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
Vvi2g422 . . . . . . . . Cmo06g01143 . Cma02g01494 Cma15g01186 Car02g01254 Car15g01075 . . Cpe05g00296 . . . . . . . . . . . . . . . . . . . Csa05g00336 Chy09g01173 . . Blo19g00299 . Bda09g00067 Bpe08g01465 . . . . Cmo02g01534 Cmo15g01250 Cma06g01116 . Car06g00953 . Cpe08g00501 Cpe13g00187 Bhi12g00330 . . . . . . Cla01g00316 Cam01g0326 Cec01g0318 Cco01g0335 Clacu01g0328 Cmu01g0312 Cre09g2199 Lsi09g00321 . . Cme09g01706
Vvi2g423 . . . . . . . . . . . . Car02g01256 . . . Cpe05g00295 . . . . . . . . . . . . . . Cone8ag0338 . . . . . Chy09g01172 . . . . . . . . . . Cmo02g01535 . . . . . . . . . . . . . . . . . . . . . . . . Cme09g01705
Vvi2g424 . . . . . . . . . . Cma02g01495 . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g00337 . . . . . . . . . . . . . . . . . . . Bhi12g00332 . . Lac11g2158 Hepe06g1598 . Lcy12g1716 Cla01g00317 Cam01g0327 Cec01g0319 Cco01g0336 Clacu01g0329 Cmu01g0313 Cre09g2198 Lsi09g00322 . . .
Vvi2g425 . . . . . . . Bma14g00575 . . Cma02g01496 Cma15g01185 Car02g01258 Car15g01073 . . Cpe05g00294 . . . . . . . . . . . . . . . . Cone6ag0735 Cone9ag0739 . Csa05g00338 Chy09g01171 . Blo03g00379 . Bda07g00507 . . Bpe11g00694 . . . Cmo02g01537 Cmo15g01249 . . . . . Cpe13g00188 Bhi12g00333 . . Lac11g2159 Hepe06g1599 . Lcy12g1717 Cla01g00318 Cam01g0328 Cec01g0320 Cco01g0337 Clacu01g0330 Cmu01g0314 Cre09g2197 Lsi09g00323 . . Cme09g01704
Vvi2g426 . . . . . . . . . . Cma02g01497 . Car02g01259 Car15g01072 . . Cpe05g00293 . . . . . . . . . . . . . . . . . Cone19ag1460 . Csa05g00339 Chy09g01170 Cme07g01592 . . . . . . . . . Cmo02g01538 Cmo15g01248 . . . . . Cpe13g00189 Bhi12g00336 . . Lac11g2160 Hepe06g1600 . Lcy12g1718 Cla01g00319 Cam01g0329 Cec01g0321 Cco01g0338 Clacu01g0331 Cmu01g0315 Cre09g2196 Lsi09g00324 Csa04g00632 . Cme09g01703
Vvi2g427 . Blo03g00184 Bda06g00062 Bda08g00545 Bpe05g00621 Bpe07g00136 . . Cmo06g00753 . . Cma15g01184 . Car15g01071 Sed05g0853 . . Bhi11g00352 Tan01g1950 Cmetu06g0320 . . . . Cla10g00327 Cam10g0339 . . Clacu10g0339 Cmu10g1178 . Cone8ag0340 Cone12ag0334 Cone6ag0734 Cone9ag0738 Lsi07g01373 Csa05g00340 Chy09g01169 Cme06g02660 . . . . . . . Bma12g00112 . . Cmo15g01247 Cma06g00729 . Car06g00649 . Cpe08g00789 Cpe13g00190 Bhi12g00340 . . . Hepe06g1202 . . Cla01g00320 Cam01g0330 Cec01g0322 Cco01g0339 Clacu01g0332 Cmu01g0316 Cre09g2195 Lsi09g00326 Csa03g00346 Chy06g01979 Cme09g01702
Vvi2g428 . . . Bda08g00546 . . . . Cmo06g00756 . . . . . Sed04g0725 . . Bhi11g00231 Tan01g1955 Cmetu06g0227 . . Mch10g1485 . Cla10g00320 Cam10g0335 Cec10g0349 Cco10g0341 Clacu10g0332 Cmu10g1172 Cre10g0582 Cone8ag0342 . . . Lsi07g01369 . . Cme06g02654 . . . . . . Bma05g00799 . . . . Cma06g00732 . Car06g00652 . Cpe08g00786 . . . . . . . . . . . . . . . . Csa03g00343 Chy06g01982 .
