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
Vvi19g994 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g995 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g996 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g997 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g998 . . . . . . . . . . Cma01g01306 Cma09g00736 Car01g01114 Car09g00646 . . Cpe02g00625 . . . . . . . Cla11g01601 Cam11g1667 Cec11g1696 . . Cmu11g1637 . . . . . Lsi04g01879 . . Cme07g00708 . . . . . . . . . Cmo01g01363 Cmo09g00728 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g999 . . . . . . . . . . Cma01g01308 Cma09g00735 Car01g01115 Car09g00645 . . Cpe02g00624 . . . . . . . Cla11g01603 Cam11g1668 Cec11g1697 Cco11g1691 Clacu11g1825 Cmu11g1638 Cre11g2052 Cone6ag0277 Cone9ag0314 . . Lsi04g01880 . . . . . . . . . . . . Cmo01g01364 Cmo09g00727 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1000 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1002 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1003 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 29362179 29371929 + CaPI482276_11g016670.1 Cam11g1667 1667
11 29371961 29375644 + CaPI482276_11g016680.1 Cam11g1668 1668
1 10382472 10388503 + Carg14779-RA Car01g01114 1114
1 10388984 10392956 + Carg14780-RA Car01g01115 1115
9 3768188 3771380 - Carg20051-RA Car09g00645 645
9 3772616 3779076 - Carg20052-RA Car09g00646 646
11 29743385 29757424 + CcPI632755_11g016910.1 Cco11g1691 1691
11 31198404 31208301 + CePI673135_11g016960.1 Cec11g1696 1696
11 31208333 31212456 + CePI673135_11g016970.1 Cec11g1697 1697
11 29385543 29399121 + ClG42_11g0182500.10 Clacu11g1825 1825
11 29693152 29699799 + ClCG11G016430.1 Cla11g01601 1601
11 29703175 29705274 + ClCG11G016450.2 Cla11g01603 1603
1 9342762 9349498 + CmaCh01G013060.1 Cma01g01306 1306
1 9351683 9355744 + CmaCh01G013080.1 Cma01g01308 1308
9 3496443 3500111 - CmaCh09G007350.1 Cma09g00735 735
9 3500142 3507709 - CmaCh09G007360.1 Cma09g00736 736
7 6202616 6209077 + MELO3C026965.2.1 Cme07g00708 708
1 10739249 10749438 + CmoCh01G013630.1 Cmo01g01363 1363
1 10749473 10752761 + CmoCh01G013640.1 Cmo01g01364 1364
9 3623881 3627511 - CmoCh09G007270.1 Cmo09g00727 727
9 3629722 3635730 - CmoCh09G007280.1 Cmo09g00728 728
11 28638285 28648130 + CmPI595203_11g016370.1 Cmu11g1637 1637
11 28648162 28651858 + CmPI595203_11g016380.1 Cmu11g1638 1638
6 1277610 1280546 - Conep06aG0027900.1 Cone6ag0277 277
9 1363083 1365732 - Conep09aG0031700.1 Cone9ag0314 314
2 3788747 3795677 - Cp4.1LG02g02500.1 Cpe02g00624 624
2 3796385 3802356 - Cp4.1LG02g02450.1 Cpe02g00625 625
11 32301919 32315245 + CrPI670011_11g020520.1 Cre11g2052 2052
4 25924179 25934544 + Lsi04G018790.1 Lsi04g01879 1879
4 25934864 25938938 + Lsi04G018800.1 Lsi04g01880 1880
19 19553943 19559065 + Vvi19g994 Vvi19g994 994
19 19592330 19597027 + Vvi19g995 Vvi19g995 995
19 19618650 19619493 + Vvi19g996 Vvi19g996 996
19 19625056 19625757 + Vvi19g997 Vvi19g997 997
19 19626825 19643204 + Vvi19g998 Vvi19g998 998
19 19655289 19660706 + Vvi19g999 Vvi19g999 999
19 19680045 19684077 - Vvi19g1000 Vvi19g1000 1000
19 19731049 19731340 - Vvi19g1001 Vvi19g1001 1001
19 19775639 19783293 + Vvi19g1002 Vvi19g1002 1002
19 19783334 19783547 - Vvi19g1003 Vvi19g1003 1003
       

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