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
Vvi5g309 . . . Bda08g00287 . . . Bma05g01038 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa06g01532 . . . Blo07g00176 Bda11g00530 . Bpe05g00840 Bpe13g00660 . Bma06g01505 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g310 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g311 . Blo12g00019 Bda03g01199 . Bpe04g01130 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa06g01530 . . . . . . Bpe05g00841 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g312 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa06g01529 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g313 . . . . . . . . . Cmo17g00306 . . . . . . . . . . . . . . . . . . . . . . . . . . Csa06g01528 . . . Blo07g00177 Bda11g00531 . . Bpe13g00659 . Bma06g01506 Sed09g0236 . . Cma08g01221 Cma17g00318 . . Cpe12g00270 . Bhi12g02075 Tan06g2655 Cmetu11g1087 . . . Lcy13g0182 . . . . . . . Lsi09g01419 . . Cme11g01997
Vvi5g314 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g315 . . Bda03g01200 . Bpe04g01131 . Bma04g01108 . . . Cma06g01493 . Car06g01284 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo06g01489 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g316 . . . . . . . . Cmo08g01196 . . . . . . Cpe08g00191 . . . . . . . . . . . . . . . Cone1ag0636 . . . Lsi05g01534 Csa06g01524 Chy11g01501 Cme06g00726 . . . Bda13g00183 . . . . . . . . . Car08g01097 Car17g00293 . . . . . . . . . Cla05g00643 Cam05g0703 Cec05g0716 Cco05g0713 Clacu05g0698 Cmu05g0665 Cre05g0738 . Csa03g01457 Chy06g00696 .
Vvi5g317 . . . . Bpe04g01132 . Bma04g01107 . . . . . . . . . . . . . . . . . Cla06g00482 Cam06g0518 Cec06g0519 Cco06g0522 Clacu06g0503 Cmu06g0505 Cre06g1275 . Cone15ag0775 . . . Csa06g01523 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g318 . . . . . . . . . . . . . . . . Cpe03g01367 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 14577694 14580316 + Bda017282.1 Bda03g01199 1199
3 14585680 14586243 + Bda017283.1 Bda03g01200 1200
8 2981416 2986846 + Bda024720.1 Bda08g00287 287
11 5569311 5584610 - Bda005265.1 Bda11g00530 530
11 5586906 5591380 + Bda005266.1 Bda11g00531 531
13 2361155 2361502 + Bda001051.1 Bda13g00183 183
12 64450508 64456176 + XM_039020046.1 Bhi12g02075 2075
7 2218146 2224625 - BLOR18108 Blo07g00176 176
7 2226888 2230117 + BLOR18109 Blo07g00177 177
12 1219568 1222191 + BLOR04038 Blo12g00019 19
4 25952180 25953224 + Bma019805.1 Bma04g01107 1107
4 25953660 25954223 - Bma019806.1 Bma04g01108 1108
5 48944562 48961341 - Bma022196.1 Bma05g01038 1038
6 51512871 51517641 - Bma024618.1 Bma06g01505 1505
6 51519384 51523555 + Bma024619.1 Bma06g01506 1506
4 9920394 9923029 + Bpe015811.1 Bpe04g01130 1130
4 9937117 9937680 + Bpe015812.1 Bpe04g01131 1131
4 9938048 9939157 - Bpe015813.1 Bpe04g01132 1132
5 21629555 21634985 - Bpe018253.1 Bpe05g00840 840
5 21637898 21640315 - Bpe018254.1 Bpe05g00841 841
13 13400047 13404640 - Bpe010360.1 Bpe13g00659 659
13 13406773 13411554 + Bpe010361.1 Bpe13g00660 660
