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
Vvi3g1016 . . . . . . . . . Cmo11g01540 . . . . . . . Bhi05g00875 . . . . . . . . . . . . . . . . . Lsi03g00751 Csa07g00560 . Cme01g00229 . . . . . . . . . . . . . . . . . . . . . . . . Cla09g01528 . . . . . . . . Chy01g00245 .
Vvi3g1017 . . . . . . . Bma12g00370 . . . . . . . . . . . . . . . . Cla10g00891 . Cec10g0954 . . . . Cone12ag0978 . . . . . . . . . Bda15g00495 . . . . . . Cmo04g00665 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1018 . . . . . . . Bma12g00369 . . . . . . . . . . . . . . . . Cla10g00890 Cam10g0915 . Cco10g0911 Clacu10g0942 Cmu10g1729 Cre10g1101 . . . . . . . . . . . . . . . . . . Cmo16g00250 . . . . Cpe14g00191 . . . . . . . . . . . . . . . . . . .
Vvi3g1019 . . . . . . . . . . . . . . . . Cpe15g00362 . . . . . . . . . . . . . . Cone12ag0977 . . . . . . . . . . . . . . . . . . . Cma19g00465 . Car19g00341 . . . . . . . . . . . . . . . . . . . .
Vvi3g1020 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1021 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo16g00480 . . . . Cpe14g00374 . . . . . . . . . . . . . . . . . . .
Vvi3g1022 . . . . . . . Bma12g00358 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1023 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1024 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1025 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
15 8063702 8064616 - Bda012323.1 Bda15g00495 495
5 29992403 29995223 + XM_039032684.1 Bhi05g00875 875
12 6184040 6186942 + Bma007285.1 Bma12g00358 358
12 6681712 6685959 + Bma007303.1 Bma12g00369 369
12 6688158 6688763 - Bma007304.1 Bma12g00370 370
10 20586267 20592091 - CaPI482276_10g009150.1 Cam10g0915 915
19 5277052 5281679 - Carg22823-RA Car19g00341 341
10 19293157 19297864 - CcPI632755_10g009110.1 Cco10g0911 911
10 21296486 21297403 + CePI673135_10g009540.1 Cec10g0954 954
1 1686229 1688711 - Chy1G002450.1 Chy01g00245 245
10 19783041 19787705 - ClG42_10g0094200.10 Clacu10g0942 942
9 30259680 30262253 - ClCG09G015560.2 Cla09g01528 1528
10 20651592 20659455 - ClCG10G009330.2 Cla10g00890 890
10 20651642 20652559 + ClCG10G009320.1 Cla10g00891 891
19 5558147 5575752 - CmaCh19G004650.1 Cma19g00465 465
1 1631539 1633753 - MELO3C018631.2.1 Cme01g00229 229
4 3298998 3313469 + CmoCh04G006650.1 Cmo04g00665 665
11 11014360 11016706 + CmoCh11G015400.1 Cmo11g01540 1540
16 1096687 1110275 - CmoCh16G002500.1 Cmo16g00250 250
16 2298110 2299948 - CmoCh16G004800.1 Cmo16g00480 480
10 20410088 20414745 - CmPI595203_10g017290.1 Cmu10g1729 1729
12 8394845 8396311 - Conep12aG0100500.1 Cone12ag0977 977
12 8398814 8399993 + Conep12aG0100600.1 Cone12ag0978 978
14 1087416 1091312 - Cp4.1LG14g05150.1 Cpe14g00191 191
14 2291980 2293818 - Cp4.1LG14g03340.1 Cpe14g00374 374
15 4824025 4829328 - Cp4.1LG15g03680.1 Cpe15g00362 362
10 22059431 22064100 - CrPI670011_10g011010.1 Cre10g1101 1101
7 4090104 4100207 + CsaV3_7G006590.1 Csa07g00560 560
3 10273779 10276422 + Lsi03G007510.1 Lsi03g00751 751
3 16773257 16775286 - Vvi3g1016 Vvi3g1016 1016
3 16956479 16957997 + Vvi3g1017 Vvi3g1017 1017
3 16968651 16983804 - Vvi3g1018 Vvi3g1018 1018
3 17028351 17034085 + Vvi3g1019 Vvi3g1019 1019
3 17152458 17154221 - Vvi3g1020 Vvi3g1020 1020
3 17161780 17168980 + Vvi3g1021 Vvi3g1021 1021
3 17178216 17218628 - Vvi3g1022 Vvi3g1022 1022
3 17241384 17241726 + Vvi3g1023 Vvi3g1023 1023
3 17271806 17276119 - Vvi3g1024 Vvi3g1024 1024
3 17278266 17287864 + Vvi3g1025 Vvi3g1025 1025
       

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