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
Vvi4g1202 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1203 . . . . . . . . . Cmo20g01091 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda14g01068 . . . Bma06g00531 . . . . Cma20g01081 . . Cpe05g01099 . Bhi10g02352 Tan07g0908 Cmetu11g1500 . . . . Cla02g00080 Cam02g0083 Cec02g0085 Cco02g0077 Clacu02g0081 Cmu02g0079 Cre02g0419 Lsi10g00698 . . Cme11g00085
Vvi4g1204 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1205 Blo04g00973 Blo16g00516 . . Bpe15g00392 Bpe13g00009 . . . Cmo20g01090 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g01352 Bda14g01063 . . Bma03g01039 . Sed01g0043 . . . Cma20g01080 . . . Cpe16g00065 Bhi10g02351 Tan07g0907 Cmetu11g1922 . . . . Cla02g00079 Cam02g0082 Cec02g0084 Cco02g0076 Clacu02g0080 Cmu02g0078 Cre02g0418 Lsi10g00699 . . Cme11g00083
Vvi4g1206 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1207 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1208 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1209 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1210 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1211 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 15391744 15407679 - Bda033151 Bda11g01352 1352
14 9141946 9144279 + Bda027878.1 Bda14g01063 1063
14 9251372 9253523 - Bda027885.1 Bda14g01068 1068
10 61584631 61588052 + XM_039044712.1 Bhi10g02351 2351
10 61630899 61634622 + XM_039046684.1 Bhi10g02352 2352
4 12183123 12185395 + BLOR13885 Blo04g00973 973
16 21032742 21041085 - BLOR07764 Blo16g00516 516
3 12141113 12143297 + Bma017398.1 Bma03g01039 1039
6 27263080 27267287 + Bma023412.1 Bma06g00531 531
13 254135 258389 - Bpe024914 Bpe13g00009 9
15 15445271 15447401 - Bpe001329.1 Bpe15g00392 392
2 1939945 1943545 + CaPI482276_02g000820.1 Cam02g0082 82
2 1952535 1955367 + CaPI482276_02g000830.1 Cam02g0083 83
2 815910 819460 + CcPI632755_02g000760.1 Cco02g0076 76
2 828367 831188 + CcPI632755_02g000770.1 Cco02g0077 77
2 821300 824857 + CePI673135_02g000840.1 Cec02g0084 84
2 836459 839285 + CePI673135_02g000850.1 Cec02g0085 85
2 822500 826090 + ClG42_02g0008000.10 Clacu02g0080 80
2 834967 837807 + ClG42_02g0008100.10 Clacu02g0081 81
2 827566 831443 + ClCG02G000750.1 Cla02g00079 79
2 841745 845481 + ClCG02G000760.2 Cla02g00080 80
20 8298392 8303269 + CmaCh20G010800.1 Cma20g01080 1080
20 8304259 8307250 + CmaCh20G010810.1 Cma20g01081 1081
11 693602 695918 + MELO3C034560.2.1 Cme11g00083 83
11 721295 724529 + MELO3C023272.2.1 Cme11g00085 85
11 30302784 30305369 - PI0017531.1 Cmetu11g1500 1500
11 30287859 30291220 - PI0024074.1 Cmetu11g1922 1922
20 10384192 10388488 + CmoCh20G010900.1 Cmo20g01090 1090
20 10389642 10392473 + CmoCh20G010910.1 Cmo20g01091 1091
2 821810 825399 + CmPI595203_02g000780.1 Cmu02g0078 78
2 834258 837098 + CmPI595203_02g000790.1 Cmu02g0079 79
5 7330666 7337757 - Cp4.1LG05g11000.1 Cpe05g01099 1099
16 1275558 1283805 - Cp4.1LG16g00690.1 Cpe16g00065 65
2 1365386 1368978 + CrPI670011_02g004180.1 Cre02g0418 418
2 1377954 1380778 + CrPI670011_02g004190.1 Cre02g0419 419
10 9757281 9762481 - Lsi10G006980.1 Lsi10g00698 698
10 9771521 9774747 - Lsi10G006990.1 Lsi10g00699 699
1 454981 457210 + Sed0015642.1 Sed01g0043 43
7 17673509 17682958 + Tan0010767.1 Tan07g0907 907
7 17673509 17683610 + Tan0010767.2 Tan07g0908 908
4 20885556 20887126 - Vvi4g1202 Vvi4g1202 1202
4 20891375 20894224 - Vvi4g1203 Vvi4g1203 1203
4 20894724 20897159 - Vvi4g1204 Vvi4g1204 1204
4 20897680 20900291 - Vvi4g1205 Vvi4g1205 1205
4 20906155 20908236 - Vvi4g1206 Vvi4g1206 1206
4 20912725 20914980 - Vvi4g1207 Vvi4g1207 1207
4 20929976 20930219 - Vvi4g1208 Vvi4g1208 1208
4 20937353 20940134 + Vvi4g1209 Vvi4g1209 1209
4 20951209 20953335 - Vvi4g1210 Vvi4g1210 1210
4 20960329 20962884 - Vvi4g1211 Vvi4g1211 1211
       

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