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
Vvi16g684 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g685 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g686 Blo06g01126 Blo15g00166 . . . . Bma10g01224 Bma14g02083 . . . . . . . . . . . . . . . . Cla01g00267 Cam01g0274 Cec01g0267 Cco01g0282 Clacu01g0274 Cmu01g0262 Cre09g2246 . . . . . . . . . Blo09g00113 . . . Bpe12g00435 Bma08g00325 . . . . . . . . . . Bhi12g00853 . . . . . . . . . . . . . . . . .
Vvi16g687 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g688 . . Bda05g00078 . Bpe03g00285 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g00284 . . Blo07g00408 Blo09g00113 . Bda15g00727 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g689 . Blo15g00167 . . . Bpe07g00938 . . . . . Cma15g01097 . Car15g01008 . . . . . . . . . . Cla01g00434 Cam01g0457 Cec01g0446 Cco01g0468 Clacu01g0456 Cmu01g0435 Cre09g2077 . . . . . . Chy09g01213 . . . Bda06g00683 . . . . Bma12g01121 . . Cmo15g01155 . . . . . Cpe13g00254 Bhi12g00510 . . Lac11g0027 Hepe06g0701 . Lcy12g0025 . . . . . . . . . . Cme09g01750
Vvi16g690 . . . . . . Bma10g01226 . . . . . . . . . . Bhi01g01318 . . . . Mch10g0152 . . . . . . . . Cone1ag1159 Cone5ag0869 . . . . . Cme06g01002 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g01714 Chy06g00949 .
Vvi16g691 . Blo15g00168 . . . Bpe07g00937 . . Cmo16g00131 . . . . . . . Cpe14g00106 . . . . . . . . . . . . . . . . . . Lsi05g01222 . . . . . Bda06g00684 . . . . . . . . Cma16g00122 . Car16g00112 . . . . . . . . . . . . . . . . . . . . .
Vvi16g692 . . . . Bpe03g00284 . Bma10g01227 . . . . . . . Sed07g1041 . . Bhi01g01317 Tan01g0248 Cmetu06g1326 . Hepe07g0155 . . . . . . . . . . . . Cone15ag0081 . . . Cme06g01003 Blo07g00407 . . . . . . Bma12g01120 . . . . . . . . . . . . . . . . . . . . . . . . Csa03g01715 . .
Vvi16g693 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 3792212 3794131 + Bda020669.1 Bda05g00078 78
6 9447641 9449948 - Bda023978.1 Bda06g00683 683
6 9453217 9454197 - Bda023979.1 Bda06g00684 684
15 10689961 10691773 - Bda012581.1 Bda15g00727 727
1 26486280 26488089 + XM_039047227.1 Bhi01g01317 1317
1 26500545 26501909 + XM_039030372.1 Bhi01g01318 1318
12 16256481 16261993 + XM_039019788.1 Bhi12g00510 510
12 25876654 25881508 - XM_039019614.1 Bhi12g00853 853
6 34730980 34732888 + BLOR17709 Blo06g01126 1126
7 7558553 7559148 + BLOR18339 Blo07g00407 407
7 7563671 7565594 - BLOR18340 Blo07g00408 408
9 2330122 2332180 + BLOR21028 Blo09g00113 113
15 1701170 1703610 + BLOR06560 Blo15g00166 166
15 1703699 1705850 - BLOR06561 Blo15g00167 167
15 1708980 1710312 - BLOR06562 Blo15g00168 168
8 4995780 4997673 - Bma027360.1 Bma08g00325 325
10 43164986 43166905 + Bma005298.1 Bma10g01224 1224
10 43372313 43373262 - Bma005304.1 Bma10g01226 1226
10 43639995 43640581 + Bma005306.1 Bma10g01227 1227
12 43478627 43479496 + Bma008467.1 Bma12g01120 1120
12 43481947 43484249 + Bma008468.1 Bma12g01121 1121
14 44195217 44197264 - Bma012893.1 Bma14g02083 2083
3 3894145 3894810 + Bpe012136.1 Bpe03g00284 284
