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
Vvi2g602 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe15g00364 . . . . . . . . . . . . . . . . . .
Vvi2g603 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo19g00168 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g604 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g605 . Blo03g00111 Bda06g01281 . . Bpe07g00226 . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0619 Cone12ag0604 . . . . . . . . Bda07g00843 . . . . Bma12g00225 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g606 . . . . . . Bma07g00974 . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag0603 . . . . . . . . . . Bpe08g00859 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g607 . Blo03g00110 . . . Bpe07g00227 . . . Cmo16g01131 . . . . . Cpe14g00895 Cpe05g00201 . . . . . . . Cla10g00185 Cam10g0191 Cec10g0196 Cco10g0198 Clacu10g0195 Cmu10g1040 Cre10g0445 . . . . . . . . . . . . . . . Bma12g00227 . . . . Cma16g01084 . . . . . . . . . . . . . . . . . . . . Chy06g02116 .
Vvi2g608 . Blo03g00109 . . . Bpe07g00228 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag0602 . . . . . . . . . . . . Bma05g00394 Bma12g00228 . . . . . . Car16g01026 . . . . . . . . . . . . . . . . . . . .
Vvi2g609 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo03g00827 . Bda07g00113 . . Bpe11g00352 . . . . . . . . . . . Bhi05g00532 . . . . . . . . . . . . . . . . .
Vvi2g610 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda09g00695 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g611 . . . . . . . Bma14g00131 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi05g00531 . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 43400791 43404653 + Bda023128.1 Bda06g01281 1281
7 1364737 1367780 - Bda025173.2 Bda07g00113 113
7 9880480 9887410 + Bda025980.1 Bda07g00843 843
9 10958567 10958973 - Bda031359.1 Bda09g00695 695
5 12488696 12490173 + XM_039031063.1 Bhi05g00531 531
5 12594468 12605442 + XM_039032234.1 Bhi05g00532 532
3 3394927 3398098 + BLOR11290 Blo03g00109 109
3 3439388 3442507 + BLOR11291 Blo03g00110 110
3 3456372 3460439 + BLOR11292 Blo03g00111 111
3 33879905 33884151 + BLOR12008 Blo03g00827 827
19 6726321 6744442 - BLOR09511 Blo19g00168 168
5 12277407 12280742 - Bma021219.1 Bma05g00394 394
7 37568814 37572737 - Bma026125.1 Bma07g00974 974
12 2952905 2956918 - Bma007114.1 Bma12g00225 225
12 2970639 2973809 - Bma007116.1 Bma12g00227 227
12 2982770 2985811 - Bma007117.1 Bma12g00228 228
14 1919440 1919757 + Bma010534.1 Bma14g00131 131
7 1588236 1592277 - Bpe021037.2 Bpe07g00226 226
7 1600268 1603293 - Bpe021038.1 Bpe07g00227 227
7 1611809 1615009 - Bpe021039.1 Bpe07g00228 228
8 10950513 10953795 - Bpe022981.1 Bpe08g00859 859
11 2558047 2561080 - Bpe003726.1 Bpe11g00352 352
10 3560519 3566670 + CaPI482276_10g001910.1 Cam10g0191 191
16 8801955 8807613 - Carg23230-RA Car16g01026 1026
10 2000341 2006335 + CcPI632755_10g001980.1 Cco10g0198 198
10 2069298 2075461 + CePI673135_10g001960.1 Cec10g0196 196
6 25364694 25368538 - Chy6G126440.1 Chy06g02116 2116
10 2312610 2317310 + ClG42_10g0019500.10 Clacu10g0195 195
10 2111246 2115500 + ClCG10G001890.2 Cla10g00185 185
16 8330917 8336050 + CmaCh16G010840.1 Cma16g01084 1084
16 8067301 8072608 + CmoCh16G011310.1 Cmo16g01131 1131
10 2464054 2468536 + CmPI595203_10g010400.1 Cmu10g1040 1040
8 6091798 6095712 - Conep08aG0064000.1 Cone8ag0619 619
12 5344233 5349567 + Conep12aG0062300.1 Cone12ag0602 602
12 5355018 5359870 + Conep12aG0062400.1 Cone12ag0603 603
12 5361468 5364723 + Conep12aG0062500.1 Cone12ag0604 604
5 1083919 1088449 - Cp4.1LG05g02070.1 Cpe05g00201 201
14 7508889 7513282 + Cp4.1LG14g08960.1 Cpe14g00895 895
15 4833021 4865442 + Cp4.1LG15g03640.1 Cpe15g00364 364
10 3420046 3425946 + CrPI670011_10g004450.1 Cre10g0445 445
2 6355688 6376881 + Vvi2g602 Vvi2g602 602
2 6378167 6384034 + Vvi2g603 Vvi2g603 603
2 6404367 6406247 - Vvi2g604 Vvi2g604 604
2 6406802 6414734 - Vvi2g605 Vvi2g605 605
2 6421695 6433453 - Vvi2g606 Vvi2g606 606
2 6442237 6449184 - Vvi2g607 Vvi2g607 607
2 6473971 6482109 - Vvi2g608 Vvi2g608 608
2 6488600 6498446 - Vvi2g609 Vvi2g609 609
2 6499781 6503935 + Vvi2g610 Vvi2g610 610
2 6504398 6504841 + Vvi2g611 Vvi2g611 611
       

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