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
Vvi17g396 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g397 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone19ag0014 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g398 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone19ag0017 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g399 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone19ag0019 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g400 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed08g2543 . . . . . . . . Bhi08g01449 Tan05g2045 . . . . . . . . . . . . . . . .
Vvi17g401 . . Bda06g00500 . . . . Bma12g00949 . . Cma10g00267 . Car10g00251 . . . . Bhi02g00039 . . . . . . Cla06g01510 Cam06g1665 Cec06g1726 Cco06g1722 Clacu06g1631 Cmu06g1580 Cre06g2390 . . . Cone19ag0020 . . . . . Blo15g00353 . . . . . . . Cmo10g00286 . . . . . . Cpe18g00729 . . . . . . . . . . . . . . Lsi06g01373 Csa01g00315 Chy02g02425 Cme02g01791
Vvi17g402 Blo04g00807 . . . . . . . . Cmo18g00014 . . . . . . . . . . . . . . . . . . . . . Cone2ag0778 . . Cone19ag0021 Lsi02g00149 Csa01g00634 . . . . . Bda14g00900 . Bpe15g00558 Bma03g00875 . . . . Cma13g01052 Cma18g00013 Car13g00885 . . . . . . . . . . Cla04g01124 Cam04g1178 Cec01g1690 Cco01g1737 Clacu04g1206 Cmu04g1185 Cre01g1483 . . . .
Vvi17g403 Blo04g00806 . . . . . . . . . Cma10g00269 Cma11g00239 Car10g00252 Car11g00218 . . Cpe04g01432 Bhi02g00041 Tan09g1983 . . . . . . . . . . . . . . . Cone19ag0022 . . . . . . . Bda14g00899 . Bpe15g00559 Bma03g00874 . . Cmo10g00287 Cmo11g00243 . . . . . Cpe18g00728 . . . . . . . . . . . . . . Lsi06g01374 Csa01g00316 . Cme02g01792
Vvi17g404 . . . . . . . . . . . . . Car11g00217 Sed12g2040 . Cpe04g01433 Bhi02g00042 Tan09g1985 Cmetu02g1376 . Hepe09g0304 . . Cla06g01511 Cam06g1666 Cec06g1727 Cco06g1724 Clacu06g1632 Cmu06g1581 Cre06g2391 . . . Cone19ag0023 . . . . . . . . . . . . . . Cmo11g00242 . . . . . . . . . . . . . . . . . . . . . Csa01g00317 Chy02g02424 Cme02g01793
Vvi17g405 Blo04g00805 . . . . Bpe13g00330 . . Cmo13g01093 Cmo18g00013 Cma10g00270 Cma11g00237 Car10g00253 Car11g00216 Sed08g0316 Cpe20g00098 Cpe04g01434 Bhi02g00043 Tan09g1986 Cmetu02g0105 . Hepe09g0303 . . . . . . . . . Cone2ag0779 Cone16ag0257 . Cone19ag0024 . . Chy12g01467 Cme12g01910 . . . Bda14g00898 . Bpe15g00560 Bma03g00873 . Sed08g2148 Cmo10g00288 Cmo11g00241 . Cma18g00012 . . . Cpe18g00727 Bhi08g01044 Tan05g2310 Cmetu12g2001 . Hepe07g2431 . . . . . . . . . Lsi06g01375 Csa01g00318 Chy02g02423 Cme02g01794
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 7108043 7116266 - Bda023750.1 Bda06g00500 500
14 6997233 7001062 - Bda027678.2 Bda14g00898 898
14 7003994 7008239 + Bda027679.1 Bda14g00899 899
14 7008825 7010285 - Bda027680.1 Bda14g00900 900
2 820962 831969 - XM_039023796.1 Bhi02g00039 39
2 870904 876116 - XM_039023131.1 Bhi02g00041 41
2 896214 901158 + XM_039022429.1 Bhi02g00042 42
2 902727 906605 + XM_039024614.1 Bhi02g00043 43
8 34123573 34127335 - XM_039040136.1 Bhi08g01044 1044
8 42588827 42592711 + XM_039040118.1 Bhi08g01449 1449
4 8331602 8335992 - BLOR13717 Blo04g00805 805
