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
Vvi1g1221 Blo01g00361 . Bda01g02182 . Bpe13g00529 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma01g00013 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1222 . . . . . . . . . Cmo18g00694 . Cma18g00705 . Car18g00651 . Cpe09g00583 . . . . . . . . . . . . . . . . . . . Lsi04g00673 . . Cme10g00650 . . . . . . . . . . . . . Car04g01844 . . . . . . . . . . Cla11g01348 Cam11g1406 Cec11g1432 Cco11g1426 Clacu11g1563 Cmu11g1384 Cre11g1804 . . . .
Vvi1g1223 . . . . . Bpe10g00789 . . Cmo04g01926 Cmo18g00693 . . . . . . Cpe01g01613 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma04g01830 . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1224 . . . . . . . . . . . Cma18g00704 . Car18g00650 Sed06g1744 Cpe09g00584 . Bhi07g01916 Tan04g0058 Cmetu10g1687 Lac13g0059 Hepe10g0100 . . . . . . . . . . . . . Lsi04g00674 . . Cme10g00651 . . . . . . . . . . . . . Car04g01845 . . . . . . . . . . Cla11g01347 Cam11g1405 Cec11g1431 Cco11g1425 Clacu11g1562 Cmu11g1383 Cre11g1803 . . . .
Vvi1g1225 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1226 Blo01g00360 . Bda01g02181 . Bpe13g00530 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma01g00012 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1227 Blo01g00359 . Bda01g02180 Bda11g00397 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g00397 . . Bma01g00011 Bma06g01354 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1228 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1229 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1230 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 57789746 57791735 - Bda004522.1 Bda01g02180 2180
1 57792234 57799345 + Bda004523.2 Bda01g02181 2181
1 57801499 57803499 - Bda004524.1 Bda01g02182 2182
11 4306450 4308599 + Bda005138.1 Bda11g00397 397
7 51224024 51227388 - XM_039035621.1 Bhi07g01916 1916
1 4247769 4249798 - BLOR00359 Blo01g00359 359
1 4250283 4257649 + BLOR00360 Blo01g00360 360
1 4260034 4262056 - BLOR00361 Blo01g00361 361
1 251922 253950 - Bma000181.1 Bma01g00011 11
1 254429 261594 + Bma000182.2 Bma01g00012 12
1 290864 292899 - Bma000184.1 Bma01g00013 13
6 50437068 50438933 + Bma024467.1 Bma06g01354 1354
10 14047584 14054977 - Bpe003094.2 Bpe10g00789 789
13 12571022 12573003 + Bpe025224 Bpe13g00529 529
13 12575290 12582445 - Bpe010234.1 Bpe13g00530 530
11 26722516 26725512 + CaPI482276_11g014050.1 Cam11g1405 1405
11 26728872 26729156 + CaPI482276_11g014060.1 Cam11g1406 1406
4 10679505 10681642 - Carg14261-RA Car04g01844 1844
4 10682204 10685696 - Carg14260-RA Car04g01845 1845
18 7786818 7787608 + Carg21233-RA Car18g00650 650
18 7788974 7789866 + Carg21234-RA Car18g00651 651
11 27014517 27017525 + CcPI632755_11g014250.1 Cco11g1425 1425
11 27020816 27021100 + CcPI632755_11g014260.1 Cco11g1426 1426
11 28469379 28472394 + CePI673135_11g014310.1 Cec11g1431 1431
11 28475743 28476027 + CePI673135_11g014320.1 Cec11g1432 1432
11 26745199 26748208 + ClG42_11g0156200.10 Clacu11g1562 1562
11 26751554 26751838 + ClG42_11g0156300.10 Clacu11g1563 1563
11 26944216 26946993 + ClCG11G013750.2 Cla11g01347 1347
11 26951079 26951826 + ClCG11G013760.1 Cla11g01348 1348
4 9235655 9241626 - CmaCh04G018300.1 Cma04g01830 1830
18 6429597 6432621 + CmaCh18G007040.1 Cma18g00704 704
18 6433535 6434464 + CmaCh18G007050.1 Cma18g00705 705
10 4160743 4161512 - MELO3C011874.2.1 Cme10g00650 650
10 4162719 4166188 - MELO3C011873.2.1 Cme10g00651 651
10 17767179 17770583 + PI0023816.1 Cmetu10g1687 1687
4 9843329 9849127 - CmoCh04G019260.1 Cmo04g01926 1926
18 8813380 8816267 + CmoCh18G006930.1 Cmo18g00693 693
18 8817471 8818270 + CmoCh18G006940.1 Cmo18g00694 694
11 25997382 26000391 + CmPI595203_11g013830.1 Cmu11g1383 1383
11 26003711 26003995 + CmPI595203_11g013840.1 Cmu11g1384 1384
1 9863363 9869081 - Cp4.1LG01g16230.1 Cpe01g01613 1613
9 4032209 4033372 - Cp4.1LG09g05990.1 Cpe09g00583 583
9 4034120 4037129 - Cp4.1LG09g05950.1 Cpe09g00584 584
11 29619041 29621984 + CrPI670011_11g018030.1 Cre11g1803 1803
11 29625074 29625358 + CrPI670011_11g018040.1 Cre11g1804 1804
10 976754 979610 - Hsped.10g01000.1 Hepe10g0100 100
13 427397 430538 + Lag0039855.1 Lac13g0059 59
4 6166414 6167648 - Lsi04G006730.1 Lsi04g00673 673
4 6169764 6174175 - Lsi04G006740.1 Lsi04g00674 674
6 42141391 42145156 - Sed0014300.1 Sed06g1744 1744
4 502943 505993 + Tan0019453.1 Tan04g0058 58
1 20690928 20695341 + Vvi1g1221 Vvi1g1221 1221
1 20701555 20702206 - Vvi1g1222 Vvi1g1222 1222
1 20703719 20708466 - Vvi1g1223 Vvi1g1223 1223
1 20708513 20711493 - Vvi1g1224 Vvi1g1224 1224
1 20711557 20712478 - Vvi1g1225 Vvi1g1225 1225
1 20714758 20734567 - Vvi1g1226 Vvi1g1226 1226
1 20746044 20750153 + Vvi1g1227 Vvi1g1227 1227
1 20751548 20752616 - Vvi1g1228 Vvi1g1228 1228
1 20752677 20755355 + Vvi1g1229 Vvi1g1229 1229
1 20766414 20771154 - Vvi1g1230 Vvi1g1230 1230
       

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