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
Vvi1g1231 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1232 . . . . . . Bma14g01987 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1233 . . . . . . . . . Cmo18g00690 . Cma18g00703 . . . . . Bhi07g01917 Tan04g0057 . . . . . . . . . . . . . . . . Lsi04g00676 . . Cme10g00654 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1234 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1235 . . . . . . . . . Cmo18g00689 . Cma18g00702 . . . . . Bhi07g01918 Tan04g0056 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1236 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1237 . . . . . . . . . Cmo18g00688 . Cma18g00701 . . . . . Bhi07g01919 Tan04g0055 . Lac13g0058 Hepe10g1522 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla11g01344 Cam11g1402 Cec11g1426 Cco11g1421 Clacu11g1559 Cmu11g1380 Cre11g1800 . . . .
Vvi1g1238 . . . . . . . . . Cmo18g00687 . Cma18g00700 . . Sed06g1745 . . Bhi07g01920 Tan04g0053 Cmetu10g0868 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1239 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1240 . . . . . . . . Cmo04g01927 . . . . . Sed06g1749 . . Bhi07g01921 Tan04g0051 Cmetu10g1689 Lac13g0056 Hepe10g1520 . . . . . . . . . . . . . Lsi04g00678 . Chy11g01760 Cme11g02293 Blo02g00171 . . . Bpe14g00771 . . . . . . Cma04g01831 . . . . . . . . . . . . Cla11g01342 Cam11g1400 Cec11g1423 Cco11g1419 Clacu11g1557 Cmu11g1378 Cre11g1798 Lsi09g01690 . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 51285988 51289670 + XM_039035973.1 Bhi07g01917 1917
7 51286590 51289673 + XM_039035974.1 Bhi07g01918 1918
7 51378605 51382589 + XM_039037009.1 Bhi07g01919 1919
7 51378605 51381764 + XM_039037010.1 Bhi07g01920 1920
7 51421909 51426926 + XM_039036803.1 Bhi07g01921 1921
2 1486096 1495845 + BLOR09901 Blo02g00171 171
14 43203384 43206857 + Bma012795.1 Bma14g01987 1987
14 5883870 5887757 + Bpe014149.1 Bpe14g00771 771
11 26654903 26667634 - CaPI482276_11g014000.1 Cam11g1400 1400
11 26683043 26687931 - CaPI482276_11g014020.1 Cam11g1402 1402
11 26950446 26954899 - CcPI632755_11g014190.1 Cco11g1419 1419
11 26973735 26978497 - CcPI632755_11g014210.1 Cco11g1421 1421
11 28411472 28420559 - CePI673135_11g014230.1 Cec11g1423 1423
11 28438198 28441758 - CePI673135_11g014260.1 Cec11g1426 1426
11 23987019 23992698 - Chy11G203400.1 Chy11g01760 1760
11 26678739 26687619 - ClG42_11g0155700.10 Clacu11g1557 1557
11 26702776 26707608 - ClG42_11g0155900.10 Clacu11g1559 1559
11 26869316 26885276 - ClCG11G013710.2 Cla11g01342 1342
11 26893080 26925270 - ClCG11G013730.1 Cla11g01344 1344
4 9243157 9248459 + CmaCh04G018310.1 Cma04g01831 1831
18 6382804 6392963 - CmaCh18G007000.1 Cma18g00700 700
18 6402209 6404067 - CmaCh18G007010.1 Cma18g00701 701
18 6407403 6409065 - CmaCh18G007020.1 Cma18g00702 702
18 6423744 6425220 - CmaCh18G007030.1 Cma18g00703 703
10 4174499 4177888 + MELO3C011872.2.1 Cme10g00654 654
11 30008597 30017621 - MELO3C022283.2.1 Cme11g02293 2293
10 17747513 17751489 - PI0017750.1 Cmetu10g0868 868
10 17732432 17737310 - PI0009696.1 Cmetu10g1689 1689
4 9850757 9855666 + CmoCh04G019270.1 Cmo04g01927 1927
18 8768982 8770762 - CmoCh18G006870.1 Cmo18g00687 687
18 8774301 8774829 - CmoCh18G006880.1 Cmo18g00688 688
18 8781950 8784209 - CmoCh18G006890.1 Cmo18g00689 689
18 8788657 8791724 - CmoCh18G006900.1 Cmo18g00690 690
11 25927324 25939812 - CmPI595203_11g013780.1 Cmu11g1378 1378
11 25954996 25959823 - CmPI595203_11g013800.1 Cmu11g1380 1380
11 29558482 29567506 - CrPI670011_11g017980.1 Cre11g1798 1798
11 29583350 29588091 - CrPI670011_11g018000.1 Cre11g1800 1800
10 51951362 51955483 - Hsped.10g15200.1 Hepe10g1520 1520
10 51960785 51963829 - Hsped.10g15220.1 Hepe10g1522 1522
13 402938 405946 - Lag0039852.1 Lac13g0056 56
13 410730 414971 - Lag0039854.1 Lac13g0058 58
4 6185301 6188956 + Lsi04G006760.1 Lsi04g00676 676
4 6198322 6200261 + Lsi04G006780.1 Lsi04g00678 678
9 25372059 25381252 - Lsi09G016900.1 Lsi09g01690 1690
6 42150399 42156621 + Sed0000878.1 Sed06g1745 1745
6 42179755 42185663 + Sed0015559.1 Sed06g1749 1749
4 455553 473205 - Tan0016593.1 Tan04g0051 51
4 478879 481785 - Tan0020610.2 Tan04g0053 53
4 483406 494288 - Tan0005715.2 Tan04g0055 55
4 483406 494288 - Tan0005715.3 Tan04g0056 56
4 487814 494288 - Tan0005715.4 Tan04g0057 57
1 20776701 20776734 - Vvi1g1231 Vvi1g1231 1231
1 20779155 20780679 - Vvi1g1232 Vvi1g1232 1232
1 20788640 20805175 + Vvi1g1233 Vvi1g1233 1233
1 20813287 20814946 + Vvi1g1234 Vvi1g1234 1234
1 20818547 20820093 + Vvi1g1235 Vvi1g1235 1235
1 20822809 20827657 + Vvi1g1236 Vvi1g1236 1236
1 20828170 20830796 + Vvi1g1237 Vvi1g1237 1237
1 20835861 20852573 + Vvi1g1238 Vvi1g1238 1238
1 20854746 20855013 + Vvi1g1239 Vvi1g1239 1239
1 20870538 20876551 + Vvi1g1240 Vvi1g1240 1240
       

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