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
Vvi16g664 Blo06g01121 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone15ag0094 . . . . . . . . . Bpe12g00429 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g665 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone15ag0093 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g666 . . Bda05g00073 . Bpe03g00288 . Bma10g01222 . Cmo16g00134 Cmo18g01269 . . . . Sed07g1105 . Cpe14g00109 Bhi01g01321 Tan01g0253 Cmetu06g1773 . Hepe07g0160 Mch10g0155 . . . . . . . . . . Cone14ag0088 Cone15ag0092 Lsi05g01227 . . . Blo07g00412 . . . . . . . . . . . Cma18g01246 Car16g00114 Car18g01152 Cpe09g00092 . . . . . . . . Cla05g00880 Cam05g0968 Cec05g0972 Cco05g0972 . Cmu05g0912 Cre05g0996 . Csa03g01710 Chy06g00946 .
Vvi16g667 Blo06g01123 Blo15g00165 . . . Bpe07g00940 . . . . Cma02g01066 . Car02g00810 . . Cpe05g00653 . . . . . . . . . . . . . . . Cone1ag1156 . Cone14ag0087 Cone15ag0091 . . . . . . Bda06g00681 Bda15g00729 . . . Bma12g01123 . Cmo02g01084 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g668 Blo06g01124 . . . . Bpe07g00939 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone15ag0090 . . . . . . Bda06g00682 Bda15g00728 . Bpe12g00434 . Bma12g01122 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g669 . . Bda05g00074 . . . . Bma14g02085 . . . . . . . . Cpe14g00108 . . . . . . . Cla01g00104 Cam01g0103 . Cco01g0105 Clacu01g0101 . Cre09g2404 . . . . . Csa05g00297 Chy09g01209 Cme06g01000 . Blo09g00110 . . . . . . . . . Cma16g00128 . . . Cpe09g00091 . . . . . . . . Cla05g00882 Cam05g0969 Cec05g0973 Cco05g0973 Clacu05g0956 Cmu05g0913 Cre05g0997 . Csa03g01711 . .
Vvi16g670 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g00122 Chy09g00982 . . . . . . . . . . . . . . . . . . Bhi12g00033 . . . . . . . . . . . . . . . . Cme09g01509
Vvi16g671 . . . . Bpe03g00287 . Bma10g01223 . Cmo16g00132 Cmo18g01270 . . . . Sed13g0125 . . Bhi01g01320 Tan01g0251 Cmetu09g0720 . Hepe07g0158 Mch10g0154 . . . . . . . . . . . Cone15ag0089 Lsi05g01226 . . . Blo07g00411 Blo09g00111 . . . . . . . . . Cma16g00126 Cma18g01247 . . . . Bhi12g00232 . . Lac11g2111 Hepe06g1560 . Lcy12g1668 . . . . . . . . . Chy06g00947 .
