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
Vvi17g406 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g407 . . . Bda15g00647 Bpe12g00506 . . . . . . . . Car11g00213 . . . . . . . . . . Cla06g01515 Cam06g1670 Cec06g1731 . Clacu06g1636 Cmu06g1584 Cre06g2395 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g408 . . . . . . . . . . . Cma11g00235 . Car11g00212 Sed12g2036 . Cpe04g01437 Bhi02g00045 Tan09g1990 Cmetu02g0800 . Hepe09g0301 . . . . . . . . . . Cone16ag0253 . . . . . . . . . . . . . . . . Cmo11g00238 . . . . . . . . . . . . . . . . . . . . Lsi06g01380 Csa01g00322 Chy02g02419 Cme02g01796
Vvi17g409 . . . . . . . . . . . . . . . . . Bhi02g00046 Tan09g1991 . . . . . . . . . . . . Cone2ag0781 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g410 . . . . . . . . . . Cma10g00273 . . . . . . Bhi02g00048 . . . . . . Cla06g01516 . . . . . . . . Cone13ag0018 . . . . . . . . . . . . . . Cmo10g00292 . . . . . . . . . . . . . . . . . . . . . . . Chy02g02418 Cme02g01797
Vvi17g411 . . Bda06g00503 . . . . . . . Cma10g00274 . Car10g00257 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo10g00293 . . . . . . Cpe18g00724 . . . . . . . . . . . . . . Lsi06g01382 Csa01g00324 Chy02g02417 Cme02g01798
Vvi17g412 . . Bda06g00505 . . . . Bma12g00953 . . . Cma11g00234 . Car11g00211 Sed08g0309 . Cpe04g01438 Bhi02g00049 Tan09g1996 Cmetu02g0986 . Hepe09g0298 . . Cla06g01517 Cam06g1673 Cec06g1734 Cco06g1730 Clacu06g1639 Cmu06g1587 Cre06g2398 Cone11ag0342 . . . . . . . . Blo15g00350 . . Bpe07g00744 . . . . . Cmo11g00237 . . . . . . . . . . . . . . . . . . . . Lsi06g01383 Csa01g00325 Chy02g02416 Cme02g01799
Vvi17g413 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g414 . . . Bda15g00639 Bpe12g00509 . . . . . . . . . . Cpe20g00278 . . . . . . . . . . . . . . . Cone2ag0786 . Cone13ag0020 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g415 . Blo16g00156 . . . Bpe13g00328 Bma06g00016 . Cmo13g01096 . . . . . . Cpe20g00095 . . . . . . . . . . . . . . . Cone2ag0788 . . . Lsi02g00146 Csa01g00629 Chy12g01471 Cme12g01913 . . . . . . . . Sed08g2145 . . Cma13g01053 . Car13g00887 . . . Bhi08g01047 Tan05g2316 Cmetu12g1391 Lac10g0192 Hepe07g2435 . . Cla04g01131 Cam04g1183 Cec01g1696 Cco01g1742 Clacu04g1211 Cmu04g1190 Cre01g1488 . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 7129622 7130133 + Bda023753.1 Bda06g00503 503
6 7149537 7156336 - Bda023756.1 Bda06g00505 505
15 9548913 9550313 + Bda012485.1 Bda15g00639 639
15 9920485 9931627 + Bda012494.1 Bda15g00647 647
2 927719 935774 + XM_039023435.1 Bhi02g00045 45
2 927721 936690 + XM_039023434.1 Bhi02g00046 46
2 1000446 1006806 + XM_039024128.1 Bhi02g00048 48
2 1007310 1012369 - XM_039022685.1 Bhi02g00049 49
