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
Vvi6g14 . . . . Bpe01g00361 . . . . . . . . . . Cpe05g00566 . . . . . . . . Cla02g02366 Cam02g2517 Cec02g2564 Cco02g2593 Clacu02g2491 Cmu02g2422 Cre02g2740 . . . Cone11ag1585 . . Chy05g00008 Cme05g00010 . Blo14g00330 . . . . . . Sed01g3427 Cmo02g01196 . Cma02g01162 . Car02g00962 . . . Bhi10g00486 Tan07g0566 . . . . . . . . . . . . . . . .
Vvi6g15 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi6g16 . . . . Bpe01g00360 . . . . . . . . . . . . . . . . . . . Cla02g02365 Cam02g2515 Cec02g2561 Cco02g2592 Clacu02g2490 Cmu02g2420 Cre02g2739 . . Cone18ag0009 Cone11ag1584 . . Chy05g00009 . Blo08g00157 Blo14g00329 . . Bpe08g00326 . Bma07g00316 Bma11g00344 . . . . . . . . . Bhi10g00484 . . . . . . . . . . . . . . . . .
Vvi6g17 . Blo03g01400 . . . . Bma14g00738 Bma07g01366 Cmo10g00832 Cmo11g00778 Cma10g00805 . . . . . Cpe18g00275 . . . . . . . . . . . . . . . . . . Lsi06g00382 . . . . . Bda07g00776 Bda09g00343 . Bpe11g00950 . . . . . Cma11g00770 . . . . Cpe04g00990 . . . . . . . Cla03g01408 Cam03g1488 Cec03g1525 . Clacu03g1510 Cmu03g2067 Cre03g1740 . Csa01g03036 Chy02g01316 Cme02g00348
Vvi6g18 . . . Bda09g01381 . Bpe08g01251 . Bma07g01365 Cmo10g00833 . Cma10g00806 . . . Sed12g1673 . Cpe18g00274 Bhi02g01728 Tan09g1013 Cmetu02g1986 . Hepe09g0976 . . . . . . . . . . . . . Lsi06g00384 . . . . . . Bda09g00344 . . . . . . . . . . . . . . . . . . . . Cla03g01191 Cam03g1197 Cec03g1292 Cco03g1261 Clacu03g1274 Cmu03g1848 . . Csa01g03037 Chy02g01317 Cme02g00349
Vvi6g19 . Blo03g01401 . . . . . Bma07g01364 Cmo10g00834 Cmo11g00779 Cma10g00807 . . . Sed08g0966 . Cpe18g00273 Bhi02g01726 Tan09g1011 Cmetu02g0710 . Hepe09g0977 . . . . . . . . . . . Cone18ag0010 Cone11ag1583 Lsi06g00387 . . . . . Bda07g00777 Bda09g00345 . Bpe11g00951 . . . . . Cma11g00771 . . . . Cpe04g00880 . . . . . . . Cla03g01405 Cam03g1485 Cec03g1522 Cco03g1518 Clacu03g1507 Cmu03g2064 Cre03g1737 . Csa01g03039 Chy02g01318 Cme02g00351
Vvi6g20 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone1ag0378 . . . . . . . Blo08g00156 . . . Bpe08g00325 . Bma07g00315 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi6g21 Blo03g01017 Blo03g01402 Bda02g00670 . . . . Bma07g01363 Cmo10g00837 Cmo11g00780 Cma10g00808 . . . . . Cpe18g00272 Bhi02g01724 . . . . . . . . . . . . . . . Cone18ag0011 Cone11ag1582 Lsi06g00388 . . . . . . Bda09g00346 . . . . . . . Cma11g00772 . . . . Cpe04g00988 . . . . . . . Cla03g01404 . . . . . . . Csa01g03041 Chy02g01319 Cme02g00352
Vvi6g22 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi6g23 . Blo03g01403 . . . . . Bma07g01362 Cmo10g00839 . Cma10g00809 . . . Sed08g0970 Cpe05g00805 . Bhi02g01722 Tan09g1009 Cmetu02g1328 . Hepe09g0981 . . . . . . . . . . . . . Lsi06g00390 . . . . . Bda07g00778 Bda09g00347 . Bpe11g00952 . . . . . Cma11g00774 . . . . Cpe04g00986 . . . . . . . Cla03g01403 Cam03g1482 Cec03g1520 Cco03g1515 Clacu03g1504 Cmu03g2061 Cre03g1735 . Csa01g03042 Chy02g01320 Cme02g00353
