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
Vvi17g196 . . . . . . . Bma12g01246 . . Cma10g00332 Cma11g00317 Car10g00314 Car11g00292 Sed08g0408 . Cpe04g01365 Bhi02g00151 Tan09g1810 Cmetu09g0719 . Hepe09g0397 . . Cla06g01415 Cam06g1568 Cec06g1628 Cco06g1620 Clacu06g1530 Cmu06g1484 Cre06g2293 . . . Cone19ag0337 . . . . . Blo15g00057 . . Bpe07g01050 . . . . Cmo10g00358 Cmo11g00322 . . . . . Cpe18g00873 . . . . . . . . . . . . . . Lsi06g01277 Csa01g00440 Chy02g02305 Cme02g01676
Vvi17g197 . . Bda06g00822 Bda15g00512 Bpe12g00695 . . Bma12g01245 . . Cma10g00331 Cma11g00316 Car10g00313 Car11g00291 . . Cpe04g01366 Bhi02g00150 Tan09g1812 . . Hepe09g0396 . . Cla06g01416 Cam06g1569 Cec06g1629 Cco06g1621 Clacu06g1531 Cmu06g1485 Cre06g2294 . . . Cone19ag0335 . . . . Blo13g00171 Blo15g00058 . . Bpe07g01049 . . Bma08g00057 . Cmo10g00357 . . . . . . . . . . . . . . . . . . . . . Lsi06g01278 Csa01g00439 Chy02g02306 Cme02g01677
Vvi17g198 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g199 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g200 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g201 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g202 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g203 . . . . . . . . . . . Cma11g00083 . . . . . . . . . . . . Cla06g01679 . . . . . . . . . . . . . . . . . . . . . . . . Cmo11g00084 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g204 Blo04g00853 Blo16g00111 . . . Bpe13g00379 Bma06g00068 . . . Cma10g00330 Cma11g00315 Car10g00312 Car11g00290 . . Cpe04g01367 Bhi02g00148 Tan09g1815 . . Hepe09g0395 . . Cla06g01417 Cam06g1570 Cec06g1630 Cco06g1622 Clacu06g1532 Cmu06g1486 Cre06g2295 . . . Cone19ag0334 . . . . Blo13g00181 . . . . Bpe15g00544 . . . Cmo10g00356 Cmo11g00320 . . . . . . . . . . . . . . . . . . . . Lsi06g01280 Csa01g00438 Chy02g02307 Cme02g01678
Vvi17g205 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 11457141 11460515 - Bda024153.1 Bda06g00822 822
15 8183462 8196227 - Bda012341.2 Bda15g00512 512
2 2707824 2723935 - XM_039023282.1 Bhi02g00148 148
2 2734154 2738870 - XM_039022414.1 Bhi02g00150 150
2 2789164 2793573 + XM_039022529.1 Bhi02g00151 151
4 9358150 9359957 - BLOR13765 Blo04g00853 853
13 6133924 6140457 + BLOR05452 Blo13g00171 171
13 6977101 6995097 - BLOR05462 Blo13g00181 181
15 451855 455575 - BLOR06451 Blo15g00057 57
15 456595 468364 + BLOR06452 Blo15g00058 58
16 2609382 2616526 + BLOR07359 Blo16g00111 111
6 1067907 1081704 - Bma022679.1 Bma06g00068 68
8 734519 739448 - Bma027053.1 Bma08g00057 57
12 45453589 45457638 - Bma008610.1 Bma12g01245 1245
12 45458527 45466959 + Bma008611.1 Bma12g01246 1246
7 15976158 15979540 - Bpe021892.1 Bpe07g01049 1049
7 15980429 15984319 + Bpe021893.1 Bpe07g01050 1050
12 12532430 12535599 + Bpe005955.1 Bpe12g00695 695
13 11535706 11550693 - Bpe006503.1 Bpe13g00379 379
15 16541010 16543684 + Bpe001479.1 Bpe15g00544 544
6 27165920 27169981 - CaPI482276_06g015680.1 Cam06g1568 1568
6 27171080 27174734 + CaPI482276_06g015690.1 Cam06g1569 1569
6 27176257 27186298 + CaPI482276_06g015700.1 Cam06g1570 1570
10 1527516 1536007 - Carg15179-RA Car10g00312 312
10 1536394 1540026 - Carg15180-RA Car10g00313 313
10 1540470 1543471 + Carg15181-RA Car10g00314 314
11 1588852 1595798 - Carg09099-RA Car11g00290 290
11 1597127 1599778 - Carg09098-RA Car11g00291 291
11 1599684 1602931 + Carg09097-RA Car11g00292 292
6 26808915 26812933 - CcPI632755_06g016200.1 Cco06g1620 1620
6 26814069 26817724 + CcPI632755_06g016210.1 Cco06g1621 1621
6 26819276 26827950 + CcPI632755_06g016220.1 Cco06g1622 1622
