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
Vvi18g1540 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1541 . . . . . . . . . . . . . . . . . . . . . . . . Cla08g00018 Cam08g0012 Cec08g0248 Cco08g0059 Clacu08g0031 Cmu08g0027 Cre08g0012 . . . . . . . . . . . . . . . . . . . . . . . . . Bhi06g00287 . . . . . . . . . . . . . Lsi08g00012 . . .
Vvi18g1542 . . . . . . . . . . . . . . . . . . . . . . . . Cla08g00017 Cam08g0011 Cec08g0249 Cco08g0058 Clacu08g0030 Cmu08g0026 Cre08g0011 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi08g00011 . . .
Vvi18g1543 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1544 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1545 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1546 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed11g1710 . . . . . . . . Bhi06g00290 Tan10g2120 Cmetu03g2111 . . . . . . . . . . . . . . .
Vvi18g1547 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1548 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1549 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi06g00292 . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 6357540 6359310 - XM_039034639.1 Bhi06g00287 287
6 6433430 6436313 - XM_039034020.1 Bhi06g00290 290
6 6500305 6502622 + XM_039035077.1 Bhi06g00292 292
8 207015 213049 + CaPI482276_08g000110.1 Cam08g0011 11
8 213680 214901 - CaPI482276_08g000120.1 Cam08g0012 12
8 603003 609101 + CcPI632755_08g000580.1 Cco08g0058 58
8 609707 610920 - CcPI632755_08g000590.1 Cco08g0059 59
8 4757052 4758270 + CePI673135_08g002480.1 Cec08g0248 248
8 4758862 4764941 - CePI673135_08g002490.1 Cec08g0249 249
8 651088 657197 + ClG42_08g0003000.10 Clacu08g0030 30
8 657804 659017 - ClG42_08g0003100.10 Clacu08g0031 31
8 456913 464041 + ClCG08G000160.1 Cla08g00017 17
8 464276 465489 - ClCG08G000170.1 Cla08g00018 18
3 26490317 26496956 - PI0022355.1 Cmetu03g2111 2111
8 568472 574576 + CmPI595203_08g000260.1 Cmu08g0026 26
8 575182 576395 - CmPI595203_08g000270.1 Cmu08g0027 27
8 354400 355178 + CrPI670011_08g000110.1 Cre08g0011 11
8 361556 363396 - CrPI670011_08g000120.1 Cre08g0012 12
8 262841 267806 + Lsi08G000110.1 Lsi08g00011 11
8 274282 276008 - Lsi08G000120.1 Lsi08g00012 12
11 32275976 32278813 - Sed0016902.1 Sed11g1710 1710
10 67572684 67575634 - Tan0021562.1 Tan10g2120 2120
18 24785526 24788535 - Vvi18g1540 Vvi18g1540 1540
18 24806055 24809727 + Vvi18g1541 Vvi18g1541 1541
18 24811606 24818958 - Vvi18g1542 Vvi18g1542 1542
18 24839030 24849802 - Vvi18g1543 Vvi18g1543 1543
18 24852932 24856629 - Vvi18g1544 Vvi18g1544 1544
18 24871392 24874057 + Vvi18g1545 Vvi18g1545 1545
18 24889178 24892076 - Vvi18g1546 Vvi18g1546 1546
18 24924816 24927056 - Vvi18g1547 Vvi18g1547 1547
18 24927148 24930210 + Vvi18g1548 Vvi18g1548 1548
18 24941767 24953370 - Vvi18g1549 Vvi18g1549 1549
       

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