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
2 47682640 47686806 + Bda006103.1 Bda02g00670 670
7 9306202 9310174 + Bda025915.1 Bda07g00776 776
7 9318203 9321958 - Bda025916.1 Bda07g00777 777
7 9326265 9329792 + Bda025917.1 Bda07g00778 778
9 4385723 4388289 + Bda030916.2 Bda09g00343 343
9 4389883 4394233 - Bda030917.1 Bda09g00344 344
9 4396954 4397259 - Bda030918.1 Bda09g00345 345
9 4403237 4405880 + Bda030919.1 Bda09g00346 346
9 4408881 4412299 + Bda030920.1 Bda09g00347 347
9 45675317 45689161 + Bda032462.1 Bda09g01381 1381
2 47264344 47269773 - XM_039023433.1 Bhi02g01722 1722
2 47320088 47323934 - XM_039024462.1 Bhi02g01724 1724
2 47388554 47392992 + XM_039024788.1 Bhi02g01726 1726
2 47518158 47523998 + XM_039024778.1 Bhi02g01728 1728
10 10824664 10829149 - XM_039045842.1 Bhi10g00484 484
10 10877261 10896905 + XM_039045653.1 Bhi10g00486 486
3 36481689 36484543 + BLOR12198 Blo03g01017 1017
3 40509649 40510770 + BLOR12581 Blo03g01400 1400
3 40513876 40524301 - BLOR12582 Blo03g01401 1401
3 40529071 40532092 + BLOR12583 Blo03g01402 1402
3 40534826 40548086 + BLOR12584 Blo03g01403 1403
8 1618090 1622389 + BLOR20326 Blo08g00156 156
8 1623958 1627226 - BLOR20327 Blo08g00157 157
14 3389176 3392046 - BLOR14647 Blo14g00329 329
14 3393072 3399454 + BLOR14648 Blo14g00330 330
7 3797293 3799314 + Bma025094.1 Bma07g00315 315
7 3800257 3804629 - Bma025095.1 Bma07g00316 316
7 49241925 49242781 - Bma026641.1 Bma07g01362 1362
7 49264505 49267477 - Bma026643.2 Bma07g01363 1363
7 49282010 49285134 + Bma026645.1 Bma07g01364 1364
7 49289730 49293970 + Bma026646.1 Bma07g01365 1365
7 49295260 49297814 - Bma026647.1 Bma07g01366 1366
11 3371673 3374578 - Bma005801.1 Bma11g00344 344
14 8161506 8165421 - Bma011206.1 Bma14g00738 738
1 2259784 2262668 - Bpe024492 Bpe01g00360 360
1 2263044 2274703 + Bpe000350.3 Bpe01g00361 361
8 1924309 1927372 + Bpe022420.1 Bpe08g00325 325
8 1928204 1931191 - Bpe022421.2 Bpe08g00326 326
8 13994374 14001476 - Bpe023375.1 Bpe08g01251 1251
11 7074405 7078474 + Bpe004288.1 Bpe11g00950 950
11 7080278 7083314 - Bpe004289.1 Bpe11g00951 951
11 7086918 7090363 + Bpe004290.1 Bpe11g00952 952
2 37493277 37498894 + CaPI482276_02g025150.1 Cam02g2515 2515
2 37520192 37530930 + CaPI482276_02g025170.1 Cam02g2517 2517
3 23739392 23743315 - CaPI482276_03g011970.1 Cam03g1197 1197
3 29727537 29740015 - CaPI482276_03g014820.1 Cam03g1482 1482
3 29768603 29772116 + CaPI482276_03g014850.1 Cam03g1485 1485
3 29792389 29796567 - CaPI482276_03g014880.1 Cam03g1488 1488
2 6770560 6780139 - Carg13979-RA Car02g00962 962
2 38168518 38173388 + CcPI632755_02g025920.1 Cco02g2592 2592
2 38178571 38202221 + CcPI632755_02g025930.1 Cco02g2593 2593
3 25218680 25222440 + CcPI632755_03g012610.1 Cco03g1261 1261
3 29727652 29740337 - CcPI632755_03g015150.1 Cco03g1515 1515
3 29774332 29778458 + CcPI632755_03g015180.1 Cco03g1518 1518
2 42605647 42611295 + CePI673135_02g025610.1 Cec02g2561 2561
2 42627178 42645414 + CePI673135_02g025640.1 Cec02g2564 2564
3 28852414 28856376 + CePI673135_03g012920.1 Cec03g1292 1292