6 29883029 29887115 - CePI673135_06g016280.1 Cec06g1628 1628
6 29888233 29892370 + CePI673135_06g016290.1 Cec06g1629 1629
6 29893431 29903173 + CePI673135_06g016300.1 Cec06g1630 1630
2 27085118 27088816 - Chy2G045720.1 Chy02g02305 2305
2 27091555 27095216 + Chy2G045730.1 Chy02g02306 2306
2 27097418 27107855 + Chy2G045740.1 Chy02g02307 2307
6 26221035 26225130 - ClG42_06g0153000.10 Clacu06g1530 1530
6 26226151 26229790 + ClG42_06g0153100.10 Clacu06g1531 1531
6 26231328 26241274 + ClG42_06g0153200.10 Clacu06g1532 1532
6 27709183 27713499 - ClCG06G014270.1 Cla06g01415 1415
6 27714520 27718561 + ClCG06G014280.2 Cla06g01416 1416
6 27719843 27730712 + ClCG06G014290.2 Cla06g01417 1417
6 30378810 30386716 - ClCG06G017180.2 Cla06g01679 1679
10 1515717 1523931 - CmaCh10G003300.1 Cma10g00330 330
10 1525204 1528254 - CmaCh10G003310.1 Cma10g00331 331
10 1528782 1532115 + CmaCh10G003320.1 Cma10g00332 332
11 405029 408909 + CmaCh11G000830.1 Cma11g00083 83
11 1566902 1573896 - CmaCh11G003150.1 Cma11g00315 315
11 1574541 1577668 - CmaCh11G003160.1 Cma11g00316 316
11 1577574 1580358 + CmaCh11G003170.1 Cma11g00317 317
2 23905359 23909302 - MELO3C017362.2.1 Cme02g01676 1676
2 23911589 23915916 + MELO3C017361.2.1 Cme02g01677 1677
2 23917126 23927822 + MELO3C017360.2.1 Cme02g01678 1678
9 5476701 5479803 + PI0017000.1 Cmetu09g0719 719
10 1612117 1614753 - CmoCh10G003560.1 Cmo10g00356 356
10 1615269 1618883 - CmoCh10G003570.1 Cmo10g00357 357
10 1619315 1622488 + CmoCh10G003580.1 Cmo10g00358 358
11 394869 398662 + CmoCh11G000840.1 Cmo11g00084 84
11 1553080 1560010 - CmoCh11G003200.1 Cmo11g00320 320
11 1564019 1567985 + CmoCh11G003220.1 Cmo11g00322 322
6 26124402 26128497 - CmPI595203_06g014840.1 Cmu06g1484 1484
6 26129518 26133162 + CmPI595203_06g014850.1 Cmu06g1485 1485
6 26134700 26144637 + CmPI595203_06g014860.1 Cmu06g1486 1486
19 2701092 2710813 + Conep19aG0034500.1 Cone19ag0334 334
19 2712257 2716926 - Conep19aG0034600.1 Cone19ag0335 335
19 2731121 2736058 + Conep19aG0034800.1 Cone19ag0337 337
4 11106219 11110349 - Cp4.1LG04g13740.1 Cpe04g01365 1365
4 11110105 11112186 + Cp4.1LG04g13700.1 Cpe04g01366 1366
4 11114105 11121444 + Cp4.1LG04g13640.1 Cpe04g01367 1367
18 7973448 7980961 - Cp4.1LG18g08760.1 Cpe18g00873 873
6 30888376 30892407 - CrPI670011_06g022930.1 Cre06g2293 2293
6 30893537 30897185 + CrPI670011_06g022940.1 Cre06g2294 2294
6 30898707 30908530 + CrPI670011_06g022950.1 Cre06g2295 2295
1 2746604 2757241 - CsaV3_1G004380.1 Csa01g00438 438
1 2758440 2763313 - CsaV3_1G004390.1 Csa01g00439 439
1 2765336 2769473 + CsaV3_1G004400.1 Csa01g00440 440
9 3540398 3548909 - Hsped.09g03950.1 Hepe09g0395 395
9 3550488 3554391 - Hsped.09g03960.1 Hepe09g0396 396
9 3555850 3564789 + Hsped.09g03970.1 Hepe09g0397 397
6 23333679 23335077 - Lsi06G012770.1 Lsi06g01277 1277
6 23338007 23343811 + Lsi06G012780.1 Lsi06g01278 1278
6 23348031 23358723 + Lsi06G012800.1 Lsi06g01280 1280
8 2465030 2471970 + Sed0008851.2 Sed08g0408 408
9 69550100 69555305 - Tan0004087.1 Tan09g1810 1810
9 69557506 69561753 + Tan0001124.2 Tan09g1812 1812
9 69562991 69580469 + Tan0011852.2 Tan09g1815 1815
17 1993492 2012416 - Vvi17g196 Vvi17g196 196
17 2017702 2033911 + Vvi17g197 Vvi17g197 197
17 2042322 2043706 - Vvi17g198 Vvi17g198 198
17 2044016 2044579 + Vvi17g199 Vvi17g199 199
17 2046548 2049008 - Vvi17g200 Vvi17g200 200
17 2054238 2088910 - Vvi17g201 Vvi17g201 201
17 2090856 2094257 - Vvi17g202 Vvi17g202 202
17 2103261 2107856 - Vvi17g203 Vvi17g203 203
17 2109306 2134845 + Vvi17g204 Vvi17g204 204
17 2135972 2148416 + Vvi17g205 Vvi17g205 205
       

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