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
Vvi1g581 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone19ag0671 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g582 . . . . . . . . . . . . . . Sed06g1715 . . Bhi07g01846 Tan04g0121 Cmetu10g1561 Lac13g0102 Hepe10g0064 . . . . . . . . . . . . . Lsi04g00639 . . Cme10g00624 Blo06g00816 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g583 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g584 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g585 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g586 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag1103 Cone19ag1091 . . . . . . . . . . . . . . . . . Cma04g01799 Cma05g00060 . Car05g00050 . . . . . . . . . . . . . . . . . . . .
Vvi1g587 Blo01g00377 Blo16g01181 Bda01g02198 . Bpe13g00515 . . Bma15g00252 . Cmo18g00714 . Cma18g00728 . Car18g00676 . Cpe09g00562 . . . . . . . . Cla05g02626 . . . . . . . . Cone8ag0712 Cone12ag0692 . Csa05g02249 Chy10g00818 . . . . . . . Bma01g00029 . . . . . . Car04g01813 . . . . . . . . . . . . . . . . . . . . .
Vvi1g588 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag1102 Cone19ag1090 . . . . . . . . . . . . . . . . . . Cma05g00059 . Car05g00049 . . . . . . . . . . . . . . . . . . . .
Vvi1g589 . Blo16g01179 . . Bpe13g01495 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag1100 Cone19ag1088 . . . . . . . . . . . . . Bma06g00591 . . . . Cma05g00057 . Car05g00045 . . . . . . . . . . . . . . . . . . . .
Vvi1g590 . Blo16g01178 . Bda11g01299 Bpe13g01493 . Bma14g01836 . . Cmo18g00716 . Cma18g00729 . Car18g00678 Sed06g1714 Cpe09g00559 Cpe01g01582 Bhi07g01841 Tan04g0127 Cmetu10g0484 Lac13g0111 Hepe10g1560 . . Cla05g02623 Cam05g2811 Cec05g2847 Cco05g2878 Clacu05g2815 Cmu05g2663 Cre05g2779 Cone13ag1098 . . . Lsi04g00635 Csa05g02252 Chy10g00821 Cme10g00610 . Blo11g01031 Bda07g01651 Bda11g01299 . . . Bma06g00592 . . . Cma04g01795 . Car04g01809 . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 57890277 57891733 + Bda004538.1 Bda01g02198 2198
7 30732809 30735032 - Bda028532.1 Bda07g01651 1651
11 13695091 13697380 - Bda007821.1 Bda11g01299 1299
7 50177345 50181136 - XM_039036135.1 Bhi07g01841 1841
7 50271134 50273799 - XM_039036214.1 Bhi07g01846 1846
1 4349598 4351188 + BLOR00377 Blo01g00377 377
6 31407292 31409684 - BLOR17399 Blo06g00816 816
11 27380020 27382166 + BLOR03907 Blo11g01031 1031
16 40329350 40331655 - BLOR21965 Blo16g01178 1178
16 40336976 40339608 - BLOR21966 Blo16g01179 1179
16 40347598 40353818 - BLOR21968 Blo16g01181 1181
1 395317 396736 + Bma030163 Bma01g00029 29
6 31643626 31646212 + Bma023518.1 Bma06g00591 591
6 31680517 31682687 + Bma023519.2 Bma06g00592 592
14 39268801 39270994 - Bma012614.1 Bma14g01836 1836
15 2515983 2517930 + Bma013237.1 Bma15g00252 252
13 12491394 12492830 - Bpe025221 Bpe13g00515 515
13 20293204 20295534 - Bpe011160.2 Bpe13g01493 1493
13 20318484 20321075 - Bpe011162.1 Bpe13g01495 1495
5 35227500 35230779 - CaPI482276_05g028110.1 Cam05g2811 2811
4 10507352 10512528 - Carg14296-RA Car04g01809 1809
4 10520448 10522419 - Carg14292-RA Car04g01813 1813
5 234837 238670 - Carg21845-RA Car05g00045 45
5 240904 246228 - Carg21849-RA Car05g00049 49
