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
Vvi17g886 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g887 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g888 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g889 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g890 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g891 Blo04g00709 . . . . . . . Cmo13g00807 . . . . . . Cpe20g00195 . . . . . . . . . . . . . . . Cone2ag0948 . . . Lsi02g00463 . Chy12g01207 Cme12g01628 . . . . . Bpe15g00664 Bma03g00757 . . . . Cma13g00776 . Car13g00622 . . . Bhi08g01692 Tan05g2896 . Lac10g0535 . . . Cla03g00320 Cam03g0336 Cec03g0328 Cco03g0342 Clacu03g0338 Cmu03g0944 Cre03g0637 . . . .
Vvi17g892 . . . . . . . . . Cmo18g00183 . . . . . Cpe20g00334 . . . . . . . . . . . . . . . Cone2ag0949 Cone16ag0052 . . Lsi02g00464 Csa01g00920 Chy12g01206 Cme12g01627 . . . . Bpe07g00876 . . . Sed08g2466 . . . Cma18g00207 Car13g00624 Car18g00201 Cpe09g00989 . Bhi08g01693 Tan05g2897 Cmetu10g1062 Lac10g0536 Hepe07g2164 . . Cla03g00321 Cam03g0337 Cec03g0329 Cco03g0343 Clacu03g0339 Cmu03g0945 Cre03g0638 . . . .
Vvi17g893 Blo04g00708 Blo16g00248 . . . Bpe13g00218 Bma06g00242 . Cmo13g00808 Cmo18g00184 . . . . . Cpe20g00333 . . . . . . . . . . . . . . . Cone2ag0950 Cone16ag0051 . . Lsi02g00466 Csa01g00921 Chy12g01205 Cme12g01626 . . Bda11g01626 Bda14g00777 . Bpe15g00167 Bma03g00756 . Sed08g2465 . . Cma13g00777 Cma18g00208 Car13g00625 Car18g00202 Cpe09g00988 . Bhi08g01694 Tan05g2898 Cmetu12g0034 Lac10g0537 Hepe07g2163 . . Cla03g00322 Cam03g0338 Cec03g0330 Cco03g0344 Clacu03g0340 Cmu03g0946 Cre03g0639 . . . .
Vvi17g894 . . . . . . Bma06g00243 . . . . . . . . . . . . . . . . . . . . . . . . . Cone16ag0050 . . . . . . . . . . . Bpe15g00666 . . Sed08g2464 . . . . . Car18g00203 . . Bhi08g01696 Tan05g2899 Cmetu12g2048 Lac10g0538 . . . . . . . . . . . . . .
Vvi17g895 . . . . . . . Bma12g01071 . . . Cma11g00050 . . . . Cpe04g01602 Bhi02g00563 . . . . . . Cla06g01725 Cam06g1915 Cec06g1965 Cco06g1969 Clacu06g1871 Cmu06g1813 Cre06g2628 . . . . . . Chy12g01593 . . . . . . . . . . . Cmo11g00052 . . . . . . . . . . . . . . . . . . . . Lsi06g01620 . Chy02g02643 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 49989275 49992789 - Bda008515.1 Bda11g01626 1626
14 5948842 5952418 - Bda027540.1 Bda14g00777 777
2 10331285 10406523 - XM_039022919.1 Bhi02g00563 563
8 47823717 47830489 + XM_039037725.1 Bhi08g01692 1692
8 47837187 47845444 + XM_039038015.1 Bhi08g01693 1693
8 47846518 47851577 + XM_039038747.1 Bhi08g01694 1694
8 47851812 47853859 - XM_039038749.1 Bhi08g01696 1696
4 6495751 6506981 - BLOR13620 Blo04g00708 708
4 6522409 6525559 - BLOR13621 Blo04g00709 709
16 5696939 5700333 + BLOR07496 Blo16g00248 248
3 6898330 6901942 - Bma017058.1 Bma03g00756 756
3 6903319 6906015 - Bma017059.1 Bma03g00757 757