8 34424088 34427854 + XM_039039406.1 Bhi08g01047 1047
15 4411882 4413264 + BLOR06744 Blo15g00350 350
16 3558556 3561702 + BLOR07404 Blo16g00156 156
6 432151 434491 + Bma022621.1 Bma06g00016 16
12 41464965 41466083 - Bma008296.1 Bma12g00953 953
7 13965727 13971226 - Bpe021589.1 Bpe07g00744 744
12 10896886 10914718 - Bpe005769.1 Bpe12g00506 506
12 10945902 10947302 - Bpe005772.1 Bpe12g00509 509
13 11121688 11124051 - Bpe006455.1 Bpe13g00328 328
4 25942834 25950092 + CaPI482276_04g011830.1 Cam04g1183 1183
6 28077431 28085635 + CaPI482276_06g016700.1 Cam06g1670 1670
6 28095494 28100353 - CaPI482276_06g016730.1 Cam06g1673 1673
10 1225310 1227709 + Carg17886-RA Car10g00257 257
11 1214930 1220135 + Carg09178-RA Car11g00211 211
11 1221165 1222911 - Carg09177-RA Car11g00212 212
11 1223065 1229080 - Carg09176-RA Car11g00213 213
13 9305432 9308223 + Carg04784-RA Car13g00887 887
1 30183080 30192385 + CcPI632755_01g017420.1 Cco01g1742 1742
6 27789743 27794612 - CcPI632755_06g017300.1 Cco06g1730 1730
1 31620090 31622898 + CePI673135_01g016960.1 Cec01g1696 1696
6 30828185 30836349 + CePI673135_06g017310.1 Cec06g1731 1731
6 30846086 30850955 - CePI673135_06g017340.1 Cec06g1734 1734
2 27885454 27890306 + Chy2G046830.1 Chy02g02416 2416
2 27892291 27894489 - Chy2G046840.1 Chy02g02417 2417
2 27895722 27898676 - Chy2G046850.1 Chy02g02418 2418
2 27900179 27908689 - Chy2G046860.1 Chy02g02419 2419
12 18654870 18657573 + Chy12G220710.1 Chy12g01471 1471
4 26295218 26297989 + ClG42_04g0121100.10 Clacu04g1211 1211
6 27129692 27137881 + ClG42_06g0163600.10 Clacu06g1636 1636
6 27147594 27152377 - ClG42_06g0163900.10 Clacu06g1639 1639
4 26526890 26530219 + ClCG04G011520.1 Cla04g01131 1131
6 28662877 28671264 + ClCG06G015340.1 Cla06g01515 1515
6 28672573 28678722 + ClCG06G015350.2 Cla06g01516 1516
6 28680595 28685665 - ClCG06G015370.1 Cla06g01517 1517
10 1214871 1217813 + CmaCh10G002730.1 Cma10g00273 273
10 1218215 1220732 + CmaCh10G002740.1 Cma10g00274 274
11 1185699 1190859 + CmaCh11G002340.1 Cma11g00234 234
11 1192528 1200933 - CmaCh11G002350.1 Cma11g00235 235
13 8007284 8014298 + CmaCh13G010530.1 Cma13g01053 1053
2 24749587 24757926 + MELO3C017261.2.1 Cme02g01796 1796
2 24759071 24762049 + MELO3C017260.2.1 Cme02g01797 1797
2 24762420 24765191 + MELO3C017259.2.1 Cme02g01798 1798
2 24767987 24773114 - MELO3C017258.2.1 Cme02g01799 1799
12 25201193 25204380 + MELO3C002058.2.1 Cme12g01913 1913
2 23092347 23101191 + PI0015293.1 Cmetu02g0800 800
2 23109029 23114098 - PI0002278.1 Cmetu02g0986 986
12 947900 951112 - PI0020081.1 Cmetu12g1391 1391
10 1297936 1300881 + CmoCh10G002920.1 Cmo10g00292 292
10 1301280 1303765 + CmoCh10G002930.1 Cmo10g00293 293
