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
Vvi3g486 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa07g00794 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g487 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme01g00019 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi11g01037 . Chy01g00024 .
Vvi3g488 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g489 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi11g01038 . . .
Vvi3g490 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g491 . . . . . . . . . Cmo11g01336 Cma02g00433 . Car02g00288 . . . . . . . . . . . Cla02g00571 Cam02g0601 Cec02g0601 Cco02g0612 Clacu02g0597 Cmu02g0595 Cre02g0924 . . . . . . . Cme01g00018 . . . . . . . . Sed01g0330 Cmo02g00435 . . . Car11g01077 . . . Bhi10g02066 Tan05g1380 Cmetu11g1580 . Hepe08g1056 . . . . . . . . . Lsi11g01039 . Chy01g00023 Cme11g00501
Vvi3g492 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g493 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g494 . . . . . . . . . Cmo11g01335 . . . . . Cpe04g00259 . . . . . . . . Cla02g00570 Cam02g0600 Cec02g0600 Cco02g0611 Clacu02g0596 Cmu02g0594 . . . . . . . . Cme01g00017 . . . . Bpe15g00885 . . . . . . . . Car11g01076 . . . . . . . . . . . . . . . . . Lsi11g01040 . Chy01g00022 .
Vvi3g495 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
10 51745909 51749789 + XM_039044362.1 Bhi10g02066 2066
15 18788290 18789450 + Bpe001806.1 Bpe15g00885 885
2 6833200 6835459 + CaPI482276_02g006000.1 Cam02g0600 600
2 6844952 6847710 + CaPI482276_02g006010.1 Cam02g0601 601
2 1943807 1946156 + Carg22973-RA Car02g00288 288
11 8361026 8362997 + Carg26378-RA Car11g01076 1076
11 8365211 8367181 + Carg26377-RA Car11g01077 1077
2 5998751 6000972 + CcPI632755_02g006110.1 Cco02g0611 611
2 6010598 6013493 + CcPI632755_02g006120.1 Cco02g0612 612
2 5892992 5895214 + CePI673135_02g006000.1 Cec02g0600 600
2 5910829 5915450 + CePI673135_02g006010.1 Cec02g0601 601
1 170353 172113 + Chy1G000220.1 Chy01g00022 22
1 173683 175467 + Chy1G000230.1 Chy01g00023 23
1 176073 178894 + Chy1G000240.1 Chy01g00024 24
2 5816122 5818315 + ClG42_02g0059600.10 Clacu02g0596 596
2 5827537 5830384 + ClG42_02g0059700.10 Clacu02g0597 597
2 6086806 6089325 + ClCG02G005590.1 Cla02g00570 570
2 6098481 6106184 + ClCG02G005600.2 Cla02g00571 571
2 2189995 2191913 + CmaCh02G004330.1 Cma02g00433 433
1 167745 169946 + MELO3C018422.2.1 Cme01g00017 17
1 170997 172887 + MELO3C018423.2.1 Cme01g00018 18
1 173497 176531 + MELO3C018424.2.1 Cme01g00019 19
11 4988488 4993039 + MELO3C021922.2.1 Cme11g00501 501
11 26877282 26881594 - PI0018558.1 Cmetu11g1580 1580
2 2270477 2270953 + CmoCh02G004350.1 Cmo02g00435 435
11 9249777 9252004 + CmoCh11G013350.1 Cmo11g01335 1335
11 9253986 9256273 + CmoCh11G013360.1 Cmo11g01336 1336
2 5722883 5725076 + CmPI595203_02g005940.1 Cmu02g0594 594
2 5734299 5737148 + CmPI595203_02g005950.1 Cmu02g0595 595
4 3204128 3206475 + Cp4.1LG04g08250.1 Cpe04g00259 259
2 6336447 6339359 + CrPI670011_02g009240.1 Cre02g0924 924
7 5554043 5556293 - CsaV3_7G008930.1 Csa07g00794 794
8 10191142 10194541 + Hsped.08g10560.1 Hepe08g1056 1056
11 17860552 17861001 - Lsi11G010370.1 Lsi11g01037 1037
11 17861645 17866700 - Lsi11G010380.1 Lsi11g01038 1038
11 17873764 17876866 - Lsi11G010390.1 Lsi11g01039 1039
11 17886117 17911596 - Lsi11G010400.1 Lsi11g01040 1040
1 2469459 2472000 + Sed0009266.1 Sed01g0330 330
5 18933012 18938722 + Tan0001706.1 Tan05g1380 1380
3 4723790 4725151 - Vvi3g486 Vvi3g486 486
3 4733146 4734032 - Vvi3g487 Vvi3g487 487
3 4741184 4748123 + Vvi3g488 Vvi3g488 488
3 4754777 4756269 - Vvi3g489 Vvi3g489 489
3 4762345 4762540 + Vvi3g490 Vvi3g490 490
3 4768404 4769397 - Vvi3g491 Vvi3g491 491
3 4770450 4771940 - Vvi3g492 Vvi3g492 492
3 4776569 4781661 - Vvi3g493 Vvi3g493 493
3 4782180 4783671 - Vvi3g494 Vvi3g494 494
3 4798767 4800935 - Vvi3g495 Vvi3g495 495
       

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