5 247380 249579 - Carg21850-RA Car05g00050 50
18 7958874 7961771 + Carg27654-RA Car18g00676 676
18 7967712 7970115 + Carg27652-RA Car18g00678 678
5 36386636 36389930 - CcPI632755_05g028780.1 Cco05g2878 2878
5 38700412 38703722 - CePI673135_05g028470.1 Cec05g2847 2847
10 14144947 14146613 + Chy10G180120.1 Chy10g00818 818
10 14175172 14177286 + Chy10G180150.1 Chy10g00821 821
5 35451239 35454541 - ClG42_05g0281500.10 Clacu05g2815 2815
5 37425096 37432555 - ClCG05G026150.2 Cla05g02623 2623
5 37443595 37445470 - ClCG05G026175.1 Cla05g02626 2626
4 9066519 9069961 - CmaCh04G017950.1 Cma04g01795 1795
4 9075767 9081213 - CmaCh04G017990.1 Cma04g01799 1799
5 230281 234605 - CmaCh05G000570.1 Cma05g00057 57
5 236463 241742 - CmaCh05G000590.1 Cma05g00059 59
5 242476 244492 - CmaCh05G000600.1 Cma05g00060 60
18 6577123 6582176 + CmaCh18G007280.1 Cma18g00728 728
18 6584833 6591763 + CmaCh18G007290.1 Cma18g00729 729
10 3904473 3908196 - MELO3C011912.2.1 Cme10g00610 610
10 3976396 3978507 + MELO3C011901.2.1 Cme10g00624 624
10 18027567 18031579 + PI0019112.1 Cmetu10g0484 484
10 17999911 18001693 + PI0027864.1 Cmetu10g1561 1561
18 8972843 8975681 + CmoCh18G007140.1 Cmo18g00714 714
18 8981016 8984509 + CmoCh18G007160.1 Cmo18g00716 716
5 35189542 35192841 - CmPI595203_05g026630.1 Cmu05g2663 2663
8 7142872 7145472 - Conep08aG0073500.1 Cone8ag0712 712
12 6310208 6312869 - Conep12aG0071500.1 Cone12ag0692 692
13 8881444 8885386 - Conep13aG0113000.1 Cone13ag1098 1098
13 8887270 8890264 - Conep13aG0113200.1 Cone13ag1100 1100
13 8893063 8896987 - Conep13aG0113400.1 Cone13ag1102 1102
13 8897423 8898710 - Conep13aG0113500.1 Cone13ag1103 1103
19 5712588 5714755 + Conep19aG0069200.1 Cone19ag0671 671
19 7916613 7924743 - Conep19aG0112200.1 Cone19ag1088 1088
19 7927386 7931746 - Conep19aG0112400.1 Cone19ag1090 1090
19 7932361 7933262 - Conep19aG0112500.1 Cone19ag1091 1091
1 9676087 9678408 - Cp4.1LG01g15920.1 Cpe01g01582 1582
9 3867260 3869958 - Cp4.1LG09g06230.1 Cpe09g00559 559
9 3876283 3883233 - Cp4.1LG09g06250.1 Cpe09g00562 562
5 38555829 38559136 - CrPI670011_05g027790.1 Cre05g2779 2779
5 25150190 25151840 + CsaV3_5G030680.1 Csa05g02249 2249
5 25177447 25180962 + CsaV3_5G030710.1 Csa05g02252 2252
10 634599 637722 - Hsped.10g00640.1 Hepe10g0064 64
10 52326361 52328645 + Hsped.10g15600.1 Hepe10g1560 1560
13 717322 718899 + Lag0039898.1 Lac13g0102 102
13 764715 766954 + Lag0039907.1 Lac13g0111 111
4 5827505 5831261 - Lsi04G006350.1 Lsi04g00635 635
4 5866620 5868736 - Lsi04G006390.1 Lsi04g00639 639
6 41845516 41849343 - Sed0022551.3 Sed06g1714 1714
6 41862678 41865743 - Sed0013142.1 Sed06g1715 1715
4 774908 776581 + Tan0021415.1 Tan04g0121 121
4 812995 815367 + Tan0005696.1 Tan04g0127 127
1 6612510 6618381 - Vvi1g581 Vvi1g581 581
1 6622466 6624298 + Vvi1g582 Vvi1g582 582
1 6624949 6628677 - Vvi1g583 Vvi1g583 583
1 6628695 6633992 - Vvi1g584 Vvi1g584 584
1 6634487 6643684 + Vvi1g585 Vvi1g585 585
1 6653069 6670306 + Vvi1g586 Vvi1g586 586
1 6670788 6674449 + Vvi1g587 Vvi1g587 587
1 6678842 6691641 + Vvi1g588 Vvi1g588 588
1 6701542 6712881 + Vvi1g589 Vvi1g589 589
1 6727674 6732296 + Vvi1g590 Vvi1g590 590
       

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