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
Vvi17g876 . . Bda06g00628 Bda15g00529 Bpe12g00680 . Bma06g00237 Bma12g01066 Cmo13g00798 Cmo18g00179 . . . . . Cpe20g00340 . . . . . . . . . . . . . . . . . Cone13ag0191 Cone19ag0186 Lsi02g00455 Csa01g00912 Chy12g01212 Cme12g02054 . Blo15g00240 Bda11g01631 . Bpe07g00869 . . Bma08g00073 Sed08g2470 . . Cma13g00769 Cma18g00203 Car13g00983 Car18g00197 Cpe09g00993 . Bhi08g01684 Tan05g2884 Cmetu12g0322 Lac10g0529 Hepe07g2171 . . Cla03g00313 Cam03g0332 Cec03g0323 Cco03g0336 Clacu03g0333 Cmu03g0939 Cre03g0633 . . . .
Vvi17g877 Blo04g00712 Blo16g00243 . . . . Bma06g00238 . Cmo13g00799 Cmo18g00180 . . . . . Cpe20g00339 . . . . . . . . . . . . . . . Cone2ag0944 Cone16ag0056 Cone13ag0192 . Lsi02g00456 Csa01g00913 Chy12g01211 Cme12g01634 . . . Bda14g00785 . Bpe15g00661 Bma03g00759 . . . . Cma13g00770 Cma18g00204 Car13g00617 Car18g00198 Cpe09g00992 . Bhi08g01685 Tan05g2886 . Lac10g0530 Hepe07g2170 . . Cla03g00314 Cam03g0333 Cec03g0324 Cco03g0337 Clacu03g0334 Cmu03g0940 Cre03g0634 . . . .
Vvi17g878 . . . . Bpe12g00681 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0193 Cone19ag0187 . . . . Blo13g00158 Blo15g00239 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g879 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g880 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g881 . Blo16g00244 . . . . Bma06g00239 . Cmo13g00800 . . . . . . Cpe20g00338 . . . . . . . . . . . . . . . . Cone16ag0055 . . Lsi02g00285 Csa01g00757 Chy12g01210 Cme12g01632 . . Bda11g01629 . . . . . Sed01g1812 . . Cma13g00771 . Car13g00618 . . . Bhi08g01369 Tan05g2119 Cmetu12g0770 Lac10g0339 Hepe07g2309 . . . . . . . . . . . . .
Vvi17g882 . Blo16g00245 . . . . Bma06g00240 . Cmo13g00801 Cmo18g00086 . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g00459 Csa01g00915 Chy12g01209 Cme12g01631 . . Bda11g01628 . . . . . . . . Cma13g00772 Cma18g00109 Car13g00619 . . . . . . . . . . Cla03g00315 Cam03g0334 Cec03g0325 Cco03g0338 Clacu03g0335 Cmu03g0941 Cre03g0635 . . . .
Vvi17g883 Blo04g00711 Blo16g00247 . . . . Bma06g00241 . Cmo13g00804 Cmo18g00181 . . . . . Cpe20g00337 . . . . . . . . . . . . . . . Cone2ag0946 Cone16ag0054 Cone13ag0195 Cone19ag0188 Lsi02g00460 Csa01g00918 . Cme12g01630 . . Bda11g01627 Bda14g00784 . Bpe15g00662 . . Sed08g2468 . . Cma13g00774 Cma18g00205 Car13g00620 Car18g00200 Cpe09g00991 . Bhi08g01687 Tan05g2890 Cmetu12g0918 Lac10g0533 Hepe07g2167 . . Cla03g00317 Cam03g0335 . . Clacu03g0336 Cmu03g0942 Cre03g0636 . . . .
Vvi17g884 Blo04g00710 . . . . . . . Cmo13g00806 . . . . . . Cpe20g00336 . . . . . . . . . . . . . . . . . Cone13ag0196 . Lsi02g00462 Csa01g00919 Chy12g01208 Cme12g01629 . . . Bda14g00783 . Bpe15g00663 Bma03g00758 . . . . Cma13g00775 . Car13g00621 . . . Bhi08g01689 . . Lac10g0534 . . . Cla03g00319 . . . Clacu03g0337 Cmu03g0943 . . . . .