Vvi2g429 Blo02g01083 . . Bda08g00547 . . . . . Cmo16g00543 . . . . . . . . . . . . . . . . . . . . . Cone8ag0343 . . Cone9ag0737 . . . . . . . . . . . . . . . . Cma16g00499 . Car16g01149 . . . . . . . . . . . . . . . . . . . .
Vvi2g430 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo03g00380 . Bda07g00029 . . . . . . . . . . Car06g00956 . . . . . . . . . . . . . . . . . . . . .
Vvi2g431 . . . . . . . Bma14g00574 Cmo06g01148 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe11g00695 . . . . . Cma06g01120 . . . Cpe08g00498 . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 645092 646104 - Bda023233.1 Bda06g00062 62
7 467471 470361 + Bda033823 Bda07g00029 29
7 6495037 6498230 - Bda025616.1 Bda07g00507 507
8 5510248 5511509 - Bda025000.1 Bda08g00545 545
8 5513072 5515037 - Bda025001.1 Bda08g00546 546
8 5522298 5523686 + Bda025002.1 Bda08g00547 547
9 1308912 1311859 + Bda030591.2 Bda09g00067 67
11 5540887 5549792 + XM_039049187.1 Bhi11g00231 231
11 8260932 8262470 - XM_039050273.1 Bhi11g00352 352
12 9514524 9521251 + XM_039050955.1 Bhi12g00330 330
12 9651548 9654429 + XM_039019699.1 Bhi12g00332 332
12 9747208 9751182 - XM_039020277.1 Bhi12g00333 333
12 9925764 9926995 + XM_039019831.1 Bhi12g00336 336
12 10448928 10452113 - XM_039020026.1 Bhi12g00340 340
2 41449733 41451326 + BLOR10813 Blo02g01083 1083
3 4497430 4498488 - BLOR11365 Blo03g00184 184
3 8867772 8875462 - BLOR11560 Blo03g00379 379
3 8875870 8877057 - BLOR11561 Blo03g00380 380
19 19015024 19029726 - BLOR09642 Blo19g00299 299
5 45240601 45242548 - Bma021902.1 Bma05g00799 799
12 1746745 1747838 + Bma006985.1 Bma12g00112 112
14 6175478 6176667 + Bma011005.1 Bma14g00574 574
14 6183209 6186416 + Bma011007.1 Bma14g00575 575
5 20140121 20141377 - Bpe018037.1 Bpe05g00621 621
7 970875 971882 + Bpe020948.1 Bpe07g00136 136
8 15372298 15374620 - Bpe023577.1 Bpe08g01465 1465
11 5347735 5351031 - Bpe004050.1 Bpe11g00694 694
11 5352874 5353617 - Bpe004051.1 Bpe11g00695 695
1 3644886 3650589 + CaPI482276_01g003260.1 Cam01g0326 326
1 3658112 3659947 + CaPI482276_01g003270.1 Cam01g0327 327
1 3666419 3669773 - CaPI482276_01g003280.1 Cam01g0328 328
1 3683540 3684517 + CaPI482276_01g003290.1 Cam01g0329 329
1 3691324 3693500 - CaPI482276_01g003300.1 Cam01g0330 330
10 5487121 5494236 + CaPI482276_10g003350.1 Cam10g0335 335
10 5517850 5518463 - CaPI482276_10g003390.1 Cam10g0339 339
2 8458346 8461146 + Carg02494-RA Car02g01254 1254
2 8463497 8464209 + Carg02492-RA Car02g01256 1256
2 8466830 8468073 - Carg02490-RA Car02g01258 1258
2 8471600 8472541 - Carg02489-RA Car02g01259 1259
6 3892111 3892995 + Carg21633-RA Car06g00649 649
6 3903791 3909874 - Carg21630-RA Car06g00652 652
6 7342139 7346018 + Carg23888-RA Car06g00953 953
