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
Vvi1g981 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g982 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi12g01051 . . . . . . . . . . . . . Lsi09g00795 Csa05g01032 . .
Vvi1g983 . . . . . . . . . . . . . . Sed06g0245 . . Bhi07g00114 Tan04g1664 Cmetu10g0662 Lac13g1622 . . . . . . . . . . . . . . . . Chy10g00123 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g984 Blo01g00392 Blo16g01097 . Bda11g01191 Bpe13g01388 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g01191 . . . Bma06g00724 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g985 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g986 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo04g02921 . . . . Car15g00248 Cpe13g00970 . . . . . . . . . . . . . . . . . Chy09g00214 .
Vvi1g987 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g988 Blo01g00443 . Bda01g02137 . . . . . Cmo04g01768 Cmo18g01142 . Cma18g01121 . Car18g01033 Sed06g1493 Cpe09g00207 Cpe01g01493 Bhi07g01520 Tan04g1033 Cmetu10g0314 Lac13g0354 Hepe10g1778 . . Cla05g02411 Cam05g2589 Cec05g2621 Cco05g2660 Clacu05g2590 Cmu05g2444 . . . . . Lsi04g00383 Csa05g02493 Chy10g01041 Cme10g00378 . . . . . Bpe02g02326 Bma01g00113 . . . . Cma04g01687 . Car04g01724 . . . . . . . . . . . . . . . . . . . . .
Vvi1g989 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe07g00641 . . . . . . . . . . . . . . . . . .
Vvi1g990 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car15g00242 Cpe13g00977 . . . . . . . . . . . . . . . . . Chy09g00204 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 57341159 57342458 + Bda004468.1 Bda01g02137 2137
11 12259266 12260330 + Bda007690.1 Bda11g01191 1191
7 6949126 6982628 - XM_039036550.1 Bhi07g00114 114
7 43848499 43851077 + XM_039035909.1 Bhi07g01520 1520
12 32070630 32080764 + XM_039019353.1 Bhi12g01051 1051
1 4433822 4439699 - BLOR00392 Blo01g00392 392
1 4909836 4911271 - BLOR00443 Blo01g00443 443
16 39453575 39469392 + BLOR21884 Blo16g01097 1097
1 1150456 1151673 - Bma000277.1 Bma01g00113 113
6 38207355 38208344 - Bma023709.1 Bma06g00724 724
2 23873537 23874940 + Bpe010141.1 Bpe02g02326 2326
13 19094764 19095999 + Bpe011049.1 Bpe13g01388 1388
5 33553299 33554819 + CaPI482276_05g025890.1 Cam05g2589 2589
4 9880848 9888298 - Carg14381-RA Car04g01724 1724
15 1351221 1352081 + Carg02223-RA Car15g00242 242
15 1365817 1367939 + Carg02229-RA Car15g00248 248
18 10672726 10675150 + Carg17297-RA Car18g01033 1033
5 34671247 34673084 + CcPI632755_05g026600.1 Cco05g2660 2660
5 37000514 37002038 + CePI673135_05g026210.1 Cec05g2621 2621
9 1733388 1735007 + Chy9G159200.1 Chy09g00204 204
9 1800474 1802838 + Chy9G159300.1 Chy09g00214 214
10 3203222 3207786 - Chy10G173170.1 Chy10g00123 123
10 15661277 15663043 - Chy10G182350.1 Chy10g01041 1041
5 33764305 33765827 + ClG42_05g0259000.10 Clacu05g2590 2590
5 35638570 35640645 + ClCG05G023900.1 Cla05g02411 2411
4 8486944 8489128 - CmaCh04G016870.1 Cma04g01687 1687
18 9105306 9107677 + CmaCh18G011210.1 Cma18g01121 1121
10 2433749 2436086 + MELO3C012133.2.1 Cme10g00378 378
10 19593661 19596032 - PI0003628.1 Cmetu10g0314 314
10 9098730 9123187 + PI0024871.4 Cmetu10g0662 662
4 8921091 8923077 - CmoCh04G017680.1 Cmo04g01768 1768
4 20709788 20712663 - CmoCh04G029210.1 Cmo04g02921 2921
18 11685382 11687394 + CmoCh18G011420.1 Cmo18g01142 1142
5 33502053 33505432 + CmPI595203_05g024440.1 Cmu05g2444 2444
1 8908389 8913964 - Cp4.1LG01g12220.1 Cpe01g01493 1493
7 4566100 4580009 - Cp4.1LG07g06440.1 Cpe07g00641 641
9 1197598 1199896 - Cp4.1LG09g02140.1 Cpe09g00207 207
13 8086024 8088493 - Cp4.1LG13g08150.1 Cpe13g00970 970
13 8104855 8105655 + Cp4.1LG13g08280.1 Cpe13g00977 977
5 9982996 9987398 - CsaV3_5G013380.1 Csa05g01032 1032
5 26608948 26611392 - CsaV3_5G033120.1 Csa05g02493 2493
10 54533608 54535769 - Hsped.10g17780.1 Hepe10g1778 1778
13 2534203 2536410 - Lag0040150.1 Lac13g0354 354
13 17499461 17507701 + Lag0041418.1 Lac13g1622 1622
4 3789205 3789802 + Lsi04G003830.1 Lsi04g00383 383
9 9086452 9087877 + Lsi09G007950.1 Lsi09g00795 795
6 1983982 2002188 - Sed0013317.2 Sed06g0245 245
6 39631795 39634953 + Sed0008420.2 Sed06g1493 1493
4 9184565 9187065 + Tan0008051.1 Tan04g1033 1033
4 34686204 34739941 + Tan0013627.1 Tan04g1664 1664
1 15015185 15030833 - Vvi1g981 Vvi1g981 981
1 15079155 15080294 - Vvi1g982 Vvi1g982 982
1 15211273 15212244 - Vvi1g983 Vvi1g983 983
1 15215061 15216231 + Vvi1g984 Vvi1g984 984
1 15219018 15223294 - Vvi1g985 Vvi1g985 985
1 15229259 15243545 + Vvi1g986 Vvi1g986 986
1 15296595 15296998 + Vvi1g987 Vvi1g987 987
1 15304652 15307940 + Vvi1g988 Vvi1g988 988
1 15308918 15323250 - Vvi1g989 Vvi1g989 989
1 15343873 15346615 + Vvi1g990 Vvi1g990 990
       

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