 Cmu05g1491 . . . . .
Vvi19g499 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g500 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g501 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo07g00909 Blo10g00824 Bda05g00725 Bda12g00903 . Bpe03g00795 . Bma14g00340 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g502 . . Bda07g00359 . . . . Bma13g01053 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe11g00546 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g503 . . . . Bpe09g00180 . . Bma13g01054 . . . . . . . . . . . . . . . . Cla10g00512 Cam10g0507 Cec10g0524 Cco10g0511 Clacu10g0528 Cmu10g1354 Cre10g0758 . . Cone14ag1140 Cone15ag1158 . Csa03g00520 . Cme06g02259 . Blo10g00825 . Bda12g00904 . . . . Sed14g0162 . . Cma04g00948 . . . . Cpe01g00859 Bhi11g00629 Tan01g1698 Cmetu12g0970 . . Mch10g1261 . . . . . . . . Lsi05g00605 . Chy06g01810 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 55622836 55626766 - Bda021867.1 Bda05g00725 725
5 55630640 55632829 + Bda021868.1 Bda05g00726 726
7 4578678 4580431 - Bda025442.1 Bda07g00357 357
7 4581080 4583326 - Bda025443.1 Bda07g00358 358
7 4590208 4594203 + Bda025444.3 Bda07g00359 359
9 5010874 5012537 - Bda030977.1 Bda09g00396 396
9 5013447 5014969 - Bda030978.1 Bda09g00397 397
9 5016007 5017427 + Bda034091 Bda09g00398 398
12 39764547 39768751 + Bda009438.1 Bda12g00903 903
12 39770394 39771970 - Bda009439.1 Bda12g00904 904
9 52273132 52278061 - XM_039043748.1 Bhi09g01887 1887
11 14644159 14649451 + XM_039049896.1 Bhi11g00629 629
3 22241677 22244535 + BLOR11745 Blo03g00564 564
3 22245360 22246643 - BLOR11746 Blo03g00565 565
3 41132293 41133695 + BLOR12629 Blo03g01448 1448
7 28035938 28039762 - BLOR18841 Blo07g00909 909
7 28055848 28058226 + BLOR18842 Blo07g00910 910
10 26079596 26083931 + BLOR02614 Blo10g00824 824
10 26084658 26090498 - BLOR02615 Blo10g00825 825
7 48601927 48603351 - Bma026575.1 Bma07g01300 1300
7 48603876 48605326 + Bma026576.1 Bma07g01301 1301
13 43224008 43228366 + Bma010173.1 Bma13g01053 1053
13 43229623 43233218 - Bma010174.1 Bma13g01054 1054
14 4227473 4231221 - Bma010761.1 Bma14g00340 340
14 4234962 4237810 + Bma010762.1 Bma14g00341 341
14 4238564 4239760 - Bma010763.1 Bma14g00342 342
14 4240134 4246408 + Bma010764.1 Bma14g00343 343
3 27908511 27912424 - Bpe012707.2 Bpe03g00795 795
8 13197844 13198391 - Bpe023252.1 Bpe08g01126 1126
8 13199886 13201380 + Bpe023253.1 Bpe08g01127 1127
9 1247563 1257219 + Bpe026209 Bpe09g00180 180
11 4167332 4174651 - Bpe003910.1 Bpe11g00543 543
11 4174919 4176226 + Bpe003911.1 Bpe11g00544 544
11 4177114 4179813 - Bpe003912.1 Bpe11g00545 545
11 4185893 4189553 + Bpe003913.1 Bpe11g00546 546
5 22833227 22835844 + CaPI482276_05g016080.1 Cam05g1608 1608
5 22836433 22838265 - CaPI482276_05g016090.1 Cam05g1609 1609
5 22838589 22847669 + CaPI482276_05g016100.1 Cam05g1610 1610
10 7544118 7550867 + CaPI482276_10g005070.1 Cam10g0507 507
9 5260492 5264295 - Carg12813-RA Car09g00859 859
9 5266068 5268453 + Carg12814-RA Car09g00860 860
9 5268646 5271758 - Carg12815-RA Car09g00861 861
16 3454928 3458534 + Carg05630-RA Car16g00545 545
16 3459289 3462717 + Carg05631-RA Car16g00546 546
5 22511454 22514076 + CcPI632755_05g016370.1 Cco05g1637 1637
