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
Vvi16g794 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g795 Blo06g01138 Blo15g00178 . . . Bpe07g00925 . . . . Cma02g01086 Cma15g01063 Car02g00827 Car15g00984 . Cpe05g00635 . . . . . . . . Cla01g00086 Cam01g0087 Cec01g0087 Cco01g0088 Clacu01g0085 Cmu01g0087 Cre09g2421 . . . . . Csa05g00099 Chy09g01395 . . . Bda06g00696 . . . . Bma12g01108 . Cmo02g01104 Cmo15g01120 . . . . . Cpe13g00280 Bhi12g00771 . . . . . . . . . . . . . Lsi09g00073 . . Cme09g01940
Vvi16g796 . . . . . . . Bma14g02036 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g797 . . . Bda07g01909 Bpe03g00161 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g798 . . Bda05g00099 . Bpe03g00256 . . . Cmo16g00094 Cmo18g01312 . . . . . . Cpe14g00074 Bhi01g01422 . . . Hepe07g0110 Mch10g0112 . . . . . . . . . . Cone14ag0047 Cone15ag0051 Lsi05g01179 . . . Blo07g00359 . . . . . . . . . . Cma16g00090 Cma18g01281 Car16g00080 . Cpe09g00057 . . . . . . . . Cla05g00929 Cam05g1016 Cec05g1020 Cco05g1016 Clacu05g1005 Cmu05g0958 Cre05g1039 . Csa03g01761 Chy06g00989 .
Vvi16g799 . . . Bda07g01910 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo09g00052 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g800 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g801 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g802 . . . . . . . . . . . . . . . . . Bhi01g01565 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g803 . . . . . . . . . . . . . . . . . . . . . . . . Cla01g00223 Cam01g0230 Cec01g0221 Cco01g0231 Clacu01g0225 Cmu01g0218 Cre09g2292 . . . . . . . . . . . . . . . . . . . . . . . . . Bhi12g00611 . . Lac11g0134 . . Lcy12g0114 . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 4973803 4975605 - Bda020704.1 Bda05g00099 99
6 9570691 9575813 + Bda023993.1 Bda06g00696 696
7 36517004 36518532 - Bda028883.1 Bda07g01909 1909
7 36532352 36533883 - Bda028885.1 Bda07g01910 1910
1 28974929 28978916 - XM_039026056.1 Bhi01g01422 1422
1 32195275 32197774 + XM_039048100.1 Bhi01g01565 1565
12 18855893 18861720 + XM_039019807.1 Bhi12g00611 611
12 23040086 23043457 - XM_039051071.1 Bhi12g00771 771
6 34836796 34838349 + BLOR17721 Blo06g01138 1138
7 5798970 5800772 + BLOR18291 Blo07g00359 359
9 872191 873759 + BLOR20967 Blo09g00052 52
15 1815177 1822031 + BLOR06572 Blo15g00178 178
12 43363445 43365277 - Bma008453.1 Bma12g01108 1108
14 43734734 43736268 + Bma012844.1 Bma14g02036 2036
3 2065798 2067342 - Bpe012006.1 Bpe03g00161 161
3 3476943 3478745 + Bpe012109.1 Bpe03g00256 256
7 15190638 15192457 - Bpe021766.1 Bpe07g00925 925
1 1159769 1163287 - CaPI482276_01g000870.1 Cam01g0087 87
1 2573682 2574314 - CaPI482276_01g002300.1 Cam01g0230 230
5 9161509 9165218 - CaPI482276_05g010160.1 Cam05g1016 1016
2 5969670 5972914 + Carg08394-RA Car02g00827 827
15 7562463 7566359 - Carg27017-RA Car15g00984 984
16 507467 509347 + Carg15099-RA Car16g00080 80
