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
Vvi19g484 . . . . Bpe09g00181 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo10g00822 . Bda12g00902 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g485 . . . Bda09g00393 . . . . . . . . . . . . . . . . . . . . Cla10g00515 Cam10g0510 Cec10g0527 Cco10g0514 Clacu10g0531 Cmu10g1357 Cre10g0761 . . Cone14ag1137 Cone15ag1155 . . . Cme06g02263 . . . . Bpe11g00537 . Bma07g01304 . Sed13g1172 . . . . . . . . Bhi11g00631 Tan01g1694 Cmetu06g0852 . . Mch10g1257 . . . . . . . . . . Chy06g01807 .
Vvi19g486 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g487 . Blo03g01446 . Bda09g00394 . . . . . . . Cma09g00943 . Car09g00857 . . . . . . . . . . . . . . . . . . . Cone14ag1138 Cone15ag1156 Lsi04g01215 . . . . . . . . . . . . . Cmo09g00941 . . . . . . . . . . . . . Cla05g01499 Cam05g1617 . Cco05g1645 Clacu05g1601 Cmu05g1498 . . . . .
Vvi19g488 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g489 . . . . . Bpe08g01130 . . . Cmo04g01021 . . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g00523 . Cme06g02261 . . . . . . . . . . . Cma04g00951 . Car04g00889 . . . . . . . . . . . . . . . . . Lsi05g00608 . . .
Vvi19g490 Blo03g00568 . Bda07g00353 . . Bpe08g01129 . . . . Cma01g01136 Cma09g00944 . Car09g00858 . Cpe06g00760 Cpe02g00765 . . . . . . . . . . . . . . . . . . Lsi04g01212 . . . . . . . Bpe11g00540 . . Bma14g00344 . Cmo01g01187 Cmo09g00942 . . . Car16g00547 . . . . . . . . . Cla05g01498 Cam05g1616 . Cco05g1644 Clacu05g1600 Cmu05g1497 . . . . .
Vvi19g491 . Blo03g01447 Bda07g00354 Bda09g00395 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi04g01210 . . . . . . . . . Bma07g01303 . . . . . . . . Cpe14g00747 . . . . . . . . Cla05g01497 Cam05g1614 . Cco05g1643 Clacu05g1597 Cmu05g1496 . . . . .
Vvi19g492 . . Bda07g00355 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe11g00542 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g493 Blo03g00567 . Bda07g00356 . . Bpe08g01128 . . . . . . . . . . . Bhi09g01888 . . . . . . . . . . . . . . . . . Lsi04g01209 . . . . . . . . . Bma07g01302 . . . . . . . . . . . . . . . . . Cla05g01495 Cam05g1612 . Cco05g1641 Clacu05g1593 Cmu05g1495 . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 4547071 4551237 + Bda033836 Bda07g00353 353
7 4555899 4556979 - Bda025439.1 Bda07g00354 354
7 4561025 4562763 - Bda025440.1 Bda07g00355 355
7 4572606 4574358 - Bda025441.1 Bda07g00356 356
9 4981407 4983562 + Bda030974.1 Bda09g00393 393
9 4984129 4987846 + Bda030975.1 Bda09g00394 394
9 5008364 5009396 - Bda030976.1 Bda09g00395 395
12 39758743 39763648 + Bda009437.1 Bda12g00902 902
9 52309898 52313294 - XM_039043202.1 Bhi09g01888 1888
11 14657189 14661101 - XM_039049973.1 Bhi11g00631 631
3 22270962 22272967 + BLOR11748 Blo03g00567 567
3 22290938 22301487 - BLOR11749 Blo03g00568 568
3 41034254 41038268 + BLOR12627 Blo03g01446 1446
3 41065637 41067337 - BLOR12628 Blo03g01447 1447
10 26056897 26061210 + BLOR02612 Blo10g00822 822
7 48606310 48607981 + Bma026577.1 Bma07g01302 1302
7 48608795 48610513 + Bma026578.1 Bma07g01303 1303
7 48613786 48615933 - Bma026579.1 Bma07g01304 1304
14 4265308 4269490 - Bma010765.1 Bma14g00344 344
8 13204816 13206537 + Bpe023254.1 Bpe08g01128 1128
8 13209461 13212176 - Bpe023255.1 Bpe08g01129 1129
8 13213753 13215906 - Bpe023256.2 Bpe08g01130 1130
9 1258728 1263069 - Bpe023851.1 Bpe09g00181 181
11 4137886 4139184 + Bpe003904.1 Bpe11g00537 537
11 4152557 4156732 + Bpe003907.1 Bpe11g00540 540
11 4164955 4166698 - Bpe003909.1 Bpe11g00542 542
5 22851671 22855969 + CaPI482276_05g016120.1 Cam05g1612 1612
5 22900513 22904612 + CaPI482276_05g016140.1 Cam05g1614 1614