Vvi17g885 . . Bda06g00630 . . . . Bma12g01067 . . . Cma11g00055 . Car11g00049 Sed08g0057 . Cpe04g01597 Bhi02g00571 Tan09g2336 Cmetu02g1589 . Hepe09g0075 . . Cla06g01719 Cam06g1909 Cec06g1959 Cco06g1963 Clacu06g1865 Cmu06g1807 Cre06g2622 . . Cone13ag0201 Cone19ag0189 . . . . . Blo15g00238 . . Bpe07g00870 . . . . . Cmo11g00057 . . . . . . . . . . . . . . . . . . . . Lsi06g01613 Csa01g00083 Chy02g02637 Cme02g02036
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 8547982 8548715 - Bda023899.1 Bda06g00628 628
6 8645838 8647505 - Bda023902.1 Bda06g00630 630
11 49994578 49997260 - Bda008516.1 Bda11g01627 1627
11 49999049 50001738 - Bda008517.1 Bda11g01628 1628
11 50002631 50007545 - Bda008518.1 Bda11g01629 1629
11 50037023 50038957 + Bda008520.1 Bda11g01631 1631
14 6032640 6039338 - Bda027549.1 Bda14g00783 783
14 6040456 6043139 - Bda027550.1 Bda14g00784 784
14 6062290 6063805 + Bda027552.1 Bda14g00785 785
15 8329608 8331397 + Bda012359.1 Bda15g00529 529
2 10825281 10828895 + XM_039022987.1 Bhi02g00571 571
8 41072398 41078141 - XM_039039159.1 Bhi08g01369 1369
8 47581619 47584524 - XM_039039941.1 Bhi08g01684 1684
8 47635954 47638519 - XM_039039482.1 Bhi08g01685 1685
8 47784628 47788987 + XM_039038344.1 Bhi08g01687 1687
8 47790145 47797333 + XM_039038833.1 Bhi08g01689 1689
4 6530088 6534994 - BLOR13622 Blo04g00710 710
4 6536445 6539117 - BLOR13623 Blo04g00711 711
4 6558464 6559778 + BLOR13624 Blo04g00712 712
13 5352606 5355698 + BLOR05439 Blo13g00158 158
15 2497860 2501531 + BLOR06632 Blo15g00238 238
15 2501906 2504790 - BLOR06633 Blo15g00239 239
15 2516486 2526421 + BLOR06634 Blo15g00240 240
16 5643367 5644896 - BLOR07491 Blo16g00243 243
16 5655868 5669486 + BLOR07492 Blo16g00244 244
16 5670276 5676536 + BLOR07493 Blo16g00245 245
16 5687818 5690465 + BLOR07495 Blo16g00247 247
3 6909215 6918411 - Bma017060.1 Bma03g00758 758
3 6924428 6925845 + Bma017061.1 Bma03g00759 759
6 3156819 3157920 - Bma022863.1 Bma06g00237 237
6 3163295 3164603 - Bma031276 Bma06g00238 238
6 3173229 3178288 + Bma022864.1 Bma06g00239 239
6 3180740 3183096 + Bma022865.1 Bma06g00240 240
6 3184952 3187622 + Bma022866.1 Bma06g00241 241
8 908833 910615 + Bma027072.1 Bma08g00073 73
12 42825365 42826456 - Bma008414.1 Bma12g01066 1066
12 42845213 42848357 - Bma030532 Bma12g01067 1067
7 14781035 14782376 - Bpe021712.2 Bpe07g00869 869
7 14785386 14788644 - Bpe021713.1 Bpe07g00870 870
12 12414618 12416383 - Bpe005939.1 Bpe12g00680 680
12 12421187 12424167 + Bpe005940.1 Bpe12g00681 681
15 17324303 17325815 - Bpe001594.1 Bpe15g00661 661
15 17329613 17332300 + Bpe001595.1 Bpe15g00662 662
15 17333284 17338184 + Bpe001596.1 Bpe15g00663 663
3 4498520 4501041 - CaPI482276_03g003320.1 Cam03g0332 332