4 8374437 8381207 + BLOR13718 Blo04g00806 806
4 8381882 8383435 - BLOR13719 Blo04g00807 807
15 4473969 4498389 + BLOR06747 Blo15g00353 353
3 8505544 8509148 - Bma017192.1 Bma03g00873 873
3 8511551 8516182 + Bma017193.2 Bma03g00874 874
3 8516859 8518766 - Bma030995 Bma03g00875 875
12 41407767 41416021 - Bma008292.3 Bma12g00949 949
13 11141841 11155700 - Bpe006457.1 Bpe13g00330 330
15 16615588 16617009 + Bpe024568 Bpe15g00558 558
15 16617569 16622248 - Bpe001493.3 Bpe15g00559 559
15 16626068 16629934 + Bpe001494.2 Bpe15g00560 560
4 25849173 25850509 - CaPI482276_04g011780.1 Cam04g1178 1178
6 28029949 28044850 - CaPI482276_06g016650.1 Cam06g1665 1665
6 28050215 28054319 + CaPI482276_06g016660.1 Cam06g1666 1666
10 1194258 1202436 - Carg17892-RA Car10g00251 251
10 1203278 1209084 - Carg17891-RA Car10g00252 252
10 1210619 1214774 + Carg17890-RA Car10g00253 253
11 1235016 1238453 - Carg09173-RA Car11g00216 216
11 1239252 1243923 - Carg09172-RA Car11g00217 217
11 1245478 1249855 + Carg09171-RA Car11g00218 218
13 9295111 9296086 - Carg04786-RA Car13g00885 885
1 30064708 30070876 - CcPI632755_01g017370.1 Cco01g1737 1737
6 27723198 27738312 - CcPI632755_06g017220.1 Cco06g1722 1722
6 27751066 27755042 + CcPI632755_06g017240.1 Cco06g1724 1724
1 31493928 31495263 - CePI673135_01g016900.1 Cec01g1690 1690
6 30780065 30794126 - CePI673135_06g017260.1 Cec06g1726 1726
6 30801333 30804950 + CePI673135_06g017270.1 Cec06g1727 1727
2 27922775 27925966 - Chy2G046900.1 Chy02g02423 2423
2 27928529 27932478 - Chy2G046910.1 Chy02g02424 2424
2 27934909 27948794 + Chy2G046920.1 Chy02g02425 2425
12 18611341 18614278 - Chy12G220670.1 Chy12g01467 1467
4 26201868 26203204 - ClG42_04g0120600.10 Clacu04g1206 1206
6 27082064 27097965 - ClG42_06g0163100.10 Clacu06g1631 1631
6 27102467 27106574 + ClG42_06g0163200.10 Clacu06g1632 1632
4 26425301 26433732 - ClCG04G011450.2 Cla04g01124 1124
6 28614671 28631022 - ClCG06G015260.2 Cla06g01510 1510
6 28635390 28646310 + ClCG06G015290.2 Cla06g01511 1511
10 1186038 1195170 - CmaCh10G002670.1 Cma10g00267 267
10 1195804 1202293 - CmaCh10G002690.1 Cma10g00269 269
10 1202046 1207348 + CmaCh10G002700.1 Cma10g00270 270
11 1207021 1218308 - CmaCh11G002370.1 Cma11g00237 237
11 1218814 1225214 + CmaCh11G002390.1 Cma11g00239 239
13 8000702 8001992 - CmaCh13G010520.1 Cma13g01052 1052
18 51874 55444 - CmaCh18G000120.1 Cma18g00012 12
18 55761 60014 - CmaCh18G000130.1 Cma18g00013 13
2 24710026 24716856 - MELO3C017266.2.1 Cme02g01791 1791
2 24718314 24724864 - MELO3C017265.2.1 Cme02g01792 1792
2 24727181 24731580 + MELO3C017264.2.1 Cme02g01793 1793
2 24733430 24738657 + MELO3C017263.2.1 Cme02g01794 1794
12 25183217 25186878 - MELO3C002061.2.1 Cme12g01910 1910
2 23076325 23080253 + PI0011303.1 Cmetu02g0105 105
2 23069831 23074439 + PI0012363.1 Cmetu02g1376 1376
12 1012366 1015995 + PI0024088.1 Cmetu12g2001 2001
10 1269742 1277593 - CmoCh10G002860.1 Cmo10g00286 286
10 1278350 1285075 - CmoCh10G002870.1 Cmo10g00287 287
10 1286166 1290164 + CmoCh10G002880.1 Cmo10g00288 288
11 1203597 1206644 - CmoCh11G002410.1 Cmo11g00241 241
11 1207879 1212376 - CmoCh11G002420.1 Cmo11g00242 242
11 1213084 1219756 + CmoCh11G002430.1 Cmo11g00243 243
