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
Vvi16g1044 Blo06g01060 . . . . . . . . . Cma02g01118 . Car02g00927 Car15g00959 . Cpe05g00600 . . . . . . . . Cla01g00044 Cam01g0041 Cec01g0040 Cco01g0042 Clacu01g0043 Cmu01g0041 Cre09g2466 . . Cone14ag0013 Cone15ag0015 . Csa05g00050 Chy09g01438 . . . . Bda15g00784 . Bpe12g00351 Bma08g00386 . . Cmo02g01146 Cmo15g01088 . . . . . Cpe13g00316 Bhi12g00638 . . . . . . . . . . . . . Lsi09g00022 . . Cme09g01984
Vvi16g1045 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone1ag0981 Cone5ag0686 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1046 Blo06g01091 . Bda05g00123 Bda07g01931 Bpe03g00235 . . . Cmo16g00058 Cmo18g01346 Cma02g01117 Cma15g01025 . Car15g00960 Sed01g3493 Cpe05g00601 Cpe14g00042 Bhi01g01483 Tan01g0107 Cmetu06g1017 Lac11g0154 Hepe07g0066 Mch10g0064 . Cla01g00045 Cam01g0042 Cec01g0041 Cco01g0043 Clacu01g0044 Cmu01g0042 Cre09g2465 Cone1ag0980 Cone5ag0685 Cone14ag0014 Cone15ag0016 . Csa05g00051 Chy09g01437 Cme06g01137 Blo07g00338 Blo09g00029 . Bda15g00760 . Bpe12g00391 . . . Cmo02g01145 Cmo15g01089 Cma16g00050 Cma18g01316 . Car18g01228 . . Bhi12g00634 . . Lac11g0154 Hepe06g1367 . Lcy12g0133 Cla05g00966 Cam05g1058 Cec05g1064 Cco05g1057 Clacu05g1051 Cmu05g1001 Cre05g1078 Lsi09g00023 Csa03g01994 Chy06g01208 Cme09g01983
Vvi16g1047 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1048 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g1 . . Bda06g00701 . . . . Bma12g01103 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa01g01001 . . . Blo15g00108 . . Bpe07g00915 . . . . . . . . . . . Cpe18g00946 . . . . . . . . . . . . . . . . . .
Vvi17g2 . Blo16g00315 . Bda15g00749 . . Bma06g00299 . . . Cma10g00005 . Car10g00003 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe15g00240 . Bma08g00287 . Cmo10g00003 . . . . . . Cpe18g00946 . . . . . . . . . . . . . . . . . .
Vvi17g3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g4 . . . . . . . . . Cmo18g00240 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo15g00183 . . . . . . . . . . . . Car18g00252 . . . . . . . . . . . . . . . . . . . .
Vvi17g5 . . . Bda15g00749 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma13g00832 . . . . . . . . . . . . Cla03g00382 Cam03g0401 Cec03g0387 Cco03g0402 Clacu03g0400 Cmu03g1005 Cre03g0697 . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 5965310 5967570 + Bda020742.1 Bda05g00123 123
6 9673937 9683050 - Bda023999.2 Bda06g00701 701
7 36823276 36825433 + Bda028911.1 Bda07g01931 1931
15 11034485 11036119 - Bda012606.1 Bda15g00749 749
15 11202090 11204050 + Bda012619.1 Bda15g00760 760
15 11693672 11697496 - Bda012642.1 Bda15g00784 784
1 30543865 30546979 + XM_039025339.1 Bhi01g01483 1483
12 19483377 19488944 + XM_039018913.1 Bhi12g00634 634
12 19552202 19557454 - XM_039050623.1 Bhi12g00638 638