5 6186026 6186364 + CaPI482276_05g007030.1 Cam05g0703 703
6 7276562 7279111 + CaPI482276_06g005180.1 Cam06g0518 518
6 9218723 9219286 + Carg17349-RA Car06g01284 1284
8 7468151 7468486 + Carg18838-RA Car08g01097 1097
17 1830115 1830450 + Carg05499-RA Car17g00293 293
5 5894495 5894833 + CcPI632755_05g007130.1 Cco05g0713 713
6 5700645 5703197 + CcPI632755_06g005220.1 Cco06g0522 522
5 5917890 5918228 + CePI673135_05g007160.1 Cec05g0716 716
6 5809450 5812001 + CePI673135_06g005190.1 Cec06g0519 519
6 4748286 4758518 + Chy6G112240.1 Chy06g00696 696
11 21697512 21709961 + Chy11G200810.1 Chy11g01501 1501
5 5916523 5916861 + ClG42_05g0069800.10 Clacu05g0698 698
6 5816347 5818897 + ClG42_06g0050300.10 Clacu06g0503 503
5 6010462 6010800 + ClCG05G006038.1 Cla05g00643 643
6 5870098 5872936 + ClCG06G005160.1 Cla06g00482 482
6 9492811 9493374 + CmaCh06G014930.1 Cma06g01493 1493
8 7489975 7496694 - CmaCh08G012210.1 Cma08g01221 1221
17 1717324 1722127 - CmaCh17G003180.1 Cma17g00318 318
6 4800504 4800854 + MELO3C006658.2.1 Cme06g00726 726
11 27912945 27918796 - MELO3C021342.2.1 Cme11g01997 1997
11 4279743 4284927 + PI0004854.1 Cmetu11g1087 1087
6 10707598 10708161 + CmoCh06G014890.1 Cmo06g01489 1489
8 7607009 7607344 + CmoCh08G011960.1 Cmo08g01196 1196
17 1859215 1864259 - CmoCh17G003060.1 Cmo17g00306 306
5 5759776 5760114 + CmPI595203_05g006650.1 Cmu05g0665 665
6 5617961 5620511 + CmPI595203_06g005050.1 Cmu06g0505 505
1 6132146 6132538 + Conep01aG0066400.1 Cone1ag0636 636
15 4653745 4657005 + Conep15aG0079000.1 Cone15ag0775 775
3 11032785 11035007 - Cp4.1LG03g11360.1 Cpe03g01367 1367
8 1286826 1287149 + Cp4.1LG08g04810.1 Cpe08g00191 191
12 1801525 1806704 - Cp4.1LG12g02810.1 Cpe12g00270 270
5 6569946 6570284 + CrPI670011_05g007380.1 Cre05g0738 738
6 6678058 6680609 + CrPI670011_06g012750.1 Cre06g1275 1275
3 10873068 10873873 + CsaV3_3G014570.1 Csa03g01457 1457
6 12775457 12778307 + CsaV3_6G017210.1 Csa06g01523 1523
6 12782588 12784518 - CsaV3_6G017220.1 Csa06g01524 1524
6 12805917 12811772 + CsaV3_6G017260.1 Csa06g01528 1528
6 12809960 12815229 - CsaV3_6G017270.1 Csa06g01529 1529
6 12817061 12822042 - CsaV3_6G017280.1 Csa06g01530 1530
6 12830137 12836573 + CsaV3_6G017300.1 Csa06g01532 1532
13 1878330 1884554 + Maker00023429 Lcy13g0182 182
5 23134084 23134419 + Lsi05G015340.1 Lsi05g01534 1534
9 22203709 22210306 - Lsi09G014190.1 Lsi09g01419 1419
9 1850524 1857220 - Sed0019081.1 Sed09g0236 236
6 79057975 79064052 - Tan0001378.1 Tan06g2655 2655
5 3051409 3053761 - Vvi5g309 Vvi5g309 309
5 3059659 3060076 - Vvi5g310 Vvi5g310 310
5 3068209 3074183 + Vvi5g311 Vvi5g311 311
5 3075714 3086112 + Vvi5g312 Vvi5g312 312
5 3086198 3099862 - Vvi5g313 Vvi5g313 313
5 3108716 3109277 + Vvi5g314 Vvi5g314 314
5 3124104 3131662 + Vvi5g315 Vvi5g315 315
5 3139278 3139844 + Vvi5g316 Vvi5g316 316
5 3146998 3150745 - Vvi5g317 Vvi5g317 317
5 3151743 3155599 + Vvi5g318 Vvi5g318 318
       

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