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
Vvi1g611 Blo01g00803 . Bda01g01762 . . . Bma14g01830 . . Cmo18g00725 . Cma18g00733 . . . Cpe09g00556 . Bhi07g01827 . . . . . . Cla05g02613 Cam05g2801 Cec05g2837 Cco05g2869 Clacu05g2804 Cmu05g2652 Cre05g2769 Cone13ag1094 . . . Lsi04g00627 Csa05g02262 Chy10g00832 Cme10g00600 . . Bda07g01646 . . Bpe02g01936 Bma01g00518 . . Cmo04g02800 . . . . . . . . . . . . . . . . . . . . . . . Chy09g00375 .
Vvi1g612 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g613 . . . . . . . Bma15g00227 . Cmo18g00727 . Cma18g00735 . Car18g00683 . Cpe09g00554 . . . . . . . . . . . . . . . Cone13ag1093 Cone19ag1081 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g614 . . . . . . . . . Cmo18g00737 . Cma18g00741 . . . . . Bhi07g01818 . . . . . . Cla05g02611 . . . . . . . . . . Lsi04g00625 Csa05g02270 Chy10g00833 Cme10g00599 Blo06g00840 . . . . . . . . . . Cma04g01787 . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g615 . . . . . . . . . . . Cma18g00746 . . . . . Bhi07g01816 . . . . . . Cla05g02610 . . . . . . . . . . Lsi04g00624 Csa05g02271 Chy10g00834 Cme10g00597 . . . . . . . . . . . Cma04g01782 . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g616 . . . . . . . . . Cmo18g00744 . Cma18g00747 . . . . . Bhi07g01813 . . . . . . Cla05g02608 . . . . . . . . . . Lsi04g00623 Csa05g02272 Chy10g00836 Cme10g00596 Blo06g00842 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g617 . . . . . . . . . Cmo18g00751 . Cma18g00748 . . . . . Bhi07g01811 . . . . . . Cla05g02607 . . . . . . . . . . Lsi04g00620 Csa05g02273 Chy10g00837 Cme10g00595 . . . . . . . . . . . Cma04g01781 . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g618 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g619 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g620 . . . . . . Bma14g01828 . . Cmo18g00756 . Cma18g00751 . Car18g00685 . Cpe09g00548 . Bhi07g01807 . . . . . . Cla05g02598 Cam05g2789 Cec05g2827 Cco05g2859 Clacu05g2791 Cmu05g2639 Cre05g2755 Cone13ag1092 . . . Lsi04g00608 Csa05g02277 Chy10g00843 Cme10g00587 . . Bda07g01644 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 53841771 53842998 + Bda004051.2 Bda01g01762 1762
7 30675675 30677225 + Bda033989 Bda07g01644 1644
7 30685341 30687292 + Bda028527.1 Bda07g01646 1646
7 49272322 49276313 + XM_039036187.1 Bhi07g01807 1807
7 49278627 49281476 - XM_039036189.1 Bhi07g01811 1811
7 49278627 49281472 - XM_039036191.1 Bhi07g01813 1813
7 49378335 49383693 - XM_039037538.1 Bhi07g01816 1816
7 49379756 49383693 - XM_039037536.1 Bhi07g01818 1818
7 49631284 49635018 + XM_039036228.1 Bhi07g01827 1827
1 12348704 12350372 - BLOR00803 Blo01g00803 803
6 31647847 31657182 - BLOR17423 Blo06g00840 840
6 31660584 31662732 - BLOR17425 Blo06g00842 842
1 4281411 4287779 - Bma000697.2 Bma01g00518 518
14 39191545 39193095 + Bma012607.1 Bma14g01828 1828
14 39203687 39207841 + Bma012609.1 Bma14g01830 1830
15 2235687 2238550 - Bma013211.1 Bma15g00227 227
2 21306801 21308007 + Bpe009761.3 Bpe02g01936 1936
5 35065468 35070100 + CaPI482276_05g027890.1 Cam05g2789 2789
5 35149567 35152104 + CaPI482276_05g028010.1 Cam05g2801 2801
18 8012272 8016654 + Carg27647-RA Car18g00683 683
18 8140298 8141884 - Carg14513-RA Car18g00685 685
5 36220308 36223909 + CcPI632755_05g028590.1 Cco05g2859 2859
5 36304338 36306875 + CcPI632755_05g028690.1 Cco05g2869 2869
5 38533681 38537592 + CePI673135_05g028270.1 Cec05g2827 2827
5 38620541 38623078 + CePI673135_05g028370.1 Cec05g2837 2837
9 3282955 3287497 - Chy9G160910.1 Chy09g00375 375
10 14255706 14258867 - Chy10G180260.1 Chy10g00832 832
10 14269029 14270787 + Chy10G180270.1 Chy10g00833 833
