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
Vvi2g632 Blo02g01002 . . Bda08g00618 Bpe05g00538 . . . Cmo06g00861 . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0618 Cone9ag0620 . . . . . . . . . . . . . . . Cma06g00839 . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g633 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g634 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g635 . . . . . . . . . Cmo16g01202 . . . . . Cpe14g00955 . Bhi11g00052 . . Lac11g2322 Hepe06g1112 . . . . . . . . . Cone8ag0466 . . . . . Chy04g00082 . Blo03g00836 Blo19g00177 . . . . . . . . Cmo19g00257 . Cma16g01151 Car06g00585 Car16g01091 . Cpe15g00220 . . . . . . . . . . . . . . . . Chy06g02135 Cme04g00106
Vvi2g636 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g637 . . . . . . Bma07g00961 . Cmo06g00662 Cmo16g01203 . . . . . Cpe14g00855 . Bhi11g00147 . . . Hepe06g1765 Mch10g1643 . . . . . . . . . . . . . . Chy04g00085 . Blo03g00838 Blo19g00178 . . . . . . . . Cmo19g00256 Cma06g00655 Cma16g01152 Car06g00584 Car16g01092 . Cpe15g00219 . . . . . . . . . . . . . . . . Chy06g02136 Cme04g00108
Vvi2g638 Blo02g00997 . . . Bpe05g00534 . . . . . . . . . . . Cpe05g00188 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma05g00385 . . . Cmo19g00479 . . . . . Cpe15g00360 . . . . . . . . . . . . . . . . . .
Vvi2g639 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda07g00815 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g640 . . . . . . . . . . . . . . . . Cpe05g00186 . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe08g00847 . . . . . Cmo19g00478 . . . . . Cpe15g00359 . . . . . . . . . . . . . . . . . .
Vvi2g641 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 9630703 9636982 - Bda033867 Bda07g00815 815
8 6344512 6346788 - Bda029084.1 Bda08g00618 618
11 1008164 1012960 - XM_039048008.1 Bhi11g00052 52
11 3375138 3383451 - XM_039048865.1 Bhi11g00147 147
2 38657372 38668108 + BLOR10727 Blo02g00997 997
2 38974730 38979657 + BLOR10732 Blo02g01002 1002
3 34084725 34085561 + BLOR12017 Blo03g00836 836
3 34108482 34111914 - BLOR12019 Blo03g00838 838
19 7583163 7584002 + BLOR09520 Blo19g00177 177
19 7602466 7606441 - BLOR09521 Blo19g00178 178
5 12144560 12152394 + Bma021210.2 Bma05g00385 385
7 36479208 36484289 - Bma026098.1 Bma07g00961 961
5 19512328 19518687 + Bpe017951.3 Bpe05g00534 534
5 19555050 19555560 + Bpe017955.1 Bpe05g00538 538
8 10807944 10810493 + Bpe022969.1 Bpe08g00847 847
6 3348786 3357555 + Carg23379-RA Car06g00584 584
6 3358808 3359518 - Carg23378-RA Car06g00585 585
16 9371877 9372602 + Carg26191-RA Car16g01091 1091
16 9376559 9384049 - Carg26192-RA Car16g01092 1092
4 850886 851704 + Chy4G068000.1 Chy04g00082 82
4 857773 861138 - Chy4G068030.1 Chy04g00085 85
6 25683354 25684100 + Chy6G126630.1 Chy06g02135 2135
6 25703791 25711781 - Chy6G126640.1 Chy06g02136 2136
6 3231771 3240251 + CmaCh06G006550.1 Cma06g00655 655
6 4618361 4625818 - CmaCh06G008390.1 Cma06g00839 839
16 8853135 8853902 + CmaCh16G011510.1 Cma16g01151 1151
16 8858536 8867165 - CmaCh16G011520.1 Cma16g01152 1152
4 850979 852335 + MELO3C003402.2.1 Cme04g00106 106
4 858647 862283 - MELO3C003404.2.1 Cme04g00108 108
6 3334907 3343642 + CmoCh06G006620.1 Cmo06g00662 662
6 4877976 4881728 - CmoCh06G008610.1 Cmo06g00861 861
16 8602724 8603500 + CmoCh16G012020.1 Cmo16g01202 1202
16 8608087 8615957 - CmoCh16G012030.1 Cmo16g01203 1203
19 1864916 1869691 + CmoCh19G002560.1 Cmo19g00256 256
19 1873601 1874377 - CmoCh19G002570.1 Cmo19g00257 257
19 5696962 5699309 - CmoCh19G004780.1 Cmo19g00478 478
19 5700837 5710039 - CmoCh19G004790.1 Cmo19g00479 479
6 3067278 3071044 + Conep06aG0063600.1 Cone6ag0618 618
8 3052220 3053167 + Conep08aG0048700.1 Cone8ag0466 466
9 2948412 2950798 + Conep09aG0063400.1 Cone9ag0620 620
5 981301 994703 + Cp4.1LG05g00140.1 Cpe05g00186 186
5 1009065 1015529 + Cp4.1LG05g02170.1 Cpe05g00188 188
14 7073358 7075469 + Cp4.1LG14g08590.1 Cpe14g00855 855
14 8063080 8063859 + Cp4.1LG14g09550.1 Cpe14g00955 955
15 1895199 1900274 + Cp4.1LG15g02210.1 Cpe15g00219 219
15 1903902 1904669 - Cp4.1LG15g02220.1 Cpe15g00220 220
15 4787008 4789765 - Cp4.1LG15g03540.1 Cpe15g00359 359
15 4791150 4799015 - Cp4.1LG15g03560.1 Cpe15g00360 360
6 59788288 59793086 + Hsped.06g11120.1 Hepe06g1112 1112
6 68749609 68754412 - Hsped.06g17650.1 Hepe06g1765 1765
11 39206232 39213897 + Lag0032960.1 Lac11g2322 2322
10 16564785 16574422 - MC10g1307 Mch10g1643 1643
2 6711942 6739053 - Vvi2g632 Vvi2g632 632
2 6743160 6747172 + Vvi2g633 Vvi2g633 633
2 6747212 6761452 + Vvi2g634 Vvi2g634 634
2 6784847 6786547 + Vvi2g635 Vvi2g635 635
2 6802672 6802882 - Vvi2g636 Vvi2g636 636
2 6802887 6816991 - Vvi2g637 Vvi2g637 637
2 6818092 6834743 - Vvi2g638 Vvi2g638 638
2 6835340 6855471 - Vvi2g639 Vvi2g639 639
2 6860936 6867964 + Vvi2g640 Vvi2g640 640
2 6868972 6869682 - Vvi2g641 Vvi2g641 641
       

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