Vvi16g672 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy09g01009 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g673 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g00532 Chy09g01010 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 3701009 3702472 + Bda020663.1 Bda05g00073 73
5 3706066 3708405 + Bda020664.1 Bda05g00074 74
6 9440978 9441337 - Bda023976.1 Bda06g00681 681
6 9442432 9443710 - Bda023977.1 Bda06g00682 682
15 10705365 10705886 + Bda033311 Bda15g00728 728
15 10721870 10722335 + Bda012583.1 Bda15g00729 729
1 26511090 26515714 - XM_039042889.1 Bhi01g01320 1320
1 26567224 26569317 - XM_039022084.1 Bhi01g01321 1321
12 615049 617588 - XM_039019248.1 Bhi12g00033 33
12 7465291 7471412 + XM_039019109.1 Bhi12g00232 232
6 34647007 34656284 - BLOR17704 Blo06g01121 1121
6 34665754 34666217 - BLOR17706 Blo06g01123 1123
6 34703526 34704090 - BLOR17707 Blo06g01124 1124
7 7641417 7643862 - BLOR18343 Blo07g00411 411
7 7645168 7646574 - BLOR18344 Blo07g00412 412
9 2187018 2189984 + BLOR21025 Blo09g00110 110
9 2258358 2265497 + BLOR21026 Blo09g00111 111
15 1685779 1696921 - BLOR06559 Blo15g00165 165
10 43136186 43137646 + Bma005294.1 Bma10g01222 1222
10 43140163 43142095 + Bma005295.1 Bma10g01223 1223
12 43496638 43497910 + Bma008470.1 Bma12g01122 1122
12 43498906 43499297 + Bma008471.1 Bma12g01123 1123
14 44243979 44245881 - Bma012896.1 Bma14g02085 2085
3 3929377 3931226 - Bpe012139.1 Bpe03g00287 287
3 3934116 3935579 - Bpe012140.1 Bpe03g00288 288
7 15270707 15271866 + Bpe021781.1 Bpe07g00939 939
7 15272828 15273217 + Bpe021782.1 Bpe07g00940 940
12 9885210 9898645 - Bpe005686.1 Bpe12g00429 429
12 10093705 10094227 - Bpe005694.1 Bpe12g00434 434
1 1335570 1345857 - CaPI482276_01g001030.1 Cam01g0103 103
5 8707535 8708992 + CaPI482276_05g009680.1 Cam05g0968 968
5 8712294 8716676 + CaPI482276_05g009690.1 Cam05g0969 969
2 5879961 5880734 - Carg08411-RA Car02g00810 810
16 685532 686986 - Carg15136-RA Car16g00114 114
18 11350274 11351701 + Carg22100-RA Car18g01152 1152
1 873173 881573 - CcPI632755_01g001050.1 Cco01g0105 105
5 8476004 8477461 + CcPI632755_05g009720.1 Cco05g0972 972
5 8480747 8485103 + CcPI632755_05g009730.1 Cco05g0973 973
5 8461252 8462709 + CePI673135_05g009720.1 Cec05g0972 972
5 8465968 8470174 + CePI673135_05g009730.1 Cec05g0973 973
6 6922203 6923633 + Chy6G114740.1 Chy06g00946 946
6 6927379 6931102 + Chy6G114750.1 Chy06g00947 947
9 12518142 12519407 + Chy9G166980.1 Chy09g00982 982
9 12696216 12698959 - Chy9G167250.1 Chy09g01009 1009
9 12703219 12704412 - Chy9G167260.1 Chy09g01010 1010
9 14226366 14230134 + Chy9G169250.1 Chy09g01209 1209
1 947349 951928 - ClG42_01g0010100.10 Clacu01g0101 101
5 8422754 8427120 + ClG42_05g0095600.10 Clacu05g0956 956
1 918198 922854 - ClCG01G001065.1 Cla01g00104 104
5 8677246 8678703 + ClCG05G008043.1 Cla05g00880 880
5 8681992 8686366 + ClCG05G008050.1 Cla05g00882 882
2 6360596 6361214 - CmaCh02G010660.1 Cma02g01066 1066
16 573031 576179 - CmaCh16G001260.1 Cma16g00126 126
16 579549 579896 - CmaCh16G001280.1 Cma16g00128 128
18 9734075 9735502 + CmaCh18G012460.1 Cma18g01246 1246
