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
Vvi3g26 . Blo15g00668 Bda06g00963 Bda08g00957 . . Bma05g00428 . . . Cma02g00365 . Car02g00233 . . . . . . . . . . . . . . . . . . . . . Cone10ag1099 Lsi10g00414 . Chy11g00338 . . . . . . Bpe05g00321 . . Sed01g0261 Cmo02g00369 . . . . . . Cpe05g01290 Bhi10g01943 Tan05g1240 Cmetu11g1701 . Hepe08g0977 . . . . . . . . . . Csa02g01306 . Cme11g00167
Vvi3g27 . . . Bda08g00958 . . Bma05g00427 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag1212 . . . . . . . . . . Bpe05g00320 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g28 Blo02g00646 . Bda06g00964 Bda08g00959 Bpe07g00497 . Bma05g00426 . . . Cma02g00364 Cma20g00811 Car02g00231 Car20g00695 . . . . . . . . . . . . . . . . . Cone12ag1182 Cone8ag1227 . . Lsi10g00416 . . . . . . . . Bpe05g00319 . . . Cmo02g00367 Cmo20g00819 . . . . Cpe16g00276 Cpe05g01292 Bhi10g01940 Tan05g1237 . . Hepe08g0974 . . . . . . . . . . Csa02g01309 . Cme11g00170
Vvi3g29 . . . . . . . . . . . . . . . . . . . . . . . . Cla02g00489 . . . . . . . . . . . Csa07g00030 . Cme01g01350 . Blo13g00536 . . . . . . . . . Cma11g01430 . . . . . . . . . . . . . . . . . . . . . Chy01g00748 .
Vvi3g30 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag1211 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g31 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g32 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g33 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g34 . . . . . . . . . . . . . . Sed05g2290 . . Bhi05g01262 Tan02g0757 Cmetu01g2730 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g35 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 27076547 27083154 + Bda022607.1 Bda06g00963 963
6 27255148 27256224 + Bda022611.1 Bda06g00964 964
8 18678618 18689026 - Bda034031 Bda08g00957 957
8 18725052 18728585 + Bda029623.1 Bda08g00958 958
8 18763743 18764830 + Bda029624.1 Bda08g00959 959
5 45539736 45553679 + XM_039032229.1 Bhi05g01262 1262
10 48383774 48385475 - XM_039046952.1 Bhi10g01940 1940
10 48430850 48435504 + XM_039044468.1 Bhi10g01943 1943
2 15245325 15247400 + BLOR10376 Blo02g00646 646
13 27193186 27194888 - BLOR05817 Blo13g00536 536
15 20045357 20058402 + BLOR07062 Blo15g00668 668
5 13638997 13640072 - Bma021268.1 Bma05g00426 426
5 13663105 13677818 - Bma021269.1 Bma05g00427 427
5 13738918 13751627 + Bma031184 Bma05g00428 428
5 16803996 16805092 - Bpe017733.1 Bpe05g00319 319
5 16817248 16820434 - Bpe017734.1 Bpe05g00320 320
5 16834991 16845263 + Bpe017735.1 Bpe05g00321 321
7 9691597 9692676 - Bpe021340.1 Bpe07g00497 497
2 1503706 1504952 - Carg27196-RA Car02g00231 231
2 1560353 1564021 + Carg24136-RA Car02g00233 233
20 3976946 3978270 - Carg25951-RA Car20g00695 695
1 5538009 5540691 - Chy1G007480.1 Chy01g00748 748
11 3047724 3051465 + Chy11G189180.1 Chy11g00338 338
2 4807358 4810362 - ClCG02G004630.1 Cla02g00489 489
2 1797272 1798853 - CmaCh02G003640.1 Cma02g00364 364
2 1808590 1812660 + CmaCh02G003650.1 Cma02g00365 365
11 9421355 9427161 - CmaCh11G014300.1 Cma11g01430 1430
20 3817823 3819388 - CmaCh20G008110.1 Cma20g00811 811
1 16873453 16876805 - MELO3C013427.2.1 Cme01g01350 1350
11 1804046 1808024 - MELO3C023347.2.1 Cme11g00167 167
11 1826644 1828431 + MELO3C023350.2.1 Cme11g00170 170
1 5763078 5775592 + PI0020747.1 Cmetu01g2730 2730
11 27906433 27910598 - PI0017217.1 Cmetu11g1701 1701
2 1855553 1857072 - CmoCh02G003670.1 Cmo02g00367 367
2 1868662 1872662 + CmoCh02G003690.1 Cmo02g00369 369
20 4050695 4052188 - CmoCh20G008190.1 Cmo20g00819 819
3 30832963 30836101 + Conep03aG0171800.1 Cone3ag1211 1211
3 30841286 30845084 - Conep03aG0171900.1 Cone3ag1212 1212
8 10361651 10363066 + Conep08aG0126500.1 Cone8ag1227 1227
10 7720732 7724720 + Conep10aG0112800.1 Cone10ag1099 1099
12 9338953 9340378 + Conep12aG0122200.1 Cone12ag1182 1182
5 9008670 9012752 - Cp4.1LG05g12920.1 Cpe05g01290 1290
5 9021238 9023083 + Cp4.1LG05g12840.1 Cpe05g01292 1292
16 4752379 4755359 + Cp4.1LG16g02750.1 Cpe16g00276 276
2 12705462 12709710 - CsaV3_2G015220.1 Csa02g01306 1306
2 12724631 12726645 + CsaV3_2G015250.1 Csa02g01309 1309
7 425377 428490 + CsaV3_7G000300.1 Csa07g00030 30
8 9152296 9154031 - Hsped.08g09740.1 Hepe08g0974 974
8 9198153 9202020 + Hsped.08g09770.1 Hepe08g0977 977
10 6279900 6284354 - Lsi10G004140.1 Lsi10g00414 414
10 6313348 6314724 + Lsi10G004160.1 Lsi10g00416 416
1 2026917 2034189 + Sed0022270.1 Sed01g0261 261
5 35448557 35459214 + Sed0010772.1 Sed05g2290 2290
2 7152912 7164258 + Tan0001963.1 Tan02g0757 757
5 12837964 12840096 - Tan0010290.2 Tan05g1237 1237
5 12931443 12935735 + Tan0020746.1 Tan05g1240 1240
3 430288 436670 - Vvi3g26 Vvi3g26 26
3 440844 445043 + Vvi3g27 Vvi3g27 27
3 452475 454201 + Vvi3g28 Vvi3g28 28
3 457047 458789 + Vvi3g29 Vvi3g29 29
3 462582 465475 - Vvi3g30 Vvi3g30 30
3 480459 480785 - Vvi3g31 Vvi3g31 31
3 484538 485522 + Vvi3g32 Vvi3g32 32
3 503105 504318 + Vvi3g33 Vvi3g33 33
3 510037 511819 + Vvi3g34 Vvi3g34 34
3 512367 513361 - Vvi3g35 Vvi3g35 35
       

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