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
Vvi1g1141 . . . . . . . . Cmo04g01910 Cmo18g00707 . Cma18g00720 . Car18g00666 . Cpe09g00569 Cpe01g01598 Bhi07g01868 . . Lac13g0089 Hepe10g1543 . . Cla05g02633 . Cec05g2863 Cco05g2895 Clacu05g2831 Cmu05g2678 . . . . . Lsi04g00654 . . Cme10g00632 Blo06g00821 Blo11g00984 . . . . . . . . . Cma04g01814 . Car04g01826 . . . . . . . . . . . . . . . . . . . . .
Vvi1g1142 . Blo16g01187 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone11ag0354 . . . . . . . . . . . . . . Bma06g00581 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1143 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1144 . . . . . Bpe10g00778 . Bma15g00243 . . . . . Car18g00665 Sed06g0134 Cpe09g00570 . Bhi07g01872 Tan04g0097 Cmetu10g0012 Lac13g0085 Hepe10g1542 . . Cla05g02634 Cam05g2827 . Cco05g2896 Clacu05g2832 Cmu05g2679 Cre05g2795 . Cone19ag1108 . . Lsi04g00655 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1145 Blo01g00371 Blo16g01188 Bda01g02190 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0728 . . . . . . . . . . . . Bma06g00580 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1146 . . . . . . Bma14g01880 . Cmo04g01911 . . . . . Sed01g1596 . Cpe01g01599 Bhi07g01873 Tan04g0096 Cmetu12g0111 Lac13g0084 Hepe10g1541 . . Cla05g02635 Cam05g2828 Cec05g2864 Cco05g2897 Clacu05g2833 Cmu05g2680 Cre05g2796 . . . . . . . Cme10g00635 . . . . . . . . . . . Cma04g01815 . Car04g01827 . . . . . . . . . . . . . . . . . . . . .
Vvi1g1147 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi04g00656 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1148 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1149 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1150 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 57859290 57861169 + Bda004531.1 Bda01g02190 2190
7 50731577 50737951 + XM_039036321.1 Bhi07g01868 1868
7 50829982 50832207 + XM_039035571.1 Bhi07g01872 1872
7 50834993 50838608 + XM_039037007.1 Bhi07g01873 1873
1 4322451 4324436 + BLOR00371 Blo01g00371 371
6 31467470 31472652 + BLOR17404 Blo06g00821 821
11 24140665 24145919 - BLOR03860 Blo11g00984 984
16 40413257 40413591 - BLOR21974 Blo16g01187 1187
16 40414658 40416612 + BLOR21975 Blo16g01188 1188
6 31154354 31156337 - Bma023504.3 Bma06g00580 580
6 31157169 31157520 + Bma023505.1 Bma06g00581 581
14 40268455 40270358 + Bma012665.1 Bma14g01880 1880
15 2443606 2445141 - Bma013229.1 Bma15g00243 243
10 13964749 13966163 + Bpe003084.2 Bpe10g00778 778
5 35335085 35346367 + CaPI482276_05g028270.1 Cam05g2827 2827
5 35349012 35352335 + CaPI482276_05g028280.1 Cam05g2828 2828
4 10581713 10587273 + Carg14279-RA Car04g01826 1826
4 10589709 10592988 + Carg14278-RA Car04g01827 1827
18 7877259 7878791 - Carg21248-RA Car18g00665 665
18 7880293 7887086 - Carg21249-RA Car18g00666 666
5 36499178 36505166 + CcPI632755_05g028950.1 Cco05g2895 2895
5 36508394 36510484 + CcPI632755_05g028960.1 Cco05g2896 2896
