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
Vvi17g226 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa01g00705 Chy12g01406 Cme12g01841 . . . . . Bpe15g00517 . . . . . . Cma18g00063 . Car18g00055 Cpe09g01121 . . . . . . . . Cla04g01057 Cam04g1099 Cec01g1614 Cco01g1659 Clacu04g1124 Cmu04g1108 Cre01g1408 . . . .
Vvi17g227 . . . Bda15g00507 Bpe12g00702 . . . . . . . Car10g00304 Car11g00278 Sed08g0393 . Cpe04g01379 Bhi02g00126 Tan09g1838 Cmetu02g0013 . Hepe09g0378 . . Cla06g01430 Cam06g1584 Cec06g1644 Cco06g1636 Clacu06g1545 Cmu06g1500 Cre06g2309 . . . Cone19ag0326 . . . . . . . . . . . Bma08g00049 . Cmo10g00348 Cmo11g00307 . . . . . . . . . . . . . . . . . . . . Lsi06g01297 Csa01g00423 Chy02g02321 Cme02g01694
Vvi17g228 Blo04g00843 . . . . . . . . Cmo18g00048 . . . . . . . . . . . . . . . . . . . . . Cone2ag0756 . . . Lsi02g00223 . . . . . . . . Bpe15g00518 Bma03g00909 . Sed01g1758 . . . Cma18g00062 . Car18g00054 Cpe09g01122 . Bhi08g01279 Tan05g2206 Cmetu04g3049 Lac10g0278 Hepe07g2363 . . Cla04g01058 Cam04g1100 Cec01g1615 Cco01g1660 Clacu04g1125 Cmu04g1109 Cre01g1409 . . . .
Vvi17g229 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda14g01079 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g230 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda14g01034 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g231 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g232 . Blo16g00117 . . . Bpe13g00373 Bma06g00062 . . . Cma10g00323 Cma11g00303 Car10g00303 Car11g00277 Sed08g0392 . Cpe04g01380 Bhi02g00125 Tan09g1839 Cmetu02g0822 . Hepe09g0377 . . Cla06g01431 Cam06g1585 Cec06g1645 Cco06g1637 Clacu06g1546 Cmu06g1501 Cre06g2310 Cone2ag0753 . . . . . . . . . Bda11g01783 . . . . . . Cmo10g00346 Cmo11g00306 . . . . . . . . . . . . . . . . . . . . Lsi06g01298 Csa01g00422 Chy02g02322 Cme02g01695
Vvi17g233 . Blo16g00120 . . . Bpe13g00372 . . Cmo13g01035 . . . . . . Cpe20g00143 . . . . . . . . . . . . . . . . . . . Lsi02g00222 Csa01g00704 Chy12g01407 Cme12g01842 . . Bda11g01782 . . . . . Sed08g2750 . . Cma13g00999 . Car13g00833 . . . Bhi08g01278 Tan05g2207 Cmetu12g0260 Lac10g0277 Hepe07g2364 . . Cla04g01059 Cam04g1102 Cec01g1616 Cco01g1662 Clacu04g1126 Cmu04g1110 Cre01g1412 . . . .
Vvi17g234 . . . . . . . . Cmo13g01036 . . . . . . Cpe20g00142 . . . . . . . . . . . . . . . Cone2ag0752 . . . Lsi02g00221 Csa01g00703 Chy12g01409 Cme12g01843 . . . . . Bpe15g00519 . . Sed01g1757 . . Cma13g01000 . Car13g00834 . . . Bhi08g01277 Tan05g2208 Cmetu12g1384 Lac10g0276 . . . Cla04g01060 Cam04g1103 Cec01g1617 Cco01g1663 Clacu04g1127 Cmu04g1111 Cre01g1413 . . . .
