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
Vvi18g350 . . . . . . . . . . . . . . . . . Bhi04g02503 . . . Hepe02g3442 . Lcy10g2333 . . . . . . . Cone4ag1361 Cone7ag1571 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla11g00767 Cam11g0801 Cec11g0783 Cco11g0789 Clacu11g1057 Cmu11g0917 Cre11g1247 . . . .
Vvi18g351 . . . . . . . . . . . . . . . . . Bhi04g02501 . . . Hepe02g3441 . Lcy10g2332 . . . . . . . . . Cone17ag1248 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla11g00766 . . . . . . . . Chy03g00065 .
Vvi18g352 . . . . . . . . . . . . . . Sed11g1510 . . Bhi04g02500 Tan11g0084 Cmetu09g1872 . Hepe02g3440 . Lcy10g2331 . . . . . . . . Cone7ag1572 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla11g00765 Cam11g0798 Cec11g0780 Cco11g0785 Clacu11g1059 Cmu11g0919 Cre11g1244 . . Chy03g00066 .
Vvi18g353 . . . . . . . . . . . . . . Sed11g2298 . . Bhi04g02498 Tan11g0086 Cmetu03g1942 . Hepe02g3439 . Lcy10g2330 . . . . . . . . . Cone17ag1247 . . . . Cme03g01869 . . . . . . . . . . . . . . . . . . . . . . . . Cla11g00763 . . . Clacu11g1060 Cmu11g0920 . . . Chy03g00067 .
Vvi18g354 . . . . . . . . . . . . . . Sed11g2297 . . Bhi04g02497 Tan11g0087 Cmetu03g1388 . Hepe02g3438 . Lcy10g2329 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla11g00761 Cam11g0795 Cec11g0776 Cco11g0782 Clacu11g1063 Cmu11g0922 Cre11g1239 . . Chy03g00068 .
Vvi18g355 . . . . . . . . Cmo04g02413 . . . . . . . . . . . . . . . . . . . . . . Cone4ag1360 Cone7ag1573 . . . . . . . . . . . . . . . . . . . Car04g02229 . Cpe01g02004 . . . . . . . . . . . . . . . . . . .
Vvi18g356 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g357 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1359 Cone7ag1574 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g358 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo18g00206 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g359 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1357 Cone7ag1576 . . . . . . Blo17g00207 . . Bda13g01510 . Bpe14g00354 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
13 38158561 38159684 + Bda000358.2 Bda13g01510 1510
4 67538096 67547409 - XM_039028472.1 Bhi04g02497 2497
4 67575253 67579275 + XM_039030495.1 Bhi04g02498 2498
4 67581168 67587764 - XM_039029744.1 Bhi04g02500 2500
4 67590574 67592933 - XM_039028436.1 Bhi04g02501 2501
4 67698053 67702094 + XM_039028133.1 Bhi04g02503 2503
17 2071542 2077071 + BLOR16028 Blo17g00207 207
18 2024436 2025857 + BLOR08694 Blo18g00206 206
14 3402902 3404177 - Bpe007011.1 Bpe14g00354 354
11 10032755 10039239 - CaPI482276_11g007950.1 Cam11g0795 795
11 10113622 10118480 - CaPI482276_11g007980.1 Cam11g0798 798
11 10175193 10178904 + CaPI482276_11g008010.1 Cam11g0801 801
4 18078153 18085717 + Carg18254-RA Car04g02229 2229
11 8929733 8937015 - CcPI632755_11g007820.1 Cco11g0782 782
11 8981864 8986716 - CcPI632755_11g007850.1 Cco11g0785 785
11 9001477 9005214 + CcPI632755_11g007890.1 Cco11g0789 789
11 9078917 9085781 - CePI673135_11g007760.1 Cec11g0776 776
11 9164652 9169509 - CePI673135_11g007800.1 Cec11g0780 780
11 9219629 9223391 + CePI673135_11g007830.1 Cec11g0783 783
3 662632 664491 + Chy3G050450.1 Chy03g00065 65
3 667300 671510 + Chy3G050460.1 Chy03g00066 66
3 674671 675825 - Chy3G050470.1 Chy03g00067 67
