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
Vvi19g204 . Blo03g01548 . . . Bpe08g01021 . . . . . . . . Sed06g0329 . Cpe02g00700 Bhi09g03433 Tan01g4390 Cmetu01g0301 . Hepe01g1389 Mch11g1066 . Cla11g01759 Cam11g1826 Cec11g1846 Cco11g1853 Clacu11g1986 . Cre11g2203 Cone6ag0150 Cone9ag0176 . . Lsi04g02069 Csa04g02340 Chy07g00071 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g205 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g206 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g207 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g208 Blo03g00667 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g209 . . . . . . . Bma13g00950 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g210 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo07g00921 . . Bda12g00870 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy06g01688 .
Vvi19g211 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g212 . . . . Bpe09g00236 . . Bma13g00952 . Cmo04g00586 . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1060 . . . . . . Blo10g00761 . Bda12g00838 . . . . . . . Cma04g00552 . Car04g00521 . . Cpe01g00494 . . . . . . . Cla05g01006 Cam05g1095 Cec05g1105 Cco05g1098 Clacu05g1091 Cmu05g1042 Cre05g1115 . . Chy06g01159 .
Vvi19g213 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
12 38014588 38018165 - Bda009356.1 Bda12g00838 838
12 39301177 39302940 - Bda009399.2 Bda12g00870 870
9 86739043 86743933 + XM_039041211.1 Bhi09g03433 3433
3 28208869 28211208 + BLOR11848 Blo03g00667 667
3 43123941 43128592 + BLOR12729 Blo03g01548 1548
7 28237792 28240103 - BLOR18853 Blo07g00921 921
10 23792715 23797817 - BLOR02551 Blo10g00761 761
13 40577149 40579440 - Bma010045.1 Bma13g00950 950
13 40629150 40632781 - Bma010047.1 Bma13g00952 952
8 12474777 12479341 - Bpe023145.1 Bpe08g01021 1021
9 1704001 1707740 + Bpe023906.1 Bpe09g00236 236
5 10017968 10023480 - CaPI482276_05g010950.1 Cam05g1095 1095
11 30796226 30801719 - CaPI482276_11g018260.1 Cam11g1826 1826
4 2930502 2934183 + Carg13186-RA Car04g00521 521
5 9787141 9792043 - CcPI632755_05g010980.1 Cco05g1098 1098
11 31220418 31226986 - CcPI632755_11g018530.1 Cco11g1853 1853
5 9775106 9780779 - CePI673135_05g011050.1 Cec05g1105 1105
11 32661245 32667488 - CePI673135_11g018460.1 Cec11g1846 1846
6 10260762 10267409 + Chy6G116870.1 Chy06g01159 1159
6 19596758 19599742 - Chy6G122160.1 Chy06g01688 1688
7 678077 682617 - Chy7G129010.1 Chy07g00071 71
5 9757543 9763343 - ClG42_05g0109100.10 Clacu05g1091 1091
11 30834779 30840150 - ClG42_11g0198600.10 Clacu11g1986 1986
5 10128284 10135940 - ClCG05G009320.1 Cla05g01006 1006
11 31209011 31214897 - ClCG11G018040.2 Cla11g01759 1759
4 2799423 2802816 + CmaCh04G005520.1 Cma04g00552 552
1 2283139 2296446 + PI0008034.1 Cmetu01g0301 301
4 2924111 2928752 + CmoCh04G005860.1 Cmo04g00586 586
5 9597909 9603794 - CmPI595203_05g010420.1 Cmu05g1042 1042
6 756007 759437 + Conep06aG0015100.1 Cone6ag0150 150
9 774554 778091 + Conep09aG0017800.1 Cone9ag0176 176
14 8937859 8940633 - Conep14aG0108100.1 Cone14ag1060 1060
1 2858116 2862946 + Cp4.1LG01g01770.1 Cpe01g00494 494
2 4421614 4426471 - Cp4.1LG02g01720.1 Cpe02g00700 700
5 10483618 10489416 - CrPI670011_05g011150.1 Cre05g1115 1115
11 33757471 33763554 - CrPI670011_11g022030.1 Cre11g2203 2203
4 23860859 23865575 - CsaV3_4G033660.1 Csa04g02340 2340
1 79094360 79099075 + Hsped.01g13890.1 Hepe01g1389 1389
4 27847744 27852634 - Lsi04G020690.1 Lsi04g02069 2069
11 7420716 7425125 - MC11g0873 Mch11g1066 1066
6 2872673 2885699 - Sed0005211.2 Sed06g0329 329
1 109011180 109015617 - Tan0010387.1 Tan01g4390 4390
19 2600505 2605072 - Vvi19g204 Vvi19g204 204
19 2605400 2606252 + Vvi19g205 Vvi19g205 205
19 2609293 2611769 - Vvi19g206 Vvi19g206 206
19 2613230 2621035 + Vvi19g207 Vvi19g207 207
19 2630095 2638598 - Vvi19g208 Vvi19g208 208
19 2643179 2661593 - Vvi19g209 Vvi19g209 209
19 2667891 2670271 - Vvi19g210 Vvi19g210 210
19 2673117 2682722 + Vvi19g211 Vvi19g211 211
19 2686235 2691922 - Vvi19g212 Vvi19g212 212
19 2699750 2702129 + Vvi19g213 Vvi19g213 213
       

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