5 22933559 22947370 - CaPI482276_05g016160.1 Cam05g1616 1616
5 22950842 22957448 - CaPI482276_05g016170.1 Cam05g1617 1617
10 7556608 7560229 - CaPI482276_10g005100.1 Cam10g0510 510
4 5104473 5108475 - Carg00064-RA Car04g00889 889
9 5246227 5250248 + Carg12811-RA Car09g00857 857
9 5252567 5253698 + Carg12812-RA Car09g00858 858
16 3462979 3467123 - Carg05632-RA Car16g00547 547
5 22533115 22537494 + CcPI632755_05g016410.1 Cco05g1641 1641
5 22601435 22605459 + CcPI632755_05g016430.1 Cco05g1643 1643
5 22642406 22647998 - CcPI632755_05g016440.1 Cco05g1644 1644
5 22649748 22658118 - CcPI632755_05g016450.1 Cco05g1645 1645
10 6139382 6143000 - CcPI632755_10g005140.1 Cco10g0514 514
10 6326014 6329621 - CePI673135_10g005270.1 Cec10g0527 527
6 21742277 21755744 + Chy6G123350.1 Chy06g01807 1807
5 22862166 22866469 + ClG42_05g0159300.10 Clacu05g1593 1593
5 22914668 22918763 + ClG42_05g0159700.10 Clacu05g1597 1597
5 22940248 22943058 - ClG42_05g0160000.10 Clacu05g1600 1600
5 22946157 22953139 - ClG42_05g0160100.10 Clacu05g1601 1601
10 6393226 6396844 - ClG42_10g0053100.10 Clacu10g0531 531
5 24133776 24138231 + ClCG05G014370.1 Cla05g01495 1495
5 24186335 24190429 + ClCG05G014390.1 Cla05g01497 1497
5 24204281 24228264 - ClCG05G014400.2 Cla05g01498 1498
5 24214842 24215192 - ClCG05G014405.1 Cla05g01499 1499
10 6796419 6802153 - ClCG10G005500.2 Cla10g00515 515
1 8319670 8323768 - CmaCh01G011360.1 Cma01g01136 1136
4 4878131 4881846 - CmaCh04G009510.1 Cma04g00951 951
9 4743218 4748799 + CmaCh09G009430.1 Cma09g00943 943
9 4749711 4754087 + CmaCh09G009440.1 Cma09g00944 944
6 29619997 29622321 - MELO3C031910.2.1 Cme06g02261 2261
6 29631264 29633194 - MELO3C032233.2.1 Cme06g02263 2263
6 26074649 26081774 + PI0021283.1 Cmetu06g0852 852
1 9641769 9645608 - CmoCh01G011870.1 Cmo01g01187 1187
4 5116317 5120964 - CmoCh04G010210.1 Cmo04g01021 1021
9 4948804 4955009 + CmoCh09G009410.1 Cmo09g00941 941
9 4955472 4956262 + CmoCh09G009420.1 Cmo09g00942 942
5 22573908 22578210 + CmPI595203_05g014950.1 Cmu05g1495 1495
5 22626249 22630342 + CmPI595203_05g014960.1 Cmu05g1496 1496
5 22649174 22654684 - CmPI595203_05g014970.1 Cmu05g1497 1497
5 22657753 22664779 - CmPI595203_05g014980.1 Cmu05g1498 1498
10 6515000 6518616 - CmPI595203_10g013570.1 Cmu10g1357 1357
14 9436152 9439480 + Conep14aG0116100.1 Cone14ag1137 1137
14 9440537 9444032 + Conep14aG0116200.1 Cone14ag1138 1138
15 9351299 9353099 + Conep15aG0118400.1 Cone15ag1155 1155
15 9355034 9358547 + Conep15aG0118500.1 Cone15ag1156 1156
2 4882718 4886887 + Cp4.1LG02g01150.1 Cpe02g00765 765
6 4799685 4810681 + Cp4.1LG06g09140.1 Cpe06g00760 760
14 5695628 5700578 + Cp4.1LG14g07460.1 Cpe14g00747 747
10 7408469 7412088 - CrPI670011_10g007610.1 Cre10g0761 761
3 4353501 4362977 - CsaV3_3G005220.1 Csa03g00523 523
4 18629166 18633813 + Lsi04G012090.1 Lsi04g01209 1209
4 18669643 18676529 + Lsi04G012100.1 Lsi04g01210 1210
4 18681480 18689152 - Lsi04G012120.1 Lsi04g01212 1212
4 18709791 18714999 - Lsi04G012150.1 Lsi04g01215 1215
5 7523449 7527881 - Lsi05G006080.1 Lsi05g00608 608
10 10196879 10204226 + MC10g1039 Mch10g1257 1257
13 15486751 15511282 + Sed0015085.1 Sed13g1172 1172
1 18034648 18038616 + Tan0016319.1 Tan01g1694 1694
19 6246784 6252551 + Vvi19g484 Vvi19g484 484
19 6254700 6263751 + Vvi19g485 Vvi19g485 485
19 6267286 6270231 + Vvi19g486 Vvi19g486 486
19 6270716 6280019 + Vvi19g487 Vvi19g487 487
19 6281780 6288420 + Vvi19g488 Vvi19g488 488
19 6288424 6294095 + Vvi19g489 Vvi19g489 489
19 6299238 6306655 + Vvi19g490 Vvi19g490 490
19 6307463 6321572 - Vvi19g491 Vvi19g491 491
19 6322179 6323029 - Vvi19g492 Vvi19g492 492
19 6323257 6327058 - Vvi19g493 Vvi19g493 493
       

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