5 22514669 22516501 - CcPI632755_05g016380.1 Cco05g1638 1638
5 22516814 22525621 + CcPI632755_05g016390.1 Cco05g1639 1639
10 6126495 6133265 + CcPI632755_10g005110.1 Cco10g0511 511
10 6313091 6319890 + CePI673135_10g005240.1 Cec10g0524 524
6 21764786 21770003 - Chy6G123380.1 Chy06g01810 1810
5 22841962 22844590 + ClG42_05g0158800.10 Clacu05g1588 1588
5 22845179 22847011 - ClG42_05g0158900.10 Clacu05g1589 1589
5 22847333 22856398 + ClG42_05g0159000.10 Clacu05g1590 1590
10 6380652 6387436 + ClG42_10g0052800.10 Clacu10g0528 528
5 24112624 24115640 + ClCG05G014340.1 Cla05g01492 1492
5 24115712 24117899 - ClCG05G014350.1 Cla05g01493 1493
5 24118177 24121152 + ClCG05G014360.2 Cla05g01494 1494
10 6782473 6790875 + ClCG10G005470.2 Cla10g00512 512
1 8310729 8315180 + CmaCh01G011340.1 Cma01g01134 1134
1 8315781 8318558 + CmaCh01G011350.1 Cma01g01135 1135
4 4870317 4875136 + CmaCh04G009480.1 Cma04g00948 948
9 4754604 4758200 - CmaCh09G009450.1 Cma09g00945 945
9 4759942 4761649 + CmaCh09G009460.1 Cma09g00946 946
9 4762645 4765783 - CmaCh09G009480.1 Cma09g00948 948
6 29609814 29615630 + MELO3C025387.2.1 Cme06g02259 2259
1 18327816 18332152 - PI0001195.1 Cmetu01g0289 289
12 1064872 1069586 + PI0028128.1 Cmetu12g0970 970
1 9634216 9637865 + CmoCh01G011850.1 Cmo01g01185 1185
1 9638578 9640527 + CmoCh01G011860.1 Cmo01g01186 1186
9 4959270 4963907 - CmoCh09G009440.1 Cmo09g00944 944
9 4965702 4967952 + CmoCh09G009450.1 Cmo09g00945 945
9 4968389 4971421 - CmoCh09G009460.1 Cmo09g00946 946
5 22553667 22556295 + CmPI595203_05g014910.1 Cmu05g1491 1491
5 22556884 22558715 - CmPI595203_05g014920.1 Cmu05g1492 1492
5 22559037 22565849 + CmPI595203_05g014930.1 Cmu05g1493 1493
10 6502427 6509208 + CmPI595203_10g013540.1 Cmu10g1354 1354
14 9450662 9455210 - Conep14aG0116400.1 Cone14ag1140 1140
15 9364071 9365638 - Conep15aG0118700.1 Cone15ag1158 1158
1 5080642 5085439 + Cp4.1LG01g08180.1 Cpe01g00859 859
2 4887998 4890872 - Cp4.1LG02g01020.1 Cpe02g00766 766
2 4891347 4895173 - Cp4.1LG02g01010.1 Cpe02g00767 767
6 4810835 4814309 - Cp4.1LG06g08860.1 Cpe06g00761 761
6 4816483 4818796 + Cp4.1LG06g08930.1 Cpe06g00762 762
6 4819288 4822257 - Cp4.1LG06g08840.1 Cpe06g00763 763
10 7395598 7402371 + CrPI670011_10g007580.1 Cre10g0758 758
3 4343806 4349530 + CsaV3_3G005200.1 Csa03g00520 520
4 18607207 18612239 + Lsi04G012050.1 Lsi04g01205 1205
4 18610628 18613564 - Lsi04G012060.1 Lsi04g01206 1206
4 18613542 18619283 + Lsi04G012070.1 Lsi04g01207 1207
5 7505723 7519847 + Lsi05G006050.1 Lsi05g00605 605
10 10226767 10233092 - MC10g1042 Mch10g1261 1261
10 37578772 37583689 + Sed0017116.1 Sed10g2110 2110
14 1867898 1880583 + Sed0021087.1 Sed14g0162 162
1 18066171 18072414 - Tan0017037.2 Tan01g1698 1698
1 91846353 91850782 + Tan0010391.1 Tan01g3346 3346
19 6327723 6329625 - Vvi19g494 Vvi19g494 494
19 6330846 6341263 - Vvi19g495 Vvi19g495 495
19 6342762 6345353 + Vvi19g496 Vvi19g496 496
19 6347040 6349633 + Vvi19g497 Vvi19g497 497
19 6349896 6356238 - Vvi19g498 Vvi19g498 498
19 6359411 6371752 - Vvi19g499 Vvi19g499 499
19 6379627 6406407 - Vvi19g500 Vvi19g500 500
19 6413979 6416816 + Vvi19g501 Vvi19g501 501
19 6416896 6422786 + Vvi19g502 Vvi19g502 502
19 6423468 6435344 - Vvi19g503 Vvi19g503 503
       

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