6 33975015 33977895 + BLOR17643 Blo06g01060 1060
6 34203091 34204789 - BLOR17674 Blo06g01091 1091
7 4366211 4368589 - BLOR18270 Blo07g00338 338
9 358877 360979 - BLOR20944 Blo09g00029 29
15 901712 906585 + BLOR06502 Blo15g00108 108
15 1900722 1912003 - BLOR06577 Blo15g00183 183
16 7968021 7972188 - BLOR07563 Blo16g00315 315
6 4444601 4445785 - Bma022941.1 Bma06g00299 299
8 3926033 3928280 - Bma027308.1 Bma08g00287 287
8 9324616 9328443 - Bma027456.1 Bma08g00386 386
12 43281329 43285514 + Bma008446.1 Bma12g01103 1103
3 3128996 3131175 - Bpe012089.1 Bpe03g00235 235
7 15101656 15103874 + Bpe021756.1 Bpe07g00915 915
12 8557165 8561002 + Bpe005606.1 Bpe12g00351 351
12 9331378 9332494 - Bpe005647.1 Bpe12g00391 391
15 13675039 13678643 - Bpe001176.1 Bpe15g00240 240
1 785358 788713 + CaPI482276_01g000410.1 Cam01g0041 41
1 793315 798848 - CaPI482276_01g000420.1 Cam01g0042 42
3 5133415 5136536 - CaPI482276_03g004010.1 Cam03g0401 401
5 9663370 9665860 + CaPI482276_05g010580.1 Cam05g1058 1058
2 6560459 6565842 - Carg14014-RA Car02g00927 927
10 17247 22177 - Carg10234-RA Car10g00003 3
15 7006775 7010113 + Carg26614-RA Car15g00959 959
15 7028201 7031426 - Carg26209-RA Car15g00960 960
18 1461304 1465988 - Carg06819-RA Car18g00252 252
18 11816241 11818504 + Carg20342-RA Car18g01228 1228
1 299198 302557 + CcPI632755_01g000420.1 Cco01g0042 42
1 307140 312771 - CcPI632755_01g000430.1 Cco01g0043 43
3 4360027 4363272 - CcPI632755_03g004020.1 Cco03g0402 402
5 9420749 9423245 + CcPI632755_05g010570.1 Cco05g1057 1057
1 327075 330438 + CePI673135_01g000400.1 Cec01g0040 40
1 335094 340289 - CePI673135_01g000410.1 Cec01g0041 41
3 4317627 4320899 - CePI673135_03g003870.1 Cec03g0387 387
5 9392488 9394969 + CePI673135_05g010640.1 Cec05g1064 1064
6 10749051 10751917 - Chy6G117360.1 Chy06g01208 1208
9 15944062 15948402 + Chy9G171530.1 Chy09g01437 1437
9 15951906 15955256 - Chy9G171540.1 Chy09g01438 1438
1 394397 397753 + ClG42_01g0004300.10 Clacu01g0043 43
1 402410 407877 - ClG42_01g0004400.10 Clacu01g0044 44
3 4448849 4452182 - ClG42_03g0040000.10 Clacu03g0400 400
5 9395563 9398054 + ClG42_05g0105100.10 Clacu05g1051 1051
1 326959 332413 + ClCG01G000430.1 Cla01g00044 44
1 336726 342333 - ClCG01G000440.1 Cla01g00045 45
3 4410543 4414558 - ClCG03G004050.2 Cla03g00382 382
5 9738714 9741609 + ClCG05G008910.1 Cla05g00966 966
2 6634770 6637841 + CmaCh02G011170.1 Cma02g01117 1117
2 6638024 6643465 - CmaCh02G011180.1 Cma02g01118 1118
10 17241 20902 - CmaCh10G000050.1 Cma10g00005 5
13 6955499 6959277 - CmaCh13G008320.1 Cma13g00832 832
15 6364490 6368025 - CmaCh15G010250.1 Cma15g01025 1025
16 219206 221834 - CmaCh16G000500.1 Cma16g00050 50
18 10105679 10108079 + CmaCh18G013160.1 Cma18g01316 1316
6 8755404 8756048 + MELO3C027375.2.1 Cme06g01137 1137
9 23683621 23688883 + MELO3C005885.2.1 Cme09g01983 1983
