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
Vvi17g756 Blo04g00735 . Bda06g00598 . . Bpe13g00240 Bma06g00220 Bma12g01038 Cmo13g00917 . . . . . . Cpe20g00243 . . . . . . . . . . . . . . . . . . . . Csa01g00850 . Cme12g01695 . . Bda11g01653 . Bpe07g00839 Bpe15g00637 Bma03g00782 . . . . Cma13g00888 Cma18g00169 Car13g00728 Car18g00160 Cpe09g01026 . Bhi08g01607 Tan05g2010 . Lac10g0448 . . . Cla01g01299 Cam01g1430 Cec01g1465 . Clacu01g1365 Cmu01g1271 Cre01g1265 . . . .
Vvi17g757 Blo04g00734 . . . . . . . . Cmo18g00128 . . . . . . . . . . . . . . . . . . . . . . Cone16ag0101 Cone13ag0142 . Lsi02g00371 Csa01g00852 Chy12g01267 Cme12g01694 . . . Bda14g00811 . Bpe15g00638 Bma03g00781 . . . . . Cma18g00170 . Car18g00161 Cpe09g01025 . Bhi08g01609 Tan05g2008 . Lac10g0449 Hepe07g2227 . . Cla01g01300 Cam01g1429 Cec01g1464 Cco01g1460 Clacu01g1366 Cmu01g1272 Cre01g1264 . . . .
Vvi17g758 Blo04g00732 . . . . Bpe13g00242 Bma06g00218 . Cmo13g00915 . . . . . . Cpe20g00245 . . . . . . . . . . . . . . . Cone2ag0909 Cone16ag0099 . . Lsi02g00374 Csa01g00855 Chy12g01265 Cme12g01692 . . Bda11g01655 Bda14g00809 . . Bma03g00779 . Sed08g2514 . . Cma13g00886 . Car13g00726 . . . Bhi08g01614 Tan05g2005 . . Hepe07g2224 . . Cla01g01302 Cam01g1428 Cec01g1461 Cco01g1462 Clacu01g1368 Cmu01g1274 Cre01g1263 . . . .
Vvi17g759 . . Bda06g00600 . . . . Bma12g01039 . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0143 . . . . . . Blo15g00266 . . Bpe07g00840 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g760 . . Bda06g00601 . . . . . . . Cma10g00123 Cma11g00093 Car10g00111 Car11g00085 . . Cpe04g01561 . . . . . . . Cla06g01665 Cam06g1850 Cec06g1902 Cco06g1907 Clacu06g1809 Cmu06g1750 Cre06g2569 . . Cone13ag0144 . . . . . . . . . Bpe07g00841 . . . . Cmo10g00127 Cmo11g00092 . . . . . Cpe18g00846 . . . . . . . . . . . . . . Lsi06g01557 Csa01g00146 Chy02g02583 .
Vvi17g761 . . Bda06g00602 Bda15g00555 . Bpe13g00243 Bma06g00217 Bma12g01040 Cmo13g00914 Cmo18g00130 . . . . . Cpe20g00246 . . . . . . . . . . . . . . . Cone2ag0910 Cone16ag0098 Cone13ag0145 Cone19ag0142 Lsi02g00376 Csa01g00856 Chy12g01264 Cme12g01691 . Blo15g00265 Bda11g01656 . Bpe07g00843 . . Bma08g00100 . . . Cma13g00885 Cma18g00172 Car13g00725 Car18g00163 Cpe09g01023 . Bhi08g01617 . . Lac10g0453 . . . Cla01g01303 Cam01g1427 Cec01g1460 Cco01g1463 Clacu01g1369 Cmu01g1275 Cre01g1262 . . . .
Vvi17g762 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g763 Blo04g00731 Blo16g00226 . . . Bpe13g00244 Bma06g00216 . Cmo13g00913 Cmo18g00131 . . . . . Cpe20g00247 . . . . . . . . . . . . . . . Cone2ag0911 Cone16ag0097 . . Lsi02g00378 Csa01g00857 Chy12g01263 Cme12g01689 . . Bda11g01657 Bda14g00808 . Bpe15g00640 . . Sed08g2516 . . Cma13g00884 Cma18g00173 Car13g00724 Car18g00164 Cpe09g01022 . Bhi08g01618 Tan05g2002 Cmetu12g1934 Lac10g0456 Hepe07g2222 . . Cla01g01304 Cam01g1426 Cec01g1459 . . Cmu01g1276 Cre01g1261 . . . .
