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
Vvi2g472 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0719 Cone9ag0722 . . . . . . . Bda09g00076 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g473 . . . . . . . Bma14g00564 . . . Cma15g01168 . Car15g01057 . . . . . . . . . . . . . . . . . . . . . . Csa05g00369 Chy09g01141 . Blo03g00389 . Bda07g00518 . . Bpe11g00705 . . . . Cmo15g01230 . . . . . . Bhi12g00368 . . Lac11g2208 Hepe06g1629 . . Cla01g00344 . . . . . . . . . Cme09g01672
Vvi2g474 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g475 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g476 . . . . . . . Bma14g00015 . . . . Car02g01268 . . . . . . . . . . . . . . . . . . . . Cone6ag0716 Cone9ag0717 . Csa05g00371 . . Blo03g00391 . . . . Bpe11g00249 . . . Cmo02g01547 . . . . . . Cpe13g00206 Bhi12g00370 . . Lac11g2214 Hepe06g1631 . Lcy12g1755 Cla01g00346 Cam01g0362 Cec01g0358 Cco01g0371 Clacu01g0365 Cmu01g0345 Cre09g2164 Lsi09g00373 . . .
Vvi2g477 Blo02g01065 . . . Bpe05g00602 . Bma07g01615 Bma14g00563 . Cmo16g01085 . Cma15g01167 Car02g01269 Car15g01056 . Cpe14g00858 . . . . . . . . . . . . . . . . . . . Lsi07g01349 . Chy09g01140 Cme06g02636 . . Bda07g00519 Bda09g00079 Bpe08g01450 Bpe11g00706 . . . Cmo02g01548 Cmo15g01229 . Cma16g01039 . Car16g00989 . . Bhi12g00575 . . . . . . . . . . . . . . Csa03g00324 Chy06g02000 Cme09g01671
Vvi2g478 Blo02g01063 Blo03g00179 . Bda08g00557 Bpe05g00601 . . . Cmo06g00774 Cmo16g01086 . Cma15g01165 . Car15g01054 . Cpe14g00859 . . . . . . . . Cla10g00301 Cam10g0313 Cec10g0324 Cco10g0316 Clacu10g0310 Cmu10g1149 Cre10g0559 Cone8ag0363 Cone12ag0353 . . Lsi07g01348 Csa05g00372 Chy09g01138 Cme06g02635 Blo03g00393 . Bda07g00023 . . . Bma05g00782 Bma12g00139 . . Cmo15g01227 Cma06g00751 . Car06g00672 Car16g00990 Cpe08g00768 Cpe13g00207 Bhi12g00371 . . Lac11g2215 Hepe06g1173 . Lcy12g1756 Cla01g00347 Cam01g0363 Cec01g0359 Cco01g0372 Clacu01g0366 Cmu01g0346 Cre09g2163 Lsi09g00374 Csa03g00323 Chy06g02001 Cme09g01669
Vvi2g479 Blo02g01062 Blo03g00178 Bda06g00051 Bda08g00558 Bpe05g00600 . . . Cmo06g00775 Cmo16g01088 . . . . . Cpe14g00860 . . . . . . . . . . . . . . . Cone8ag0364 Cone12ag0355 Cone6ag0714 Cone9ag0714 Lsi07g01347 . . Cme06g02634 . . . . . . Bma05g00781 Bma12g00140 . . . Cma06g00752 Cma16g01040 Car06g00673 Car16g00991 Cpe08g00767 . . . . . . . . . . . . . . . . Csa03g00322 Chy06g02002 .
Vvi2g480 . . . . . Bpe07g00148 . . . Cmo16g01089 . . . . . Cpe14g00861 . . . . . . . . Cla10g00299 Cam10g0312 Cec10g0322 Cco10g0315 Clacu10g0309 Cmu10g1148 Cre10g0558 . . Cone6ag0712 Cone9ag0713 Lsi07g01344 . . Cme06g02631 . . . . . . . Bma12g00141 . . . . Cma16g01041 . Car16g00992 . . . . . . . . . . . . . . . . . Csa03g00319 . .