3 4514431 4516454 - CaPI482276_03g003330.1 Cam03g0333 333
3 4532490 4546066 + CaPI482276_03g003340.1 Cam03g0334 334
3 4550117 4553251 + CaPI482276_03g003350.1 Cam03g0335 335
6 30039973 30043376 - CaPI482276_06g019090.1 Cam06g1909 1909
11 278596 281791 + Carg20187-RA Car11g00049 49
13 7884129 7885674 - Carg07565-RA Car13g00617 617
13 7890191 7895636 + Carg07566-RA Car13g00618 618
13 7896195 7899405 + Carg07567-RA Car13g00619 619
13 7901651 7904468 + Carg07568-RA Car13g00620 620
13 7905764 7912987 + Carg07569-RA Car13g00621 621
13 9800364 9801572 - Carg04688-RA Car13g00983 983
18 1114686 1116522 - Carg06764-RA Car18g00197 197
18 1127035 1129011 - Carg06765-RA Car18g00198 198
18 1137822 1142735 + Carg06767-RA Car18g00200 200
3 3712772 3715282 - CcPI632755_03g003360.1 Cco03g0336 336
3 3728773 3730798 - CcPI632755_03g003370.1 Cco03g0337 337
3 3746931 3760733 + CcPI632755_03g003380.1 Cco03g0338 338
6 29773961 29777391 - CcPI632755_06g019630.1 Cco06g1963 1963
3 3654277 3656796 - CePI673135_03g003230.1 Cec03g0323 323
3 3676051 3678066 - CePI673135_03g003240.1 Cec03g0324 324
3 3694216 3708396 + CePI673135_03g003250.1 Cec03g0325 325
6 32853606 32857021 - CePI673135_06g019590.1 Cec06g1959 1959
2 29433752 29436703 - Chy2G049040.1 Chy02g02637 2637
12 16812102 16820273 - Chy12G218080.1 Chy12g01208 1208
12 16821631 16830597 - Chy12G218090.1 Chy12g01209 1209
12 16832897 16838531 - Chy12G218100.1 Chy12g01210 1210
12 16852088 16854005 + Chy12G218110.1 Chy12g01211 1211
12 16865750 16867698 + Chy12G218120.1 Chy12g01212 1212
3 3813855 3816376 - ClG42_03g0033300.10 Clacu03g0333 333
3 3829960 3831959 - ClG42_03g0033400.10 Clacu03g0334 334
3 3848822 3862443 + ClG42_03g0033500.10 Clacu03g0335 335
3 3866465 3869596 + ClG42_03g0033600.10 Clacu03g0336 336
3 3871139 3878710 + ClG42_03g0033700.10 Clacu03g0337 337
6 29090820 29094223 - ClG42_06g0186500.10 Clacu06g1865 1865
3 3746140 3750800 - ClCG03G003310.1 Cla03g00313 313
3 3763924 3766384 - ClCG03G003320.1 Cla03g00314 314
3 3783212 3799935 + ClCG03G003330.2 Cla03g00315 315
3 3802077 3806626 + ClCG03G003370.1 Cla03g00317 317
3 3807694 3815374 + ClCG03G003390.1 Cla03g00319 319
6 30721570 30724962 - ClCG06G017610.2 Cla06g01719 1719
11 275086 280862 + CmaCh11G000550.1 Cma11g00055 55
13 6642698 6644762 - CmaCh13G007690.1 Cma13g00769 769
13 6648875 6650534 - CmaCh13G007700.1 Cma13g00770 770
13 6655560 6660781 + CmaCh13G007710.1 Cma13g00771 771
13 6661388 6664899 + CmaCh13G007720.1 Cma13g00772 772
13 6667950 6670629 + CmaCh13G007740.1 Cma13g00774 774
13 6671253 6678249 + CmaCh13G007750.1 Cma13g00775 775
18 534850 539480 - CmaCh18G001090.1 Cma18g00109 109
18 1098369 1100438 - CmaCh18G002030.1 Cma18g00203 203
18 1108778 1110867 - CmaCh18G002040.1 Cma18g00204 204