Vvi17g235 . Blo16g00122 . . . Bpe13g00371 Bma06g00060 . . . Cma10g00322 . Car10g00302 . . . . Bhi02g00122 Tan09g1841 . . . . . Cla06g01432 Cam06g1586 Cec06g1646 Cco06g1638 Clacu06g1547 Cmu06g1502 Cre06g2311 . . . . . . . . . . Bda11g01781 . . . . . . Cmo10g00345 . . . . . . . . . . . . . . . . . . . . . Lsi06g01299 Csa01g00420 Chy02g02324 Cme02g01696
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 52670274 52674755 + Bda008703.1 Bda11g01781 1781
11 52675550 52679306 - Bda008704.1 Bda11g01782 1782
11 52682657 52724769 - Bda008705.1 Bda11g01783 1783
14 8716235 8717431 + Bda027844.1 Bda14g01034 1034
14 9446081 9446659 + Bda027902.1 Bda14g01079 1079
15 8157843 8160405 - Bda012336.1 Bda15g00507 507
2 2282523 2286869 + XM_039023654.1 Bhi02g00122 122
2 2370782 2377451 - XM_039023543.1 Bhi02g00125 125
2 2407637 2409893 - XM_039024181.1 Bhi02g00126 126
8 39178880 39184599 + XM_039037996.1 Bhi08g01277 1277
8 39185118 39188372 - XM_039039787.1 Bhi08g01278 1278
8 39274978 39276675 - XM_039039711.1 Bhi08g01279 1279
4 9182179 9183287 - BLOR13755 Blo04g00843 843
16 2727376 2732321 + BLOR07365 Blo16g00117 117
16 2748345 2752564 + BLOR07368 Blo16g00120 120
16 2768111 2772407 - BLOR07370 Blo16g00122 122
3 9055134 9056192 - Bma030999 Bma03g00909 909
6 964605 970064 + Bma022671.1 Bma06g00060 60
6 1001008 1007727 - Bma022673.1 Bma06g00062 62
8 685071 687486 - Bma027044.1 Bma08g00049 49
12 12568385 12570901 + Bpe005962.1 Bpe12g00702 702
13 11459158 11463150 + Bpe024938 Bpe13g00371 371
13 11469296 11472672 - Bpe006497.1 Bpe13g00372 372
13 11474536 11485440 - Bpe006498.1 Bpe13g00373 373
15 16359413 16361908 + Bpe001450.1 Bpe15g00517 517
15 16362933 16363968 + Bpe001451.1 Bpe15g00518 518
15 16365026 16368425 - Bpe001452.1 Bpe15g00519 519
4 25146678 25149809 + CaPI482276_04g010990.1 Cam04g1099 1099
4 25152960 25154517 + CaPI482276_04g011000.1 Cam04g1100 1100
4 25169294 25172466 + CaPI482276_04g011020.1 Cam04g1102 1102
4 25172497 25177929 - CaPI482276_04g011030.1 Cam04g1103 1103
6 27321806 27323529 + CaPI482276_06g015840.1 Cam06g1584 1584
6 27327299 27332453 + CaPI482276_06g015850.1 Cam06g1585 1585
6 27336301 27339962 - CaPI482276_06g015860.1 Cam06g1586 1586
10 1485726 1492034 + Carg15169-RA Car10g00302 302
10 1492035 1497766 - Carg15170-RA Car10g00303 303
10 1498604 1500602 - Carg15171-RA Car10g00304 304
11 1517513 1523521 - Carg09112-RA Car11g00277 277
11 1524541 1526393 - Carg09111-RA Car11g00278 278
13 9014869 9017502 + Carg04839-RA Car13g00833 833
13 9017532 9021547 - Carg04838-RA Car13g00834 834
18 275566 276999 + Carg06619-RA Car18g00054 54
18 280015 282964 - Carg06620-RA Car18g00055 55
1 29360858 29364007 + CcPI632755_01g016590.1 Cco01g1659 1659
1 29366289 29368052 + CcPI632755_01g016600.1 Cco01g1660 1660
1 29383121 29386428 + CcPI632755_01g016620.1 Cco01g1662 1662
1 29386459 29391875 - CcPI632755_01g016630.1 Cco01g1663 1663
6 26973055 26974782 + CcPI632755_06g016360.1 Cco06g1636 1636
6 26978448 26983589 + CcPI632755_06g016370.1 Cco06g1637 1637
6 26986615 26990276 - CcPI632755_06g016380.1 Cco06g1638 1638
1 30796802 30799953 + CePI673135_01g016140.1 Cec01g1614 1614
1 30803084 30804816 + CePI673135_01g016150.1 Cec01g1615 1615