3 33282079 33295108 - CePI673135_03g015200.1 Cec03g1520 1520
3 33322383 33327928 + CePI673135_03g015220.1 Cec03g1522 1522
3 33348702 33352849 - CePI673135_03g015250.1 Cec03g1525 1525
2 9727912 9732611 + Chy2G035830.1 Chy02g01316 1316
2 9734749 9741628 - Chy2G035840.1 Chy02g01317 1317
2 9745412 9753912 - Chy2G035850.1 Chy02g01318 1318
2 9766783 9769517 + Chy2G035860.1 Chy02g01319 1319
2 9773032 9778708 + Chy2G035870.1 Chy02g01320 1320
5 56106 66751 - Chy5G090540.1 Chy05g00008 8
5 71545 90589 + Chy5G090550.1 Chy05g00009 9
2 37738117 37743566 + ClG42_02g0249000.10 Clacu02g2490 2490
2 37748745 37775410 + ClG42_02g0249100.10 Clacu02g2491 2491
3 24468751 24472708 + ClG42_03g0127400.10 Clacu03g1274 1274
3 28607648 28619953 - ClG42_03g0150400.10 Clacu03g1504 1504
3 28647448 28650960 + ClG42_03g0150700.10 Clacu03g1507 1507
3 28671213 28674962 - ClG42_03g0151000.10 Clacu03g1510 1510
2 38686297 38692446 + ClCG02G024430.2 Cla02g02365 2365
2 38697072 38724616 + ClCG02G024440.2 Cla02g02366 2366
3 25191734 25196180 + ClCG03G012380.1 Cla03g01191 1191
3 29525424 29529279 - ClCG03G014590.2 Cla03g01403 1403
3 29538919 29541910 - ClCG03G014600.1 Cla03g01404 1404
3 29556530 29561195 + ClCG03G014610.2 Cla03g01405 1405
3 29582113 29586579 - ClCG03G014640.2 Cla03g01408 1408
2 6847843 6857267 - CmaCh02G011620.1 Cma02g01162 1162
10 3720953 3727350 + CmaCh10G008050.1 Cma10g00805 805
10 3727762 3733335 - CmaCh10G008060.1 Cma10g00806 806
10 3735100 3738884 - CmaCh10G008070.1 Cma10g00807 807
10 3743932 3746990 + CmaCh10G008080.1 Cma10g00808 808
10 3747317 3752459 + CmaCh10G008090.1 Cma10g00809 809
11 3747253 3751132 + CmaCh11G007700.1 Cma11g00770 770
11 3751220 3756305 - CmaCh11G007710.1 Cma11g00771 771
11 3759324 3762825 + CmaCh11G007720.1 Cma11g00772 772
11 3764223 3767701 + CmaCh11G007740.1 Cma11g00774 774
2 2868768 2875482 + MELO3C015563.2.1 Cme02g00348 348
2 2876161 2883283 - MELO3C015564.2.1 Cme02g00349 349
2 2895334 2899855 - MELO3C015566.2.1 Cme02g00351 351
2 2910613 2914466 + MELO3C015567.2.1 Cme02g00352 352
2 2917852 2923563 + MELO3C015568.2.1 Cme02g00353 353
5 80087 97478 - MELO3C014731.2.1 Cme05g00010 10
2 3006154 3011148 - PI0009383.1 Cmetu02g0710 710
2 3032630 3038393 + PI0002615.1 Cmetu02g1328 1328
2 2992927 3000523 - PI0001265.1 Cmetu02g1986 1986
2 7155506 7165047 - CmoCh02G011960.1 Cmo02g01196 1196
10 3916893 3923204 + CmoCh10G008320.1 Cmo10g00832 832
10 3923527 3929116 - CmoCh10G008330.1 Cmo10g00833 833
10 3931400 3934887 - CmoCh10G008340.1 Cmo10g00834 834
10 3941622 3943250 + CmoCh10G008370.1 Cmo10g00837 837
10 3944731 3948942 + CmoCh10G008390.1 Cmo10g00839 839
11 3811378 3825571 + CmoCh11G007780.1 Cmo11g00778 778
11 3824506 3831024 - CmoCh11G007790.1 Cmo11g00779 779
11 3834396 3844054 + CmoCh11G007800.1 Cmo11g00780 780
2 37601828 37607278 + CmPI595203_02g024200.1 Cmu02g2420 2420
2 37628392 37639121 + CmPI595203_02g024220.1 Cmu02g2422 2422
3 24853720 24857676 + CmPI595203_03g018480.1 Cmu03g1848 1848
