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
Vvi1g1331 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1332 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1333 Blo01g00158 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0659 Cone15ag0670 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1334 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1335 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1336 . . . Bda11g00375 . . . . . . . . . . . . . . . . . . . . Cla06g00163 Cam06g0050 Cec06g0182 Cco06g0175 Clacu06g0176 Cmu06g0171 Cre06g0945 Cone14ag0658 Cone15ag0668 . . . Csa04g00246 . Cme11g02360 . . . Bda11g00375 . . . Bma06g01331 Sed07g0131 . . . . . . . Cpe03g01189 Bhi12g02397 Tan06g1451 Cmetu11g1663 . . . . . . . . . . . . . Chy07g01528 Cme07g01972
Vvi1g1337 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe03g01185 . . . . . . . . . . . . . . . . . Cme07g01977
Vvi1g1338 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1339 . . . . Bpe13g00826 . . . . . . . . . . . . . . . . . . . Cla06g00162 Cam06g0051 Cec06g0181 Cco06g0174 Clacu06g0175 Cmu06g0170 Cre06g0944 . . . . . . Chy11g01826 Cme11g02361 Blo02g00204 . . . . . . Bma06g01330 Sed09g0330 . . . . . . . . Bhi12g02396 Tan06g1449 Cmetu11g2046 . Hepe03g1165 . . . . . . . . . . . Chy07g01536 Cme07g01979
Vvi1g1340 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 4152959 4154927 - Bda005114.1 Bda11g00375 375
12 75673241 75679736 - XM_039019749.1 Bhi12g02396 2396
12 75772279 75775232 + XM_039051027.1 Bhi12g02397 2397
1 2144259 2145345 - BLOR00158 Blo01g00158 158
2 1864512 1881591 + BLOR09934 Blo02g00204 204
6 50269961 50274977 - Bma024441.1 Bma06g01330 1330
6 50284856 50286867 - Bma024442.1 Bma06g01331 1331
13 14532108 14537584 + Bpe010517.1 Bpe13g00826 826
6 2357214 2359752 - CaPI482276_06g000500.1 Cam06g0050 50
6 2385501 2391297 + CaPI482276_06g000510.1 Cam06g0051 51
6 1783902 1789777 - CcPI632755_06g001740.1 Cco06g0174 174
6 1816092 1818782 + CcPI632755_06g001750.1 Cco06g0175 175
6 1810824 1816574 - CePI673135_06g001810.1 Cec06g0181 181
6 1842787 1845469 + CePI673135_06g001820.1 Cec06g0182 182
7 19545555 19549480 - Chy7G143580.1 Chy07g01528 1528
7 19607780 19622567 + Chy7G143660.1 Chy07g01536 1536
11 24629950 24635345 + Chy11G204060.1 Chy11g01826 1826
6 1954727 1960565 - ClG42_06g0017500.10 Clacu06g0175 175
6 1985878 1988432 + ClG42_06g0017600.10 Clacu06g0176 176
6 1828593 1834393 - ClCG06G001790.1 Cla06g00162 162
6 1860012 1863060 + ClCG06G001800.1 Cla06g00163 163
7 24856471 24862839 - MELO3C017797.2.1 Cme07g01972 1972
7 24894226 24896981 + MELO3C017802.2.1 Cme07g01977 1977
7 24916504 24925625 + MELO3C017803.2.1 Cme07g01979 1979
11 30595070 30598347 - MELO3C022348.2.1 Cme11g02360 2360
11 30615632 30621233 + MELO3C022349.2.1 Cme11g02361 2361
11 1456273 1459441 + PI0001525.1 Cmetu11g1663 1663
11 1429573 1434920 - PI0014539.1 Cmetu11g2046 2046
6 1750055 1755850 - CmPI595203_06g001700.1 Cmu06g0170 170
6 1781232 1783786 + CmPI595203_06g001710.1 Cmu06g0171 171
14 3365197 3367334 - Conep14aG0067200.1 Cone14ag0658 658
14 3374889 3376892 - Conep14aG0067300.1 Cone14ag0659 659
15 3560722 3563299 - Conep15aG0068100.1 Cone15ag0668 668
15 3564539 3565928 - Conep15aG0068300.1 Cone15ag0670 670
3 9702531 9705871 - Cp4.1LG03g13180.1 Cpe03g01185 1185
3 9732446 9736048 + Cp4.1LG03g13220.1 Cpe03g01189 1189
6 2853748 2859543 - CrPI670011_06g009440.1 Cre06g0944 944
6 2883833 2886525 + CrPI670011_06g009450.1 Cre06g0945 945
4 1493876 1500668 + CsaV3_4G002460.1 Csa04g00246 246
3 65267852 65274541 + Hsped.03g11650.1 Hepe03g1165 1165
7 1202934 1206506 - Sed0027998.2 Sed07g0131 131
9 2976707 2984211 - Sed0023362.1 Sed09g0330 330
6 19402214 19408004 - Tan0013568.1 Tan06g1449 1449
6 19497406 19500564 + Tan0014912.2 Tan06g1451 1451
1 22279453 22280781 + Vvi1g1331 Vvi1g1331 1331
1 22299989 22304575 - Vvi1g1332 Vvi1g1332 1332
1 22304969 22308253 - Vvi1g1333 Vvi1g1333 1333
1 22308445 22311511 - Vvi1g1334 Vvi1g1334 1334
1 22323504 22323657 + Vvi1g1335 Vvi1g1335 1335
1 22328029 22331014 + Vvi1g1336 Vvi1g1336 1336
1 22336321 22338766 + Vvi1g1337 Vvi1g1337 1337
1 22356345 22356408 + Vvi1g1338 Vvi1g1338 1338
1 22356990 22364888 + Vvi1g1339 Vvi1g1339 1339
1 22388039 22389199 + Vvi1g1340 Vvi1g1340 1340
       

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