Vvi17g764 . . Bda06g00606 . . . . Bma12g01041 Cmo13g00912 Cmo18g00133 . . . . . Cpe20g00248 . . . . . . . . . . . . . . . Cone2ag0912 Cone16ag0096 . Cone19ag0143 Lsi02g00379 Csa01g00858 . Cme12g01688 . . . . Bpe07g00844 . . . Sed08g2518 . . Cma13g00882 Cma18g00175 Car13g00722 Car18g00165 . . Bhi08g01620 Tan05g2000 Cmetu12g1450 Lac10g0457 Hepe07g2221 . . Cla01g01305 . . Cco01g1464 Clacu01g1370 Cmu01g1277 . . . . .
Vvi17g765 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 8203902 8206655 - Bda023862.1 Bda06g00598 598
6 8211716 8214268 + Bda023864.1 Bda06g00600 600
6 8215568 8217094 + Bda023865.1 Bda06g00601 601
6 8222811 8225884 - Bda023867.1 Bda06g00602 602
6 8267095 8269364 + Bda023872.1 Bda06g00606 606
11 50564361 50567057 - Bda008545.1 Bda11g01653 1653
11 50632821 50639112 + Bda008549.1 Bda11g01655 1655
11 50639562 50642592 - Bda008550.1 Bda11g01656 1656
11 50681135 50683542 + Bda008551.1 Bda11g01657 1657
14 6213274 6215702 - Bda027576.1 Bda14g00808 808
14 6216618 6219772 - Bda027577.1 Bda14g00809 809
14 6246584 6257222 + Bda027580.1 Bda14g00811 811
15 8675523 8678558 + Bda012392.1 Bda15g00555 555
8 46091544 46095493 - XM_039038136.1 Bhi08g01607 1607
8 46100115 46118382 - XM_039038789.1 Bhi08g01609 1609
8 46184514 46190432 + XM_039038676.1 Bhi08g01614 1614
8 46193395 46197111 - XM_039039426.1 Bhi08g01617 1617
8 46224752 46229378 + XM_039039425.1 Bhi08g01618 1618
8 46235189 46238614 + XM_039040154.1 Bhi08g01620 1620
4 6788069 6789931 - BLOR13643 Blo04g00731 731
4 6791446 6794965 - BLOR13644 Blo04g00732 732
4 6833180 6852912 + BLOR13646 Blo04g00734 734
4 6854391 6857078 + BLOR13647 Blo04g00735 735
15 2848875 2852016 + BLOR06659 Blo15g00265 265
15 2853866 2859378 - BLOR06660 Blo15g00266 266
16 5088631 5091064 - BLOR07474 Blo16g00226 226
3 7194080 7197268 - Bma017083.1 Bma03g00779 779
3 7213162 7225484 + Bma017086.1 Bma03g00781 781
3 7227881 7230310 + Bma017087.1 Bma03g00782 782
6 2573262 2575678 - Bma022830.1 Bma06g00216 216
6 2577921 2581012 + Bma022831.1 Bma06g00217 217
6 2581339 2585708 - Bma022832.1 Bma06g00218 218
6 2610352 2613105 + Bma022835.1 Bma06g00220 220
8 1212884 1215952 + Bma027100.1 Bma08g00100 100
12 42445870 42448582 - Bma008386.1 Bma12g01038 1038
12 42453818 42456289 + Bma030528 Bma12g01039 1039
12 42462244 42465414 - Bma030529 Bma12g01040 1040
12 42467556 42470967 + Bma008387.1 Bma12g01041 1041
7 14582525 14585320 - Bpe021683.1 Bpe07g00839 839
7 14587052 14589598 + Bpe021684.1 Bpe07g00840 840
7 14591081 14592616 + Bpe021685.1 Bpe07g00841 841
7 14594929 14598027 - Bpe021687.1 Bpe07g00843 843
7 14601583 14603817 + Bpe021688.1 Bpe07g00844 844
13 10391581 10394340 - Bpe006362.1 Bpe13g00240 240
13 10398757 10401547 + Bpe006364.1 Bpe13g00242 242
13 10401834 10404865 - Bpe024933 Bpe13g00243 243
13 10407660 10410083 + Bpe006365.1 Bpe13g00244 244
15 17164850 17167474 - Bpe001570.1 Bpe15g00637 637
15 17168853 17179326 - Bpe001571.1 Bpe15g00638 638