Vvi2g481 . . . . . . . . Cmo06g01164 . . Cma15g01164 . Car15g01052 . . . . . . . . . . . . . . . . . . Cone12ag0356 Cone6ag0711 . . Csa05g00376 Chy09g01136 . Blo03g00394 . Bda07g00021 . . Bpe11g00252 . . . . Cmo15g01226 Cma06g01139 . Car06g00977 . Cpe08g00483 Cpe13g00209 Bhi12g00374 . . . . . . Cla01g00349 Cam01g0365 Cec01g0361 Cco01g0375 Clacu01g0368 Cmu01g0348 Cre09g2162 Lsi09g00376 . . Cme09g01667
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 547830 552712 - Bda023223.1 Bda06g00051 51
7 345316 346149 + Bda025075.1 Bda07g00021 21
7 364461 365901 + Bda025077.1 Bda07g00023 23
7 6622145 6623869 - Bda025628.1 Bda07g00518 518
7 6644662 6646965 + Bda025629.1 Bda07g00519 519
8 5674909 5675979 - Bda029015.1 Bda08g00557 557
8 5678832 5680215 + Bda029016.1 Bda08g00558 558
9 1425158 1425700 - Bda030604.1 Bda09g00076 76
9 1477786 1480086 + Bda030610.1 Bda09g00079 79
12 11754906 11757326 - XM_039018964.1 Bhi12g00368 368
12 11925667 11933295 + XM_039019909.1 Bhi12g00370 370
12 12023569 12025752 - XM_039019998.1 Bhi12g00371 371
12 12134860 12136025 - XM_039019246.1 Bhi12g00374 374
12 18205574 18209432 + XM_039051256.1 Bhi12g00575 575
2 40843207 40844569 - BLOR10792 Blo02g01062 1062
2 40864130 40865693 + BLOR10793 Blo02g01063 1063
2 40889487 40891529 - BLOR10795 Blo02g01065 1065
3 4430765 4432367 - BLOR11359 Blo03g00178 178
3 4437393 4438934 + BLOR11360 Blo03g00179 179
3 9451121 9452845 - BLOR11570 Blo03g00389 389
3 9752847 9760854 + BLOR11572 Blo03g00391 391
3 9883403 9885136 - BLOR11574 Blo03g00393 393
3 9996675 9997217 - BLOR11575 Blo03g00394 394
5 44747404 44748783 - Bma021880.1 Bma05g00781 781
5 44751572 44752987 + Bma021881.1 Bma05g00782 782
7 51662972 51665272 - Bma026912.1 Bma07g01615 1615
12 2003738 2005335 - Bma007016.1 Bma12g00139 139
12 2008399 2014277 + Bma007017.2 Bma12g00140 140
12 2024730 2027579 + Bma007018.1 Bma12g00141 141
14 174333 177257 - Bma010418.1 Bma14g00015 15
14 6040989 6043292 - Bma010993.1 Bma14g00563 563
14 6055263 6056987 + Bma010994.1 Bma14g00564 564
5 20018075 20019445 - Bpe018017.1 Bpe05g00600 600
5 20022132 20023674 + Bpe018018.1 Bpe05g00601 601
5 20024828 20026867 - Bpe018019.1 Bpe05g00602 602
7 1046709 1051518 + Bpe020958.1 Bpe07g00148 148
8 15250057 15252357 + Bpe023563.1 Bpe08g01450 1450
11 1732347 1735253 + Bpe003623.1 Bpe11g00249 249
11 1773760 1774595 - Bpe003627.1 Bpe11g00252 252
11 5426625 5428349 - Bpe004061.1 Bpe11g00705 705
11 5439029 5441332 + Bpe004062.1 Bpe11g00706 706
1 4058800 4061891 + CaPI482276_01g003620.1 Cam01g0362 362
1 4070127 4071622 - CaPI482276_01g003630.1 Cam01g0363 363
