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
Vvi2g832 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g833 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g834 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g835 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g836 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g837 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g838 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g839 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g840 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g841 . . Bda06g01229 Bda08g00650 Bpe05g00507 Bpe07g00249 Bma07g00967 Bma14g00108 Cmo06g00612 Cmo16g01257 . . . . . Cpe14g01000 . . . . . . . . Cla10g00111 Cam10g0106 Cec10g0115 Cco10g0116 Clacu10g0112 Cmu10g0959 Cre10g0369 . . . . Lsi07g01140 . . Cme06g02416 Blo03g00811 . Bda07g00143 . . . Bma05g00692 Bma12g00251 . . . Cma06g00605 Cma16g01211 Car06g00540 Car16g01139 . . . . . . . . . . . . . . . . . Csa03g00110 Chy06g02195 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 42357103 42361205 - Bda023057.1 Bda06g01229 1229
7 1759668 1760659 - Bda025209.1 Bda07g00143 143
8 6759120 6761858 + Bda029112.1 Bda08g00650 650
3 33497112 33498641 + BLOR11992 Blo03g00811 811
5 40473448 40476178 - Bma021755.1 Bma05g00692 692
7 37103081 37105006 - Bma026108.1 Bma07g00967 967
12 3228306 3232260 + Bma007143.1 Bma12g00251 251
14 1466252 1468674 + Bma010513.1 Bma14g00108 108
5 19259308 19262048 - Bpe025815 Bpe05g00507 507
7 1768412 1772327 + Bpe021060.1 Bpe07g00249 249
10 2637708 2644225 - CaPI482276_10g001060.1 Cam10g0106 106
6 3033872 3039781 - Carg16292-RA Car06g00540 540
16 9732501 9738168 + Carg23570-RA Car16g01139 1139
10 1050446 1056950 - CcPI632755_10g001160.1 Cco10g0116 116
10 1063611 1070044 - CePI673135_10g001150.1 Cec10g0115 115
6 26183861 26187685 + Chy6G127230.1 Chy06g02195 2195
10 1364837 1371317 - ClG42_10g0011200.10 Clacu10g0112 112
10 1093492 1099900 - ClCG10G001080.1 Cla10g00111 111
6 2928656 2932678 - CmaCh06G006050.1 Cma06g00605 605
16 9181602 9187627 + CmaCh16G012110.1 Cma16g01211 1211
6 31284780 31292020 - MELO3C013800.2.1 Cme06g02416 2416
6 3019440 3025456 - CmoCh06G006120.1 Cmo06g00612 612
16 8964554 8970308 + CmoCh16G012570.1 Cmo16g01257 1257
10 1515878 1522354 - CmPI595203_10g009590.1 Cmu10g0959 959
14 8438601 8444368 + Cp4.1LG14g09910.1 Cpe14g01000 1000
10 2478535 2485075 - CrPI670011_10g003690.1 Cre10g0369 369
3 860991 867400 - CsaV3_3G001100.1 Csa03g00110 110
7 16845671 16852353 - Lsi07G011400.1 Lsi07g01140 1140
2 14338051 14338661 - Vvi2g832 Vvi2g832 832
2 14386732 14387420 + Vvi2g833 Vvi2g833 833
2 14455263 14456243 + Vvi2g834 Vvi2g834 834
2 14478818 14480844 + Vvi2g835 Vvi2g835 835
2 14558289 14566882 + Vvi2g836 Vvi2g836 836
2 14614996 14616258 + Vvi2g837 Vvi2g837 837
2 14619390 14622613 - Vvi2g838 Vvi2g838 838
2 14622644 14635079 - Vvi2g839 Vvi2g839 839
2 14717665 14717734 - Vvi2g840 Vvi2g840 840
2 14819756 14824676 + Vvi2g841 Vvi2g841 841
       

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