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
Vvi2g622 . Blo03g00108 . . . Bpe07g00230 . . Cmo06g00860 . . . . . Sed07g1320 . . Bhi11g00108 Tan01g2131 Cmetu06g0814 . . . . . . . . . . . . . . . Lsi07g01233 . . Cme06g02502 . . . . . . . Bma12g00230 . . . Cma06g00838 . . . . . . . . . . . . . . . . . . . . Csa03g00207 . .
Vvi2g623 . . . . . . . . . . . . . . . . . Bhi11g00109 Tan01g2132 . . Hepe06g1060 . . . . . . . . . . Cone12ag0439 . . Lsi07g01232 . . Cme06g02501 . . . . . . . Bma12g00258 . . . . . . . . . . . . . . . . . . . . . . . . Csa03g00206 . .
Vvi2g624 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g625 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g626 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo19g00382 . . . . . . Bhi05g00519 . . . . . . . . . . . . . . . . .
Vvi2g627 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g628 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g629 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g630 . Blo03g00121 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0450 Cone12ag0440 . . . . Chy04g00051 . . . . . . . . . . . . . . . . . . . . . . . . . Cla09g01175 Cam09g1240 Cec09g1256 Cco09g1286 . . Cre09g1204 . Csa03g04649 . Cme04g00065
Vvi2g631 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 12298785 12304513 + XM_039033078.1 Bhi05g00519 519
11 2608259 2611448 - XM_039047429.1 Bhi11g00108 108
11 2616801 2617923 - XM_039047633.1 Bhi11g00109 109
3 3376781 3377842 - BLOR11289 Blo03g00108 108
3 3619187 3620886 - BLOR11302 Blo03g00121 121
12 3019879 3021253 + Bma007120.1 Bma12g00230 230
12 3347258 3349776 - Bma007152.1 Bma12g00258 258
7 1634038 1635348 + Bpe021041.1 Bpe07g00230 230
9 14202977 14206199 - CaPI482276_09g012400.1 Cam09g1240 1240
9 14098488 14101754 - CcPI632755_09g012860.1 Cco09g1286 1286
9 14230134 14233538 - CePI673135_09g012560.1 Cec09g1256 1256
4 565264 567389 + Chy4G067690.1 Chy04g00051 51
9 14172897 14176393 - ClCG09G012380.1 Cla09g01175 1175
6 4606804 4610632 - CmaCh06G008380.1 Cma06g00838 838
4 498019 500390 + MELO3C003371.2.1 Cme04g00065 65
6 32001139 32004294 + MELO3C013877.2.1 Cme06g02501 2501
6 32006531 32009870 + MELO3C013878.2.1 Cme06g02502 2502
6 29364182 29366986 - PI0009512.1 Cmetu06g0814 814
6 4868730 4871914 - CmoCh06G008600.1 Cmo06g00860 860
19 3778375 3783947 + CmoCh19G003820.1 Cmo19g00382 382
8 2867253 2868970 + Conep08aG0046800.1 Cone8ag0450 450
12 2615219 2617770 - Conep12aG0045400.1 Cone12ag0439 439
12 2627841 2629375 + Conep12aG0045500.1 Cone12ag0440 440
9 14270888 14274244 - CrPI670011_09g012040.1 Cre09g1204 1204
3 1623204 1627365 + CsaV3_3G002060.1 Csa03g00206 206
3 1629567 1633054 + CsaV3_3G002070.1 Csa03g00207 207
3 40386206 40389290 - CsaV3_3G049550.1 Csa03g04649 4649
6 58855464 58858285 + Hsped.06g10600.1 Hepe06g1060 1060
7 17981484 17984937 + Lsi07G012320.1 Lsi07g01232 1232
7 17988362 17991674 + Lsi07G012330.1 Lsi07g01233 1233
7 10063254 10066936 - Sed0018988.1 Sed07g1320 1320
1 24628048 24631346 - Tan0018794.1 Tan01g2131 2131
1 24628048 24631346 - Tan0018794.2 Tan01g2132 2132
2 6657870 6661876 - Vvi2g622 Vvi2g622 622
2 6666038 6670079 - Vvi2g623 Vvi2g623 623
2 6675173 6677663 + Vvi2g624 Vvi2g624 624
2 6679455 6679611 - Vvi2g625 Vvi2g625 625
2 6680634 6681662 - Vvi2g626 Vvi2g626 626
2 6683685 6683850 - Vvi2g627 Vvi2g627 627
2 6687938 6688022 - Vvi2g628 Vvi2g628 628
2 6688050 6695865 - Vvi2g629 Vvi2g629 629
2 6705374 6707155 + Vvi2g630 Vvi2g630 630
2 6707242 6711024 - Vvi2g631 Vvi2g631 631
       

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