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
Vvi17g146 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g147 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g148 . . . . . . . . . . Cma10g00073 Cma11g00047 Car10g00062 Car11g00041 . . Cpe04g01604 Bhi02g00541 Tan09g2354 . . Hepe09g0064 . . Cla06g01729 Cam06g1919 Cec06g1969 Cco06g1973 Clacu06g1875 Cmu06g1817 Cre06g2632 Cone2ag0961 Cone16ag0030 . Cone19ag0198 . . . . . . . . . . . . . Cmo10g00070 Cmo11g00047 . . . . . . . . . . . . . . . . . . . . Lsi06g01627 Csa01g00072 Chy02g02648 Cme02g02048
Vvi17g149 . Blo16g00263 . . . Bpe13g00206 Bma06g00250 . Cmo13g00825 Cmo18g00200 . . . . . Cpe20g00318 . . . . . . . . . . . . . . . . Cone16ag0032 . . Lsi02g00484 Csa01g00946 Chy12g01184 Cme12g01605 . . Bda11g01605 . . . . . . . . Cma13g00793 . Car13g00641 Car18g00217 Cpe09g00974 . . . . . . . . Cla03g00341 Cam03g0357 Cec03g0348 Cco03g0362 Clacu03g0358 Cmu03g0963 Cre03g0656 . . . .
Vvi17g150 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone16ag0033 . . . . . . . . . Bda14g01374 . Bpe15g00208 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g151 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0210 Cone19ag0197 . . . . . Blo15g00063 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g152 . . . . . Bpe13g00208 . . Cmo13g00822 . . . . . . Cpe20g00320 . . . . . . . . . . . . . . . Cone2ag0959 . . . Lsi02g00483 . . . . . Bda11g01607 . . . . . . . . Cma13g00791 . Car13g00639 . . . . . . . . . . Cla03g00340 Cam03g0355 Cec03g0346 Cco03g0361 Clacu03g0356 Cmu03g0961 Cre03g0654 . . . .
Vvi17g153 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g154 . . Bda06g00738 . . . . Bma12g01074 . . . Cma11g00049 Car10g00063 Car11g00042 . . Cpe04g01603 Bhi02g00543 . . . Hepe09g0065 . . Cla06g01728 Cam06g1918 Cec06g1968 Cco06g1972 Clacu06g1874 Cmu06g1816 Cre06g2631 . . Cone13ag0209 Cone19ag0196 . . . . . . . . Bpe07g00881 . . . . Cmo10g00071 Cmo11g00050 . . . . . . . . . . . . . . . . . . . . Lsi06g01625 Csa01g00073 Chy02g02647 .
Vvi17g155 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 10032733 10036998 + Bda024043.1 Bda06g00738 738
11 49672773 49675576 + Bda008486.1 Bda11g01605 1605
11 49688349 49690401 + Bda008488.1 Bda11g01607 1607
14 16217670 16219682 + Bda011076.1 Bda14g01374 1374
2 10238454 10239747 + XM_039023854.1 Bhi02g00541 541
2 10311935 10318520 + XM_039024347.1 Bhi02g00543 543
15 501607 504058 - BLOR06457 Blo15g00063 63
16 6134110 6137034 - BLOR07511 Blo16g00263 263
6 3438898 3441694 + Bma022880.1 Bma06g00250 250
12 43025800 43030003 - Bma008421.2 Bma12g01074 1074
7 14913513 14918046 - Bpe021724.1 Bpe07g00881 881
13 10082510 10085275 + Bpe006329.2 Bpe13g00206 206
13 10156131 10158186 + Bpe024931 Bpe13g00208 208
15 13172579 13174565 - Bpe001146.1 Bpe15g00208 208
3 4710600 4713431 - CaPI482276_03g003550.1 Cam03g0355 355
3 4725657 4728851 - CaPI482276_03g003570.1 Cam03g0357 357
6 30132141 30139095 - CaPI482276_06g019180.1 Cam06g1918 1918
6 30143948 30145692 - CaPI482276_06g019190.1 Cam06g1919 1919
10 283099 283613 + Carg10294-RA Car10g00062 62
10 286116 293083 + Carg10295-RA Car10g00063 63
11 219329 220714 + Carg20179-RA Car11g00041 41
11 221395 227089 + Carg20180-RA Car11g00042 42
13 8001403 8003897 - Carg07587-RA Car13g00639 639
13 8005520 8009283 - Carg07589-RA Car13g00641 641
18 1225556 1230019 - Carg06784-RA Car18g00217 217
3 3925346 3928207 - CcPI632755_03g003610.1 Cco03g0361 361
3 3930565 3943588 - CcPI632755_03g003620.1 Cco03g0362 362
6 29866858 29872528 - CcPI632755_06g019720.1 Cco06g1972 1972
6 29879352 29881126 - CcPI632755_06g019730.1 Cco06g1973 1973
3 3874235 3877041 - CePI673135_03g003460.1 Cec03g0346 346
3 3889011 3892201 - CePI673135_03g003480.1 Cec03g0348 348
6 32946020 32953041 - CePI673135_06g019680.1 Cec06g1968 1968