1 4091549 4092290 - CaPI482276_01g003650.1 Cam01g0365 365
10 5220390 5232862 - CaPI482276_10g003120.1 Cam10g0312 312
10 5240777 5245028 + CaPI482276_10g003130.1 Cam10g0313 313
2 8505841 8507357 - Carg02480-RA Car02g01268 1268
2 8513079 8515439 - Carg02479-RA Car02g01269 1269
6 3999165 4000675 - Carg21610-RA Car06g00672 672
6 4005002 4006823 - Carg21609-RA Car06g00673 673
6 7483110 7483838 - Carg23912-RA Car06g00977 977
15 8311061 8311809 + Carg16691-RA Car15g01052 1052
15 8319419 8321233 + Carg16689-RA Car15g01054 1054
15 8333636 8335966 - Carg16687-RA Car15g01056 1056
15 8339688 8341424 + Carg16686-RA Car15g01057 1057
16 8395986 8398226 + Carg25281-RA Car16g00989 989
16 8399708 8406908 - Carg25280-RA Car16g00990 990
16 8410688 8414083 - Carg25279-RA Car16g00991 991
16 8415376 8420082 + Carg25278-RA Car16g00992 992
1 3724066 3727147 + CcPI632755_01g003710.1 Cco01g0371 371
1 3734961 3736465 - CcPI632755_01g003720.1 Cco01g0372 372
1 3756632 3757373 - CcPI632755_01g003750.1 Cco01g0375 375
10 3671426 3684697 - CcPI632755_10g003150.1 Cco10g0315 315
10 3692283 3694977 + CcPI632755_10g003160.1 Cco10g0316 316
1 3733728 3736831 + CePI673135_01g003580.1 Cec01g0358 358
1 3744724 3746219 - CePI673135_01g003590.1 Cec01g0359 359
1 3769839 3770580 - CePI673135_01g003610.1 Cec01g0361 361
10 3859601 3872658 - CePI673135_10g003220.1 Cec10g0322 322
10 3880067 3882755 + CePI673135_10g003240.1 Cec10g0324 324
6 23974261 23976477 + Chy6G125280.1 Chy06g02000 2000
6 23985568 23989957 - Chy6G125290.1 Chy06g02001 2001
6 23992301 23994458 - Chy6G125300.1 Chy06g02002 2002
9 13588874 13589615 + Chy9G168520.1 Chy09g01136 1136
9 13601291 13602804 + Chy9G168540.1 Chy09g01138 1138
9 13633256 13635625 - Chy9G168560.1 Chy09g01140 1140
9 13646780 13648522 + Chy9G168570.1 Chy09g01141 1141
1 3689713 3692789 + ClG42_01g0036500.10 Clacu01g0365 365
1 3701075 3702571 - ClG42_01g0036600.10 Clacu01g0366 366
1 3723439 3724180 - ClG42_01g0036800.10 Clacu01g0368 368
10 3966244 3979249 - ClG42_10g0030900.10 Clacu10g0309 309
10 3987018 3989425 + ClG42_10g0031000.10 Clacu10g0310 310
1 3741072 3743012 - ClCG01G003560.1 Cla01g00344 344
1 3803998 3807413 + ClCG01G003610.2 Cla01g00346 346
1 3815494 3817533 - ClCG01G003620.1 Cla01g00347 347
1 3837691 3838735 - ClCG01G003640.1 Cla01g00349 349
10 3888777 3900192 - ClCG10G003160.2 Cla10g00299 299
10 3910416 3921377 + ClCG10G003180.2 Cla10g00301 301
6 3800354 3801938 - CmaCh06G007510.1 Cma06g00751 751
6 3807191 3809906 - CmaCh06G007520.1 Cma06g00752 752
6 7670809 7671840 - CmaCh06G011390.1 Cma06g01139 1139
