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
Vvi19g34 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g35 . . . . . . . Bma13g00921 . Cmo04g00709 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo10g00721 . Bda12g00811 . . . . . . . Cma04g00661 . . . . Cpe01g00596 . . . . . . . . . . . . . . . . . .
Vvi19g36 Blo03g00706 . . . . . . . . . Cma01g01268 . Car01g01085 Car09g00596 . Cpe06g00526 Cpe02g00654 Bhi09g03565 . . . Hepe01g1465 . . Cla11g01689 Cam11g1753 Cec11g1777 Cco11g1779 Clacu11g1913 Cmu11g1724 Cre11g2134 Cone6ag0209 Cone9ag0237 . . Lsi04g01980 Csa04g02257 . Cme07g00501 . . . . Bpe11g00439 . . Bma14g00274 . Cmo01g01322 Cmo09g00657 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g37 . . Bda07g00349 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00827 . .
Vvi19g38 . . . . . . . . . Cmo04g00710 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma04g00662 . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g39 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe01g00597 . . . . . . . . . . . . . . . Csa04g00826 . .
Vvi19g40 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g41 . . . . Bpe09g00269 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1025 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g42 . . . . . . . . . . . . . . . . . Bhi09g03558 . . . Hepe01g1461 . . . . . . . . . . . . . . . . Cme07g00504 . . . . . Bpe03g00881 . . . . . . . . . . . . . . . . . . Cla07g00984 . . . . . . . . . .
Vvi19g43 . . . . . . . . . . . . . . . . . Bhi09g03556 . . . . . . . . . . . . . . . . . . . . . Blo07g01002 . . . . . . . . . . . . . Car16g00424 . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 4522679 4526009 + Bda033834 Bda07g00349 349
12 37344195 37346499 - Bda009320.1 Bda12g00811 811
9 89292923 89305513 + XM_039042137.1 Bhi09g03556 3556
9 89335314 89349624 + XM_039040536.1 Bhi09g03558 3558
9 89438431 89441446 - XM_039040283.1 Bhi09g03565 3565
3 29860845 29863009 - BLOR11887 Blo03g00706 706
7 29603550 29610396 + BLOR18934 Blo07g01002 1002
10 22825477 22832559 - BLOR02511 Blo10g00721 721
13 39621689 39623983 - Bma009998.1 Bma13g00921 921
14 3260569 3262726 - Bma030650 Bma14g00274 274
3 28580832 28583144 + Bpe012786.1 Bpe03g00881 881
9 2003456 2008540 + Bpe023940.2 Bpe09g00269 269
11 3327525 3329697 + Bpe024755 Bpe11g00439 439
11 30086384 30089537 + CaPI482276_11g017530.1 Cam11g1753 1753
1 10164027 10166304 - Carg14749-RA Car01g01085 1085
9 3393849 3396920 - Carg03079-RA Car09g00596 596
16 2649297 2652626 - Carg11391-RA Car16g00424 424
11 30502002 30505149 + CcPI632755_11g017790.1 Cco11g1779 1779
11 31956003 31959136 + CePI673135_11g017770.1 Cec11g1777 1777
11 30122882 30126017 + ClG42_11g0191300.10 Clacu11g1913 1913
7 26039257 26054254 + ClCG07G010320.2 Cla07g00984 984
11 30460606 30464135 + ClCG11G017210.1 Cla11g01689 1689
1 9136742 9139310 - CmaCh01G012680.1 Cma01g01268 1268
4 3368788 3373007 - CmaCh04G006610.1 Cma04g00661 661
4 3373405 3375506 - CmaCh04G006620.1 Cma04g00662 662
7 4146761 4150295 + MELO3C025669.2.1 Cme07g00501 501
7 4173782 4174770 + MELO3C025667.2.1 Cme07g00504 504
1 10509125 10511414 - CmoCh01G013220.1 Cmo01g01322 1322
4 3511668 3515617 - CmoCh04G007090.1 Cmo04g00709 709
4 3516087 3518092 - CmoCh04G007100.1 Cmo04g00710 710
9 3296461 3299749 - CmoCh09G006570.1 Cmo09g00657 657
11 29375921 29379054 + CmPI595203_11g017240.1 Cmu11g1724 1724
6 988793 990437 - Conep06aG0021100.1 Cone6ag0209 209
9 1003097 1004771 - Conep09aG0024000.1 Cone9ag0237 237
14 8554124 8555809 - Conep14aG0104500.1 Cone14ag1025 1025
1 3436458 3442169 - Cp4.1LG01g00650.1 Cpe01g00596 596
1 3442537 3444858 - Cp4.1LG01g00670.1 Cpe01g00597 597
2 4049767 4052985 + Cp4.1LG02g02180.1 Cpe02g00654 654
6 3161830 3167778 - Cp4.1LG06g05300.1 Cpe06g00526 526
11 33036432 33039574 + CrPI670011_11g021340.1 Cre11g2134 2134
4 5779957 5781619 - CsaV3_4G008260.1 Csa04g00826 826
4 5787010 5790674 - CsaV3_4G008270.1 Csa04g00827 827
4 23197540 23201105 + CsaV3_4G032830.1 Csa04g02257 2257
1 79885916 79897617 + Hsped.01g14610.1 Hepe01g1461 1461
1 79962142 79965182 - Hsped.01g14650.1 Hepe01g1465 1465
4 26855033 26858324 + Lsi04G019800.1 Lsi04g01980 1980
19 374954 375178 - Vvi19g34 Vvi19g34 34
19 375193 383468 - Vvi19g35 Vvi19g35 35
19 419929 427216 + Vvi19g36 Vvi19g36 36
19 427491 430727 - Vvi19g37 Vvi19g37 37
19 434142 434694 - Vvi19g38 Vvi19g38 38
19 434982 456680 - Vvi19g39 Vvi19g39 39
19 468847 472363 - Vvi19g40 Vvi19g40 40
19 473473 478208 - Vvi19g41 Vvi19g41 41
19 481018 491501 - Vvi19g42 Vvi19g42 42
19 494246 496540 - Vvi19g43 Vvi19g43 43
       

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