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
Vvi17g906 . . . . Bpe12g00683 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone2ag0953 Cone16ag0045 . . . . . . . . . . . . . Bma08g00071 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g907 . . Bda06g00631 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0202 Cone19ag0190 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g908 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0203 Cone19ag0191 . . . . . . Bda11g01622 . . Bpe15g00195 Bma03g01280 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g909 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g910 . . . . . . . . Cmo13g00812 . . . . . . Cpe20g00330 . . . . . . . . . . . . . . . . Cone16ag0044 . . Lsi02g00472 Csa01g00929 Chy12g01198 Cme12g01622 . . . . . Bpe15g00197 Bma03g01277 . Sed08g2461 . . Cma13g00780 . Car13g00628 . . . Bhi08g01705 Tan05g2912 Cmetu12g0083 . . . . Cla03g00328 Cam03g0345 Cec03g0336 Cco03g0349 Clacu03g0346 Cmu03g0952 Cre03g0644 . . . .
Vvi17g911 . . . . . . . . . Cmo18g00191 . . . . . . . . . . . . . . . . . . . . . . Cone16ag0043 . . Lsi02g00474 Csa01g00931 Chy12g01196 Cme12g01619 . . . . . Bpe15g00199 Bma03g01275 . Sed01g1592 . . . Cma18g00215 . Car18g00100 Cpe09g00983 . Bhi08g01707 Tan05g2915 Cmetu12g0042 Lac10g0545 Hepe07g2155 . . Cla03g00330 Cam03g0346 Cec03g0337 Cco03g0351 Clacu03g0347 Cmu03g0953 Cre03g0646 . . . .
Vvi17g912 . . . . Bpe12g00682 . . . Cmo13g00813 Cmo18g00192 . . . . . Cpe20g00329 . . . . . . . . . . . . . . . Cone2ag0954 Cone16ag0042 . . . Csa01g00932 Chy12g01195 Cme12g01618 Blo13g00159 . . . . . . Bma08g00127 Sed02g1603 . . Cma13g00781 Cma18g00216 Car13g00630 Car18g00209 Cpe09g00982 . Bhi08g01708 Tan05g2917 Cmetu12g0851 Lac10g0546 Hepe07g2154 . . . . . . . . . . . . .
Vvi17g913 . Blo16g00252 . . . Bpe13g00214 Bma06g00245 . Cmo13g00814 . . . . . . Cpe20g00328 . . . . . . . . . . . . . . . . Cone16ag0041 . . Lsi02g00475 Csa01g00933 Chy12g01194 Cme12g01617 . . Bda11g01613 . . . . . Sed08g2459 . . Cma13g00782 . Car13g00631 . . . Bhi08g01709 Tan05g2923 Cmetu12g0722 Lac10g0547 Hepe07g2153 . . Cla03g00331 Cam03g0347 Cec03g0338 Cco03g0353 Clacu03g0348 Cmu03g0954 Cre03g0647 . . . .
Vvi17g914 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g915 . Blo16g00253 . . . Bpe13g00213 Bma06g00246 . Cmo13g00816 Cmo18g00193 . . . . . Cpe20g00326 . . . . . . . . . . . . . . . Cone2ag0956 Cone16ag0039 . . Lsi02g00476 Csa01g00935 Chy12g01193 Cme12g01615 . . Bda11g01612 . . . . . . . . Cma13g00784 Cma18g00217 Car13g00633 Car18g00211 Cpe09g00980 . . . . . . . . Cla03g00334 Cam03g0349 Cec03g0340 Cco03g0355 Clacu03g0350 Cmu03g0956 Cre03g0649 . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 8700456 8701966 + Bda023905.1 Bda06g00631 631
11 49796443 49798448 + Bda008494.1 Bda11g01612 1612
11 49801386 49805633 - Bda008495.2 Bda11g01613 1613
11 49964881 49969301 + Bda008511.1 Bda11g01622 1622
8 47906244 47925621 - XM_039038191.1 Bhi08g01705 1705
8 47930520 47933957 - XM_039039626.1 Bhi08g01707 1707
8 47969868 47973404 + XM_039037635.1 Bhi08g01708 1708
8 47974295 47981825 + XM_039039199.1 Bhi08g01709 1709
13 5358271 5361780 - BLOR05440 Blo13g00159 159
16 5884911 5890597 + BLOR07500 Blo16g00252 252
16 5890963 5892988 - BLOR07501 Blo16g00253 253
3 22702485 22703755 + Bma017746.2 Bma03g01275 1275
3 22731926 22738566 - Bma017750.1 Bma03g01277 1277
3 22763886 22768730 + Bma017753.1 Bma03g01280 1280