6 7360341 7365172 - Carg23891-RA Car06g00956 956
15 8423647 8424814 + Carg16671-RA Car15g01071 1071
15 8425962 8426915 - Carg16670-RA Car15g01072 1072
15 8431646 8432665 + Carg16669-RA Car15g01073 1073
15 8437266 8441205 - Carg16667-RA Car15g01075 1075
16 9796146 9797565 + Carg19492-RA Car16g01149 1149
1 3291700 3296725 + CcPI632755_01g003350.1 Cco01g0335 335
1 3305174 3307075 + CcPI632755_01g003360.1 Cco01g0336 336
1 3314290 3317639 - CcPI632755_01g003370.1 Cco01g0337 337
1 3335450 3336421 + CcPI632755_01g003380.1 Cco01g0338 338
1 3343207 3345318 - CcPI632755_01g003390.1 Cco01g0339 339
10 3975944 3982876 + CcPI632755_10g003410.1 Cco10g0341 341
1 3260637 3266399 + CePI673135_01g003180.1 Cec01g0318 318
1 3274280 3276120 + CePI673135_01g003190.1 Cec01g0319 319
1 3282408 3285752 - CePI673135_01g003200.1 Cec01g0320 320
1 3299417 3300400 + CePI673135_01g003210.1 Cec01g0321 321
1 3314083 3316248 - CePI673135_01g003220.1 Cec01g0322 322
10 4147773 4155015 + CePI673135_10g003490.1 Cec10g0349 349
6 23805963 23806888 + Chy6G125070.1 Chy06g01979 1979
6 23818540 23824073 - Chy6G125100.1 Chy06g01982 1982
9 13884835 13886558 + Chy9G168850.1 Chy09g01169 1169
9 13890136 13891008 - Chy9G168860.1 Chy09g01170 1170
9 13902223 13905333 + Chy9G168870.1 Chy09g01171 1171
9 13909382 13910925 - Chy9G168880.1 Chy09g01172 1172
9 13921137 13925972 - Chy9G168890.1 Chy09g01173 1173
1 3259190 3264881 + ClG42_01g0032800.10 Clacu01g0328 328
1 3272279 3274117 + ClG42_01g0032900.10 Clacu01g0329 329
1 3280582 3283920 - ClG42_01g0033000.10 Clacu01g0330 330
1 3305625 3306605 + ClG42_01g0033100.10 Clacu01g0331 331
1 3313546 3315713 - ClG42_01g0033200.10 Clacu01g0332 332
10 4249842 4256903 + ClG42_10g0033200.10 Clacu10g0332 332
10 4289137 4290691 - ClG42_10g0033900.10 Clacu10g0339 339
1 3354653 3359932 + ClCG01G003280.2 Cla01g00316 316
1 3367560 3369984 + ClCG01G003290.2 Cla01g00317 317
1 3375565 3379876 - ClCG01G003300.2 Cla01g00318 318
1 3403378 3404346 + ClCG01G003310.1 Cla01g00319 319
1 3414812 3416980 - ClCG01G003320.1 Cla01g00320 320
10 4197258 4203618 + ClCG10G003400.1 Cla10g00320 320
10 4236919 4248019 - ClCG10G003470.1 Cla10g00327 327
2 8539914 8543899 + CmaCh02G014940.1 Cma02g01494 1494
2 8544313 8546016 + CmaCh02G014950.1 Cma02g01495 1495
2 8546031 8549806 - CmaCh02G014960.1 Cma02g01496 1496
2 8553111 8554046 - CmaCh02G014970.1 Cma02g01497 1497
6 3697164 3698385 + CmaCh06G007290.1 Cma06g00729 729
6 3706241 3712939 - CmaCh06G007320.1 Cma06g00732 732
6 7524448 7530761 + CmaCh06G011160.1 Cma06g01116 1116
6 7542308 7544123 - CmaCh06G011200.1 Cma06g01120 1120
15 7491843 7495404 + CmaCh15G011840.1 Cma15g01184 1184
15 7501492 7505110 + CmaCh15G011850.1 Cma15g01185 1185
15 7507315 7511349 - CmaCh15G011860.1 Cma15g01186 1186