1 30819974 30823203 + CePI673135_01g016160.1 Cec01g1616 1616
1 30823234 30828675 - CePI673135_01g016170.1 Cec01g1617 1617
6 30044496 30046220 + CePI673135_06g016440.1 Cec06g1644 1644
6 30049923 30055103 + CePI673135_06g016450.1 Cec06g1645 1645
6 30057774 30062723 - CePI673135_06g016460.1 Cec06g1646 1646
2 27214670 27216388 + Chy2G045880.1 Chy02g02321 2321
2 27219005 27225234 + Chy2G045890.1 Chy02g02322 2322
2 27228602 27232355 - Chy2G045910.1 Chy02g02324 2324
12 18177956 18180388 + Chy12G220060.1 Chy12g01406 1406
12 18183583 18185458 + Chy12G220070.1 Chy12g01407 1407
12 18186890 18191608 - Chy12G220090.1 Chy12g01409 1409
4 25518098 25521225 + ClG42_04g0112400.10 Clacu04g1124 1124
4 25523935 25525679 + ClG42_04g0112500.10 Clacu04g1125 1125
4 25540043 25543630 + ClG42_04g0112600.10 Clacu04g1126 1126
4 25543643 25549008 - ClG42_04g0112700.10 Clacu04g1127 1127
6 26378343 26380066 + ClG42_06g0154500.10 Clacu06g1545 1545
6 26383850 26389023 + ClG42_06g0154600.10 Clacu06g1546 1546
6 26391522 26396806 - ClG42_06g0154700.10 Clacu06g1547 1547
4 25741819 25745017 + ClCG04G010740.2 Cla04g01057 1057
4 25748946 25750863 + ClCG04G010750.1 Cla04g01058 1058
4 25765434 25768809 + ClCG04G010760.1 Cla04g01059 1059
4 25769117 25774044 - ClCG04G010770.2 Cla04g01060 1060
6 27875280 27877713 + ClCG06G014430.1 Cla06g01430 1430
6 27880842 27887529 + ClCG06G014440.2 Cla06g01431 1431
6 27890621 27894697 - ClCG06G014450.2 Cla06g01432 1432
10 1474986 1480173 + CmaCh10G003220.1 Cma10g00322 322
10 1480125 1488890 - CmaCh10G003230.1 Cma10g00323 323
11 1497323 1506187 - CmaCh11G003030.1 Cma11g00303 303
13 7722261 7724915 + CmaCh13G009990.1 Cma13g00999 999
13 7725033 7728896 - CmaCh13G010000.1 Cma13g01000 1000
18 264340 266190 - CmaCh18G000620.1 Cma18g00062 62
18 268209 277347 - CmaCh18G000630.1 Cma18g00063 63
2 24033249 24035388 + MELO3C017348.2.1 Cme02g01694 1694
2 24037350 24042817 + MELO3C017347.2.1 Cme02g01695 1695
2 24044701 24048615 - MELO3C017346.2.1 Cme02g01696 1696
12 24756875 24759486 + MELO3C002123.2.1 Cme12g01841 1841
12 24762052 24765257 + MELO3C002122.2.1 Cme12g01842 1842
12 24765518 24770236 - MELO3C002121.2.1 Cme12g01843 1843
2 22457779 22459930 + PI0025530.1 Cmetu02g0013 13
2 22462261 22468024 + PI0026055.1 Cmetu02g0822 822
4 6373205 6374855 + PI0011815.1 Cmetu04g3049 3049
12 1469342 1472648 - PI0025922.1 Cmetu12g0260 260
12 1463797 1469357 + PI0022441.1 Cmetu12g1384 1384
10 1564937 1569445 + CmoCh10G003450.1 Cmo10g00345 345
10 1569527 1575695 - CmoCh10G003460.1 Cmo10g00346 346
10 1576542 1578648 - CmoCh10G003480.1 Cmo10g00348 348
11 1480836 1486760 - CmoCh11G003060.1 Cmo11g00306 306
11 1487679 1494096 - CmoCh11G003070.1 Cmo11g00307 307
13 8714454 8717178 + CmoCh13G010350.1 Cmo13g01035 1035
13 8717250 8721081 - CmoCh13G010360.1 Cmo13g01036 1036
18 307778 309513 + CmoCh18G000480.1 Cmo18g00048 48
4 25698888 25702013 + CmPI595203_04g011080.1 Cmu04g1108 1108
4 25705089 25706830 + CmPI595203_04g011090.1 Cmu04g1109 1109
4 25721598 25724742 + CmPI595203_04g011100.1 Cmu04g1110 1110
4 25724755 25730120 - CmPI595203_04g011110.1 Cmu04g1111 1111
6 26281613 26283336 + CmPI595203_06g015000.1 Cmu06g1500 1500
