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
Vvi17g246 Blo04g00839 Blo16g00126 . . . Bpe13g00367 Bma06g00055 . Cmo13g01039 Cmo18g00045 . . . . . Cpe20g00140 . . . . . . . . . . . . . . . . . . . Lsi02g00219 Csa01g00700 Chy12g01412 Cme12g01846 . . Bda11g01780 . . Bpe15g00536 Bma03g00904 . Sed08g2749 . . Cma13g01003 Cma18g00058 Car13g00838 Car18g00051 Cpe09g01124 Cpe18g00872 Bhi08g01272 Tan05g2214 Cmetu12g0241 Lac10g0273 . . . Cla04g01062 Cam04g1105 Cec01g1619 Cco01g1666 Clacu04g1130 Cmu04g1114 Cre01g1415 . . . .
Vvi17g247 . . . Bda15g00505 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda14g00999 . . . Bma08g00047 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g248 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g249 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g250 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g251 . . Bda06g00814 . . . . Bma12g01237 . . . Cma11g00300 . Car11g00274 . . Cpe04g01383 Bhi02g00118 Tan09g1845 Cmetu02g0604 . . . . . . . . . . . . . Cone13ag0330 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme02g01702
Vvi17g252 . . . . . . . . . . . Cma11g00299 . . Sed08g0385 . . Bhi02g00117 Tan09g1846 Cmetu02g0734 . Hepe09g0371 . . Cla06g01435 Cam06g1590 Cec06g1650 Cco06g1642 Clacu06g1551 Cmu06g1506 Cre06g2315 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi06g01302 . . .
Vvi17g253 . . . . . . . . . . . . . . . . Cpe04g01384 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme02g01703
Vvi17g254 . . . Bda15g00504 . . . . . . Cma10g00319 Cma11g00298 Car10g00299 Car11g00272 . . Cpe04g01385 Bhi02g00116 . . . . . . Cla06g01436 Cam06g1591 Cec06g1651 Cco06g1643 Clacu06g1552 Cmu06g1507 Cre06g2316 . . . . . . . . Blo13g00180 . . . . . . . . Cmo10g00341 Cmo11g00303 . . . . . . . . . . . . . . . . . . . . Lsi06g01303 . . .
Vvi17g255 . . . . . . . . . . Cma10g00316 Cma11g00297 . . . . . Bhi02g00115 . . . Hepe09g0239 . . Cla06g01437 Cam06g1592 Cec06g1652 Cco06g1644 Clacu06g1553 Cmu06g1508 Cre06g2318 . . . . . . . . . . . . Bpe07g01043 . . . . Cmo10g00340 Cmo11g00302 . . . . . . . . . . . . . . . . . . . . . Csa01g00419 Chy02g02327 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 11402233 11403344 + Bda024145.1 Bda06g00814 814
11 52655314 52660119 - Bda008702.1 Bda11g01780 1780
14 8384469 8385836 + Bda027805.1 Bda14g00999 999
15 8133713 8136846 - Bda033302 Bda15g00504 504
15 8137806 8143661 - Bda012334.1 Bda15g00505 505
2 2094367 2098217 + XM_039024207.1 Bhi02g00115 115
2 2107290 2112847 - XM_039024379.1 Bhi02g00116 116
2 2122602 2124290 + XM_039023882.1 Bhi02g00117 117
2 2124499 2127787 - XM_039023881.1 Bhi02g00118 118
8 39006841 39025056 - XM_039038778.1 Bhi08g01272 1272
4 9082701 9097364 - BLOR13751 Blo04g00839 839
13 6894448 6896498 + BLOR05461 Blo13g00180 180
16 2862452 2878734 + BLOR07374 Blo16g00126 126
3 8971403 8976391 - Bma017229.1 Bma03g00904 904
6 885048 894238 - Bma022666.1 Bma06g00055 55
8 668568 669602 - Bma027042.1 Bma08g00047 47
12 45373076 45374918 + Bma008603.1 Bma12g01237 1237
7 15945033 15948057 - Bpe021886.3 Bpe07g01043 1043
13 11427618 11435452 - Bpe006493.1 Bpe13g00367 367
15 16501481 16506441 - Bpe001471.1 Bpe15g00536 536
4 25202744 25211658 + CaPI482276_04g011050.1 Cam04g1105 1105
6 27372713 27374008 - CaPI482276_06g015900.1 Cam06g1590 1590
6 27375969 27380645 + CaPI482276_06g015910.1 Cam06g1591 1591
6 27382251 27387360 - CaPI482276_06g015920.1 Cam06g1592 1592
10 1460610 1469985 - Carg15166-RA Car10g00299 299
11 1498123 1501978 - Carg09117-RA Car11g00272 272
11 1505185 1506994 - Carg09115-RA Car11g00274 274
13 9032041 9042987 + Carg04834-RA Car13g00838 838
18 231843 240211 - Carg22735-RA Car18g00051 51
1 29417113 29426227 + CcPI632755_01g016660.1 Cco01g1666 1666
6 27029622 27030916 - CcPI632755_06g016420.1 Cco06g1642 1642
6 27032917 27037104 + CcPI632755_06g016430.1 Cco06g1643 1643
6 27038744 27043166 - CcPI632755_06g016440.1 Cco06g1644 1644