6 3239740 3245016 + Bma022870.1 Bma06g00242 242
6 3246284 3247256 - Bma022871.1 Bma06g00243 243
12 42888248 42937043 + Bma008418.1 Bma12g01071 1071
7 14869374 14881418 - Bpe021719.1 Bpe07g00876 876
13 10219885 10223537 - Bpe006340.1 Bpe13g00218 218
15 12145707 12148684 - Bpe001104.1 Bpe15g00167 167
15 17340506 17343229 + Bpe001597.1 Bpe15g00664 664
15 17354714 17355733 - Bpe001599.1 Bpe15g00666 666
3 4554814 4571406 + CaPI482276_03g003360.1 Cam03g0336 336
3 4575301 4582980 + CaPI482276_03g003370.1 Cam03g0337 337
3 4584671 4588884 + CaPI482276_03g003380.1 Cam03g0338 338
6 30084644 30119702 + CaPI482276_06g019150.1 Cam06g1915 1915
13 7913823 7917690 + Carg07570-RA Car13g00622 622
13 7926930 7932064 + Carg07572-RA Car13g00624 624
13 7933068 7936577 + Carg07573-RA Car13g00625 625
18 1148147 1155128 + Carg06768-RA Car18g00201 201
18 1158157 1162114 + Carg06769-RA Car18g00202 202
18 1162739 1165215 - Carg06770-RA Car18g00203 203
3 3769635 3786136 + CcPI632755_03g003420.1 Cco03g0342 342
3 3790006 3797995 + CcPI632755_03g003430.1 Cco03g0343 343
3 3799382 3803612 + CcPI632755_03g003440.1 Cco03g0344 344
6 29819166 29854445 + CcPI632755_06g019690.1 Cco06g1969 1969
3 3716671 3733015 + CePI673135_03g003280.1 Cec03g0328 328
3 3736932 3744913 + CePI673135_03g003290.1 Cec03g0329 329
3 3746301 3750532 + CePI673135_03g003300.1 Cec03g0330 330
6 32898396 32933521 + CePI673135_06g019650.1 Cec06g1965 1965
2 29473072 29505974 + Chy2G049100.1 Chy02g02643 2643
12 16787366 16791530 - Chy12G218050.1 Chy12g01205 1205
12 16792783 16800016 - Chy12G218060.1 Chy12g01206 1206
12 16804314 16809966 - Chy12G218070.1 Chy12g01207 1207
12 19494960 19495772 + Chy12G221930.1 Chy12g01593 1593
3 3881578 3887853 + ClG42_03g0033800.10 Clacu03g0338 338
3 3891599 3900390 + ClG42_03g0033900.10 Clacu03g0339 339
3 3901126 3905303 + ClG42_03g0034000.10 Clacu03g0340 340
6 29135470 29169926 + ClG42_06g0187100.10 Clacu06g1871 1871
3 3818094 3825010 + ClCG03G003400.1 Cla03g00320 320
3 3828150 3836490 + ClCG03G003410.2 Cla03g00321 321
3 3837345 3842406 + ClCG03G003420.2 Cla03g00322 322
6 30768245 30804399 + ClCG06G017700.2 Cla06g01725 1725
11 223878 256605 - CmaCh11G000500.1 Cma11g00050 50
13 6679120 6685614 + CmaCh13G007760.1 Cma13g00776 776
13 6687078 6702758 + CmaCh13G007770.1 Cma13g00777 777
18 1129465 1136458 + CmaCh18G002070.1 Cma18g00207 207
18 1138585 1142149 + CmaCh18G002080.1 Cma18g00208 208
12 23421827 23426479 - MELO3C002328.2.1 Cme12g01626 1626
12 23427548 23435122 - MELO3C002327.2.1 Cme12g01627 1627
12 23438839 23444572 - MELO3C002326.2.1 Cme12g01628 1628
10 17532406 17536745 + PI0024078.1 Cmetu10g1062 1062
12 2905660 2909789 + PI0000677.1 Cmetu12g0034 34
12 2910478 2911927 - PI0004873.1 Cmetu12g2048 2048
11 215531 247857 - CmoCh11G000520.1 Cmo11g00052 52
13 7599838 7606882 + CmoCh13G008070.1 Cmo13g00807 807
