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
Vvi2g652 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g653 . Blo03g00080 Bda06g01276 Bda08g00622 . . . . . Cmo16g01120 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme06g02487 . . . . . . . . . . . . Cma16g01071 . Car16g01017 . . . . . . . . . . . . . . . . . . . .
Vvi2g654 . . . . . . . . Cmo06g00870 . . . . . . . . . . . . . . . . . . . . . . Cone8ag0617 . . . Lsi07g01219 . . . . . . . . . . . . . . Cma06g00845 . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g655 . . . . . . . . . . Cma02g01600 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo19g00470 . . . . . Cpe15g00350 . . . . . . . Cla09g01154 Cam09g1214 Cec09g1236 Cco09g1257 . . Cre09g1175 . . . .
Vvi2g656 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g657 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g658 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo19g00461 . . . . . Cpe15g00347 . . . . . . . . . . . . . . . . . .
Vvi2g659 . Blo03g00059 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda07g00775 . . . . . . . Cmo19g00460 . . . . . Cpe15g00346 . . . . . . . . . . . . . . . . . .
Vvi2g660 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g661 . . . Bda08g00626 Bpe05g00532 . Bma07g00945 . Cmo06g00876 . Cma02g01606 . Car02g01366 . . . Cpe05g00184 . . . . . . . Cla10g00172 Cam10g0171 Cec10g0180 Cco10g0180 Clacu10g0175 Cmu10g1023 Cre10g0429 . . . . . . . Cme06g02480 . . . Bda09g00708 Bpe08g00846 . Bma05g00715 . . Cmo02g01650 . Cma06g00849 . . . . . . . . . . . . . . . . . . . . Csa03g04620 . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 43367904 43372633 - Bda023123.1 Bda06g01276 1276
7 9284622 9286504 + Bda025914.1 Bda07g00775 775
8 6381269 6386145 + Bda034007 Bda08g00622 622
8 6423408 6423884 - Bda029090.1 Bda08g00626 626
9 11307095 11307760 - Bda031376.1 Bda09g00708 708
3 2206831 2213329 + BLOR11240 Blo03g00059 59
3 2712736 2714705 + BLOR11261 Blo03g00080 80
5 41370129 41370686 + Bma021791.1 Bma05g00715 715
7 35697695 35698360 + Bma026075.1 Bma07g00945 945
5 19499197 19499754 + Bpe017949.1 Bpe05g00532 532
8 10799015 10799686 + Bpe022968.1 Bpe08g00846 846
9 13521134 13523032 - CaPI482276_09g012140.1 Cam09g1214 1214
10 3347797 3348387 + CaPI482276_10g001710.1 Cam10g0171 171
2 9044173 9044904 - Carg08833-RA Car02g01366 1366
16 8658307 8663459 - Carg23221-RA Car16g01017 1017
9 13306496 13308377 - CcPI632755_09g012570.1 Cco09g1257 1257
10 1780666 1781256 + CcPI632755_10g001800.1 Cco10g0180 180
9 13421050 13422943 - CePI673135_09g012360.1 Cec09g1236 1236
10 1804596 1805186 + CePI673135_10g001800.1 Cec10g0180 180
10 2077282 2077872 + ClG42_10g0017500.10 Clacu10g0175 175
9 13458542 13460689 - ClCG09G012170.1 Cla09g01154 1154
10 1837362 1837952 + ClCG10G001720.1 Cla10g00172 172
2 9093206 9095825 + CmaCh02G016000.1 Cma02g01600 1600
2 9146091 9146813 - CmaCh02G016060.1 Cma02g01606 1606
6 4695235 4700773 + CmaCh06G008450.1 Cma06g00845 845
6 4722305 4722850 - CmaCh06G008490.1 Cma06g00849 849
16 8200291 8205722 - CmaCh16G010710.1 Cma16g01071 1071
6 31794978 31796323 + MELO3C013858.2.1 Cme06g02480 2480
6 31828616 31838218 - MELO3C013864.2.1 Cme06g02487 2487
2 9518170 9518787 - CmoCh02G016500.1 Cmo02g01650 1650
6 4960566 4966137 + CmoCh06G008700.1 Cmo06g00870 870
6 4987437 4987982 - CmoCh06G008760.1 Cmo06g00876 876
16 7922076 7927369 - CmoCh16G011200.1 Cmo16g01120 1120
19 5546173 5555044 + CmoCh19G004600.1 Cmo19g00460 460
19 5555067 5560214 - CmoCh19G004610.1 Cmo19g00461 461
19 5625026 5628359 + CmoCh19G004700.1 Cmo19g00470 470
10 2228215 2228805 + CmPI595203_10g010230.1 Cmu10g1023 1023
8 6061228 6066602 + Conep08aG0063800.1 Cone8ag0617 617
5 969896 970624 + Cp4.1LG05g00120.1 Cpe05g00184 184
15 4647442 4658722 + Cp4.1LG15g03400.1 Cpe15g00346 346
15 4656000 4661848 - Cp4.1LG15g03460.1 Cpe15g00347 347
15 4719565 4722725 + Cp4.1LG15g03480.1 Cpe15g00350 350
9 13543520 13545420 - CrPI670011_09g011750.1 Cre09g1175 1175
10 3201973 3202563 + CrPI670011_10g004290.1 Cre10g0429 429
3 40137845 40139161 + CsaV3_3G049260.1 Csa03g04620 4620
7 17767030 17774349 - Lsi07G012190.1 Lsi07g01219 1219
2 7043739 7046954 + Vvi2g652 Vvi2g652 652
2 7060027 7078684 - Vvi2g653 Vvi2g653 653
2 7100432 7117056 - Vvi2g654 Vvi2g654 654
2 7118007 7119801 + Vvi2g655 Vvi2g655 655
2 7149351 7159858 - Vvi2g656 Vvi2g656 656
2 7180185 7183125 - Vvi2g657 Vvi2g657 657
2 7184233 7189385 + Vvi2g658 Vvi2g658 658
2 7190723 7217114 - Vvi2g659 Vvi2g659 659
2 7229352 7231070 + Vvi2g660 Vvi2g660 660
2 7241429 7242900 + Vvi2g661 Vvi2g661 661
       

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