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
Vvi4g1362 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1363 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1 . . . . . . . . . Cmo17g00383 . . . . . . . . . . . . . . Cla06g00399 Cam06g0420 Cec06g0428 Cco06g0428 Clacu06g0407 Cmu06g0407 Cre06g1186 . . . . . . Chy11g01605 . . . . . . . . . Sed09g0632 . . . Cma17g00394 . Car17g00365 Cpe12g00345 . Bhi12g01983 Tan06g2808 Cmetu11g2556 . . . Lcy12g0895 . . . . . . . Lsi09g01519 . . Cme11g02111
Vvi5g2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g3 . . Bda03g01197 . Bpe04g01126 . . . . . Cma06g01582 . . . Sed02g0487 Cpe08g00136 . Bhi01g01119 Tan10g1105 Cmetu06g2035 . . . . . . . . . . . Cone14ag0686 . . . Lsi05g01396 . . Cme06g00822 . . . . . . . . . Cmo06g01578 . . . . . . . . . . . . . . Cla05g00729 Cam05g0798 Cec05g0805 Cco05g0807 Clacu05g0787 Cmu05g0750 Cre05g0826 . Csa03g01545 Chy06g00781 .
Vvi5g4 Blo01g00046 . . Bda08g00326 . . . Bma05g01013 . . . . Car06g01340 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda13g00229 . Bpe13g00710 Bma02g00941 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g6 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g7 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g8 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe13g00710 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 14510541 14518217 - Bda017280.1 Bda03g01197 1197
8 3366107 3366971 - Bda024765.1 Bda08g00326 326
13 2885944 2886577 + Bda001108.1 Bda13g00229 229
1 21813063 21814572 + XM_039021406.1 Bhi01g01119 1119
12 62471468 62503637 - XM_039018704.1 Bhi12g01983 1983
1 610816 613721 + BLOR00046 Blo01g00046 46
2 49318301 49320251 - Bma015735.1 Bma02g00941 941
5 48616047 48618485 - Bma022168.1 Bma05g01013 1013
4 9758205 9767370 + Bpe015806.1 Bpe04g01126 1126
13 13673173 13674224 + Bpe025234 Bpe13g00710 710
5 7053777 7055412 + CaPI482276_05g007980.1 Cam05g0798 798
6 6331461 6350346 + CaPI482276_06g004200.1 Cam06g0420 420
6 9616840 9620369 + Carg25649-RA Car06g01340 1340
17 2326040 2339950 - Carg05572-RA Car17g00365 365
5 6788886 6790718 + CcPI632755_05g008070.1 Cco05g0807 807
6 4697245 4714977 + CcPI632755_06g004280.1 Cco06g0428 428
5 6795491 6798706 + CePI673135_05g008050.1 Cec05g0805 805
6 4840206 4860340 + CePI673135_06g004280.1 Cec06g0428 428
6 5486192 5487155 + Chy6G113090.1 Chy06g00781 781
11 22599378 22612588 - Chy11G201850.1 Chy11g01605 1605
5 6761131 6762755 + ClG42_05g0078700.10 Clacu05g0787 787
6 4869740 4888606 + ClG42_06g0040700.10 Clacu06g0407 407
5 6913770 6920155 + ClCG05G006790.2 Cla05g00729 729
6 4894948 4913414 + ClCG06G004280.1 Cla06g00399 399
6 9891202 9893033 + CmaCh06G015820.1 Cma06g01582 1582
17 2220854 2238323 - CmaCh17G003940.1 Cma17g00394 394
6 5628870 5630780 + MELO3C006744.2.1 Cme06g00822 822
11 28713961 28728067 - MELO3C021240.2.1 Cme11g02111 2111
6 5727232 5728312 + PI0024662.1 Cmetu06g2035 2035
11 3453544 3467327 + PI0013814.1 Cmetu11g2556 2556
6 11096046 11097516 + CmoCh06G015780.1 Cmo06g01578 1578
17 2368870 2383591 - CmoCh17G003830.1 Cmo17g00383 383
5 6617021 6618645 + CmPI595203_05g007500.1 Cmu05g0750 750
6 4664963 4683822 + CmPI595203_06g004070.1 Cmu06g0407 407
14 3548900 3549756 - Conep14aG0070100.1 Cone14ag0686 686
8 877859 881125 - Cp4.1LG08g05410.1 Cpe08g00136 136
12 2307256 2321990 - Cp4.1LG12g03480.1 Cpe12g00345 345
5 7426061 7428028 + CrPI670011_05g008260.1 Cre05g0826 826
6 5721313 5740233 + CrPI670011_06g011860.1 Cre06g1186 1186
3 11538638 11539612 + CsaV3_3G015450.1 Csa03g01545 1545
12 12777844 12792167 - Maker00025007 Lcy12g0895 895
5 21806546 21808682 - Lsi05G013960.1 Lsi05g01396 1396
9 23296207 23311465 - Lsi09G015190.1 Lsi09g01519 1519
2 42220658 42225260 + Sed0003794.1 Sed02g0487 487
9 7901915 7915661 - Sed0008409.1 Sed09g0632 632
6 80158040 80182226 - Tan0012260.1 Tan06g2808 2808
10 10672090 10674244 + Tan0012508.1 Tan10g1105 1105
4 23835409 23843626 + Vvi4g1362 Vvi4g1362 1362
4 23844523 23862507 - Vvi4g1363 Vvi4g1363 1363
5 0 12798 - Vvi5g1 Vvi5g1 1
5 18118 18457 + Vvi5g2 Vvi5g2 2
5 19030 27806 - Vvi5g3 Vvi5g3 3
5 32005 36655 + Vvi5g4 Vvi5g4 4
5 65306 83720 + Vvi5g5 Vvi5g5 5
5 83802 84482 - Vvi5g6 Vvi5g6 6
5 85361 86460 - Vvi5g7 Vvi5g7 7
5 86823 89944 + Vvi5g8 Vvi5g8 8
       

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