15 7378510 7379545 + CmaCh15G011640.1 Cma15g01164 1164
15 7385938 7387897 + CmaCh15G011650.1 Cma15g01165 1165
15 7400296 7402617 - CmaCh15G011670.1 Cma15g01167 1167
15 7409133 7410869 + CmaCh15G011680.1 Cma15g01168 1168
16 7985007 7987238 + CmaCh16G010390.1 Cma16g01039 1039
16 7993215 8000853 - CmaCh16G010400.1 Cma16g01040 1040
16 8001842 8007924 + CmaCh16G010410.1 Cma16g01041 1041
6 33497210 33500638 - MELO3C013984.2.1 Cme06g02631 2631
6 33510259 33513682 + MELO3C013988.2.1 Cme06g02634 2634
6 33518418 33520111 + MELO3C013989.2.1 Cme06g02635 2635
6 33530611 33532836 - MELO3C013990.2.1 Cme06g02636 2636
9 21361529 21362656 + MELO3C005581.2.1 Cme09g01667 1667
9 21373509 21375584 + MELO3C005583.2.1 Cme09g01669 1669
9 21406119 21409007 - MELO3C005585.2.1 Cme09g01671 1671
9 21420665 21422407 + MELO3C005586.2.1 Cme09g01672 1672
2 8962878 8964247 - CmoCh02G015470.1 Cmo02g01547 1547
2 8970023 8972380 - CmoCh02G015480.1 Cmo02g01548 1548
6 4024868 4026386 - CmoCh06G007740.1 Cmo06g00774 774
6 4030461 4033159 - CmoCh06G007750.1 Cmo06g00775 775
6 8919314 8920373 - CmoCh06G011640.1 Cmo06g01164 1164
15 8455017 8456104 + CmoCh15G012260.1 Cmo15g01226 1226
15 8463264 8465233 + CmoCh15G012270.1 Cmo15g01227 1227
15 8477099 8479417 - CmoCh15G012290.1 Cmo15g01229 1229
15 8483570 8485306 + CmoCh15G012300.1 Cmo15g01230 1230
16 7675800 7678037 + CmoCh16G010850.1 Cmo16g01085 1085
16 7685711 7688795 - CmoCh16G010860.1 Cmo16g01086 1086
16 7693243 7696620 - CmoCh16G010880.1 Cmo16g01088 1088
16 7697908 7702323 + CmoCh16G010890.1 Cmo16g01089 1089
1 3636515 3639591 + CmPI595203_01g003450.1 Cmu01g0345 345
1 3647867 3649363 - CmPI595203_01g003460.1 Cmu01g0346 346
1 3670438 3671179 - CmPI595203_01g003480.1 Cmu01g0348 348
10 4084562 4097587 - CmPI595203_10g011480.1 Cmu10g1148 1148
10 4105280 4108395 + CmPI595203_10g011490.1 Cmu10g1149 1149
6 3585444 3586204 + Conep06aG0073300.1 Cone6ag0711 711
6 3586400 3588849 - Conep06aG0073400.1 Cone6ag0712 712
6 3592930 3595495 - Conep06aG0073600.1 Cone6ag0714 714
6 3602577 3605372 - Conep06aG0073800.1 Cone6ag0716 716
6 3621542 3623000 + Conep06aG0074100.1 Cone6ag0719 719
8 2140242 2142366 - Conep08aG0037900.1 Cone8ag0363 363
8 2148379 2151126 + Conep08aG0038000.1 Cone8ag0364 364
9 3416653 3419024 - Conep09aG0073000.1 Cone9ag0713 713
9 3420134 3422580 - Conep09aG0073100.1 Cone9ag0714 714
9 3432049 3433173 - Conep09aG0073400.1 Cone9ag0717 717
9 3448579 3450031 + Conep09aG0073900.1 Cone9ag0722 722
12 1974249 1984661 - Conep12aG0036800.1 Cone12ag0353 353
12 1997334 2000119 + Conep12aG0037000.1 Cone12ag0355 355
12 2000191 2000989 - Conep12aG0037100.1 Cone12ag0356 356
