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
Vvi5g989 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g990 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g991 . Blo12g00110 Bda03g01132 . Bpe04g01075 . Bma04g01170 . . Cmo17g00087 . . . . . . . . . . . . . . Cla06g00784 Cam06g0838 Cec06g0853 Cco06g0867 Clacu06g0841 Cmu06g0813 Cre06g1593 . . . . . Csa02g00898 . . . . . . . . . . . . . . Cma17g00080 . Car17g00074 Cpe12g00074 . Bhi12g01467 . . . . . . . . . . . . . Lsi09g01114 . . .
Vvi5g992 . . . . . . . . . . . Cma14g01901 . Car14g01702 . Cpe08g00404 Cpe03g01601 Bhi01g00219 . . . . . . . . . . . . . . Cone5ag1828 . . Lsi05g01850 . . Cme06g00375 . . Bda11g00343 . . Bpe13g00863 . Bma06g01277 . Cmo06g01246 Cmo14g01954 . . . . . . . . . . . . . Cla05g00340 Cam05g0372 Cec05g0376 Cco05g0377 Clacu05g0366 Cmu05g0351 Cre05g0415 . Csa03g01087 Chy06g00356 .
Vvi5g993 . . . . . . . . . . . Cma14g01900 Car06g01062 Car14g01701 Sed12g0370 Cpe08g00403 Cpe03g01600 Bhi01g00220 Tan10g0508 Cmetu06g2263 . Hepe05g1767 . Lcy11g1781 . . . . . . . . . . . Lsi05g01849 . . Cme06g00376 . . . . . . . . . Cmo06g01247 Cmo14g01953 . . . . . . . . . . . . . Cla05g00342 Cam05g0373 Cec05g0377 Cco05g0378 Clacu05g0367 Cmu05g0352 Cre05g0416 . Csa03g01088 Chy06g00357 .
Vvi5g994 . . . . . . . . . . . Cma14g01899 Car06g01063 Car14g01700 Sed02g1510 Cpe08g00402 Cpe03g01599 Bhi01g00222 Tan10g0511 Cmetu06g0585 . Hepe05g1766 . Lcy11g1779 . . . . . . . . . . . Lsi05g01848 . . Cme06g00377 . . Bda11g00344 . . Bpe13g00862 . Bma06g01278 . Cmo06g01248 Cmo14g01952 . . . . . . . . . . . . . Cla05g00343 Cam05g0374 Cec05g0378 Cco05g0379 Clacu05g0368 Cmu05g0353 Cre05g0417 . Csa03g01089 Chy06g00358 .
Vvi5g995 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g996 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g997 . . Bda03g01131 . Bpe04g01074 . Bma04g01171 . . Cmo17g00086 . . . . . . . . . . . . . . Cla06g00785 Cam06g0840 Cec06g0855 Cco06g0869 Clacu06g0843 Cmu06g0815 Cre06g1595 . . . . . Csa02g00897 . . . . . . . . . . . . . . Cma17g00079 . Car17g00073 Cpe12g00073 . Bhi12g01466 . . . . . Lcy13g0479 . . . . . . . Lsi09g01113 . . .
Vvi5g998 . . . . . . . . . . . Cma14g01898 Car06g01064 Car14g01699 . Cpe08g00401 Cpe03g01597 Bhi01g00223 . . . . . . . . . . . . . . . . . Lsi05g01846 . . Cme06g00378 . . Bda11g00345 . . Bpe13g00861 . Bma06g01279 . Cmo06g01249 Cmo14g01951 . . . . . . . . . . . . . Cla05g00345 Cam05g0375 Cec05g0379 Cco05g0380 Clacu05g0369 Cmu05g0354 Cre05g0418 . Csa03g01090 Chy06g00360 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 11917772 11920784 + Bda033518 Bda03g01131 1131
3 11921879 11932218 - Bda017182.1 Bda03g01132 1132
11 3840579 3842033 + Bda005075.1 Bda11g00343 343
11 3843018 3858552 - Bda005076.1 Bda11g00344 344
11 3860060 3863845 + Bda005077.2 Bda11g00345 345
1 4132888 4136181 + XM_039036304.1 Bhi01g00219 219
1 4136655 4139978 - XM_039036331.1 Bhi01g00220 220
1 4162618 4187439 - XM_039036025.1 Bhi01g00222 222
1 4243700 4248498 + XM_039044561.1 Bhi01g00223 223
12 47538473 47544092 + XM_039051268.1 Bhi12g01466 1466
12 47545125 47553069 - XM_039051267.1 Bhi12g01467 1467
12 7927434 7942132 + BLOR04129 Blo12g00110 110
4 30215376 30228894 + Bma031132 Bma04g01170 1170
4 30229719 30244517 - Bma019906.2 Bma04g01171 1171
6 49865176 49866624 + Bma024386.1 Bma06g01277 1277
6 49867583 49882482 - Bma024387.1 Bma06g01278 1278