6 3260459 3267277 + Bma022873.1 Bma06g00245 245
6 3273131 3275151 - Bma022874.1 Bma06g00246 246
8 885030 890685 + Bma027070.1 Bma08g00071 71
8 1630703 1635713 + Bma031419 Bma08g00127 127
12 12425501 12428631 - Bpe005941.1 Bpe12g00682 682
12 12429653 12435502 - Bpe005942.1 Bpe12g00683 683
13 10194599 10196608 + Bpe006335.2 Bpe13g00213 213
13 10199257 10203403 - Bpe006336.1 Bpe13g00214 214
15 13021747 13026639 - Bpe001133.1 Bpe15g00195 195
15 13048659 13055261 + Bpe001135.1 Bpe15g00197 197
15 13077038 13078409 - Bpe001137.2 Bpe15g00199 199
3 4610385 4620790 - CaPI482276_03g003450.1 Cam03g0345 345
3 4624155 4627155 - CaPI482276_03g003460.1 Cam03g0346 346
3 4629965 4640492 + CaPI482276_03g003470.1 Cam03g0347 347
3 4644846 4647241 - CaPI482276_03g003490.1 Cam03g0349 349
13 7946844 7954673 - Carg07576-RA Car13g00628 628
13 7956804 7958454 + Carg07578-RA Car13g00630 630
13 7958875 7965398 + Carg07579-RA Car13g00631 631
13 7967162 7970691 - Carg07581-RA Car13g00633 633
18 539090 543697 - Carg06665-RA Car18g00100 100
18 1186155 1187927 + Carg06776-RA Car18g00209 209
18 1192902 1195363 - Carg06778-RA Car18g00211 211
3 3825892 3835141 - CcPI632755_03g003490.1 Cco03g0349 349
3 3836584 3841562 - CcPI632755_03g003510.1 Cco03g0351 351
3 3848707 3854864 + CcPI632755_03g003530.1 Cco03g0353 353
3 3859216 3861591 - CcPI632755_03g003550.1 Cco03g0355 355
3 3772935 3782355 - CePI673135_03g003360.1 Cec03g0336 336
3 3785745 3788732 - CePI673135_03g003370.1 Cec03g0337 337
3 3791474 3801986 + CePI673135_03g003380.1 Cec03g0338 338
3 3806335 3808732 - CePI673135_03g003400.1 Cec03g0340 340
12 16732675 16735068 + Chy12G217930.1 Chy12g01193 1193
12 16735716 16745107 - Chy12G217940.1 Chy12g01194 1194
12 16746772 16749925 - Chy12G217950.1 Chy12g01195 1195
12 16751786 16754385 + Chy12G217960.1 Chy12g01196 1196
12 16757310 16766460 + Chy12G217980.1 Chy12g01198 1198
3 3927634 3937071 - ClG42_03g0034600.10 Clacu03g0346 346
3 3940467 3943462 - ClG42_03g0034700.10 Clacu03g0347 347
3 3946251 3956781 + ClG42_03g0034800.10 Clacu03g0348 348
3 3961083 3963468 - ClG42_03g0035000.10 Clacu03g0350 350
3 3864080 3873577 - ClCG03G003490.1 Cla03g00328 328
3 3877289 3880284 - ClCG03G003510.2 Cla03g00330 330
3 3882959 3893896 + ClCG03G003520.1 Cla03g00331 331
3 3897703 3900399 - ClCG03G003540.2 Cla03g00334 334
13 6709579 6717436 - CmaCh13G007800.1 Cma13g00780 780
13 6717877 6721679 + CmaCh13G007810.1 Cma13g00781 781
13 6722564 6728258 + CmaCh13G007820.1 Cma13g00782 782
13 6730931 6733620 - CmaCh13G007840.1 Cma13g00784 784
18 1160471 1164024 - CmaCh18G002150.1 Cma18g00215 215
18 1164929 1171737 + CmaCh18G002160.1 Cma18g00216 216
18 1172418 1174881 - CmaCh18G002170.1 Cma18g00217 217
12 23368627 23371238 + MELO3C002338.2.1 Cme12g01615 1615
12 23374217 23381749 - MELO3C002336.2.1 Cme12g01617 1617
12 23382734 23386229 - MELO3C002335.2.1 Cme12g01618 1618
12 23387403 23390420 + MELO3C002334.2.1 Cme12g01619 1619
12 23393268 23402568 + MELO3C002332.2.1 Cme12g01622 1622
12 2941753 2944817 - PI0005464.2 Cmetu12g0042 42
12 2929530 2938535 - PI0001802.1 Cmetu12g0083 83
12 2951462 2957778 + PI0020121.1 Cmetu12g0722 722
12 2946575 2950090 + PI0014963.1 Cmetu12g0851 851
13 7630642 7638395 - CmoCh13G008120.1 Cmo13g00812 812
13 7638540 7641884 + CmoCh13G008130.1 Cmo13g00813 813
13 7642453 7648278 + CmoCh13G008140.1 Cmo13g00814 814
13 7650878 7654319 - CmoCh13G008160.1 Cmo13g00816 816
18 1291926 1295433 - CmoCh18G001910.1 Cmo18g00191 191
