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
Vvi1g421 . . . . . . . . . . . Cma04g00039 . . Sed06g0211 . . Bhi07g00288 Tan04g1613 Cmetu09g0102 Lac13g1501 Hepe01g0469 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma04g02089 Cma15g00941 Car04g02028 Car15g00884 . . . . . . . . . . . . . . . . . Csa05g01220 . .
Vvi1g422 . . . . . . Bma14g01597 . . . . . . . . . . . . . . . . . Cla07g00622 Cam07g0642 . Cco07g0699 . Cmu07g0670 Cre07g1019 Cone13ag0764 . . . Lsi04g01153 . . Cme10g01515 . Blo11g00729 . . Bpe11g01604 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g423 . . . . . . . . . . . Cma04g00044 . . . . . Bhi07g00298 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g424 . . . . . . . . . . . . . . Sed06g0201 . . Bhi07g00299 Tan04g1602 Cmetu10g0245 . Hepe01g0476 . . . . . . . . . . . . . Lsi04g01160 . . Cme10g01534 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g425 . . . . . . . . . . . . . . . . . Bhi07g00300 . . Lac13g1488 . . . Cla07g00633 Cam07g0653 Cec07g0712 Cco07g0712 Clacu07g0653 Cmu07g0680 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g426 . . . . . . Bma14g01598 . . . . Cma04g00042 . . . . . . . . . . . . Cla07g00638 Cam07g0656 Cec07g0713 Cco07g0716 Clacu07g0657 Cmu07g0682 . Cone13ag0763 Cone19ag0767 . . Lsi04g01162 . . Cme10g01536 . Blo11g00728 . . . . . . . . . . . . . . Cpe04g01376 . . . . . . . . . . . . . . . . . .
Vvi1g427 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g428 . . . . Bpe13g01031 . . . . Cmo18g00957 . Cma18g00956 . Car18g00873 . Cpe09g00366 . . . . . . . . Cla07g00640 Cam07g0663 Cec07g0715 Cco07g0718 Clacu07g0661 Cmu07g0684 Cre07g1032 . . Cone6ag0396 Cone9ag0422 Lsi04g01163 Csa05g02704 Chy10g01230 Cme10g01537 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g429 . . . . . Bpe10g00920 . . . . . Cma04g00029 . . . . . . . . . . . . . . . . . . . Cone13ag0762 Cone19ag0766 . . . . . Cme10g01474 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01026 . .
Vvi1g430 . . . . . . . . . . . Cma04g00028 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01025 . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 12969474 12975709 - XM_039037137.1 Bhi07g00288 288
7 13234650 13237099 - XM_039037204.1 Bhi07g00298 298
7 13244890 13246715 + XM_039037330.1 Bhi07g00299 299
7 13244899 13246715 + XM_039037331.1 Bhi07g00300 300
11 9332928 9341304 + BLOR03604 Blo11g00728 728
11 9365441 9402183 + BLOR03605 Blo11g00729 729
14 33050792 33063747 - Bma012290.1 Bma14g01597 1597
14 33078541 33083084 - Bma012291.1 Bma14g01598 1598
10 14812954 14823654 - Bpe003223.3 Bpe10g00920 920
11 12118098 12135028 + Bpe024849 Bpe11g01604 1604
13 16002457 16003796 - Bpe010712.1 Bpe13g01031 1031
7 12067751 12075471 + CaPI482276_07g006420.1 Cam07g0642 642
7 12646940 12648316 - CaPI482276_07g006530.1 Cam07g0653 653
7 12837282 12843024 + CaPI482276_07g006560.1 Cam07g0656 656
7 12993037 12995050 - CaPI482276_07g006630.1 Cam07g0663 663
4 16323750 16325746 + Carg27270-RA Car04g02028 2028
15 5258409 5260863 + Carg24910-RA Car15g00884 884
18 9699564 9703847 + Carg18999-RA Car18g00873 873
7 12407692 12415547 + CcPI632755_07g006990.1 Cco07g0699 699
7 13126714 13128084 - CcPI632755_07g007120.1 Cco07g0712 712
7 13272636 13278391 + CcPI632755_07g007160.1 Cco07g0716 716
7 13371365 13373421 - CcPI632755_07g007180.1 Cco07g0718 718
7 13180596 13181966 - CePI673135_07g007120.1 Cec07g0712 712
7 13395452 13399155 + CePI673135_07g007130.1 Cec07g0713 713
7 13466051 13468074 - CePI673135_07g007150.1 Cec07g0715 715