1 30853062 30863179 + CePI673135_01g016190.1 Cec01g1619 1619
6 30101832 30103167 - CePI673135_06g016500.1 Cec06g1650 1650
6 30105212 30110423 + CePI673135_06g016510.1 Cec06g1651 1651
6 30111139 30115900 - CePI673135_06g016520.1 Cec06g1652 1652
2 27256449 27259265 + Chy2G045940.1 Chy02g02327 2327
12 18213333 18222814 + Chy12G220120.1 Chy12g01412 1412
4 25574266 25583325 + ClG42_04g0113000.10 Clacu04g1130 1130
6 26428750 26430044 - ClG42_06g0155100.10 Clacu06g1551 1551
6 26432049 26436740 + ClG42_06g0155200.10 Clacu06g1552 1552
6 26438364 26442703 - ClG42_06g0155300.10 Clacu06g1553 1553
4 25795571 25808564 + ClCG04G010790.2 Cla04g01062 1062
6 27926213 27927934 - ClCG06G014490.1 Cla06g01435 1435
6 27929686 27935272 + ClCG06G014500.2 Cla06g01436 1436
6 27936273 27949922 - ClCG06G014510.1 Cla06g01437 1437
10 1436992 1440984 + CmaCh10G003160.1 Cma10g00316 316
10 1447108 1456805 - CmaCh10G003190.1 Cma10g00319 319
11 1473820 1476583 + CmaCh11G002970.1 Cma11g00297 297
11 1477703 1481876 - CmaCh11G002980.1 Cma11g00298 298
11 1483599 1484338 + CmaCh11G002990.1 Cma11g00299 299
11 1485826 1487359 - CmaCh11G003000.1 Cma11g00300 300
13 7739614 7751145 + CmaCh13G010030.1 Cma13g01003 1003
18 245718 253891 - CmaCh18G000580.1 Cma18g00058 58
2 24094172 24098425 - MELO3C017340.2.1 Cme02g01702 1702
2 24094306 24095783 + MELO3C017341.2.1 Cme02g01703 1703
12 24787993 24798536 + MELO3C002118.2.1 Cme12g01846 1846
2 22494288 22496783 + PI0011868.1 Cmetu02g0604 604
2 22497116 22498504 - PI0014336.1 Cmetu02g0734 734
12 1432536 1444346 - PI0022318.2 Cmetu12g0241 241
10 1535480 1538244 + CmoCh10G003400.1 Cmo10g00340 340
10 1537400 1543490 - CmoCh10G003410.1 Cmo10g00341 341
11 1456477 1459813 + CmoCh11G003020.1 Cmo11g00302 302
11 1460967 1465189 - CmoCh11G003030.1 Cmo11g00303 303
13 8731867 8742276 + CmoCh13G010390.1 Cmo13g01039 1039
18 282587 291332 - CmoCh18G000450.1 Cmo18g00045 45
4 25755352 25764410 + CmPI595203_04g011140.1 Cmu04g1114 1114
6 26332020 26333314 - CmPI595203_06g015060.1 Cmu06g1506 1506
6 26335316 26340004 + CmPI595203_06g015070.1 Cmu06g1507 1507
6 26341628 26345967 - CmPI595203_06g015080.1 Cmu06g1508 1508
13 2761001 2763155 + Conep13aG0034900.1 Cone13ag0330 330
4 11202920 11205216 + Cp4.1LG04g13840.1 Cpe04g01383 1383
4 11205731 11207383 - Cp4.1LG04g13870.1 Cpe04g01384 1384
4 11207918 11212437 + Cp4.1LG04g13780.1 Cpe04g01385 1385
9 9658470 9667131 + Cp4.1LG09g11260.1 Cpe09g01124 1124
18 7971397 7972842 - Cp4.1LG18g08690.1 Cpe18g00872 872
20 780993 792963 - Cp4.1LG20g01530.1 Cpe20g00140 140
1 27406444 27416410 + CrPI670011_01g014150.1 Cre01g1415 1415
6 31098298 31099593 - CrPI670011_06g023150.1 Cre06g2315 2315
6 31101608 31106393 + CrPI670011_06g023160.1 Cre06g2316 2316
6 31115197 31121928 - CrPI670011_06g023180.1 Cre06g2318 2318
1 2622473 2626066 - CsaV3_1G004190.1 Csa01g00419 419
1 4428900 4440320 - CsaV3_1G007000.1 Csa01g00700 700
9 2076335 2082733 + Hsped.09g02390.1 Hepe09g0239 239
9 3298201 3302033 + Hsped.09g03710.1 Hepe09g0371 371
10 2068512 2079931 - Lag0024318.1 Lac10g0273 273
2 1799171 1814070 - Lsi02G002190.1 Lsi02g00219 219
6 23562948 23564527 - Lsi06G013020.1 Lsi06g01302 1302
6 23571443 23575648 + Lsi06G013030.1 Lsi06g01303 1303
8 2332067 2335053 + Sed0005841.1 Sed08g0385 385
8 39160409 39170070 - Sed0018744.1 Sed08g2749 2749
5 73134898 73145878 + Tan0018792.1 Tan05g2214 2214
9 69804482 69806403 + Tan0012226.1 Tan09g1845 1845
9 69807788 69809295 - Tan0005928.1 Tan09g1846 1846
17 2618186 2673179 + Vvi17g246 Vvi17g246 246
17 2676006 2681814 + Vvi17g247 Vvi17g247 247
17 2681863 2684238 + Vvi17g248 Vvi17g248 248
17 2684890 2685735 + Vvi17g249 Vvi17g249 249
17 2692100 2698566 - Vvi17g250 Vvi17g250 250
17 2700965 2703196 + Vvi17g251 Vvi17g251 251
17 2703714 2704981 - Vvi17g252 Vvi17g252 252
17 2707208 2720616 - Vvi17g253 Vvi17g253 253
17 2724697 2742734 + Vvi17g254 Vvi17g254 254
17 2743721 2767609 - Vvi17g255 Vvi17g255 255
       

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