18 1296102 1303320 + CmoCh18G001920.1 Cmo18g00192 192
18 1304259 1306718 - CmoCh18G001930.1 Cmo18g00193 193
3 4141106 4151069 - CmPI595203_03g009520.1 Cmu03g0952 952
3 4154589 4157584 - CmPI595203_03g009530.1 Cmu03g0953 953
3 4160372 4170897 + CmPI595203_03g009540.1 Cmu03g0954 954
3 4175197 4177582 - CmPI595203_03g009560.1 Cmu03g0956 956
2 35159780 35163597 + Conep02aG0198700.1 Cone2ag0953 953
2 35164231 35166926 + Conep02aG0198800.1 Cone2ag0954 954
2 35170073 35172434 - Conep02aG0199000.1 Cone2ag0956 956
13 1255198 1256349 - Conep13aG0020700.1 Cone13ag0202 202
13 1256737 1260047 - Conep13aG0020800.1 Cone13ag0203 203
16 225534 227690 + Conep16aG0003900.1 Cone16ag0039 39
16 230356 233532 - Conep16aG0004100.1 Cone16ag0041 41
16 234315 237221 - Conep16aG0004200.1 Cone16ag0042 42
16 240650 241260 + Conep16aG0004300.1 Cone16ag0043 43
16 242637 247550 - Conep16aG0004400.1 Cone16ag0044 44
16 247764 251078 + Conep16aG0004500.1 Cone16ag0045 45
19 1197647 1199274 - Conep19aG0019600.1 Cone19ag0190 190
19 1199545 1202688 - Conep19aG0019700.1 Cone19ag0191 191
9 8708853 8711286 + Cp4.1LG09g09720.1 Cpe09g00980 980
9 8715349 8718424 - Cp4.1LG09g09850.1 Cpe09g00982 982
9 8719188 8722986 + Cp4.1LG09g09730.1 Cpe09g00983 983
20 1834547 1837930 + Cp4.1LG20g03160.1 Cpe20g00326 326
20 1840163 1845879 - Cp4.1LG20g03310.1 Cpe20g00328 328
20 1846756 1849960 - Cp4.1LG20g03300.1 Cpe20g00329 329
20 1851195 1859610 + Cp4.1LG20g03170.1 Cpe20g00330 330
3 5344820 5354244 - CrPI670011_03g006440.1 Cre03g0644 644
3 5357609 5360632 - CrPI670011_03g006460.1 Cre03g0646 646
3 5363419 5374032 + CrPI670011_03g006470.1 Cre03g0647 647
3 5378454 5380849 - CrPI670011_03g006490.1 Cre03g0649 649
1 5779491 5789171 - CsaV3_1G009290.1 Csa01g00929 929
1 5791730 5794868 - CsaV3_1G009310.1 Csa01g00931 931
1 5796145 5800014 + CsaV3_1G009320.1 Csa01g00932 932
1 5800683 5807878 + CsaV3_1G009330.1 Csa01g00933 933
1 5809379 5813401 - CsaV3_1G009350.1 Csa01g00935 935
7 65799281 65804304 - Hsped.07g21530.1 Hepe07g2153 2153
7 65805494 65808815 - Hsped.07g21540.1 Hepe07g2154 2154
7 65814690 65818202 + Hsped.07g21550.1 Hepe07g2155 2155
10 4220913 4224784 - Lag0024590.1 Lac10g0545 545
10 4228055 4231203 + Lag0024591.1 Lac10g0546 546
10 4232686 4238610 + Lag0024592.1 Lac10g0547 547
2 3923878 3934595 - Lsi02G004720.1 Lsi02g00472 472
2 3937759 3940955 - Lsi02G004740.1 Lsi02g00474 474
2 3944421 3960799 + Lsi02G004750.1 Lsi02g00475 475
2 3960291 3963317 - Lsi02G004760.1 Lsi02g00476 476
1 11536235 11539517 - Sed0019471.1 Sed01g1592 1592
2 51529902 51534315 - Sed0001471.1 Sed02g1603 1603
8 37537479 37552740 - Sed0024107.1 Sed08g2459 2459
8 37556452 37565136 + Sed0011232.1 Sed08g2461 2461
5 81361687 81372573 - Tan0001016.1 Tan05g2912 2912
5 81375854 81379473 - Tan0012159.2 Tan05g2915 2915
5 81382792 81385964 - Tan0020680.2 Tan05g2917 2917
5 81441823 81447535 + Tan0002357.1 Tan05g2923 2923
17 12367009 12375117 + Vvi17g906 Vvi17g906 906
17 12376734 12378241 - Vvi17g907 Vvi17g907 907
17 12379861 12388649 - Vvi17g908 Vvi17g908 908
17 12455523 12456465 + Vvi17g909 Vvi17g909 909
17 12479097 12494428 + Vvi17g910 Vvi17g910 910
17 12494825 12498377 - Vvi17g911 Vvi17g911 911
17 12501667 12507105 + Vvi17g912 Vvi17g912 912
17 12508379 12516414 + Vvi17g913 Vvi17g913 913
17 12527467 12530386 + Vvi17g914 Vvi17g914 914
17 12530663 12532984 - Vvi17g915 Vvi17g915 915
       

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