13 7608227 7620373 + CmoCh13G008080.1 Cmo13g00808 808
18 1259893 1266830 + CmoCh18G001830.1 Cmo18g00183 183
18 1268440 1272145 + CmoCh18G001840.1 Cmo18g00184 184
3 4095670 4101943 + CmPI595203_03g009440.1 Cmu03g0944 944
3 4105702 4114493 + CmPI595203_03g009450.1 Cmu03g0945 945
3 4115229 4119405 + CmPI595203_03g009460.1 Cmu03g0946 946
6 29038063 29073133 + CmPI595203_06g018130.1 Cmu06g1813 1813
2 35135541 35138617 + Conep02aG0198200.1 Cone2ag0948 948
2 35142677 35149109 + Conep02aG0198300.1 Cone2ag0949 949
2 35149649 35152719 + Conep02aG0198400.1 Cone2ag0950 950
16 264717 266364 + Conep16aG0005000.1 Cone16ag0050 50
16 266827 269740 - Conep16aG0005100.1 Cone16ag0051 51
16 271626 278089 - Conep16aG0005200.1 Cone16ag0052 52
4 12446130 12479397 + Cp4.1LG04g16090.1 Cpe04g01602 1602
9 8741032 8744959 - Cp4.1LG09g09820.1 Cpe09g00988 988
9 8747642 8754711 - Cp4.1LG09g09800.1 Cpe09g00989 989
20 1125507 1126788 + Cp4.1LG20g01880.1 Cpe20g00195 195
20 1869479 1873279 - Cp4.1LG20g03260.1 Cpe20g00333 333
20 1874271 1881881 - Cp4.1LG20g03240.1 Cpe20g00334 334
3 5287102 5303651 + CrPI670011_03g006370.1 Cre03g0637 637
3 5307597 5315279 + CrPI670011_03g006380.1 Cre03g0638 638
3 5316961 5321194 + CrPI670011_03g006390.1 Cre03g0639 639
6 33864106 33899641 + CrPI670011_06g026280.1 Cre06g2628 2628
1 5746354 5754071 + CsaV3_1G009200.1 Csa01g00920 920
1 5755151 5759299 + CsaV3_1G009210.1 Csa01g00921 921
7 65864008 65868362 - Hsped.07g21630.1 Hepe07g2163 2163
7 65872869 65881193 - Hsped.07g21640.1 Hepe07g2164 2164
10 4156065 4163010 + Lag0024580.1 Lac10g0535 535
10 4169149 4176475 + Lag0024581.1 Lac10g0536 536
10 4178558 4182599 + Lag0024582.1 Lac10g0537 537
10 4183463 4183873 - Lag0024583.1 Lac10g0538 538
2 3878531 3885686 + Lsi02G004630.1 Lsi02g00463 463
2 3888416 3896591 + Lsi02G004640.1 Lsi02g00464 464
2 3900167 3902739 + Lsi02G004660.1 Lsi02g00466 466
6 26512684 26554114 + Lsi06G016200.1 Lsi06g01620 1620
8 37578260 37579561 + Sed0025558.1 Sed08g2464 2464
8 37580438 37585199 - Sed0021120.1 Sed08g2465 2465
8 37587657 37595149 - Sed0007345.1 Sed08g2466 2466
5 81312200 81321509 + Tan0010785.2 Tan05g2896 2896
5 81326147 81334062 + Tan0020026.1 Tan05g2897 2897
5 81335382 81340422 + Tan0019379.1 Tan05g2898 2898
5 81340624 81342733 - Tan0018422.1 Tan05g2899 2899
17 11874603 11876146 - Vvi17g886 Vvi17g886 886
17 11912231 11912950 + Vvi17g887 Vvi17g887 887
17 11917356 11918658 - Vvi17g888 Vvi17g888 888
17 11926720 11926825 + Vvi17g889 Vvi17g889 889
17 11927364 11927493 - Vvi17g890 Vvi17g890 890
17 11958349 11967045 + Vvi17g891 Vvi17g891 891
17 11978866 11993275 + Vvi17g892 Vvi17g892 892
17 11993838 12000969 + Vvi17g893 Vvi17g893 893
17 12001517 12004913 - Vvi17g894 Vvi17g894 894
17 12030875 12098518 - Vvi17g895 Vvi17g895 895
       

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