15 17196778 17199029 + Bpe001573.1 Bpe15g00640 640
1 27770972 27784046 - CaPI482276_01g014260.1 Cam01g1426 1426
1 27793135 27796291 + CaPI482276_01g014270.1 Cam01g1427 1427
1 27802120 27806673 - CaPI482276_01g014280.1 Cam01g1428 1428
1 27830323 27852630 + CaPI482276_01g014290.1 Cam01g1429 1429
1 27856934 27860618 + CaPI482276_01g014300.1 Cam01g1430 1430
6 29588124 29590638 + CaPI482276_06g018500.1 Cam06g1850 1850
10 529820 531433 - Carg10343-RA Car10g00111 111
11 457101 458949 - Carg20223-RA Car11g00085 85
13 8386566 8388519 - Carg07672-RA Car13g00722 722
13 8392788 8395986 - Carg07674-RA Car13g00724 724
13 8397225 8400757 + Carg07675-RA Car13g00725 725
13 8400842 8406700 - Carg07676-RA Car13g00726 726
13 8417047 8420370 + Carg07678-RA Car13g00728 728
18 869626 872913 - Carg06726-RA Car18g00160 160
18 875161 885956 - Carg06727-RA Car18g00161 161
18 891626 895794 - Carg06729-RA Car18g00163 163
18 897176 900799 + Carg06730-RA Car18g00164 164
18 901871 907218 + Carg06731-RA Car18g00165 165
1 26370643 26388059 - CcPI632755_01g014600.1 Cco01g1460 1460
1 26439814 26444401 + CcPI632755_01g014620.1 Cco01g1462 1462
1 26450301 26453454 - CcPI632755_01g014630.1 Cco01g1463 1463
1 26462706 26475770 + CcPI632755_01g014640.1 Cco01g1464 1464
6 29324449 29326957 + CcPI632755_06g019070.1 Cco06g1907 1907
1 29224586 29237789 - CePI673135_01g014590.1 Cec01g1459 1459
1 29244422 29248566 + CePI673135_01g014600.1 Cec01g1460 1460
1 29254449 29259013 - CePI673135_01g014610.1 Cec01g1461 1461
1 29295557 29308860 + CePI673135_01g014640.1 Cec01g1464 1464
1 29313133 29315535 + CePI673135_01g014650.1 Cec01g1465 1465
6 32389217 32391723 + CePI673135_06g019020.1 Cec06g1902 1902
2 29074772 29077135 + Chy2G048500.1 Chy02g02583 2583
12 17209459 17221401 - Chy12G218630.1 Chy12g01263 1263
12 17224495 17227668 + Chy12G218640.1 Chy12g01264 1264
12 17230913 17235346 - Chy12G218650.1 Chy12g01265 1265
12 17252612 17269636 + Chy12G218670.1 Chy12g01267 1267
1 24957378 24959774 - ClG42_01g0136500.10 Clacu01g1365 1365
1 24964254 24977503 - ClG42_01g0136600.10 Clacu01g1366 1366
1 25012600 25017194 + ClG42_01g0136800.10 Clacu01g1368 1368
1 25023010 25026176 - ClG42_01g0136900.10 Clacu01g1369 1369
1 25035206 25049780 + ClG42_01g0137000.10 Clacu01g1370 1370
6 28644731 28647245 + ClG42_06g0180900.10 Clacu06g1809 1809
1 26309180 26313252 - ClCG01G013160.1 Cla01g01299 1299
1 26317509 26331633 - ClCG01G013170.2 Cla01g01300 1300
1 26369501 26375686 + ClCG01G013190.1 Cla01g01302 1302
1 26380826 26384610 - ClCG01G013200.2 Cla01g01303 1303
1 26392672 26397287 + ClCG01G013210.2 Cla01g01304 1304
1 26399299 26406086 + ClCG01G013220.2 Cla01g01305 1305
6 30238153 30240665 + ClCG06G017050.1 Cla06g01665 1665
10 544778 546196 - CmaCh10G001230.1 Cma10g00123 123
11 458271 460121 - CmaCh11G000930.1 Cma11g00093 93
13 7147000 7148749 - CmaCh13G008820.1 Cma13g00882 882
