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
Vvi1g701 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g702 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo04g02836 . . . . . Cpe13g00900 . . . . . . . . . . . . . . . . . Chy09g00338 .
Vvi1g703 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g704 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag0643 . . . . . . . . . . . . . . . . Cma05g00011 . . . . . . . . . . . . . . . . . . . . . .
Vvi1g705 . . Bda01g02222 Bda11g01265 Bpe13g00496 . . . . Cmo18g00804 . Cma18g00800 . Car18g00731 Sed08g1391 Cpe09g00503 Cpe01g01530 Bhi07g01727 Tan04g1231 Cmetu04g2853 Lac13g0202 Hepe10g1642 . . Cla05g02540 Cam05g2730 Cec05g2761 Cco05g2801 Clacu05g2731 Cmu05g2584 Cre05g2698 Cone13ag1039 Cone19ag1029 Cone8ag0661 Cone12ag0642 Lsi04g00548 Csa05g02338 Chy10g00905 Cme10g00521 . . . Bda11g01265 . . Bma01g00049 Bma06g00622 . . . Cma04g01731 . Car04g01764 . . . . . . . . . . . . . . . . . . . . .
Vvi1g706 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g707 . . . . . . Bma14g01793 . . . . . . . Sed01g1019 . Cpe01g01529 Bhi07g01725 Tan04g1230 Cmetu09g1229 Lac13g0203 Hepe10g1643 . . Cla05g02539 Cam05g2729 Cec05g2760 Cco05g2800 Clacu05g2730 Cmu05g2583 Cre05g2697 Cone13ag1038 . . . Lsi04g00547 Csa05g02339 Chy10g00906 Cme10g00520 . Blo11g00915 Bda07g01601 . . . . . . Cmo04g02843 . Cma04g01730 . Car04g01763 . . . . . . . . . . . . . . . . . . . Chy09g00330 .
Vvi1g708 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g709 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g710 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 58049132 58050844 + Bda004562.2 Bda01g02222 2222
7 29684270 29686094 + Bda028470.1 Bda07g01601 1601
11 13293941 13297564 - Bda007782.2 Bda11g01265 1265
7 47701181 47705825 + XM_039037484.1 Bhi07g01725 1725
7 47705892 47713580 - XM_039037485.1 Bhi07g01727 1727
11 18870466 18872376 + BLOR03791 Blo11g00915 915
1 534473 536477 + Bma000217.1 Bma01g00049 49
6 32838828 32842418 + Bma023563.1 Bma06g00622 622
14 38531797 38533667 + Bma012564.1 Bma14g01793 1793
13 12370981 12373748 - Bpe010207.2 Bpe13g00496 496
5 34603361 34607017 + CaPI482276_05g027290.1 Cam05g2729 2729
5 34607503 34611343 - CaPI482276_05g027300.1 Cam05g2730 2730
4 10097941 10101749 + Carg14342-RA Car04g01763 1763
4 10100707 10103391 - Carg14341-RA Car04g01764 1764
18 8437870 8440643 + Carg14467-RA Car18g00731 731
5 35745596 35749233 + CcPI632755_05g028000.1 Cco05g2800 2800
5 35749730 35753579 - CcPI632755_05g028010.1 Cco05g2801 2801
5 38059940 38063622 + CePI673135_05g027600.1 Cec05g2760 2760
5 38064118 38067966 - CePI673135_05g027610.1 Cec05g2761 2761
9 2865074 2867054 + Chy9G160460.1 Chy09g00330 330
9 2955913 2964998 + Chy9G160540.1 Chy09g00338 338
10 14748006 14757478 + Chy10G180990.1 Chy10g00905 905