6 49884072 49887920 + Bma024388.1 Bma06g01279 1279
4 8220724 8223665 + Bpe015746.1 Bpe04g01074 1074
4 8224706 8240278 - Bpe015747.1 Bpe04g01075 1075
13 14778079 14781695 - Bpe025253 Bpe13g00861 861
13 14783446 14798915 + Bpe010549.1 Bpe13g00862 862
13 14799883 14801320 - Bpe010550.1 Bpe13g00863 863
5 3423236 3425971 + CaPI482276_05g003720.1 Cam05g0372 372
5 3427178 3430542 - CaPI482276_05g003730.1 Cam05g0373 373
5 3432606 3451105 - CaPI482276_05g003740.1 Cam05g0374 374
5 3455849 3460193 + CaPI482276_05g003750.1 Cam05g0375 375
6 11823765 11836683 + CaPI482276_06g008380.1 Cam06g0838 838
6 11846885 11852350 - CaPI482276_06g008400.1 Cam06g0840 840
6 7985843 7989231 - Carg06297-RA Car06g01062 1062
6 7990139 8007002 - Carg06296-RA Car06g01063 1063
6 8008858 8013618 + Carg06295-RA Car06g01064 1064
14 13502753 13506669 - Carg24766-RA Car14g01699 1699
14 13508505 13522701 + Carg24767-RA Car14g01700 1700
14 13523368 13526697 + Carg24768-RA Car14g01701 1701
14 13526950 13528870 - Carg24769-RA Car14g01702 1702
17 423671 428272 + Carg10159-RA Car17g00073 73
17 428592 436840 - Carg10158-RA Car17g00074 74
5 3054816 3057784 + CcPI632755_05g003770.1 Cco05g0377 377
5 3059039 3062375 - CcPI632755_05g003780.1 Cco05g0378 378
5 3064259 3083112 - CcPI632755_05g003790.1 Cco05g0379 379
5 3085215 3091788 + CcPI632755_05g003800.1 Cco05g0380 380
6 10685995 10697663 + CcPI632755_06g008670.1 Cco06g0867 867
6 10708731 10714148 - CcPI632755_06g008690.1 Cco06g0869 869
5 3067005 3070178 + CePI673135_05g003760.1 Cec05g0376 376
5 3071294 3074598 - CePI673135_05g003770.1 Cec05g0377 377
5 3076352 3094933 - CePI673135_05g003780.1 Cec05g0378 378
5 3099694 3103697 + CePI673135_05g003790.1 Cec05g0379 379
6 10745375 10758221 + CePI673135_06g008530.1 Cec06g0853 853
6 10769108 10774665 - CePI673135_06g008550.1 Cec06g0855 855
6 2375333 2377045 + Chy6G108840.1 Chy06g00356 356
6 2379542 2380888 - Chy6G108850.1 Chy06g00357 357
6 2382125 2397684 - Chy6G108860.1 Chy06g00358 358
6 2411715 2415663 + Chy6G108880.1 Chy06g00360 360
5 3137199 3139815 + ClG42_05g0036600.10 Clacu05g0366 366
5 3141055 3144429 - ClG42_05g0036700.10 Clacu05g0367 367
5 3150620 3165002 - ClG42_05g0036800.10 Clacu05g0368 368
5 3167267 3174110 + ClG42_05g0036900.10 Clacu05g0369 369
6 10458563 10471594 + ClG42_06g0084100.10 Clacu06g0841 841
6 10481769 10487240 - ClG42_06g0084300.10 Clacu06g0843 843
5 3080963 3083664 + ClCG05G003240.1 Cla05g00340 340
5 3084846 3088220 - ClCG05G003255.1 Cla05g00342 342
5 3090097 3109297 - ClCG05G003260.1 Cla05g00343 343
5 3114428 3118994 + ClCG05G003285.1 Cla05g00345 345
6 10779648 10793828 + ClCG06G008040.2 Cla06g00784 784
6 10798022 10810951 - ClCG06G008050.2 Cla06g00785 785
14 13421397 13426132 - CmaCh14G018980.1 Cma14g01898 1898
14 13427901 13436338 + CmaCh14G018990.1 Cma14g01899 1899
14 13437921 13441336 + CmaCh14G019000.1 Cma14g01900 1900
14 13441909 13445069 - CmaCh14G019010.1 Cma14g01901 1901
17 386769 397095 + CmaCh17G000790.1 Cma17g00079 79
17 397533 405667 - CmaCh17G000800.1 Cma17g00080 80
6 2334218 2337566 + MELO3C006305.2.1 Cme06g00375 375
6 2338016 2341130 - MELO3C006306.2.1 Cme06g00376 376
6 2341817 2365024 - MELO3C006307.2.1 Cme06g00377 377
6 2367962 2372868 + MELO3C006309.2.1 Cme06g00378 378
6 2553764 2575512 - PI0020972.1 Cmetu06g0585 585
6 2549465 2552580 - PI0008716.1 Cmetu06g2263 2263
6 9419475 9422279 + CmoCh06G012460.1 Cmo06g01246 1246
6 9423235 9426593 - CmoCh06G012470.1 Cmo06g01247 1247