18 9737142 9739755 + CmaCh18G012470.1 Cma18g01247 1247
6 7159458 7162505 + MELO3C006909.2.1 Cme06g01000 1000
9 20235669 20238509 + MELO3C005428.2.1 Cme09g01509 1509
6 7125909 7128146 + PI0006697.1 Cmetu06g1773 1773
9 2149878 2153923 - PI0003125.1 Cmetu09g0720 720
2 6591357 6591971 - CmoCh02G010840.1 Cmo02g01084 1084
16 617793 619560 - CmoCh16G001320.1 Cmo16g00132 132
16 621700 623157 - CmoCh16G001340.1 Cmo16g00134 134
18 12352537 12353964 + CmoCh18G012690.1 Cmo18g01269 1269
18 12355388 12358026 + CmoCh18G012700.1 Cmo18g01270 1270
5 8264860 8266317 + CmPI595203_05g009120.1 Cmu05g0912 912
5 8269604 8273956 + CmPI595203_05g009130.1 Cmu05g0913 913
1 55714129 55715060 - Conep01aG0120500.1 Cone1ag1156 1156
14 439732 440497 + Conep14aG0009000.1 Cone14ag0087 87
14 440845 443001 - Conep14aG0009100.1 Cone14ag0088 88
15 463196 466293 - Conep15aG0009100.1 Cone15ag0089 89
15 467618 468329 + Conep15aG0009200.1 Cone15ag0090 90
15 469546 470180 + Conep15aG0009300.1 Cone15ag0091 91
15 470825 472336 - Conep15aG0009400.1 Cone15ag0092 92
15 473362 475007 - Conep15aG0009500.1 Cone15ag0093 93
15 475652 480820 + Conep15aG0009600.1 Cone15ag0094 94
5 3977030 3980454 + Cp4.1LG05g06460.1 Cpe05g00653 653
9 527520 530223 - Cp4.1LG09g00970.1 Cpe09g00091 91
9 531877 533304 - Cp4.1LG09g00920.1 Cpe09g00092 92
14 594103 597243 - Cp4.1LG14g06010.1 Cpe14g00108 108
14 598176 600494 - Cp4.1LG14g06120.1 Cpe14g00109 109
5 9147963 9149420 + CrPI670011_05g009960.1 Cre05g0996 996
5 9153894 9158257 + CrPI670011_05g009970.1 Cre05g0997 997
9 43404474 43408902 + CrPI670011_09g024040.1 Cre09g2404 2404
3 12814883 12817876 + CsaV3_3G017100.1 Csa03g01710 1710
3 12820046 12824122 + CsaV3_3G017110.1 Csa03g01711 1711
5 617527 619981 - CsaV3_5G001220.1 Csa05g00122 122
5 1869686 1873208 - CsaV3_5G002970.1 Csa05g00297 297
5 3404889 3406928 - CsaV3_5G005320.1 Csa05g00532 532
6 66320650 66325613 - Hsped.06g15600.1 Hepe06g1560 1560
7 1447886 1453473 - Hsped.07g01580.1 Hepe07g0158 158
7 1457287 1459368 - Hsped.07g01600.1 Hepe07g0160 160
11 37074560 37079505 - Lag0032749.1 Lac11g2111 2111
12 37096288 37102267 - Maker00029339 Lcy12g1668 1668
5 20146334 20152611 - Lsi05G012260.1 Lsi05g01226 1226
5 20159648 20161105 - Lsi05G012270.1 Lsi05g01227 1227
10 945393 950901 - MC10g_new0024 Mch10g0154 154
10 951679 954508 - MC10g_new0025 Mch10g0155 155
7 8111369 8113747 + Sed0008807.1 Sed07g1105 1105
13 815906 820016 + Sed0019719.2 Sed13g0125 125
1 2155530 2158832 - Tan0003445.1 Tan01g0251 251
1 2164901 2167013 - Tan0004239.1 Tan01g0253 253
16 16950217 16957354 - Vvi16g664 Vvi16g664 664
16 16962309 16964099 + Vvi16g665 Vvi16g665 665
16 16971498 16973459 + Vvi16g666 Vvi16g666 666
16 16976682 16977766 - Vvi16g667 Vvi16g667 667
16 16983230 16985468 - Vvi16g668 Vvi16g668 668
16 16992465 16995367 + Vvi16g669 Vvi16g669 669
16 17001569 17012208 + Vvi16g670 Vvi16g670 670
16 17013690 17015121 + Vvi16g671 Vvi16g671 671
16 17017498 17020870 + Vvi16g672 Vvi16g672 672
16 17021166 17025232 + Vvi16g673 Vvi16g673 673
       

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