13 7153110 7156092 - CmaCh13G008840.1 Cma13g00884 884
13 7158062 7161660 + CmaCh13G008850.1 Cma13g00885 885
13 7162122 7168136 - CmaCh13G008860.1 Cma13g00886 886
13 7177987 7181938 + CmaCh13G008880.1 Cma13g00888 888
18 851404 854694 - CmaCh18G001690.1 Cma18g00169 169
18 856894 868487 - CmaCh18G001700.1 Cma18g00170 170
18 873560 877248 - CmaCh18G001720.1 Cma18g00172 172
18 878630 883325 + CmaCh18G001730.1 Cma18g00173 173
18 887074 889706 + CmaCh18G001750.1 Cma18g00175 175
12 23784485 23787752 - MELO3C002272.2.1 Cme12g01688 1688
12 23792839 23796967 - MELO3C002271.2.1 Cme12g01689 1689
12 23801716 23805247 + MELO3C002270.2.1 Cme12g01691 1691
12 23807349 23813886 - MELO3C002269.2.1 Cme12g01692 1692
12 23827947 23840369 + MELO3C002267.2.1 Cme12g01694 1694
12 23841986 23845706 + MELO3C002265.2.1 Cme12g01695 1695
12 2506439 2509717 + PI0013147.1 Cmetu12g1450 1450
12 2497303 2500792 + PI0029079.1 Cmetu12g1934 1934
10 581873 582704 - CmoCh10G001270.1 Cmo10g00127 127
11 450531 452379 - CmoCh11G000920.1 Cmo11g00092 92
13 8081018 8083314 - CmoCh13G009120.1 Cmo13g00912 912
13 8086452 8090225 - CmoCh13G009130.1 Cmo13g00913 913
13 8091354 8095114 + CmoCh13G009140.1 Cmo13g00914 914
13 8095554 8101479 - CmoCh13G009150.1 Cmo13g00915 915
13 8112129 8115452 + CmoCh13G009170.1 Cmo13g00917 917
18 914635 932617 - CmoCh18G001280.1 Cmo18g00128 128
18 937564 942936 - CmoCh18G001300.1 Cmo18g00130 130
18 942951 946613 + CmoCh18G001310.1 Cmo18g00131 131
18 950710 953740 + CmoCh18G001330.1 Cmo18g00133 133
1 25296931 25299327 - CmPI595203_01g012710.1 Cmu01g1271 1271
1 25303749 25317004 - CmPI595203_01g012720.1 Cmu01g1272 1272
1 25345869 25356607 + CmPI595203_01g012740.1 Cmu01g1274 1274
1 25362415 25365569 - CmPI595203_01g012750.1 Cmu01g1275 1275
1 25374610 25380933 + CmPI595203_01g012760.1 Cmu01g1276 1276
1 25385349 25389175 + CmPI595203_01g012770.1 Cmu01g1277 1277
6 28546631 28549146 + CmPI595203_06g017500.1 Cmu06g1750 1750
2 34900850 34906050 + Conep02aG0193900.1 Cone2ag0909 909
2 34906514 34909349 - Conep02aG0194000.1 Cone2ag0910 910
2 34913737 34916229 + Conep02aG0194100.1 Cone2ag0911 911
2 34919164 34921195 + Conep02aG0194200.1 Cone2ag0912 912
13 895821 902921 - Conep13aG0014700.1 Cone13ag0142 142
13 904826 907482 + Conep13aG0014800.1 Cone13ag0143 143
13 909075 910852 + Conep13aG0014900.1 Cone13ag0144 144
13 911231 914750 - Conep13aG0015000.1 Cone13ag0145 145
16 535203 536325 - Conep16aG0009700.1 Cone16ag0096 96
16 540011 542873 - Conep16aG0009800.1 Cone16ag0097 97
16 545209 549585 + Conep16aG0009900.1 Cone16ag0098 98
16 553672 558924 - Conep16aG0010100.1 Cone16ag0099 99
16 576156 583305 + Conep16aG0010300.1 Cone16ag0101 101
19 787906 791377 - Conep19aG0014800.1 Cone19ag0142 142
19 795211 796996 + Conep19aG0014900.1 Cone19ag0143 143
4 12236961 12238815 + Cp4.1LG04g15550.1 Cpe04g01561 1561
9 9009038 9012641 - Cp4.1LG09g10260.1 Cpe09g01022 1022
9 9014219 9017832 + Cp4.1LG09g10230.1 Cpe09g01023 1023
