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
Vvi3g236 . . Bda06g00459 . . . . Bma12g00863 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car11g01408 . . . . . . . . . . . . . . . . . . . . .
Vvi3g237 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g238 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g239 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo04g00601 Blo13g00482 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g240 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g241 . . . . . . . Bma12g00864 . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi10g00822 . . . . . . . . . . . Sed05g3473 . . . . . . . . Bhi10g01234 Tan05g1067 Cmetu11g0438 . Hepe08g0332 . . . . . . . . . . . . Cme11g01219
Vvi3g242 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi10g00823 . . . Blo04g00600 . . . . . . . Sed01g0639 . . . . . . . . Bhi10g01233 Tan05g1068 Cmetu11g1383 . Hepe08g0331 . . . . . . . . . . . . Cme11g01221
Vvi3g243 . . . . Bpe07g00697 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag1227 . Lsi10g00824 . . . . . . . . . . . . . . . . . . . . Bhi10g01232 . . . . . . . . . . . . . . . . Cme11g01222
Vvi3g244 . Blo15g00399 . . . . . Bma12g00903 Cmo19g00799 . . . . . Sed05g2188 . . Bhi05g01617 Tan02g0599 Cmetu01g2685 . . . . Cla02g00372 . . Cco02g0382 Clacu02g0371 Cmu02g0368 Cre02g0701 . . . Cone10ag1225 . Csa07g00160 . Cme01g01176 . . . . . . . . . . . Cma11g01348 . . . . . . . . . . . . . . . . . . . Lsi11g01261 . Chy01g00630 .
Vvi3g245 . Blo15g00400 . . . . . Bma12g00902 Cmo19g00800 . . . . . . . . Bhi05g01616 . . . . . . Cla02g00371 . . . Clacu02g0370 Cmu02g0367 Cre02g0700 . . . . Lsi10g00825 Csa07g00161 . Cme01g01175 . . . . . . . . . . . Cma11g01347 Cma19g00784 . . . . . . . . . . . . . . . . . . Lsi11g01264 . Chy01g00628 Cme11g01223
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 6640286 6644784 - Bda023703.1 Bda06g00459 459
5 53098643 53099497 + XM_039031276.1 Bhi05g01616 1616
5 53100540 53101904 + XM_039031657.1 Bhi05g01617 1617
10 27605335 27610440 - XM_039045958.1 Bhi10g01232 1232
10 27727069 27731525 - XM_039045084.1 Bhi10g01233 1233
10 27782815 27788097 - XM_039046919.1 Bhi10g01234 1234
4 5164305 5167653 - BLOR13512 Blo04g00600 600
4 5193974 5197001 + BLOR13513 Blo04g00601 601
13 25699684 25703128 - BLOR05763 Blo13g00482 482
15 5649152 5649994 - BLOR06793 Blo15g00399 399
15 5698955 5707968 - BLOR06794 Blo15g00400 400
12 39564798 39569380 - Bma008183.1 Bma12g00863 863
12 39597324 39598962 + Bma008184.1 Bma12g00864 864
12 40387495 40390608 + Bma008231.2 Bma12g00902 902
12 40402501 40403367 + Bma008232.1 Bma12g00903 903
7 13586974 13596447 + Bpe021544.1 Bpe07g00697 697
11 11533512 11534867 + Carg18124-RA Car11g01408 1408
2 3474340 3484911 + CcPI632755_02g003820.1 Cco02g0382 382
1 4414154 4415005 + Chy1G006280.1 Chy01g00628 628
1 4418666 4419556 + Chy1G006300.1 Chy01g00630 630
2 3355667 3356521 + ClG42_02g0037000.10 Clacu02g0370 370
2 3359169 3360680 + ClG42_02g0037100.10 Clacu02g0371 371
2 3567021 3567872 + ClCG02G003599.1 Cla02g00371 371
2 3571457 3572311 + ClCG02G024600.1 Cla02g00372 372
11 8933147 8934265 + CmaCh11G013470.1 Cma11g01347 1347
11 8936577 8937428 + CmaCh11G013480.1 Cma11g01348 1348
19 7639048 7639931 - CmaCh19G007840.1 Cma19g00784 784
1 14967070 14967924 + MELO3C013284.2.1 Cme01g01175 1175
1 14977127 14978156 + MELO3C013286.2.1 Cme01g01176 1176
11 18442134 18453892 + MELO3C013632.2.1 Cme11g01219 1219
11 18516464 18521133 + MELO3C013634.2.1 Cme11g01221 1221
11 18583545 18589583 + MELO3C013635.2.1 Cme11g01222 1222
11 18623032 18624671 + MELO3C013636.2.1 Cme11g01223 1223
1 4680503 4681351 + PI0024898.1 Cmetu01g2685 2685
11 12473781 12482381 - PI0017522.1 Cmetu11g0438 438
11 12406362 12409520 - PI0023181.1 Cmetu11g1383 1383
19 7964186 7965034 - CmoCh19G007990.1 Cmo19g00799 799
19 7966943 7967785 - CmoCh19G008000.1 Cmo19g00800 800
2 3349475 3350329 + CmPI595203_02g003670.1 Cmu02g0367 367
2 3352978 3354489 + CmPI595203_02g003680.1 Cmu02g0368 368
3 31055108 31059322 + Conep03aG0173400.1 Cone3ag1227 1227
10 9204204 9205109 + Conep10aG0126000.1 Cone10ag1225 1225
2 3920086 3920940 + CrPI670011_02g007000.1 Cre02g0700 700
2 3923634 3924488 + CrPI670011_02g007010.1 Cre02g0701 701
7 1363959 1364846 - CsaV3_7G001600.1 Csa07g00160 160
7 1366069 1366920 - CsaV3_7G001610.1 Csa07g00161 161
8 2969153 2974124 - Hsped.08g03310.1 Hepe08g0331 331
8 2995639 3000845 - Hsped.08g03320.1 Hepe08g0332 332
10 11327352 11332090 + Lsi10G008220.1 Lsi10g00822 822
10 11376759 11381037 + Lsi10G008230.1 Lsi10g00823 823
10 11440193 11446427 + Lsi10G008240.1 Lsi10g00824 824
10 11535514 11537267 + Lsi10G008250.1 Lsi10g00825 825
11 21250340 21251233 - Lsi11G012610.1 Lsi11g01261 1261
11 21258145 21258999 - Lsi11G012640.1 Lsi11g01264 1264
1 4652355 4656802 + Sed0024395.1 Sed01g0639 639
5 34701350 34702195 + Sed0027956.1 Sed05g2188 2188
5 43527741 43534508 + Sed0018198.1 Sed05g3473 3473
2 5301018 5305052 + Tan0022354.1 Tan02g0599 599
5 9223127 9227267 + Tan0011514.1 Tan05g1067 1067
5 9293472 9298398 + Tan0004445.1 Tan05g1068 1068
3 2313914 2331028 - Vvi3g236 Vvi3g236 236
3 2334481 2338229 - Vvi3g237 Vvi3g237 237
3 2338608 2344688 - Vvi3g238 Vvi3g238 238
3 2346117 2352506 - Vvi3g239 Vvi3g239 239
3 2372021 2379593 + Vvi3g240 Vvi3g240 240
3 2380379 2384597 + Vvi3g241 Vvi3g241 241
3 2403126 2409026 + Vvi3g242 Vvi3g242 242
3 2413496 2420431 + Vvi3g243 Vvi3g243 243
3 2421824 2430563 - Vvi3g244 Vvi3g244 244
3 2434388 2439692 - Vvi3g245 Vvi3g245 245
       

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