18 1120663 1123593 + CmaCh18G002050.1 Cma18g00205 205
2 26433938 26437468 - MELO3C026235.2.1 Cme02g02036 2036
12 23445866 23454203 - MELO3C002325.2.1 Cme12g01629 1629
12 23454586 23459223 - MELO3C002324.2.1 Cme12g01630 1630
12 23462000 23466163 - MELO3C002322.2.1 Cme12g01631 1631
12 23467569 23473574 - MELO3C002321.2.1 Cme12g01632 1632
12 23484887 23487773 + MELO3C002319.2.1 Cme12g01634 1634
12 26044146 26088074 + MELO3C001921.2.1 Cme12g02054 2054
2 24734010 24737163 - PI0011260.1 Cmetu02g1589 1589
12 2827381 2829949 - PI0026442.1 Cmetu12g0322 322
12 1908246 1913103 - PI0019642.1 Cmetu12g0770 770
12 2871411 2876127 + PI0026459.1 Cmetu12g0918 918
11 267953 274322 + CmoCh11G000570.1 Cmo11g00057 57
13 7560951 7563236 - CmoCh13G007980.1 Cmo13g00798 798
13 7568287 7569912 - CmoCh13G007990.1 Cmo13g00799 799
13 7574387 7580237 + CmoCh13G008000.1 Cmo13g00800 800
13 7580948 7584363 + CmoCh13G008010.1 Cmo13g00801 801
13 7587336 7589351 + CmoCh13G008040.1 Cmo13g00804 804
13 7591778 7598939 + CmoCh13G008060.1 Cmo13g00806 806
18 578419 582439 - CmoCh18G000860.1 Cmo18g00086 86
18 1225731 1226651 - CmoCh18G001790.1 Cmo18g00179 179
18 1237313 1239311 - CmoCh18G001800.1 Cmo18g00180 180
18 1249537 1253664 + CmoCh18G001810.1 Cmo18g00181 181
3 4027933 4030454 - CmPI595203_03g009390.1 Cmu03g0939 939
3 4044022 4046023 - CmPI595203_03g009400.1 Cmu03g0940 940
3 4062870 4076536 + CmPI595203_03g009410.1 Cmu03g0941 941
3 4080550 4083684 + CmPI595203_03g009420.1 Cmu03g0942 942
3 4085226 4092797 + CmPI595203_03g009430.1 Cmu03g0943 943
6 28994075 28997467 - CmPI595203_06g018070.1 Cmu06g1807 1807
2 35120894 35122787 - Conep02aG0197800.1 Cone2ag0944 944
2 35131176 35134838 + Conep02aG0198000.1 Cone2ag0946 946
13 1199789 1201149 - Conep13aG0019600.1 Cone13ag0191 191
13 1209138 1211056 - Conep13aG0019700.1 Cone13ag0192 192
13 1215781 1220844 + Conep13aG0019800.1 Cone13ag0193 193
13 1228834 1230360 + Conep13aG0020000.1 Cone13ag0195 195
13 1235904 1240079 + Conep13aG0020100.1 Cone13ag0196 196
13 1251470 1254320 - Conep13aG0020600.1 Cone13ag0201 201
16 279373 282850 - Conep16aG0005400.1 Cone16ag0054 54
16 284681 294141 - Conep16aG0005500.1 Cone16ag0055 55
16 296641 298507 + Conep16aG0005600.1 Cone16ag0056 56
19 1174936 1176273 - Conep19aG0019200.1 Cone19ag0186 186
19 1178428 1183474 + Conep19aG0019300.1 Cone19ag0187 187
19 1185878 1189529 + Conep19aG0019400.1 Cone19ag0188 188
19 1194003 1197024 - Conep19aG0019500.1 Cone19ag0189 189
4 12423747 12427212 - Cp4.1LG04g15980.1 Cpe04g01597 1597
9 8770367 8775390 - Cp4.1LG09g09930.1 Cpe09g00991 991
9 8789668 8791706 + Cp4.1LG09g09910.1 Cpe09g00992 992
9 8801639 8803689 + Cp4.1LG09g09900.1 Cpe09g00993 993
20 1890307 1897915 - Cp4.1LG20g03450.1 Cpe20g00336 336