8 3101520 3102289 + Cp4.1LG08g01930.1 Cpe08g00483 483
8 6144444 6147246 + Cp4.1LG08g07620.1 Cpe08g00767 767
8 6150435 6153593 + Cp4.1LG08g07610.1 Cpe08g00768 768
13 1576254 1579723 + Cp4.1LG13g01920.1 Cpe13g00206 206
13 1581424 1583720 - Cp4.1LG13g01960.1 Cpe13g00207 207
13 1590844 1591955 - Cp4.1LG13g02140.1 Cpe13g00209 209
14 7100691 7102931 + Cp4.1LG14g08520.1 Cpe14g00858 858
14 7110310 7112162 - Cp4.1LG14g08600.1 Cpe14g00859 859
14 7116341 7119389 - Cp4.1LG14g08630.1 Cpe14g00860 860
14 7120628 7125080 + Cp4.1LG14g08570.1 Cpe14g00861 861
9 40624774 40625515 + CrPI670011_09g021620.1 Cre09g2162 2162
9 40644956 40646452 + CrPI670011_09g021630.1 Cre09g2163 2163
9 40658669 40661935 - CrPI670011_09g021640.1 Cre09g2164 2164
10 5059733 5072905 - CrPI670011_10g005580.1 Cre10g0558 558
10 5080719 5083831 + CrPI670011_10g005590.1 Cre10g0559 559
3 2678986 2682698 - CsaV3_3G003190.1 Csa03g00319 319
3 2691048 2694338 + CsaV3_3G003220.1 Csa03g00322 322
3 2699024 2700738 + CsaV3_3G003230.1 Csa03g00323 323
3 2708083 2711518 - CsaV3_3G003240.1 Csa03g00324 324
5 2367404 2369983 - CsaV3_5G003690.1 Csa05g00369 369
5 2407805 2411594 + CsaV3_5G003710.1 Csa05g00371 371
5 2414868 2417473 - CsaV3_5G003720.1 Csa05g00372 372
5 2428666 2429997 - CsaV3_5G003760.1 Csa05g00376 376
6 61102111 61103570 + Hsped.06g11730.1 Hepe06g1173 1173
6 67149519 67151260 - Hsped.06g16290.1 Hepe06g1629 1629
6 67188201 67192111 + Hsped.06g16310.1 Hepe06g1631 1631
11 38167913 38169649 - Lag0032846.1 Lac11g2208 2208
11 38209901 38213000 + Lag0032852.1 Lac11g2214 2214
11 38219693 38222745 - Lag0032853.1 Lac11g2215 2215
12 38338180 38341572 + Maker00003061 Lcy12g1755 1755
12 38348340 38350657 - Maker00003058 Lcy12g1756 1756
7 19610554 19619053 - Lsi07G013440.1 Lsi07g01344 1344
7 19630756 19634491 + Lsi07G013470.1 Lsi07g01347 1347
7 19641120 19642714 + Lsi07G013480.1 Lsi07g01348 1348
7 19661986 19664208 - Lsi07G013490.1 Lsi07g01349 1349
9 3916468 3919624 + Lsi09G003730.1 Lsi09g00373 373
9 3929757 3931841 - Lsi09G003740.1 Lsi09g00374 374
9 3958441 3959588 - Lsi09G003760.1 Lsi09g00376 376
2 4642111 4643844 - Vvi2g472 Vvi2g472 472
2 4666523 4667903 + Vvi2g473 Vvi2g473 473
2 4671232 4672854 + Vvi2g474 Vvi2g474 474
2 4681633 4682139 + Vvi2g475 Vvi2g475 475
2 4685337 4693209 - Vvi2g476 Vvi2g476 476
2 4699450 4704222 - Vvi2g477 Vvi2g477 477
2 4713634 4718456 - Vvi2g478 Vvi2g478 478
2 4730225 4736741 + Vvi2g479 Vvi2g479 479
2 4737980 4745369 + Vvi2g480 Vvi2g480 480
2 4745515 4746562 - Vvi2g481 Vvi2g481 481
       

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