9 9022976 9034320 + Cp4.1LG09g10200.1 Cpe09g01025 1025
9 9036480 9039767 + Cp4.1LG09g10240.1 Cpe09g01026 1026
18 7799652 7801265 + Cp4.1LG18g08330.1 Cpe18g00846 846
20 1372941 1376267 - Cp4.1LG20g02430.1 Cpe20g00243 243
20 1386587 1392312 + Cp4.1LG20g02500.1 Cpe20g00245 245
20 1392890 1396441 - Cp4.1LG20g02590.1 Cpe20g00246 246
20 1397984 1401562 + Cp4.1LG20g02460.1 Cpe20g00247 247
20 1404401 1407618 + Cp4.1LG20g02480.1 Cpe20g00248 248
1 25800895 25814013 - CrPI670011_01g012610.1 Cre01g1261 1261
1 25823300 25826449 + CrPI670011_01g012620.1 Cre01g1262 1262
1 25832419 25837016 - CrPI670011_01g012630.1 Cre01g1263 1263
1 25859804 25883182 + CrPI670011_01g012640.1 Cre01g1264 1264
1 25887575 25891700 + CrPI670011_01g012650.1 Cre01g1265 1265
6 33370192 33372714 + CrPI670011_06g025690.1 Cre06g2569 2569
1 884566 886903 - CsaV3_1G001460.1 Csa01g00146 146
1 5321745 5326440 - CsaV3_1G008500.1 Csa01g00850 850
1 5327853 5340570 - CsaV3_1G008520.1 Csa01g00852 852
1 5356685 5362947 + CsaV3_1G008550.1 Csa01g00855 855
1 5365097 5368975 - CsaV3_1G008560.1 Csa01g00856 856
1 5371307 5375970 + CsaV3_1G008570.1 Csa01g00857 857
1 5376360 5384021 + CsaV3_1G008580.1 Csa01g00858 858
7 66580257 66582688 - Hsped.07g22210.1 Hepe07g2221 2221
7 66588478 66592323 - Hsped.07g22220.1 Hepe07g2222 2222
7 66604822 66609471 - Hsped.07g22240.1 Hepe07g2224 2224
7 66654258 66666414 + Hsped.07g22270.1 Hepe07g2227 2227
10 3506847 3510260 - Lag0024493.1 Lac10g0448 448
10 3513101 3534664 - Lag0024494.1 Lac10g0449 449
10 3570935 3574194 - Lag0024498.1 Lac10g0453 453
10 3584121 3587333 + Lag0024501.1 Lac10g0456 456
10 3592400 3594431 + Lag0024502.1 Lac10g0457 457
2 3196590 3217853 - Lsi02G003710.1 Lsi02g00371 371
2 3242172 3248433 + Lsi02G003740.1 Lsi02g00374 374
2 3252077 3256220 - Lsi02G003760.1 Lsi02g00376 376
2 3260754 3271246 + Lsi02G003780.1 Lsi02g00378 378
2 3272349 3275508 + Lsi02G003790.1 Lsi02g00379 379
6 25997955 25999673 + Lsi06G015570.1 Lsi06g01557 1557
8 37901717 37907945 + Sed0021778.1 Sed08g2514 2514
8 37917076 37921308 + Sed0024030.1 Sed08g2516 2516
8 37925517 37929083 + Sed0025875.2 Sed08g2518 2518
5 69885115 69889158 - Tan0011614.3 Tan05g2000 2000
5 69892424 69896344 - Tan0005562.1 Tan05g2002 2002
5 69974347 69981178 - Tan0017552.2 Tan05g2005 2005
5 70051763 70073273 + Tan0003683.2 Tan05g2008 2008
5 70075182 70080880 + Tan0013221.1 Tan05g2010 2010
17 9722891 9727154 - Vvi17g756 Vvi17g756 756
17 9731584 9760223 - Vvi17g757 Vvi17g757 757
17 9805984 9812712 + Vvi17g758 Vvi17g758 758
17 9828364 9840079 + Vvi17g759 Vvi17g759 759
17 9841307 9843240 + Vvi17g760 Vvi17g760 760
17 9846862 9851923 - Vvi17g761 Vvi17g761 761
17 9862858 9868352 - Vvi17g762 Vvi17g762 762
17 9879459 9885641 + Vvi17g763 Vvi17g763 763
17 9888228 9891951 + Vvi17g764 Vvi17g764 764
17 9893077 9898404 - Vvi17g765 Vvi17g765 765
       

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