13 9008398 9011549 - CmoCh13G010930.1 Cmo13g01093 1093
18 51520 55053 - CmoCh18G000130.1 Cmo18g00013 13
18 55383 57528 - CmoCh18G000140.1 Cmo18g00014 14
4 26383646 26384982 - CmPI595203_04g011850.1 Cmu04g1185 1185
6 26990678 27006574 - CmPI595203_06g015800.1 Cmu06g1580 1580
6 27011076 27015185 + CmPI595203_06g015810.1 Cmu06g1581 1581
2 33769646 33771408 + Conep02aG0180500.1 Cone2ag0778 778
2 33772721 33776497 + Conep02aG0180600.1 Cone2ag0779 779
16 2835222 2839577 + Conep16aG0260600.1 Cone16ag0257 257
19 120984 122220 + Conep19aG0001700.1 Cone19ag0014 14
19 145957 149586 - Conep19aG0002000.1 Cone19ag0017 17
19 157077 158150 - Conep19aG0002200.1 Cone19ag0019 19
19 165548 176423 - Conep19aG0002300.1 Cone19ag0020 20
19 182268 183290 + Conep19aG0002400.1 Cone19ag0021 21
19 183285 186850 - Conep19aG0002500.1 Cone19ag0022 22
19 188243 190404 + Conep19aG0002600.1 Cone19ag0023 23
19 190767 192571 + Conep19aG0002700.1 Cone19ag0024 24
4 11460899 11468039 - Cp4.1LG04g14240.1 Cpe04g01432 1432
4 11468740 11473656 + Cp4.1LG04g14170.1 Cpe04g01433 1433
4 11474286 11477518 + Cp4.1LG04g14370.1 Cpe04g01434 1434
18 7121401 7125381 - Cp4.1LG18g07360.1 Cpe18g00727 727
18 7126233 7133109 + Cp4.1LG18g07280.1 Cpe18g00728 728
18 7133789 7142442 + Cp4.1LG18g07270.1 Cpe18g00729 729
20 517144 520555 + Cp4.1LG20g01000.1 Cpe20g00098 98
1 28032838 28034981 - CrPI670011_01g014830.1 Cre01g1483 1483
6 31791511 31806509 - CrPI670011_06g023900.1 Cre06g2390 2390
6 31811924 31815571 + CrPI670011_06g023910.1 Cre06g2391 2391
1 1952410 1960679 - CsaV3_1G003150.1 Csa01g00315 315
1 1961757 1968368 - CsaV3_1G003160.1 Csa01g00316 316
1 1970502 1974453 + CsaV3_1G003170.1 Csa01g00317 317
1 1976470 1980581 + CsaV3_1G003180.1 Csa01g00318 318
1 4041091 4042702 + CsaV3_1G006340.1 Csa01g00634 634
7 68682471 68686243 - Hsped.07g24310.1 Hepe07g2431 2431
9 2632440 2636491 - Hsped.09g03030.1 Hepe09g0303 303
9 2637355 2642178 - Hsped.09g03040.1 Hepe09g0304 304
2 1252533 1254331 + Lsi02G001490.1 Lsi02g00149 149
6 24290281 24291592 - Lsi06G013730.1 Lsi06g01373 1373
6 24324051 24330447 - Lsi06G013740.1 Lsi06g01374 1374
6 24336639 24349543 + Lsi06G013750.1 Lsi06g01375 1375
8 1897524 1902103 - Sed0006970.1 Sed08g0316 316
8 35387286 35392042 - Sed0026229.2 Sed08g2148 2148
8 38087592 38090553 - Sed0027046.2 Sed08g2543 2543
12 31245521 31250943 - Sed0023319.1 Sed12g2040 2040
5 70692482 70695497 - Tan0017666.3 Tan05g2045 2045
5 74608838 74612587 - Tan0012041.1 Tan05g2310 2310
9 70595402 70602385 - Tan0005694.3 Tan09g1983 1983
9 70617323 70622569 + Tan0004452.2 Tan09g1985 1985
9 70627371 70631943 + Tan0022688.1 Tan09g1986 1986
17 4798762 4799730 - Vvi17g396 Vvi17g396 396
17 4802272 4803138 - Vvi17g397 Vvi17g397 397
17 4806534 4817448 - Vvi17g398 Vvi17g398 398
17 4820278 4826327 + Vvi17g399 Vvi17g399 399
17 4829689 4831828 - Vvi17g400 Vvi17g400 400
17 4833305 4884217 - Vvi17g401 Vvi17g401 401
17 4885700 4888937 + Vvi17g402 Vvi17g402 402
17 4889730 4906088 - Vvi17g403 Vvi17g403 403
17 4910753 4920747 + Vvi17g404 Vvi17g404 404
17 4921250 4931711 + Vvi17g405 Vvi17g405 405
       

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