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
Vvi2g782 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g783 . . . Bda08g00648 Bpe05g00509 . . . . . . . Car02g01404 . . . Cpe05g00147 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma05g00694 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g784 . . Bda06g01235 . . Bpe07g00244 Bma07g01005 . Cmo06g00621 Cmo16g01249 . . . . . Cpe14g00994 . . . . . . . . Cla10g00118 Cam10g0115 Cec10g0124 Cco10g0124 Clacu10g0121 Cmu10g0968 Cre10g0378 . . . . Lsi07g01149 . . Cme06g02425 . . . . . . . Bma12g00247 . . . Cma06g00614 Cma16g01202 Car06g00547 Car16g01132 . . . . . . . . . . . . . . . . . Csa03g00119 Chy06g02185 .
Vvi2g785 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g786 . . . . . . . Bma14g00071 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo03g00893 . Bda07g00066 . . Bpe11g00304 . . . . Cmo19g00221 . . . . . Cpe15g00179 . . . . . . . . . . . . . . . . . .
Vvi2g787 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g788 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g789 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g790 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0546 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g791 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 42430161 42434912 - Bda023065.1 Bda06g01235 1235
7 900180 902804 + Bda025123.1 Bda07g00066 66
8 6710973 6712761 + Bda029109.1 Bda08g00648 648
3 34855723 34858536 - BLOR12074 Blo03g00893 893
5 40707521 40709306 - Bma021763.1 Bma05g00694 694
7 40046367 40051730 - Bma026175.1 Bma07g01005 1005
12 3202476 3207169 + Bma007139.1 Bma12g00247 247
14 875393 877978 + Bma010475.1 Bma14g00071 71
5 19278488 19280233 - Bpe017927.2 Bpe05g00509 509
7 1738890 1743599 + Bpe021055.2 Bpe07g00244 244
11 2228801 2231408 + Bpe003678.1 Bpe11g00304 304
10 2746190 2750975 + CaPI482276_10g001150.1 Cam10g0115 115
2 9236654 9239342 - Carg08871-RA Car02g01404 1404
6 3109625 3113945 + Carg23416-RA Car06g00547 547
16 9683707 9691165 - Carg23577-RA Car16g01132 1132
10 1153711 1158479 + CcPI632755_10g001240.1 Cco10g0124 124
10 1167189 1171957 + CePI673135_10g001240.1 Cec10g0124 124
6 26093073 26097653 - Chy6G127130.1 Chy06g02185 2185
10 1469047 1473835 + ClG42_10g0012100.10 Clacu10g0121 121
10 1199621 1205778 + ClCG10G001170.1 Cla10g00118 118
6 2993687 2998223 + CmaCh06G006140.1 Cma06g00614 614
16 9131910 9139993 - CmaCh16G012020.1 Cma16g01202 1202
6 31368518 31373276 + MELO3C013809.2.1 Cme06g02425 2425
6 3085733 3090484 + CmoCh06G006210.1 Cmo06g00621 621
16 8911800 8920474 - CmoCh16G012490.1 Cmo16g01249 1249
19 1483825 1493237 + CmoCh19G002210.1 Cmo19g00221 221
10 1620329 1625106 + CmPI595203_10g009680.1 Cmu10g0968 968
8 4038403 4043094 + Conep08aG0056700.1 Cone8ag0546 546
5 769508 772491 + Cp4.1LG05g00410.1 Cpe05g00147 147
14 8381699 8392126 - Cp4.1LG14g09990.1 Cpe14g00994 994
15 1464272 1473627 + Cp4.1LG15g01680.1 Cpe15g00179 179
10 2581125 2585882 + CrPI670011_10g003780.1 Cre10g0378 378
3 947266 952507 + CsaV3_3G001190.1 Csa03g00119 119
7 16966726 16973201 + Lsi07G011490.1 Lsi07g01149 1149
2 12528920 12532950 + Vvi2g782 Vvi2g782 782
2 12649057 12674003 - Vvi2g783 Vvi2g783 783
2 12674905 12697098 + Vvi2g784 Vvi2g784 784
2 12702813 12703038 - Vvi2g785 Vvi2g785 785
2 12710239 12715877 - Vvi2g786 Vvi2g786 786
2 12756221 12764275 - Vvi2g787 Vvi2g787 787
2 12800306 12817428 + Vvi2g788 Vvi2g788 788
2 12817477 12826831 - Vvi2g789 Vvi2g789 789
2 12946347 12964317 - Vvi2g790 Vvi2g790 790
2 13004263 13012644 - Vvi2g791 Vvi2g791 791
       

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