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
Vvi2g182 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g183 . . . . . . . . . . . . . . . . . . . . . . . . Cla07g01081 Cam07g1419 Cec07g1240 Cco07g1218 Clacu07g1143 Cmu07g1125 Cre07g1502 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g184 . . . Bda08g00453 . . . . . . Cma02g00920 Cma15g01289 Car02g00670 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo02g00928 Cmo15g01360 . . . . . Cpe13g00098 . . . . . . . . . . . . . . . . . Cme09g01852
Vvi2g185 Blo02g01162 . . . . Bpe07g00059 . . . . Cma02g00919 . Car02g00669 Car15g01252 . . . . . . . . . . . . . . . . . Cone8ag0235 Cone12ag0240 . . . . . . . . . . . . . Bma12g00618 . Cmo02g00927 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g186 . Blo03g00260 Bda06g00160 Bda08g00452 . Bpe07g00058 . . . Cmo16g00578 . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0869 Cone9ag0875 . . . Cme07g01524 . . . . . . Bma05g00889 Bma12g00619 . . . . Cma16g00529 . . . . . . . . . . . . . . . . . . . Csa04g00683 Chy07g01126 .
Vvi2g187 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0234 . . . . . . . . . Bda07g01938 . . . . Bma12g00620 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g188 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g189 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0233 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g190 . . Bda06g00162 . Bpe05g00708 Bpe07g00057 . . Cmo06g00603 Cmo16g00577 . . . . . Cpe14g00447 . . . . . . . . Cla07g01080 Cam07g1420 Cec07g1236 Cco07g1216 Clacu07g1141 Cmu07g1123 Cre07g1500 . . . . . . . Cme07g01523 . . . . . . . . . . . Cma06g00596 Cma16g00528 . . . . . . . . . . . . . . . . . . . . Chy07g01125 .
Vvi2g191 Blo02g01163 Blo03g00261 . Bda08g00451 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma05g00891 Bma12g00621 . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00684 . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 2306869 2309705 + Bda023362.1 Bda06g00160 160
6 2337739 2341628 + Bda023364.2 Bda06g00162 162
7 36869637 36871852 + Bda028917.1 Bda07g01938 1938
8 4639458 4642959 - Bda024901.1 Bda08g00451 451
8 4663800 4666738 - Bda024902.1 Bda08g00452 452
8 4675371 4676609 + Bda024904.1 Bda08g00453 453
2 43265588 43266814 - BLOR10892 Blo02g01162 1162
2 43290674 43294142 + BLOR10893 Blo02g01163 1163
3 5480339 5486749 + BLOR11441 Blo03g00260 260
3 5488587 5492392 + BLOR11442 Blo03g00261 261
5 46692209 46694371 + Bma022007.1 Bma05g00889 889
5 46706732 46710246 + Bma022009.2 Bma05g00891 891
12 27457740 27458787 - Bma007794.1 Bma12g00618 618
12 27459040 27462002 + Bma007795.1 Bma12g00619 619
12 27463041 27464774 + Bma007796.1 Bma12g00620 620
12 27467195 27472405 + Bma007797.1 Bma12g00621 621
5 20652962 20656471 + Bpe018121.1 Bpe05g00708 708
7 462325 466200 - Bpe020869.1 Bpe07g00057 57
7 471137 474033 - Bpe020870.1 Bpe07g00058 58
7 474756 475804 + Bpe020871.2 Bpe07g00059 59