3 29002597 29014908 - CmPI595203_03g020610.1 Cmu03g2061 2061
3 29042394 29045906 + CmPI595203_03g020640.1 Cmu03g2064 2064
3 29066145 29069896 - CmPI595203_03g020670.1 Cmu03g2067 2067
1 3222659 3226176 + Conep01aG0039800.1 Cone1ag0378 378
11 10970530 10973273 - Conep11aG0163300.1 Cone11ag1582 1582
11 10974154 10978719 - Conep11aG0163400.1 Cone11ag1583 1583
11 10987044 10990602 - Conep11aG0163700.1 Cone11ag1584 1584
11 10995446 11005099 + Conep11aG0163800.1 Cone11ag1585 1585
18 69871 72477 + Conep18aG0000900.1 Cone18ag0009 9
18 77275 82168 + Conep18aG0001000.1 Cone18ag0010 10
18 83797 85367 + Conep18aG0001100.1 Cone18ag0011 11
4 8061708 8068409 - Cp4.1LG04g12500.1 Cpe04g00880 880
4 8890965 8894870 - Cp4.1LG04g11450.1 Cpe04g00986 986
4 8899180 8902638 - Cp4.1LG04g11300.1 Cpe04g00988 988
4 8911432 8916382 - Cp4.1LG04g11310.1 Cpe04g00990 990
5 3413492 3425408 + Cp4.1LG05g05570.1 Cpe05g00566 566
5 4995124 4998516 - Cp4.1LG05g08060.1 Cpe05g00805 805
18 4326061 4335083 - Cp4.1LG18g02700.1 Cpe18g00272 272
18 4339566 4345590 + Cp4.1LG18g02640.1 Cpe18g00273 273
18 4346872 4352454 + Cp4.1LG18g02820.1 Cpe18g00274 274
18 4353569 4359446 - Cp4.1LG18g02990.1 Cpe18g00275 275
2 40522166 40527737 + CrPI670011_02g027390.1 Cre02g2739 2739
2 40532918 40556501 + CrPI670011_02g027400.1 Cre02g2740 2740
3 34138071 34141947 - CrPI670011_03g017350.1 Cre03g1735 1735
3 34171730 34176511 + CrPI670011_03g017370.1 Cre03g1737 1737
3 34196960 34200688 - CrPI670011_03g017400.1 Cre03g1740 1740
1 26459013 26465432 + CsaV3_1G041520.1 Csa01g03036 3036
1 26465624 26472982 - CsaV3_1G041530.1 Csa01g03037 3037
1 26477184 26482188 - CsaV3_1G041550.1 Csa01g03039 3039
1 26493868 26496958 + CsaV3_1G041570.1 Csa01g03041 3041
1 26498374 26504077 + CsaV3_1G041580.1 Csa01g03042 3042
9 9959671 9966848 - Hsped.09g09760.1 Hepe09g0976 976
9 9972823 9977447 - Hsped.09g09770.1 Hepe09g0977 977
9 10054287 10058783 + Hsped.09g09810.1 Hepe09g0981 981
6 4209827 4213834 + Lsi06G003820.1 Lsi06g00382 382
6 4216995 4224665 - Lsi06G003840.1 Lsi06g00384 384
6 4243244 4247310 - Lsi06G003870.1 Lsi06g00387 387
6 4273350 4277492 + Lsi06G003880.1 Lsi06g00388 388
6 4287428 4293566 + Lsi06G003900.1 Lsi06g00390 390
1 63329066 63346843 + Sed0010489.1 Sed01g3427 3427
8 8909309 8913934 - Sed0021339.1 Sed08g0966 966
8 9047947 9053098 + Sed0021995.1 Sed08g0970 970
12 27946260 27953434 + Sed0008695.1 Sed12g1673 1673
7 9235627 9257409 - Tan0019285.2 Tan07g0566 566
9 62170425 62176026 - Tan0018789.1 Tan09g1009 1009
9 62231789 62236564 + Tan0002205.1 Tan09g1011 1011
9 62250336 62257590 + Tan0021340.2 Tan09g1013 1013
6 264279 274992 - Vvi6g14 Vvi6g14 14
6 290038 291140 + Vvi6g15 Vvi6g15 15
6 300268 307086 + Vvi6g16 Vvi6g16 16
6 311447 317888 + Vvi6g17 Vvi6g17 17
6 318043 325141 - Vvi6g18 Vvi6g18 18
6 326464 331217 - Vvi6g19 Vvi6g19 19
6 344488 349182 - Vvi6g20 Vvi6g20 20
6 355719 359838 + Vvi6g21 Vvi6g21 21
6 364395 365387 + Vvi6g22 Vvi6g22 22
6 368930 374770 + Vvi6g23 Vvi6g23 23
       

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