1 674500 677024 - CcPI632755_01g000880.1 Cco01g0088 88
1 2188192 2188824 - CcPI632755_01g002310.1 Cco01g0231 231
5 8921146 8927143 - CcPI632755_05g010160.1 Cco05g1016 1016
1 723601 726299 - CePI673135_01g000870.1 Cec01g0087 87
1 2168879 2169508 - CePI673135_01g002210.1 Cec01g0221 221
5 8903498 8907259 - CePI673135_05g010200.1 Cec05g1020 1020
6 7313070 7316229 - Chy6G115170.1 Chy06g00989 989
9 15670767 15673472 + Chy9G171110.1 Chy09g01395 1395
1 770411 776077 - ClG42_01g0008500.10 Clacu01g0085 85
1 2190175 2190807 - ClG42_01g0022500.10 Clacu01g0225 225
5 8878097 8881848 - ClG42_05g0100500.10 Clacu05g1005 1005
1 734581 739353 - ClCG01G000850.2 Cla01g00086 86
1 2216262 2216894 - ClCG01G002280.1 Cla01g00223 223
5 9170232 9179019 - ClCG05G008520.1 Cla05g00929 929
2 6456584 6463085 + CmaCh02G010860.1 Cma02g01086 1086
15 6746473 6750759 - CmaCh15G010630.1 Cma15g01063 1063
16 398509 400621 + CmaCh16G000900.1 Cma16g00090 90
18 9910798 9914109 - CmaCh18G012810.1 Cma18g01281 1281
9 23422320 23425579 + MELO3C005845.2.1 Cme09g01940 1940
2 6683312 6690306 + CmoCh02G011040.1 Cmo02g01104 1104
15 7787850 7791642 - CmoCh15G011200.1 Cmo15g01120 1120
16 438121 440122 + CmoCh16G000940.1 Cmo16g00094 94
18 12528364 12530111 - CmoCh18G013120.1 Cmo18g01312 1312
1 714837 718268 - CmPI595203_01g000870.1 Cmu01g0087 87
1 2143259 2143891 - CmPI595203_01g002180.1 Cmu01g0218 218
5 8723283 8727038 - CmPI595203_05g009580.1 Cmu05g0958 958
14 303359 305182 + Conep14aG0004900.1 Cone14ag0047 47
15 319195 321009 + Conep15aG0005300.1 Cone15ag0051 51
5 3883241 3888960 - Cp4.1LG05g06360.1 Cpe05g00635 635
9 350056 351727 + Cp4.1LG09g00500.1 Cpe09g00057 57
13 2214111 2218418 + Cp4.1LG13g02750.1 Cpe13g00280 280
14 407677 409913 + Cp4.1LG14g06430.1 Cpe14g00074 74
5 9604209 9607976 - CrPI670011_05g010390.1 Cre05g1039 1039
9 42146618 42147250 + CrPI670011_09g022920.1 Cre09g2292 2292
9 43595903 43599463 + CrPI670011_09g024210.1 Cre09g2421 2421
3 13182164 13185586 - CsaV3_3G017610.1 Csa03g01761 1761
5 494629 498287 - CsaV3_5G000990.1 Csa05g00099 99
7 1043993 1047066 + Hsped.07g01100.1 Hepe07g0110 110
11 1229495 1234428 + Lag0030772.1 Lac11g0134 134
12 1455598 1462352 + Maker00038973 Lcy12g0114 114
5 19718362 19722474 + Lsi05G011790.1 Lsi05g01179 1179
9 616334 619116 - Lsi09G000730.1 Lsi09g00073 73
10 667514 670561 + MC10g_new0018 Mch10g0112 112
16 18473349 18474919 + Vvi16g794 Vvi16g794 794
16 18484089 18489671 + Vvi16g795 Vvi16g795 795
16 18494016 18495759 + Vvi16g796 Vvi16g796 796
16 18501786 18503389 + Vvi16g797 Vvi16g797 797
16 18530209 18534998 - Vvi16g798 Vvi16g798 798
16 18554740 18556254 - Vvi16g799 Vvi16g799 799
16 18632561 18634313 + Vvi16g800 Vvi16g800 800
16 18657280 18659016 + Vvi16g801 Vvi16g801 801
16 18685818 18687767 + Vvi16g802 Vvi16g802 802
16 18691677 18698719 + Vvi16g803 Vvi16g803 803
       

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