16 2546331 2551268 + CmaCh16G004990.1 Cma16g00499 499
6 33692165 33699467 + MELO3C014009.2.1 Cme06g02654 2654
6 33714951 33716330 - MELO3C014013.2.1 Cme06g02660 2660
7 21711618 21712728 - MELO3C016318.2.1 Cme07g01592 1592
9 21654358 21656546 + MELO3C005613.2.1 Cme09g01702 1702
9 21658834 21660034 - MELO3C005614.2.1 Cme09g01703 1703
9 21675623 21679524 + MELO3C005615.2.1 Cme09g01704 1704
9 21683430 21685920 - MELO3C005616.2.1 Cme09g01705 1705
9 21690768 21696345 - MELO3C005617.2.1 Cme09g01706 1706
6 27963124 27969397 - PI0022480.1 Cmetu06g0227 227
6 27953885 27954891 + PI0015901.1 Cmetu06g0320 320
2 8913207 8915531 + CmoCh02G015340.1 Cmo02g01534 1534
2 8917178 8917965 + CmoCh02G015350.1 Cmo02g01535 1535
2 8920715 8924289 - CmoCh02G015370.1 Cmo02g01537 1537
2 8927839 8928729 - CmoCh02G015380.1 Cmo02g01538 1538
6 3913410 3914294 + CmoCh06G007530.1 Cmo06g00753 753
6 3922689 3929488 - CmoCh06G007560.1 Cmo06g00756 756
6 8774826 8779967 + CmoCh06G011430.1 Cmo06g01143 1143
6 8792394 8795627 - CmoCh06G011480.1 Cmo06g01148 1148
15 8565520 8570002 + CmoCh15G012470.1 Cmo15g01247 1247
15 8571185 8572075 - CmoCh15G012480.1 Cmo15g01248 1248
15 8576869 8579860 + CmoCh15G012490.1 Cmo15g01249 1249
15 8582334 8586940 - CmoCh15G012500.1 Cmo15g01250 1250
16 2636864 2642110 + CmoCh16G005430.1 Cmo16g00543 543
1 3215247 3220948 + CmPI595203_01g003120.1 Cmu01g0312 312
1 3228310 3230149 + CmPI595203_01g003130.1 Cmu01g0313 313
1 3236615 3239964 - CmPI595203_01g003140.1 Cmu01g0314 314
1 3257719 3258690 + CmPI595203_01g003150.1 Cmu01g0315 315
1 3265472 3267584 - CmPI595203_01g003160.1 Cmu01g0316 316
10 4392370 4399431 + CmPI595203_10g011720.1 Cmu10g1172 1172
10 4435963 4436763 - CmPI595203_10g011780.1 Cmu10g1178 1178
6 3709224 3710316 + Conep06aG0075700.1 Cone6ag0734 734
6 3711942 3715320 + Conep06aG0075800.1 Cone6ag0735 735
8 1937942 1939379 + Conep08aG0035400.1 Cone8ag0338 338
8 1951447 1952424 - Conep08aG0035600.1 Cone8ag0340 340
8 1955149 1958600 - Conep08aG0035800.1 Cone8ag0342 342
8 1961632 1962948 + Conep08aG0035900.1 Cone8ag0343 343
9 3510433 3511636 - Conep09aG0075400.1 Cone9ag0737 737
9 3513641 3514994 + Conep09aG0075500.1 Cone9ag0738 738
9 3515500 3518664 + Conep09aG0075600.1 Cone9ag0739 739
12 1836858 1837867 - Conep12aG0034900.1 Cone12ag0334 334
19 9476968 9479345 - Conep19aG0150100.1 Cone19ag1460 1460
5 1645439 1646374 + Cp4.1LG05g03790.1 Cpe05g00293 293
5 1651209 1656676 + Cp4.1LG05g03890.1 Cpe05g00294 294
5 1654053 1656842 - Cp4.1LG05g03690.1 Cpe05g00295 295
5 1658238 1661010 - Cp4.1LG05g03740.1 Cpe05g00296 296
8 3222108 3231492 + Cp4.1LG08g01840.1 Cpe08g00498 498
8 3241950 3246574 - Cp4.1LG08g01730.1 Cpe08g00501 501
8 6247664 6255736 + Cp4.1LG08g07780.1 Cpe08g00786 786