11 1183223 1188575 + CmoCh11G002370.1 Cmo11g00237 237
11 1189558 1197545 - CmoCh11G002380.1 Cmo11g00238 238
13 9022105 9025997 + CmoCh13G010960.1 Cmo13g01096 1096
4 26476781 26479840 + CmPI595203_04g011900.1 Cmu04g1190 1190
6 27038312 27046502 + CmPI595203_06g015840.1 Cmu06g1584 1584
6 27056214 27060997 - CmPI595203_06g015870.1 Cmu06g1587 1587
2 33800647 33808578 + Conep02aG0180800.1 Cone2ag0781 781
2 33846130 33847854 - Conep02aG0181300.1 Cone2ag0786 786
2 33874814 33877064 + Conep02aG0181500.1 Cone2ag0788 788
11 1676019 1677624 - Conep11aG0035100.1 Cone11ag0342 342
13 114829 118068 + Conep13aG0002000.1 Cone13ag0018 18
13 124501 125979 - Conep13aG0002200.1 Cone13ag0020 20
16 2763429 2765245 - Conep16aG0260200.1 Cone16ag0253 253
4 11483335 11491364 + Cp4.1LG04g14380.1 Cpe04g01437 1437
4 11492770 11497917 - Cp4.1LG04g14440.1 Cpe04g01438 1438
18 7106818 7113679 - Cp4.1LG18g07350.1 Cpe18g00724 724
20 502453 506187 - Cp4.1LG20g01060.1 Cpe20g00095 95
20 1558254 1559889 - Cp4.1LG20g02770.1 Cpe20g00278 278
1 28142080 28144847 + CrPI670011_01g014880.1 Cre01g1488 1488
6 31839619 31847780 + CrPI670011_06g023950.1 Cre06g2395 2395
6 31857409 31862276 - CrPI670011_06g023980.1 Cre06g2398 2398
1 1992123 2002518 + CsaV3_1G003220.1 Csa01g00322 322
1 2007039 2010064 + CsaV3_1G003240.1 Csa01g00324 324
1 2011263 2016703 - CsaV3_1G003250.1 Csa01g00325 325
1 4011421 4014889 - CsaV3_1G006290.1 Csa01g00629 629
7 68724108 68727731 + Hsped.07g24350.1 Hepe07g2435 2435
9 2592837 2598323 + Hsped.09g02980.1 Hepe09g0298 298
9 2609181 2616003 - Hsped.09g03010.1 Hepe09g0301 301
10 1476479 1483772 - Lag0024237.1 Lac10g0192 192
2 1196001 1199685 - Lsi02G001460.1 Lsi02g00146 146
6 24378354 24387817 + Lsi06G013800.1 Lsi06g01380 1380
6 24392156 24395744 + Lsi06G013820.1 Lsi06g01382 1382
6 24400379 24405624 - Lsi06G013830.1 Lsi06g01383 1383
8 1869612 1875868 + Sed0011544.1 Sed08g0309 309
8 35372671 35377299 - Sed0027849.2 Sed08g2145 2145
12 31212861 31220664 - Sed0016449.1 Sed12g2036 2036
5 74693411 74696983 + Tan0008677.2 Tan05g2316 2316
9 70644093 70652880 + Tan0018155.1 Tan09g1990 1990
9 70644093 70652880 + Tan0018155.2 Tan09g1991 1991
9 70675490 70680636 - Tan0018461.1 Tan09g1996 1996
17 4931760 4931943 - Vvi17g406 Vvi17g406 406
17 4959315 4963930 + Vvi17g407 Vvi17g407 407
17 4964451 4975759 + Vvi17g408 Vvi17g408 408
17 5013389 5014780 + Vvi17g409 Vvi17g409 409
17 5104508 5107475 + Vvi17g410 Vvi17g410 410
17 5107490 5115700 + Vvi17g411 Vvi17g411 411
17 5125969 5136309 - Vvi17g412 Vvi17g412 412
17 5144244 5149804 + Vvi17g413 Vvi17g413 413
17 5149855 5151301 - Vvi17g414 Vvi17g414 414
17 5154402 5159799 + Vvi17g415 Vvi17g415 415
       

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