6 26287120 26292293 + CmPI595203_06g015010.1 Cmu06g1501 1501
6 26294834 26300118 - CmPI595203_06g015020.1 Cmu06g1502 1502
2 33318226 33321401 + Conep02aG0176900.1 Cone2ag0752 752
2 33321803 33329301 - Conep02aG0177000.1 Cone2ag0753 753
2 33367093 33368767 + Conep02aG0177300.1 Cone2ag0756 756
19 2610202 2612433 - Conep19aG0033700.1 Cone19ag0326 326
4 11183850 11186002 + Cp4.1LG04g13770.1 Cpe04g01379 1379
4 11186944 11193119 + Cp4.1LG04g13800.1 Cpe04g01380 1380
9 9636486 9639831 + Cp4.1LG09g11160.1 Cpe09g01121 1121
9 9643331 9644754 - Cp4.1LG09g11210.1 Cpe09g01122 1122
20 803788 809676 + Cp4.1LG20g01400.1 Cpe20g00142 142
20 807317 810537 - Cp4.1LG20g01540.1 Cpe20g00143 143
1 27350646 27353805 + CrPI670011_01g014080.1 Cre01g1408 1408
1 27356926 27358674 + CrPI670011_01g014090.1 Cre01g1409 1409
1 27372904 27376767 + CrPI670011_01g014120.1 Cre01g1412 1412
1 27376798 27383987 - CrPI670011_01g014130.1 Cre01g1413 1413
6 31046776 31048498 + CrPI670011_06g023090.1 Cre06g2309 2309
6 31052339 31057516 + CrPI670011_06g023100.1 Cre06g2310 2310
6 31061302 31065203 - CrPI670011_06g023110.1 Cre06g2311 2311
1 2633327 2639484 + CsaV3_1G004200.1 Csa01g00420 420
1 2640319 2646163 - CsaV3_1G004220.1 Csa01g00422 422
1 2647667 2650211 - CsaV3_1G004230.1 Csa01g00423 423
1 4456446 4462653 + CsaV3_1G007030.1 Csa01g00703 703
1 4461984 4465405 - CsaV3_1G007040.1 Csa01g00704 704
1 4468088 4470523 - CsaV3_1G007050.1 Csa01g00705 705
7 68000379 68002385 + Hsped.07g23630.1 Hepe07g2363 2363
7 68018674 68022321 + Hsped.07g23640.1 Hepe07g2364 2364
9 3350875 3357451 - Hsped.09g03770.1 Hepe09g0377 377
9 3361490 3363863 - Hsped.09g03780.1 Hepe09g0378 378
10 2101604 2106591 + Lag0024321.1 Lac10g0276 276
10 2107308 2110488 - Lag0024322.1 Lac10g0277 277
10 2113946 2114254 - Lag0024323.1 Lac10g0278 278
2 1848383 1853614 + Lsi02G002210.1 Lsi02g00221 221
2 1854174 1857591 - Lsi02G002220.1 Lsi02g00222 222
2 1864174 1866009 - Lsi02G002230.1 Lsi02g00223 223
6 23514810 23516577 + Lsi06G012970.1 Lsi06g01297 1297
6 23519986 23525272 + Lsi06G012980.1 Lsi06g01298 1298
6 23526756 23531278 - Lsi06G012990.1 Lsi06g01299 1299
1 12790694 12796200 + Sed0024498.1 Sed01g1757 1757
1 12799166 12804187 - Sed0000492.1 Sed01g1758 1758
8 2359988 2366884 - Sed0001638.1 Sed08g0392 392
8 2370465 2373370 - Sed0006313.1 Sed08g0393 393
8 39180187 39184276 - Sed0023689.1 Sed08g2750 2750
5 73013439 73018349 + Tan0019350.1 Tan05g2206 2206
5 73042193 73045411 + Tan0012085.1 Tan05g2207 2207
5 73045809 73051176 - Tan0000036.1 Tan05g2208 2208
9 69745296 69747600 + Tan0018165.1 Tan09g1838 1838
9 69751345 69757351 + Tan0019421.1 Tan09g1839 1839
9 69757843 69762768 - Tan0010854.2 Tan09g1841 1841
17 2388618 2393012 + Vvi17g226 Vvi17g226 226
17 2401129 2403917 + Vvi17g227 Vvi17g227 227
17 2414102 2416028 - Vvi17g228 Vvi17g228 228
17 2449847 2450462 - Vvi17g229 Vvi17g229 229
17 2457850 2459785 - Vvi17g230 Vvi17g230 230
17 2459940 2464219 - Vvi17g231 Vvi17g231 231
17 2475547 2490062 + Vvi17g232 Vvi17g232 232
17 2495807 2498821 + Vvi17g233 Vvi17g233 233
17 2499559 2504322 - Vvi17g234 Vvi17g234 234
17 2505972 2509710 - Vvi17g235 Vvi17g235 235
       

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