8 6263251 6264135 - Cp4.1LG08g07870.1 Cpe08g00789 789
13 1468337 1472843 + Cp4.1LG13g01770.1 Cpe13g00187 187
13 1474852 1478422 - Cp4.1LG13g01890.1 Cpe13g00188 188
13 1482909 1483862 + Cp4.1LG13g01780.1 Cpe13g00189 189
13 1485047 1486197 - Cp4.1LG13g02000.1 Cpe13g00190 190
9 41044988 41047159 + CrPI670011_09g021950.1 Cre09g2195 2195
9 41054202 41055164 - CrPI670011_09g021960.1 Cre09g2196 2196
9 41069640 41072994 + CrPI670011_09g021970.1 Cre09g2197 2197
9 41080316 41082180 - CrPI670011_09g021980.1 Cre09g2198 2198
9 41090544 41095619 - CrPI670011_09g021990.1 Cre09g2199 2199
10 5318697 5325909 + CrPI670011_10g005820.1 Cre10g0582 582
3 2841421 2849807 + CsaV3_3G003430.1 Csa03g00343 343
3 2855660 2857112 - CsaV3_3G003460.1 Csa03g00346 346
4 4228853 4230655 + CsaV3_4G006320.1 Csa04g00632 632
5 2144062 2149675 + CsaV3_5G003360.1 Csa05g00336 336
5 2152767 2155983 + CsaV3_5G003370.1 Csa05g00337 337
5 2158867 2162801 - CsaV3_5G003380.1 Csa05g00338 338
5 2170952 2172029 + CsaV3_5G003390.1 Csa05g00339 339
5 2174486 2176590 - CsaV3_5G003400.1 Csa05g00340 340
6 61549136 61550889 - Hsped.06g12020.1 Hepe06g1202 1202
6 66802648 66805480 + Hsped.06g15980.1 Hepe06g1598 1598
6 66807451 66810762 - Hsped.06g15990.1 Hepe06g1599 1599
6 66836760 66837635 - Hsped.06g16000.1 Hepe06g1600 1600
11 37642868 37645488 + Lag0032796.1 Lac11g2158 2158
11 37649980 37653227 - Lag0032797.1 Lac11g2159 2159
11 37668240 37669178 - Lag0032798.1 Lac11g2160 2160
12 37721052 37724790 + Maker00003033 Lcy12g1716 1716
12 37735786 37739811 - Maker00003080 Lcy12g1717 1717
12 37753080 37759400 - Maker00003008 Lcy12g1718 1718
7 19875322 19882989 + Lsi07G013690.1 Lsi07g01369 1369
7 19983160 19994538 - Lsi07G013730.1 Lsi07g01373 1373
9 3331222 3338153 + Lsi09G003210.1 Lsi09g00321 321
9 3347872 3350441 + Lsi09G003220.1 Lsi09g00322 322
9 3356813 3360385 - Lsi09G003230.1 Lsi09g00323 323
9 3372145 3373044 + Lsi09G003240.1 Lsi09g00324 324
9 3404485 3407388 - Lsi09G003260.1 Lsi09g00326 326
10 14807279 14814760 - MC10g1170 Mch10g1485 1485
4 5886323 5901330 - Sed0026462.2 Sed04g0725 725
5 6796719 6798177 - Sed0022083.1 Sed05g0853 853
1 21473742 21475261 - Tan0015071.1 Tan01g1950 1950
1 21635515 21641737 - Tan0011413.1 Tan01g1955 1955
2 4197373 4209047 + Vvi2g422 Vvi2g422 422
2 4225245 4227170 + Vvi2g423 Vvi2g423 423
2 4231192 4232794 + Vvi2g424 Vvi2g424 424
2 4234842 4244059 - Vvi2g425 Vvi2g425 425
2 4246952 4247870 - Vvi2g426 Vvi2g426 426
2 4249303 4250807 - Vvi2g427 Vvi2g427 427
2 4251597 4260954 - Vvi2g428 Vvi2g428 428
2 4282245 4283948 + Vvi2g429 Vvi2g429 429
2 4287649 4290952 + Vvi2g430 Vvi2g430 430
2 4296412 4298771 - Vvi2g431 Vvi2g431 431
       

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