10 16945531 16947779 - Chy10G184240.1 Chy10g01230 1230
7 11769988 11771358 - ClG42_07g0065300.10 Clacu07g0653 653
7 11992018 11997519 + ClG42_07g0065700.10 Clacu07g0657 657
7 12145662 12147659 - ClG42_07g0066100.10 Clacu07g0661 661
7 11487918 11500787 + ClCG07G006500.2 Cla07g00622 622
7 12182324 12183694 - ClCG07G006600.1 Cla07g00633 633
7 12421762 12426630 + ClCG07G006650.2 Cla07g00638 638
7 12593269 12595791 - ClCG07G006670.1 Cla07g00640 640
4 133752 145001 + CmaCh04G000280.1 Cma04g00028 28
4 145507 161885 - CmaCh04G000290.1 Cma04g00029 29
4 215669 217930 - CmaCh04G000390.1 Cma04g00039 39
4 221872 224635 + CmaCh04G000420.1 Cma04g00042 42
4 225862 227930 - CmaCh04G000440.1 Cma04g00044 44
4 14499939 14501662 + CmaCh04G020890.1 Cma04g02089 2089
15 4997473 5000029 + CmaCh15G009410.1 Cma15g00941 941
18 8145039 8148261 + CmaCh18G009560.1 Cma18g00956 956
10 18270658 18298489 + MELO3C018345.2.1 Cme10g01474 1474
10 19087347 19133619 + MELO3C018322.2.1 Cme10g01515 1515
10 19508446 19509840 - MELO3C018309.2.1 Cme10g01534 1534
10 19536359 19542328 - MELO3C018306.2.1 Cme10g01536 1536
10 19598017 19600719 - MELO3C018305.2.1 Cme10g01537 1537
9 4923765 4925528 + PI0017309.1 Cmetu09g0102 102
10 8031521 8032650 + PI0011994.1 Cmetu10g0245 245
18 10663741 10667660 + CmoCh18G009570.1 Cmo18g00957 957
7 11269140 11277046 + CmPI595203_07g006700.1 Cmu07g0670 670
7 11914260 11915630 - CmPI595203_07g006800.1 Cmu07g0680 680
7 12136067 12141809 + CmPI595203_07g006820.1 Cmu07g0682 682
7 12289954 12291949 - CmPI595203_07g006840.1 Cmu07g0684 684
6 1919005 1921097 + Conep06aG0040500.1 Cone6ag0396 396
9 1944622 1949364 + Conep09aG0043200.1 Cone9ag0422 422
13 7185580 7193893 - Conep13aG0078700.1 Cone13ag0762 762
13 7194257 7197768 + Conep13aG0078800.1 Cone13ag0763 763
13 7198301 7203979 + Conep13aG0078900.1 Cone13ag0764 764
19 6221028 6232395 - Conep19aG0078800.1 Cone19ag0766 766
19 6232714 6235849 + Conep19aG0078900.1 Cone19ag0767 767
4 11169248 11175288 + Cp4.1LG04g13790.1 Cpe04g01376 1376
9 2197184 2202556 - Cp4.1LG09g03770.1 Cpe09g00366 366
7 13204617 13212520 + CrPI670011_07g010190.1 Cre07g1019 1019
7 14141234 14143204 - CrPI670011_07g010320.1 Cre07g1032 1032
5 9837251 9853359 + CsaV3_5G013310.1 Csa05g01025 1025
5 9862240 9895376 - CsaV3_5G013320.1 Csa05g01026 1026
5 12811044 12817222 + CsaV3_5G015440.1 Csa05g01220 1220
5 27853470 27856708 - CsaV3_5G035230.1 Csa05g02704 2704
1 61314157 61320731 - Hsped.01g04690.1 Hepe01g0469 469
1 61636502 61639261 + Hsped.01g04760.1 Hepe01g0476 476
13 14954900 14956378 - Lag0041284.1 Lac13g1488 1488
13 15180740 15189011 + Lag0041297.1 Lac13g1501 1501
4 16162742 16187030 + Lsi04G011530.1 Lsi04g01153 1153
4 16703808 16705184 - Lsi04G011600.1 Lsi04g01160 1160
4 16742281 16747234 - Lsi04G011620.1 Lsi04g01162 1162
4 16797077 16798953 - Lsi04G011630.1 Lsi04g01163 1163
6 1526872 1528620 - Sed0020091.1 Sed06g0201 201
6 1565784 1571598 + Sed0007127.1 Sed06g0211 211
4 27615559 27617189 - Tan0007582.1 Tan04g1602 1602
4 28785786 28790609 + Tan0022173.1 Tan04g1613 1613
1 4488300 4491290 - Vvi1g421 Vvi1g421 421
1 4493672 4545871 - Vvi1g422 Vvi1g422 422
1 4546686 4556121 + Vvi1g423 Vvi1g423 423
1 4557701 4559021 + Vvi1g424 Vvi1g424 424
1 4559806 4564709 + Vvi1g425 Vvi1g425 425
1 4565333 4574753 - Vvi1g426 Vvi1g426 426
1 4583156 4585054 - Vvi1g427 Vvi1g427 427
1 4585733 4591099 - Vvi1g428 Vvi1g428 428
1 4612429 4635979 + Vvi1g429 Vvi1g429 429
1 4638277 4649298 - Vvi1g430 Vvi1g430 430
       

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