6 9427359 9444568 - CmoCh06G012480.1 Cmo06g01248 1248
6 9446395 9451632 + CmoCh06G012490.1 Cmo06g01249 1249
14 14414203 14417661 - CmoCh14G019510.1 Cmo14g01951 1951
14 14419353 14433663 + CmoCh14G019520.1 Cmo14g01952 1952
14 14434035 14436621 + CmoCh14G019530.1 Cmo14g01953 1953
14 14437564 14440629 - CmoCh14G019540.1 Cmo14g01954 1954
17 452012 461618 + CmoCh17G000860.1 Cmo17g00086 86
17 462714 470840 - CmoCh17G000870.1 Cmo17g00087 87
5 2975695 2978484 + CmPI595203_05g003510.1 Cmu05g0351 351
5 2979551 2982925 - CmPI595203_05g003520.1 Cmu05g0352 352
5 2984979 3003482 - CmPI595203_05g003530.1 Cmu05g0353 353
5 3008243 3012574 + CmPI595203_05g003540.1 Cmu05g0354 354
6 10274839 10290451 + CmPI595203_06g008130.1 Cmu06g0813 813
6 10297899 10303370 - CmPI595203_06g008150.1 Cmu06g0815 815
5 12887388 12888368 - Conep05aG0188600.1 Cone5ag1828 1828
3 12317491 12321790 - Cp4.1LG03g17940.1 Cpe03g01597 1597
3 12324560 12337842 + Cp4.1LG03g17990.1 Cpe03g01599 1599
3 12338054 12340798 + Cp4.1LG03g18060.1 Cpe03g01600 1600
3 12341931 12345043 - Cp4.1LG03g17920.1 Cpe03g01601 1601
8 2551636 2557424 - Cp4.1LG08g02730.1 Cpe08g00401 401
8 2559650 2576232 + Cp4.1LG08g02770.1 Cpe08g00402 402
8 2577024 2580419 + Cp4.1LG08g02750.1 Cpe08g00403 403
8 2581777 2584731 - Cp4.1LG08g02710.1 Cpe08g00404 404
12 432523 436925 + Cp4.1LG12g00690.1 Cpe12g00073 73
12 437064 445770 - Cp4.1LG12g00750.1 Cpe12g00074 74
5 3753926 3757957 + CrPI670011_05g004150.1 Cre05g0415 415
5 3759269 3762638 - CrPI670011_05g004160.1 Cre05g0416 416
5 3764516 3783074 - CrPI670011_05g004170.1 Cre05g0417 417
5 3785328 3792113 + CrPI670011_05g004180.1 Cre05g0418 418
6 11381961 11393984 + CrPI670011_06g015930.1 Cre06g1593 1593
6 11405861 11411334 - CrPI670011_06g015950.1 Cre06g1595 1595
2 8353030 8361659 + CsaV3_2G011130.1 Csa02g00897 897
2 8359606 8366890 - CsaV3_2G011140.1 Csa02g00898 898
3 8618992 8622530 + CsaV3_3G010870.1 Csa03g01087 1087
3 8622738 8626436 - CsaV3_3G010880.1 Csa03g01088 1088
3 8626561 8649887 - CsaV3_3G010890.1 Csa03g01089 1089
3 8653223 8658459 + CsaV3_3G010900.1 Csa03g01090 1090
5 67957539 67980634 + Hsped.05g17660.1 Hepe05g1766 1766
5 67980707 67988026 + Hsped.05g17670.1 Hepe05g1767 1767
11 41591476 41596241 + Maker00031972 Lcy11g1779 1779
11 41618356 41620955 + Maker00032071 Lcy11g1781 1781
13 5694689 5702061 + Maker00023353 Lcy13g0479 479
5 25705627 25709391 - Lsi05G018460.1 Lsi05g01846 1846
5 25714550 25719484 + Lsi05G018480.1 Lsi05g01848 1848
5 25722076 25743604 + Lsi05G018490.1 Lsi05g01849 1849
5 25744698 25747533 - Lsi05G018500.1 Lsi05g01850 1850
9 17843839 17849813 + Lsi09G011130.1 Lsi09g01113 1113
9 17850749 17865194 - Lsi09G011140.1 Lsi09g01114 1114
2 50921316 50942462 + Sed0007147.2 Sed02g1510 1510
12 2246768 2252915 - Sed0002608.1 Sed12g0370 370
10 4090918 4096070 - Tan0004630.1 Tan10g0508 508
10 4097160 4120109 - Tan0015482.3 Tan10g0511 511
5 16999342 16999891 - Vvi5g989 Vvi5g989 989
5 17008193 17037290 + Vvi5g990 Vvi5g990 990
5 17060020 17088912 + Vvi5g991 Vvi5g991 991
5 17090552 17104721 + Vvi5g992 Vvi5g992 992
5 17105411 17127003 - Vvi5g993 Vvi5g993 993
5 17144367 17217606 - Vvi5g994 Vvi5g994 994
5 17239624 17245674 + Vvi5g995 Vvi5g995 995
5 17246942 17250635 + Vvi5g996 Vvi5g996 996
5 17250963 17270067 - Vvi5g997 Vvi5g997 997
5 17290605 17357547 + Vvi5g998 Vvi5g998 998
       

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