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
Vvi3g976 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g977 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo16g00263 . . . . Cpe14g00202 . . . . . . . . . . . . . . . . . . .
Vvi3g978 . . . . . . . . . . . . . . . . . . . . . . . . Cla10g00895 Cam10g0919 Cec10g0957 Cco10g0917 Clacu10g0948 Cmu10g1733 Cre10g1109 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g979 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g980 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g981 . . . . . . . . . Cmo11g01477 . . . . Sed10g1872 Cpe04g00372 Cpe15g00366 Bhi05g00901 Tan02g1189 Cmetu01g2487 Lac12g0060 Hepe02g0730 . . . . . . . . . . . . . Lsi03g00730 . . . . . Bda15g00493 . . . . . . . . Cma11g01659 Cma19g00468 Car11g01180 Car19g00344 . . . . . . . . . Cla09g01565 Cam09g1596 Cec09g1718 Cco09g1775 . . Cre09g1612 . . . .
Vvi3g982 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g983 . . . . . . . . . . . . . . Sed06g0768 . . Bhi05g00899 Tan02g1190 Cmetu01g0153 Lac12g0059 Hepe02g0731 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g984 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g985 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag0989 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
15 8059195 8060277 - Bda012321.1 Bda15g00493 493
5 31530867 31534678 - XM_039032875.1 Bhi05g00899 899
5 31550248 31551526 + XM_039032185.1 Bhi05g00901 901
9 26984990 26986063 + CaPI482276_09g015960.1 Cam09g1596 1596
10 20729377 20735055 + CaPI482276_10g009190.1 Cam10g0919 919
11 9561590 9562573 - Carg26463-RA Car11g01180 1180
19 5318670 5325527 + Carg22820-RA Car19g00344 344
9 30362491 30363558 - CcPI632755_09g017750.1 Cco09g1775 1775
10 19447530 19459807 + CcPI632755_10g009170.1 Cco10g0917 917
9 32202019 32203080 - CePI673135_09g017180.1 Cec09g1718 1718
10 21440547 21445717 + CePI673135_10g009570.1 Cec10g0957 957
10 20020528 20027401 + ClG42_10g0094800.10 Clacu10g0948 948
9 31119992 31121071 - ClCG09G015940.1 Cla09g01565 1565
10 20898104 20904977 + ClCG10G009370.2 Cla10g00895 895
11 10914692 10915678 + CmaCh11G016590.1 Cma11g01659 1659
19 5612484 5619942 + CmaCh19G004680.1 Cma19g00468 468
1 1719444 1723865 + PI0018346.1 Cmetu01g0153 153
1 1515484 1516867 + PI0023017.1 Cmetu01g2487 2487
11 10443138 10444130 - CmoCh11G014770.1 Cmo11g01477 1477
16 1165773 1168877 + CmoCh16G002630.1 Cmo16g00263 263
10 20648383 20655653 + CmPI595203_10g017330.1 Cmu10g1733 1733
12 8449064 8450499 + Conep12aG0101700.1 Cone12ag0989 989
4 4386496 4387479 - Cp4.1LG04g07030.1 Cpe04g00372 372
14 1139196 1142744 + Cp4.1LG14g05220.1 Cpe14g00202 202
15 4874155 4875138 + Cp4.1LG15g03610.1 Cpe15g00366 366
9 32949660 32950739 - CrPI670011_09g016120.1 Cre09g1612 1612
10 22245421 22251841 + CrPI670011_10g011090.1 Cre10g1109 1109
2 8018562 8019910 - Hsped.02g07300.1 Hepe02g0730 730
2 8023146 8027302 + Hsped.02g07310.1 Hepe02g0731 731
12 697025 700150 - Lag0014431.1 Lac12g0059 59
12 718700 719776 + Lag0014432.1 Lac12g0060 60
3 9827304 9828347 - Lsi03G007300.1 Lsi03g00730 730
6 8129431 8132270 - Sed0021578.1 Sed06g0768 768
10 35599711 35600994 + Sed0007105.1 Sed10g1872 1872
2 27586647 27588180 - Tan0010830.1 Tan02g1189 1189
2 27883229 27888051 + Tan0000752.1 Tan02g1190 1190
3 15321427 15321811 + Vvi3g976 Vvi3g976 976
3 15345489 15354975 + Vvi3g977 Vvi3g977 977
3 15416130 15426803 + Vvi3g978 Vvi3g978 978
3 15465127 15465860 + Vvi3g979 Vvi3g979 979
3 15520675 15521254 + Vvi3g980 Vvi3g980 980
3 15529866 15532548 - Vvi3g981 Vvi3g981 981
3 15558812 15562236 - Vvi3g982 Vvi3g982 982
3 15582921 15585234 + Vvi3g983 Vvi3g983 983
3 15596923 15598147 + Vvi3g984 Vvi3g984 984
3 15617476 15621957 + Vvi3g985 Vvi3g985 985
       

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