3 690781 714274 + Chy3G050480.1 Chy03g00068 68
11 13122486 13126264 - ClG42_11g0105700.10 Clacu11g1057 1057
11 13155701 13160553 + ClG42_11g0105900.10 Clacu11g1059 1059
11 13162371 13165545 - ClG42_11g0106000.10 Clacu11g1060 1060
11 13237308 13243698 + ClG42_11g0106300.10 Clacu11g1063 1063
11 10920689 10927337 - ClCG11G007960.2 Cla11g00761 761
11 11001577 11006476 + ClCG11G007980.2 Cla11g00763 763
11 11009733 11014585 - ClCG11G008000.2 Cla11g00765 765
11 11018251 11020122 - ClCG11G008010.1 Cla11g00766 766
11 11044432 11048536 + ClCG11G008020.2 Cla11g00767 767
3 26921041 26925752 + MELO3C011022.2.1 Cme03g01869 1869
3 25831695 25840309 - PI0011455.1 Cmetu03g1388 1388
3 25853034 25855915 + PI0020822.2 Cmetu03g1942 1942
9 6398583 6406098 - PI0013709.1 Cmetu09g1872 1872
4 17951968 17959889 + CmoCh04G024130.1 Cmo04g02413 2413
11 12451618 12455395 - CmPI595203_11g009170.1 Cmu11g0917 917
11 12484828 12489680 + CmPI595203_11g009190.1 Cmu11g0919 919
11 12491502 12494677 - CmPI595203_11g009200.1 Cmu11g0920 920
11 12566564 12572953 + CmPI595203_11g009220.1 Cmu11g0922 922
4 11055676 11056425 + Conep04aG0140500.1 Cone4ag1357 1357
4 11062167 11063958 + Conep04aG0140700.1 Cone4ag1359 1359
4 11064088 11067029 - Conep04aG0140800.1 Cone4ag1360 1360
4 11074928 11077590 + Conep04aG0140900.1 Cone4ag1361 1361
7 10767935 10770268 - Conep07aG0161800.1 Cone7ag1571 1571
7 10770613 10774729 + Conep07aG0161900.1 Cone7ag1572 1572
7 10776979 10785219 + Conep07aG0162000.1 Cone7ag1573 1573
7 10785457 10787097 - Conep07aG0162100.1 Cone7ag1574 1574
7 10796340 10798294 - Conep07aG0162300.1 Cone7ag1576 1576
17 8985951 8990242 - Conep17aG0127800.1 Cone17ag1247 1247
17 8986190 8988082 + Conep17aG0127900.1 Cone17ag1248 1248
1 17096280 17106462 + Cp4.1LG01g19940.1 Cpe01g02004 2004
11 10696574 10703500 - CrPI670011_11g012390.1 Cre11g1239 1239
11 10780782 10785643 - CrPI670011_11g012440.1 Cre11g1244 1244
11 10838716 10842475 + CrPI670011_11g012470.1 Cre11g1247 1247
2 83751071 83758459 - Hsped.02g34380.1 Hepe02g3438 3438
2 83766264 83770733 + Hsped.02g34390.1 Hepe02g3439 3439
2 83771440 83776893 - Hsped.02g34400.1 Hepe02g3440 3440
2 83779436 83781729 - Hsped.02g34410.1 Hepe02g3441 3441
2 83782925 83788497 + Hsped.02g34420.1 Hepe02g3442 3442
10 46898668 46904329 - Maker00039581 Lcy10g2329 2329
10 46915465 46917865 + Maker00039647 Lcy10g2330 2330
10 46918639 46924566 - Maker00039143 Lcy10g2331 2331
10 46926389 46928260 - Maker00039540 Lcy10g2332 2332
10 46929371 46933420 + Maker00039483 Lcy10g2333 2333
11 30753912 30762744 - Sed0016314.1 Sed11g1510 1510
11 36057275 36066645 - Sed0017864.1 Sed11g2297 2297
11 36072792 36076096 + Sed0017821.1 Sed11g2298 2298
11 960394 966035 + Tan0011155.1 Tan11g0084 84
11 967047 971419 - Tan0008108.2 Tan11g0086 86
11 986377 994910 + Tan0001256.1 Tan11g0087 87
18 3900384 3905806 - Vvi18g350 Vvi18g350 350
18 3906072 3907917 + Vvi18g351 Vvi18g351 351
18 3911380 3917340 + Vvi18g352 Vvi18g352 352
18 3918202 3923619 - Vvi18g353 Vvi18g353 353
18 3924181 3930364 + Vvi18g354 Vvi18g354 354
18 3937856 3949317 + Vvi18g355 Vvi18g355 355
18 3949803 3956472 + Vvi18g356 Vvi18g356 356
18 3956773 3960560 - Vvi18g357 Vvi18g357 357
18 3963410 3965374 - Vvi18g358 Vvi18g358 358
18 3976068 3979749 - Vvi18g359 Vvi18g359 359
       

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