7 28735365 28739035 + CaPI482276_07g014190.1 Cam07g1419 1419
7 28764969 28768960 + CaPI482276_07g014200.1 Cam07g1420 1420
2 5002952 5005364 + Carg08554-RA Car02g00669 669
2 5007246 5015357 + Carg08553-RA Car02g00670 670
15 9766582 9768060 + Carg20790-RA Car15g01252 1252
7 26003702 26007693 - CcPI632755_07g012160.1 Cco07g1216 1216
7 26040274 26045675 - CcPI632755_07g012180.1 Cco07g1218 1218
7 27865103 27869094 - CePI673135_07g012360.1 Cec07g1236 1236
7 27906177 27911626 - CePI673135_07g012400.1 Cec07g1240 1240
7 16156637 16160624 - Chy7G139550.1 Chy07g01125 1125
7 16172100 16175257 - Chy7G139560.1 Chy07g01126 1126
7 26031053 26035044 - ClG42_07g0114100.10 Clacu07g1141 1141
7 26066074 26071439 - ClG42_07g0114300.10 Clacu07g1143 1143
7 27410322 27414757 - ClCG07G011370.1 Cla07g01080 1080
7 27438593 27452453 - ClCG07G011380.2 Cla07g01081 1081
2 5473398 5480745 + CmaCh02G009190.1 Cma02g00919 919
2 5482126 5484966 + CmaCh02G009200.1 Cma02g00920 920
6 2881162 2884562 + CmaCh06G005960.1 Cma06g00596 596
15 8181182 8183634 + CmaCh15G012890.1 Cma15g01289 1289
16 2695380 2699223 - CmaCh16G005280.1 Cma16g00528 528
16 2705166 2710249 - CmaCh16G005290.1 Cma16g00529 529
7 21065003 21069575 - MELO3C016260.2.1 Cme07g01523 1523
7 21080767 21084481 - MELO3C016262.2.1 Cme07g01524 1524
9 22741769 22744190 + MELO3C005760.2.1 Cme09g01852 1852
2 5695413 5697958 + CmoCh02G009270.1 Cmo02g00927 927
2 5700632 5703452 + CmoCh02G009280.1 Cmo02g00928 928
6 2972044 2975927 + CmoCh06G006030.1 Cmo06g00603 603
15 9301295 9304152 + CmoCh15G013600.1 Cmo15g01360 1360
16 2791791 2795653 - CmoCh16G005770.1 Cmo16g00577 577
16 2802485 2806807 - CmoCh16G005780.1 Cmo16g00578 578
7 26279345 26283336 - CmPI595203_07g011230.1 Cmu07g1123 1123
7 26314340 26319704 - CmPI595203_07g011250.1 Cmu07g1125 1125
6 4439684 4441751 + Conep06aG0089600.1 Cone6ag0869 869
8 1332920 1342683 - Conep08aG0024200.1 Cone8ag0233 233
8 1343157 1345150 - Conep08aG0024300.1 Cone8ag0234 234
8 1346759 1348295 + Conep08aG0024400.1 Cone8ag0235 235
9 4263438 4265582 + Conep09aG0089700.1 Cone9ag0875 875
12 1295881 1297270 + Conep12aG0024500.1 Cone12ag0240 240
13 712130 716322 - Cp4.1LG13g01040.1 Cpe13g00098 98
14 2792768 2796752 - Cp4.1LG14g02590.1 Cpe14g00447 447
7 30238849 30242840 - CrPI670011_07g015000.1 Cre07g1500 1500
7 30275626 30281126 - CrPI670011_07g015020.1 Cre07g1502 1502
4 4633029 4636833 + CsaV3_4G006830.1 Csa04g00683 683
4 4646625 4651248 + CsaV3_4G006840.1 Csa04g00684 684
2 1803176 1803783 - Vvi2g182 Vvi2g182 182
2 1804244 1812371 + Vvi2g183 Vvi2g183 183
2 1812387 1814056 - Vvi2g184 Vvi2g184 184
2 1817152 1820380 - Vvi2g185 Vvi2g185 185
2 1820995 1826505 + Vvi2g186 Vvi2g186 186
2 1827631 1830534 + Vvi2g187 Vvi2g187 187
2 1831754 1832406 - Vvi2g188 Vvi2g188 188
2 1834523 1837791 - Vvi2g189 Vvi2g189 189
2 1842258 1843381 + Vvi2g190 Vvi2g190 190
2 1850586 1857501 + Vvi2g191 Vvi2g191 191
       

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