10 14757977 14761207 - Chy10G181000.1 Chy10g00906 906
5 34810960 34814618 + ClG42_05g0273000.10 Clacu05g2730 2730
5 34815108 34818804 - ClG42_05g0273100.10 Clacu05g2731 2731
5 36747445 36751101 + ClCG05G025320.2 Cla05g02539 2539
5 36751591 36759394 - ClCG05G025330.2 Cla05g02540 2540
4 8700030 8704022 + CmaCh04G017300.1 Cma04g01730 1730
4 8703199 8707858 - CmaCh04G017310.1 Cma04g01731 1731
5 44166 48743 + CmaCh05G000110.1 Cma05g00011 11
18 7030407 7036753 + CmaCh18G008000.1 Cma18g00800 800
10 3355394 3359166 + MELO3C011998.2.1 Cme10g00520 520
10 3358260 3363023 - MELO3C011997.2.1 Cme10g00521 521
4 9388801 9392043 - PI0022203.1 Cmetu04g2853 2853
9 20779272 20782310 + PI0028080.1 Cmetu09g1229 1229
4 20276632 20285590 - CmoCh04G028360.1 Cmo04g02836 2836
4 20313160 20315248 - CmoCh04G028430.1 Cmo04g02843 2843
18 9492720 9495246 + CmoCh18G008040.1 Cmo18g00804 804
5 34548954 34552615 + CmPI595203_05g025830.1 Cmu05g2583 2583
5 34553106 34556777 - CmPI595203_05g025840.1 Cmu05g2584 2584
8 6597006 6600549 - Conep08aG0068400.1 Cone8ag0661 661
12 5868359 5877062 - Conep12aG0066500.1 Cone12ag0642 642
12 5887303 5891130 + Conep12aG0066600.1 Cone12ag0643 643
13 8609558 8611628 + Conep13aG0106900.1 Cone13ag1038 1038
13 8612445 8613958 - Conep13aG0107000.1 Cone13ag1039 1039
19 7662477 7665189 - Conep19aG0106100.1 Cone19ag1029 1029
1 9161179 9165930 + Cp4.1LG01g15230.1 Cpe01g01529 1529
1 9162799 9167006 - Cp4.1LG01g15310.1 Cpe01g01530 1530
9 3341603 3344569 - Cp4.1LG09g05050.1 Cpe09g00503 503
13 7689434 7701521 - Cp4.1LG13g08930.1 Cpe13g00900 900
5 37902873 37906521 + CrPI670011_05g026970.1 Cre05g2697 2697
5 37907004 37910772 - CrPI670011_05g026980.1 Cre05g2698 2698
5 25748877 25752521 + CsaV3_5G031570.1 Csa05g02338 2338
5 25751891 25756218 - CsaV3_5G031580.1 Csa05g02339 2339
10 53118625 53122588 + Hsped.10g16420.1 Hepe10g1642 1642
10 53123061 53125655 - Hsped.10g16430.1 Hepe10g1643 1643
13 1398664 1401683 + Lag0039998.1 Lac13g0202 202
13 1402154 1405018 - Lag0039999.1 Lac13g0203 203
4 5024874 5029573 + Lsi04G005470.1 Lsi04g00547 547
4 5029328 5032808 - Lsi04G005480.1 Lsi04g00548 548
1 7582626 7586572 + Sed0004042.1 Sed01g1019 1019
8 28403539 28413818 - Sed0009809.3 Sed08g1391 1391
4 11674381 11676775 + Tan0005709.1 Tan04g1230 1230
4 11677239 11697746 - Tan0001821.1 Tan04g1231 1231
1 8010190 8012475 + Vvi1g701 Vvi1g701 701
1 8012585 8021182 - Vvi1g702 Vvi1g702 702
1 8036640 8038012 - Vvi1g703 Vvi1g703 703
1 8038364 8044353 - Vvi1g704 Vvi1g704 704
1 8065296 8071309 + Vvi1g705 Vvi1g705 705
1 8079674 8080776 - Vvi1g706 Vvi1g706 706
1 8083561 8085999 - Vvi1g707 Vvi1g707 707
1 8096450 8100142 + Vvi1g708 Vvi1g708 708
1 8105310 8106237 + Vvi1g709 Vvi1g709 709
1 8106259 8107501 + Vvi1g710 Vvi1g710 710
       

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