20 1898532 1903109 - Cp4.1LG20g03430.1 Cpe20g00337 337
20 1904233 1913653 - Cp4.1LG20g03460.1 Cpe20g00338 338
20 1918062 1919705 + Cp4.1LG20g03360.1 Cpe20g00339 339
20 1924872 1927143 + Cp4.1LG20g03370.1 Cpe20g00340 340
3 5229909 5232430 - CrPI670011_03g006330.1 Cre03g0633 633
3 5246066 5248094 - CrPI670011_03g006340.1 Cre03g0634 634
3 5264544 5278356 + CrPI670011_03g006350.1 Cre03g0635 635
3 5282426 5285557 + CrPI670011_03g006360.1 Cre03g0636 636
6 33818850 33822268 - CrPI670011_06g026220.1 Cre06g2622 2622
1 517369 520358 + CsaV3_1G000830.1 Csa01g00083 83
1 4810928 4814629 - CsaV3_1G007570.1 Csa01g00757 757
1 5680088 5682761 - CsaV3_1G009120.1 Csa01g00912 912
1 5694974 5697739 - CsaV3_1G009130.1 Csa01g00913 913
1 5716330 5720773 + CsaV3_1G009150.1 Csa01g00915 915
1 5721955 5726721 + CsaV3_1G009180.1 Csa01g00918 918
1 5726954 5735122 + CsaV3_1G009190.1 Csa01g00919 919
7 65907114 65912560 - Hsped.07g21670.1 Hepe07g2167 2167
7 65960580 65962960 + Hsped.07g21700.1 Hepe07g2170 2170
7 65990531 65993486 + Hsped.07g21710.1 Hepe07g2171 2171
7 67410069 67416316 + Hsped.07g23090.1 Hepe07g2309 2309
9 661144 664761 + Hsped.09g00750.1 Hepe09g0075 75
10 2663263 2669676 - Lag0024384.1 Lac10g0339 339
10 4088635 4090695 - Lag0024574.1 Lac10g0529 529
10 4115298 4116805 - Lag0024575.1 Lac10g0530 530
10 4143739 4146873 + Lag0024578.1 Lac10g0533 533
10 4146906 4154760 + Lag0024579.1 Lac10g0534 534
2 2444544 2450612 - Lsi02G002850.1 Lsi02g00285 285
2 3802559 3805654 - Lsi02G004550.1 Lsi02g00455 455
2 3822873 3826272 - Lsi02G004560.1 Lsi02g00456 456
2 3852661 3854853 + Lsi02G004590.1 Lsi02g00459 459
2 3856909 3861030 + Lsi02G004600.1 Lsi02g00460 460
2 3862245 3875584 + Lsi02G004620.1 Lsi02g00462 462
6 26465791 26472847 - Lsi06G016130.1 Lsi06g01613 1613
1 13263286 13269060 - Sed0027713.1 Sed01g1812 1812
8 329041 334032 + Sed0019566.2 Sed08g0057 57
8 37601902 37606324 - Sed0025036.2 Sed08g2468 2468
8 37614422 37617576 + Sed0021827.1 Sed08g2470 2470
5 71888907 71898537 + Tan0020658.2 Tan05g2119 2119
5 81224562 81227561 - Tan0011432.1 Tan05g2884 2884
5 81256955 81259028 - Tan0006837.2 Tan05g2886 2886
5 81294952 81299955 + Tan0000609.2 Tan05g2890 2890
9 73113091 73116558 - Tan0009626.1 Tan09g2336 2336
17 11642833 11645637 - Vvi17g876 Vvi17g876 876
17 11674723 11676881 - Vvi17g877 Vvi17g877 877
17 11694436 11701341 + Vvi17g878 Vvi17g878 878
17 11716241 11717170 + Vvi17g879 Vvi17g879 879
17 11735838 11738219 + Vvi17g880 Vvi17g880 880
17 11757260 11766550 + Vvi17g881 Vvi17g881 881
17 11776047 11781289 + Vvi17g882 Vvi17g882 882
17 11783302 11799500 + Vvi17g883 Vvi17g883 883
17 11826628 11853120 + Vvi17g884 Vvi17g884 884
17 11856662 11860209 - Vvi17g885 Vvi17g885 885
       

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