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
Vvi18g500 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g501 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g502 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g503 . . Bda01g00913 . . . . . . Cmo12g00150 . . . Car12g00178 . . Cpe07g00166 Bhi04g00925 . . . . . . . . . . . . . . . . . . . . . . Blo18g00104 . . Bpe02g01152 Bpe05g00432 Bma01g00979 . . . . Cma12g00197 . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g504 . . Bda01g00912 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone9ag1448 . . . . . . . . . . Bpe02g01151 . Bma01g01373 Bma02g00111 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g505 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g506 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g507 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g508 . Blo12g00731 . Bda03g00457 . Bpe04g00418 Bma04g00432 . . . Cma01g01645 Cma09g00593 . . . Cpe06g00454 . . . . . . . . . . . . . . . Cone6ag1532 . . . Lsi04g02278 Csa03g04491 Chy04g00209 . . . . . . . . . Sed14g1000 Cmo01g01695 Cmo09g00579 . . . Car09g00524 . . Bhi09g02496 Tan01g3850 Cmetu01g2584 . Hepe01g2168 Mch11g0707 . Cla11g01422 Cam11g1478 Cec11g1508 Cco11g1504 Clacu11g1639 Cmu11g1457 Cre11g1875 . . . Cme04g00239
Vvi18g509 . . Bda01g00911 . . . . . . Cmo12g00151 . . . Car12g00179 . . Cpe07g00167 . . . . . . . . . . . . . . Cone4ag1298 Cone7ag0856 . . . . . . Blo17g00098 . . . Bpe02g01150 . . Bma02g00112 . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 42144461 42147759 - Bda003052.1 Bda01g00911 911
1 42151035 42151816 + Bda003053.1 Bda01g00912 912
1 42153305 42155099 + Bda003054.3 Bda01g00913 913
3 3955831 3956802 + Bda016425.1 Bda03g00457 457
4 23687908 23691430 - XM_039029586.1 Bhi04g00925 925
9 67500948 67502495 - XM_039042845.1 Bhi09g02496 2496
12 25648738 25649709 - BLOR04750 Blo12g00731 731
17 774926 806065 + BLOR15919 Blo17g00098 98
18 944900 946449 - BLOR08592 Blo18g00104 104
1 9660404 9661863 + Bma001203.1 Bma01g00979 979
1 21241731 21242524 - Bma001713.1 Bma01g01373 1373
2 1020575 1021356 - Bma014567.1 Bma02g00111 111
2 1031212 1032342 + Bma014568.1 Bma02g00112 112
4 3549207 3550151 + Bma018900.1 Bma04g00432 432
2 15107315 15110643 - Bpe009010.1 Bpe02g01150 1150
2 15119063 15119856 + Bpe009011.1 Bpe02g01151 1151
2 15121187 15122127 + Bpe009012.1 Bpe02g01152 1152
4 2702898 2703869 + Bpe015103.1 Bpe04g00418 418
5 18764785 18766463 - Bpe017851.1 Bpe05g00432 432
11 27517492 27518913 - CaPI482276_11g014780.1 Cam11g1478 1478
9 2941902 2949666 - Carg03006-RA Car09g00524 524
12 1099895 1102872 - Carg22516-RA Car12g00178 178
12 1106121 1108703 + Carg22515-RA Car12g00179 179
11 27861368 27863029 - CcPI632755_11g015040.1 Cco11g1504 1504
11 29292589 29293998 - CePI673135_11g015080.1 Cec11g1508 1508
4 1917871 1918878 + Chy4G069270.1 Chy04g00209 209
11 27545497 27547974 - ClG42_11g0163900.10 Clacu11g1639 1639
11 27775757 27779332 - ClCG11G014550.2 Cla11g01422 1422
1 11266079 11267074 - CmaCh01G016450.1 Cma01g01645 1645
9 2744449 2750733 - CmaCh09G005930.1 Cma09g00593 593
12 915950 918990 - CmaCh12G001970.1 Cma12g00197 197
4 1883858 1887994 + MELO3C003525.2.1 Cme04g00239 239
1 1625950 1630674 + PI0015433.1 Cmetu01g2584 2584
1 12741391 12742386 - CmoCh01G016950.1 Cmo01g01695 1695
9 2830537 2839156 - CmoCh09G005790.1 Cmo09g00579 579
12 975836 978831 - CmoCh12G001500.1 Cmo12g00150 150
12 982096 985704 + CmoCh12G001510.1 Cmo12g00151 151
11 26798373 26799789 - CmPI595203_11g014570.1 Cmu11g1457 1457
4 10714434 10717904 - Conep04aG0134400.1 Cone4ag1298 1298
6 12056940 12057929 + Conep06aG0159100.1 Cone6ag1532 1532
7 6546748 6550582 + Conep07aG0088500.1 Cone7ag0856 856
9 10738704 10740444 + Conep09aG0149100.1 Cone9ag1448 1448
6 2642771 2651802 - Cp4.1LG06g04060.1 Cpe06g00454 454
7 986064 989019 - Cp4.1LG07g01640.1 Cpe07g00166 166
7 992248 996230 + Cp4.1LG07g01680.1 Cpe07g00167 167
11 30417842 30419250 - CrPI670011_11g018750.1 Cre11g1875 1875
3 39120447 39122733 - CsaV3_3G047970.1 Csa03g04491 4491
1 86325876 86327507 - Hsped.01g21680.1 Hepe01g2168 2168
4 29808025 29809032 - Lsi04G022780.1 Lsi04g02278 2278
11 4661078 4661788 - MC11g0596 Mch11g0707 707
14 19422381 19423499 - Sed0016245.1 Sed14g1000 1000
1 103252616 103253997 - Tan0020438.1 Tan01g3850 3850
18 5651900 5652908 + Vvi18g500 Vvi18g500 500
18 5652914 5653524 + Vvi18g501 Vvi18g501 501
18 5657907 5661024 - Vvi18g502 Vvi18g502 502
18 5663287 5667315 - Vvi18g503 Vvi18g503 503
18 5668080 5668815 - Vvi18g504 Vvi18g504 504
18 5674195 5679787 - Vvi18g505 Vvi18g505 505
18 5679789 5681129 - Vvi18g506 Vvi18g506 506
18 5683705 5685041 + Vvi18g507 Vvi18g507 507
18 5687067 5688394 - Vvi18g508 Vvi18g508 508
18 5694492 5711399 + Vvi18g509 Vvi18g509 509
       

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