10 14271100 14278653 - Chy10G180280.1 Chy10g00834 834
10 14284128 14286060 - Chy10G180300.1 Chy10g00836 836
10 14288655 14291420 - Chy10G180310.1 Chy10g00837 837
10 14331788 14333332 - Chy10G180370.1 Chy10g00843 843
5 35277107 35280598 + ClG42_05g0279100.10 Clacu05g2791 2791
5 35368005 35370542 + ClG42_05g0280400.10 Clacu05g2804 2804
5 37231395 37235116 + ClCG05G025900.1 Cla05g02598 2598
5 37288721 37291113 - ClCG05G025975.1 Cla05g02607 2607
5 37303566 37306340 - ClCG05G025978.1 Cla05g02608 2608
5 37315144 37327846 - ClCG05G025990.2 Cla05g02610 2610
5 37322308 37325014 + ClCG05G026000.2 Cla05g02611 2611
5 37339391 37342450 + ClCG05G026040.1 Cla05g02613 2613
4 8976316 8978222 - CmaCh04G017810.1 Cma04g01781 1781
4 8991584 8993198 - CmaCh04G017820.1 Cma04g01782 1782
4 9010240 9012644 + CmaCh04G017870.1 Cma04g01787 1787
18 6626007 6636960 - CmaCh18G007330.1 Cma18g00733 733
18 6641734 6646275 + CmaCh18G007350.1 Cma18g00735 735
18 6679052 6687116 - CmaCh18G007410.1 Cma18g00741 741
18 6699586 6704953 - CmaCh18G007460.1 Cma18g00746 746
18 6709254 6711608 - CmaCh18G007470.1 Cma18g00747 747
18 6718521 6720261 - CmaCh18G007480.1 Cma18g00748 748
18 6738908 6743571 - CmaCh18G007510.1 Cma18g00751 751
10 3777455 3782003 + MELO3C034149.2.1 Cme10g00587 587
10 3799636 3802016 - MELO3C011930.2.1 Cme10g00595 595
10 3804018 3806248 - MELO3C011929.2.1 Cme10g00596 596
10 3808996 3811261 - MELO3C011928.2.1 Cme10g00597 597
10 3817059 3819055 - MELO3C011926.2.1 Cme10g00599 599
10 3825102 3828779 + MELO3C011925.2.1 Cme10g00600 600
4 20118369 20123644 + CmoCh04G028000.1 Cmo04g02800 2800
18 9022257 9025991 - CmoCh18G007250.1 Cmo18g00725 725
18 9030217 9034675 + CmoCh18G007270.1 Cmo18g00727 727
18 9093495 9095456 - CmoCh18G007370.1 Cmo18g00737 737
18 9146840 9148513 - CmoCh18G007440.1 Cmo18g00744 744
18 9185496 9187281 - CmoCh18G007510.1 Cmo18g00751 751
18 9199406 9200992 - CmoCh18G007560.1 Cmo18g00756 756
5 35015439 35018929 + CmPI595203_05g026390.1 Cmu05g2639 2639
5 35106305 35108842 + CmPI595203_05g026520.1 Cmu05g2652 2652
13 8837738 8840567 + Conep13aG0112400.1 Cone13ag1092 1092
13 8846710 8850106 - Conep13aG0112500.1 Cone13ag1093 1093
13 8851639 8855025 + Conep13aG0112600.1 Cone13ag1094 1094
19 7874669 7876913 - Conep19aG0111400.1 Cone19ag1081 1081
9 3677564 3682207 + Cp4.1LG09g06340.1 Cpe09g00548 548
9 3818068 3822272 - Cp4.1LG09g06210.1 Cpe09g00554 554
9 3832854 3837511 + Cp4.1LG09g06300.1 Cpe09g00556 556
5 38373221 38377861 + CrPI670011_05g027550.1 Cre05g2755 2755
5 38475260 38477798 + CrPI670011_05g027690.1 Cre05g2769 2769
5 25249531 25253237 - CsaV3_5G030810.1 Csa05g02262 2262
5 25298556 25301650 - CsaV3_5G030890.1 Csa05g02270 2270
5 25309859 25312628 + CsaV3_5G030900.1 Csa05g02271 2271
5 25316097 25318576 - CsaV3_5G030910.1 Csa05g02272 2272
5 25327936 25330556 + CsaV3_5G030920.1 Csa05g02273 2273
5 25343682 25345986 - CsaV3_5G030960.1 Csa05g02277 2277
4 5600067 5601611 + Lsi04G006080.1 Lsi04g00608 608
4 5672264 5674667 + Lsi04G006200.1 Lsi04g00620 620
4 5705523 5708313 + Lsi04G006230.1 Lsi04g00623 623
4 5708822 5710894 - Lsi04G006240.1 Lsi04g00624 624
4 5718525 5720995 - Lsi04G006250.1 Lsi04g00625 625
4 5738272 5740777 + Lsi04G006270.1 Lsi04g00627 627
1 6977774 6982566 - Vvi1g611 Vvi1g611 611
1 6982613 6986592 - Vvi1g612 Vvi1g612 612
1 6988613 6993527 + Vvi1g613 Vvi1g613 613
1 6994566 7007375 - Vvi1g614 Vvi1g614 614
1 7007864 7024648 - Vvi1g615 Vvi1g615 615
1 7027703 7030273 - Vvi1g616 Vvi1g616 616
1 7031054 7050240 - Vvi1g617 Vvi1g617 617
1 7066223 7070866 + Vvi1g618 Vvi1g618 618
1 7071570 7079766 - Vvi1g619 Vvi1g619 619
1 7085349 7086909 - Vvi1g620 Vvi1g620 620
       

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