6 32957955 32959597 - CePI673135_06g019690.1 Cec06g1969 1969
2 29516699 29522303 - Chy2G049140.1 Chy02g02647 2647
2 29526582 29527102 - Chy2G049150.1 Chy02g02648 2648
12 16667488 16670268 + Chy12G217840.1 Chy12g01184 1184
3 4026799 4029619 - ClG42_03g0035600.10 Clacu03g0356 356
3 4042059 4045252 - ClG42_03g0035800.10 Clacu03g0358 358
6 29182980 29189934 - ClG42_06g0187400.10 Clacu06g1874 1874
6 29194791 29196543 - ClG42_06g0187500.10 Clacu06g1875 1875
3 3966401 3969640 - ClCG03G003600.1 Cla03g00340 340
3 3971460 3985558 - ClCG03G003610.1 Cla03g00341 341
6 30817363 30823030 - ClCG06G017730.1 Cla06g01728 1728
6 30829781 30831530 - ClCG06G017740.2 Cla06g01729 1729
10 291739 305414 + CmaCh10G000730.1 Cma10g00073 73
11 210860 211354 + CmaCh11G000470.1 Cma11g00047 47
11 217982 223266 + CmaCh11G000490.1 Cma11g00049 49
13 6762635 6765213 - CmaCh13G007910.1 Cma13g00791 791
13 6766961 6770703 - CmaCh13G007930.1 Cma13g00793 793
2 26508685 26510162 + MELO3C026223.2.1 Cme02g02048 2048
12 23303176 23306408 + MELO3C035535.2.1 Cme12g01605 1605
10 319459 325897 + CmoCh10G000700.1 Cmo10g00070 70
10 328504 334350 + CmoCh10G000710.1 Cmo10g00071 71
11 206748 207834 + CmoCh11G000470.1 Cmo11g00047 47
11 209826 215281 + CmoCh11G000500.1 Cmo11g00050 50
13 7686133 7688885 - CmoCh13G008220.1 Cmo13g00822 822
13 7690457 7694238 - CmoCh13G008250.1 Cmo13g00825 825
18 1339080 1343170 - CmoCh18G002000.1 Cmo18g00200 200
3 4240666 4243486 - CmPI595203_03g009610.1 Cmu03g0961 961
3 4255927 4259120 - CmPI595203_03g009630.1 Cmu03g0963 963
6 29085455 29092469 - CmPI595203_06g018160.1 Cmu06g1816 1816
6 29097365 29099115 - CmPI595203_06g018170.1 Cmu06g1817 1817
2 35182163 35184548 - Conep02aG0199300.1 Cone2ag0959 959
2 35192211 35193669 - Conep02aG0199500.1 Cone2ag0961 961
13 1341013 1346060 - Conep13aG0021400.1 Cone13ag0209 209
13 1354774 1359175 + Conep13aG0021500.1 Cone13ag0210 210
16 195244 196960 + Conep16aG0003000.1 Cone16ag0030 30
16 199550 201966 + Conep16aG0003200.1 Cone16ag0032 32
16 203104 205787 + Conep16aG0003300.1 Cone16ag0033 33
19 1228958 1234045 - Conep19aG0020200.1 Cone19ag0196 196
19 1240182 1244484 + Conep19aG0020300.1 Cone19ag0197 197
19 1244491 1245780 - Conep19aG0020400.1 Cone19ag0198 198
4 12476972 12485596 - Cp4.1LG04g16120.1 Cpe04g01603 1603
4 12486027 12487534 - Cp4.1LG04g16150.1 Cpe04g01604 1604
9 8675363 8681070 + Cp4.1LG09g09760.1 Cpe09g00974 974
20 1796227 1799694 + Cp4.1LG20g03200.1 Cpe20g00318 318
20 1801383 1803523 + Cp4.1LG20g03190.1 Cpe20g00320 320
3 5442830 5445643 - CrPI670011_03g006540.1 Cre03g0654 654
3 5457704 5460897 - CrPI670011_03g006560.1 Cre03g0656 656
6 33912287 33919910 - CrPI670011_06g026310.1 Cre06g2631 2631
6 33924069 33925721 - CrPI670011_06g026320.1 Cre06g2632 2632
1 428413 430044 + CsaV3_1G000720.1 Csa01g00072 72
1 433234 440378 + CsaV3_1G000730.1 Csa01g00073 73
1 5872757 5878503 - CsaV3_1G009460.1 Csa01g00946 946
9 543461 544833 + Hsped.09g00640.1 Hepe09g0064 64
9 549981 554303 + Hsped.09g00650.1 Hepe09g0065 65
2 4038393 4042355 - Lsi02G004830.1 Lsi02g00483 483
2 4044869 4058378 - Lsi02G004840.1 Lsi02g00484 484
6 26566199 26572030 - Lsi06G016250.1 Lsi06g01625 1625
6 26577801 26579257 - Lsi06G016270.1 Lsi06g01627 1627
9 73273758 73275137 - Tan0005617.1 Tan09g2354 2354
17 1307824 1308955 - Vvi17g146 Vvi17g146 146
17 1309751 1312896 - Vvi17g147 Vvi17g147 147
17 1314625 1323288 + Vvi17g148 Vvi17g148 148
17 1326720 1332448 + Vvi17g149 Vvi17g149 149
17 1336724 1339729 + Vvi17g150 Vvi17g150 150
17 1342829 1345896 - Vvi17g151 Vvi17g151 151
17 1351756 1355016 + Vvi17g152 Vvi17g152 152
17 1364233 1365304 + Vvi17g153 Vvi17g153 153
17 1370138 1381495 + Vvi17g154 Vvi17g154 154
17 1382387 1394519 + Vvi17g155 Vvi17g155 155
       

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