9 23691780 23696644 - MELO3C005886.2.1 Cme09g01984 1984
6 8116832 8120081 - PI0016513.1 Cmetu06g1017 1017
2 6934865 6937943 + CmoCh02G011450.1 Cmo02g01145 1145
2 6938209 6943527 - CmoCh02G011460.1 Cmo02g01146 1146
10 42347 60365 - CmoCh10G000030.1 Cmo10g00003 3
15 7225033 7229647 + CmoCh15G010880.1 Cmo15g01088 1088
15 7241794 7245354 - CmoCh15G010890.1 Cmo15g01089 1089
16 242264 245230 - CmoCh16G000580.1 Cmo16g00058 58
18 1586990 1592025 - CmoCh18G002400.1 Cmo18g00240 240
18 12739181 12741541 + CmoCh18G013460.1 Cmo18g01346 1346
1 339239 342594 + CmPI595203_01g000410.1 Cmu01g0041 41
1 347287 352741 - CmPI595203_01g000420.1 Cmu01g0042 42
3 4662832 4666165 - CmPI595203_03g010050.1 Cmu03g1005 1005
5 9241125 9243612 + CmPI595203_05g010010.1 Cmu05g1001 1001
1 54911997 54914932 + Conep01aG0102500.1 Cone1ag0980 980
1 54916307 54919043 - Conep01aG0102600.1 Cone1ag0981 981
5 2933931 2936826 + Conep05aG0070900.1 Cone5ag0685 685
5 2937701 2940824 - Conep05aG0071000.1 Cone5ag0686 686
14 108232 111296 + Conep14aG0001400.1 Cone14ag0013 13
14 112197 114919 - Conep14aG0001500.1 Cone14ag0014 14
15 121032 125193 + Conep15aG0001600.1 Cone15ag0015 15
15 125619 128352 - Conep15aG0001700.1 Cone15ag0016 16
5 3645757 3651500 + Cp4.1LG05g06020.1 Cpe05g00600 600
5 3652067 3655029 - Cp4.1LG05g06070.1 Cpe05g00601 601
13 2728877 2733546 - Cp4.1LG13g03170.1 Cpe13g00316 316
14 223595 226955 - Cp4.1LG14g06720.1 Cpe14g00042 42
18 8315112 8320149 + Cp4.1LG18g09300.1 Cpe18g00946 946
3 5877321 5880582 - CrPI670011_03g006970.1 Cre03g0697 697
5 10103828 10106338 + CrPI670011_05g010780.1 Cre05g1078 1078
9 43976047 43981671 + CrPI670011_09g024650.1 Cre09g2465 2465
9 43986185 43989546 - CrPI670011_09g024660.1 Cre09g2466 2466
1 6222195 6223646 + CsaV3_1G010010.1 Csa01g01001 1001
3 15703537 15707297 - CsaV3_3G019940.1 Csa03g01994 1994
5 229072 232419 + CsaV3_5G000500.1 Csa05g00050 50
5 235332 240442 - CsaV3_5G000510.1 Csa05g00051 51
6 63939918 63942880 + Hsped.06g13670.1 Hepe06g1367 1367
7 602499 605853 - Hsped.07g00660.1 Hepe07g0066 66
11 1433242 1438786 + Lag0030792.1 Lac11g0154 154
12 1659503 1665847 + Maker00039006 Lcy12g0133 133
9 188335 193330 + Lsi09G000220.1 Lsi09g00022 22
9 197201 202177 - Lsi09G000230.1 Lsi09g00023 23
10 342442 345721 - MC10g0059 Mch10g0064 64
1 64019311 64025518 - Sed0018706.1 Sed01g3493 3493
1 1054518 1057902 - Tan0016494.1 Tan01g0107 107
16 21963903 21968096 + Vvi16g1044 Vvi16g1044 1044
16 21971523 21974662 + Vvi16g1045 Vvi16g1045 1045
16 21975852 21979103 - Vvi16g1046 Vvi16g1046 1046
16 22015152 22015892 - Vvi16g1047 Vvi16g1047 1047
16 22031590 22038414 + Vvi16g1048 Vvi16g1048 1048
17 9171 13753 + Vvi17g1 Vvi17g1 1
17 23970 30618 + Vvi17g2 Vvi17g2 2
17 31532 34781 - Vvi17g3 Vvi17g3 3
17 34821 36451 + Vvi17g4 Vvi17g4 4
17 37071 39024 - Vvi17g5 Vvi17g5 5
       

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