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
Vvi18g800 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo17g00837 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g801 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo17g00834 . Bda08g01332 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi08g01450 . . .
Vvi18g802 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g803 . . . . . . . . . Cmo12g00462 . . . . . . . . . . . . . . . . . . . . . Cone4ag1561 . . . . . . Cme03g02011 . . Bda08g01330 . . . . . . . . Cma12g00521 . . . . . . . . . . . . . . . . . . . Lsi08g01449 . Chy03g01516 .
Vvi18g804 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma05g00092 . . . . . . . Cpe11g00167 . . . . . . . . . . . . . . . . . . .
Vvi18g805 . . . . . . . . . Cmo12g00461 . . . Car12g00493 . . Cpe07g00464 . . . . . . . . . . . . . . . . . . . . . Cme03g02010 . . Bda08g01329 . . . . Bma05g00093 . . . Cma12g00520 . . . Cpe11g00168 . . . . . . . . . . . . . . . Lsi08g01448 . Chy03g01515 .
Vvi18g806 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g807 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo17g00833 . . . . . Bma01g00779 Bma05g00094 . . . . . . . Cpe11g00169 . . . . . . . . . . . . . . . . . . .
Vvi18g808 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g809 . Blo12g00948 . Bda03g00222 . Bpe04g00189 Bma04g00176 . . . . Cma09g00214 . . . Cpe06g00149 . . . . . . . . . . . . . . . . . . Cone20ag0175 Lsi04g01580 Csa04g02389 . . . . . . . . . . . . Cmo09g00207 . . . Car09g00182 . . Bhi09g03347 . . . . . . Cla05g02022 Cam05g2172 Cec05g2188 Cco05g2236 Clacu05g2165 Cmu05g2033 Cre05g2161 . . Chy07g00115 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 1715125 1722419 + Bda016166.1 Bda03g00222 222
8 53173447 53175430 + Bda030369.1 Bda08g01329 1329
8 53316309 53333585 + Bda030373.1 Bda08g01330 1330
8 53470500 53472159 - Bda034051 Bda08g01332 1332
9 85643164 85668967 + XM_039041646.1 Bhi09g03347 3347
12 27623571 27630531 - BLOR04967 Blo12g00948 948
17 27200641 27202620 - BLOR08379 Blo17g00833 833
17 27223699 27229925 - BLOR08380 Blo17g00834 834
17 27347621 27349619 - BLOR08383 Blo17g00837 837
1 7154841 7156886 - Bma001002.1 Bma01g00779 779
4 1469959 1475897 + Bma018623.7 Bma04g00176 176
5 3017049 3019277 - Bma020785.1 Bma05g00092 92
5 3051559 3053550 - Bma020786.1 Bma05g00093 93
5 3123731 3125734 - Bma020788.5 Bma05g00094 94
4 1216758 1258483 + Bpe014909.3 Bpe04g00189 189
5 30114819 30127873 - CaPI482276_05g021720.1 Cam05g2172 2172
9 922470 934058 - Carg08766-RA Car09g00182 182
12 3103506 3112992 + Carg25835-RA Car12g00493 493
5 31104209 31117426 - CcPI632755_05g022360.1 Cco05g2236 2236
5 33466403 33479740 - CePI673135_05g021880.1 Cec05g2188 2188
3 17467508 17471936 + Chy3G064950.1 Chy03g01515 1515
3 17474391 17477452 + Chy3G064960.1 Chy03g01516 1516
7 1009937 1016355 - Chy7G129450.1 Chy07g00115 115
5 30313708 30326792 - ClG42_05g0216500.10 Clacu05g2165 2165
5 31969351 31981662 - ClCG05G019730.2 Cla05g02022 2022
9 910547 926903 - CmaCh09G002140.1 Cma09g00214 214
12 2706243 2709623 + CmaCh12G005200.1 Cma12g00520 520
12 2712991 2714448 + CmaCh12G005210.1 Cma12g00521 521
3 27813457 27818301 + MELO3C010889.2.1 Cme03g02010 2010
3 27820271 27823081 + MELO3C010888.2.1 Cme03g02011 2011
9 959974 972423 - CmoCh09G002070.1 Cmo09g00207 207
12 2840074 2843657 + CmoCh12G004610.1 Cmo12g00461 461
12 2847475 2850219 + CmoCh12G004620.1 Cmo12g00462 462
5 30048093 30061177 - CmPI595203_05g020330.1 Cmu05g2033 2033
4 11989741 11991826 + Conep04aG0161300.1 Cone4ag1561 1561
20 762527 768622 - Conep20aG0018300.1 Cone20ag0175 175
6 801694 818637 - Cp4.1LG06g01560.1 Cpe06g00149 149
7 2982821 2992503 + Cp4.1LG07g04510.1 Cpe07g00464 464
11 911945 914776 - Cp4.1LG11g01800.1 Cpe11g00167 167
11 916752 917418 - Cp4.1LG11g01810.1 Cpe11g00168 168
11 917767 919103 - Cp4.1LG11g01820.1 Cpe11g00169 169
5 33380173 33393324 - CrPI670011_05g021610.1 Cre05g2161 2161
4 24209898 24216453 - CsaV3_4G034150.1 Csa04g02389 2389
4 23350571 23360086 + Lsi04G015800.1 Lsi04g01580 1580
8 22671489 22677362 + Lsi08G014480.1 Lsi08g01448 1448
8 22680945 22685112 + Lsi08G014490.1 Lsi08g01449 1449
8 22690568 22694738 + Lsi08G014500.1 Lsi08g01450 1450
18 9238034 9246098 - Vvi18g800 Vvi18g800 800
18 9246450 9251294 - Vvi18g801 Vvi18g801 801
18 9254404 9256571 - Vvi18g802 Vvi18g802 802
18 9265010 9267331 - Vvi18g803 Vvi18g803 803
18 9273801 9288920 - Vvi18g804 Vvi18g804 804
18 9289406 9306119 - Vvi18g805 Vvi18g805 805
18 9306604 9313005 + Vvi18g806 Vvi18g806 806
18 9313561 9332778 - Vvi18g807 Vvi18g807 807
18 9335609 9335990 + Vvi18g808 Vvi18g808 808
18 9336601 9346057 + Vvi18g809 Vvi18g809 809
       

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