5 36513093 36516427 + CcPI632755_05g028970.1 Cco05g2897 2897
5 38808714 38814676 + CePI673135_05g028630.1 Cec05g2863 2863
5 38817941 38826010 + CePI673135_05g028640.1 Cec05g2864 2864
5 35560298 35566262 + ClG42_05g0283100.10 Clacu05g2831 2831
5 35569993 35571552 + ClG42_05g0283200.10 Clacu05g2832 2832
5 35574020 35577407 + ClG42_05g0283300.10 Clacu05g2833 2833
5 37535790 37541754 + ClCG05G026280.2 Cla05g02633 2633
5 37544946 37547044 + ClCG05G026285.1 Cla05g02634 2634
5 37549512 37552899 + ClCG05G026290.1 Cla05g02635 2635
4 9140791 9147219 + CmaCh04G018140.1 Cma04g01814 1814
4 9149255 9152123 + CmaCh04G018150.1 Cma04g01815 1815
18 6515218 6526652 - CmaCh18G007200.1 Cma18g00720 720
10 4026934 4032059 + MELO3C011894.2.1 Cme10g00632 632
10 4045840 4047815 + MELO3C011891.2.1 Cme10g00635 635
10 17900339 17902866 - PI0009056.1 Cmetu10g0012 12
12 4962888 4966212 - PI0019745.1 Cmetu12g0111 111
4 9742902 9748788 + CmoCh04G019100.1 Cmo04g01910 1910
4 9751158 9754479 + CmoCh04G019110.1 Cmo04g01911 1911
18 8908612 8919029 - CmoCh18G007070.1 Cmo18g00707 707
5 35298663 35304627 + CmPI595203_05g026780.1 Cmu05g2678 2678
5 35308358 35309917 + CmPI595203_05g026790.1 Cmu05g2679 2679
5 35312385 35315775 + CmPI595203_05g026800.1 Cmu05g2680 2680
8 7309890 7312674 + Conep08aG0075200.1 Cone8ag0728 728
11 1737231 1737739 - Conep11aG0036400.1 Cone11ag0354 354
19 7994042 7996292 + Conep19aG0114200.1 Cone19ag1108 1108
1 9756152 9770227 + Cp4.1LG01g16000.1 Cpe01g01598 1598
1 9772238 9775861 + Cp4.1LG01g15990.1 Cpe01g01599 1599
9 3931604 3938789 + Cp4.1LG09g06160.1 Cpe09g00569 569
9 3939953 3942039 + Cp4.1LG09g06110.1 Cpe09g00570 570
5 38662581 38673209 + CrPI670011_05g027950.1 Cre05g2795 2795
5 38675747 38679019 + CrPI670011_05g027960.1 Cre05g2796 2796
10 52136644 52141681 - Hsped.10g15410.1 Hepe10g1541 1541
10 52144414 52146557 - Hsped.10g15420.1 Hepe10g1542 1542
10 52149272 52155091 - Hsped.10g15430.1 Hepe10g1543 1543
13 616402 620433 - Lag0039880.1 Lac13g0084 84
13 622506 624065 - Lag0039881.1 Lac13g0085 85
13 644195 644928 - Lag0039885.1 Lac13g0089 89
4 5978596 5984384 + Lsi04G006540.1 Lsi04g00654 654
4 5987831 5989390 + Lsi04G006550.1 Lsi04g00655 655
4 5992685 5996516 + Lsi04G006560.1 Lsi04g00656 656
1 11572033 11577023 + Sed0005184.1 Sed01g1596 1596
6 953096 953539 + Sed0028237.1 Sed06g0134 134
4 672909 678260 - Tan0012888.1 Tan04g0096 96
4 682100 683809 - Tan0017353.1 Tan04g0097 97
1 19526695 19532390 + Vvi1g1141 Vvi1g1141 1141
1 19533131 19534966 - Vvi1g1142 Vvi1g1142 1142
1 19543649 19546789 + Vvi1g1143 Vvi1g1143 1143
1 19548425 19557950 + Vvi1g1144 Vvi1g1144 1144
1 19565566 19569566 + Vvi1g1145 Vvi1g1145 1145
1 19570004 19571923 + Vvi1g1146 Vvi1g1146 1146
1 19574854 19576375 - Vvi1g1147 Vvi1g1147 1147
1 19576382 19577202 - Vvi1g1148 Vvi1g1148 1148
1 19577701 19585175 + Vvi1g1149 Vvi1g1149 1149
1 19586823 19601973 + Vvi1g1150 Vvi1g1150 1150
       

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