3 3895792 3897709 - Bpe012137.1 Bpe03g00285 285
7 15260357 15261430 + Bpe021779.1 Bpe07g00937 937
7 15264246 15266571 + Bpe021780.1 Bpe07g00938 938
12 10114472 10116355 + Bpe005695.1 Bpe12g00435 435
1 3060156 3062382 + CaPI482276_01g002740.1 Cam01g0274 274
1 4870377 4874105 - CaPI482276_01g004570.1 Cam01g0457 457
15 7883481 7886140 + Carg23184-RA Car15g01008 1008
16 676908 677829 + Carg15134-RA Car16g00112 112
1 2696380 2698521 + CcPI632755_01g002820.1 Cco01g0282 282
1 4568614 4572400 - CcPI632755_01g004680.1 Cco01g0468 468
1 2668713 2670934 + CePI673135_01g002670.1 Cec01g0267 267
1 4593620 4597355 - CePI673135_01g004460.1 Cec01g0446 446
6 6946502 6947189 - Chy6G114770.1 Chy06g00949 949
9 14259472 14261455 - Chy9G169290.1 Chy09g01213 1213
1 2676366 2678598 + ClG42_01g0027400.10 Clacu01g0274 274
1 4516992 4520789 - ClG42_01g0045600.10 Clacu01g0456 456
1 2741029 2743826 + ClCG01G002750.1 Cla01g00267 267
1 4693647 4697813 - ClCG01G004420.1 Cla01g00434 434
15 6987825 6990099 + CmaCh15G010970.1 Cma15g01097 1097
16 567975 568905 + CmaCh16G001220.1 Cma16g00122 122
6 7173617 7174808 - MELO3C006912.2.1 Cme06g01002 1002
6 7182450 7183792 - MELO3C006914.2.1 Cme06g01003 1003
9 22002747 22005182 - MELO3C005663.2.1 Cme09g01750 1750
6 7149745 7151039 - PI0027421.1 Cmetu06g1326 1326
15 8077062 8079883 + CmoCh15G011550.1 Cmo15g01155 1155
16 612380 617437 + CmoCh16G001310.1 Cmo16g00131 131
1 2629309 2631541 + CmPI595203_01g002620.1 Cmu01g0262 262
1 4473795 4477592 - CmPI595203_01g004350.1 Cmu01g0435 435
1 55724090 55725489 - Conep01aG0120800.1 Cone1ag1159 1159
5 3697180 3700154 - Conep05aG0089500.1 Cone5ag0869 869
15 432797 433680 - Conep15aG0008300.1 Cone15ag0081 81
13 1972164 1975169 - Cp4.1LG13g02500.1 Cpe13g00254 254
14 587879 588757 + Cp4.1LG14g06050.1 Cpe14g00106 106
9 39839735 39843539 + CrPI670011_09g020770.1 Cre09g2077 2077
9 41660502 41662727 - CrPI670011_09g022460.1 Cre09g2246 2246
3 12831127 12832171 - CsaV3_3G017140.1 Csa03g01714 1714
3 12833581 12835061 - CsaV3_3G017150.1 Csa03g01715 1715
5 1761660 1767852 + CsaV3_5G002840.1 Csa05g00284 284
6 51400365 51404021 + Hsped.06g07010.1 Hepe06g0701 701
7 1439353 1440708 + Hsped.07g01550.1 Hepe07g0155 155
11 236964 239494 - Lag0030665.1 Lac11g0027 27
12 532924 535533 - Maker00038573 Lcy12g0025 25
5 20130370 20131886 + Lsi05G012220.1 Lsi05g01222 1222
10 940190 941417 + MC10g0129 Mch10g0152 152
7 7519775 7521825 + Sed0005792.1 Sed07g1041 1041
1 2146705 2147868 + Tan0001526.1 Tan01g0248 248
16 17152641 17152908 - Vvi16g684 Vvi16g684 684
16 17157529 17157868 - Vvi16g685 Vvi16g685 685
16 17168324 17169388 + Vvi16g686 Vvi16g686 686
16 17185800 17186091 - Vvi16g687 Vvi16g687 687
16 17206673 17208766 + Vvi16g688 Vvi16g688 688
16 17209236 17213204 - Vvi16g689 Vvi16g689 689
16 17218592 17219856 - Vvi16g690 Vvi16g690 690
16 17226708 17238324 - Vvi16g691 Vvi16g691 691
16 17238816 17239970 - Vvi16g692 Vvi16g692 692
16 17245530 17247214 - Vvi16g693 Vvi16g693 693
       

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