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
Vvi1g1361 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1362 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1363 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1364 . Blo16g00697 Bda01g02080 Bda11g00371 Bpe13g00834 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00215 . . . . . Bda11g00371 . . . Bma06g01323 . . . . . . . . . . . . . . . . . . . . . . . . . Chy07g01554 Cme07g02001
Vvi1g1365 . . . Bda11g00370 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g00370 Bpe14g00823 . . Bma06g01322 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1366 . . . . . . . . . . . . . . . . . . . . . . . . Cla06g00154 Cam06g0062 Cec06g0170 Cco06g0164 Clacu06g0164 Cmu06g0160 Cre06g0936 . . . . . . Chy11g01835 Cme11g02371 . . . . . . . . Sed09g0343 . . . . . . . . Bhi12g02382 Tan06g1433 Cmetu11g1216 . Hepe03g1178 . . . . . . . . . Lsi09g01772 . . .
Vvi1g1367 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy11g01836 Cme11g02372 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1368 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0642 Cone15ag0652 . . . Csa04g00214 . . . . . . Bpe14g00826 . . . . . . . . . . . Cpe03g01171 . . . . . . . . . . . . . . . . Chy07g01555 Cme07g02002
Vvi1g1369 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00213 . . Blo02g00215 . . . . . . . . . . . . . . . Cpe03g01170 . . . . . . . . . . . . . . . . Chy07g01556 Cme07g02003
Vvi1g1370 . Blo16g00694 . . . . . . . . . . . . . . . . . . . . . . Cla06g00153 . Cec06g0169 Cco06g0163 Clacu06g0163 . Cre06g0935 . . . . . . Chy11g01838 Cme11g02374 . . . . . . . . Sed09g0344 . . . . . . Cpe17g00947 . Bhi12g02381 Tan06g1432 Cmetu11g0098 . . . . . . . . . . . Lsi09g01773 . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 57016457 57019848 + Bda004408.1 Bda01g02080 2080
11 4052956 4054734 + Bda005107.1 Bda11g00370 370
11 4056047 4058091 - Bda005108.1 Bda11g00371 371
12 75160979 75161881 - XM_039019357.1 Bhi12g02381 2381
12 75241183 75241692 + XM_039019182.1 Bhi12g02382 2382
2 2023853 2025949 + BLOR09945 Blo02g00215 215
16 26713934 26714403 + BLOR07942 Blo16g00694 694
16 26809091 26812775 - BLOR07945 Blo16g00697 697
6 50195810 50197753 + Bma024431.1 Bma06g01322 1322
6 50199104 50201263 - Bma024432.1 Bma06g01323 1323
13 14601133 14603276 + Bpe010524.1 Bpe13g00834 834
14 6213414 6214961 - Bpe014200.1 Bpe14g00823 823
14 6229785 6234194 + Bpe014203.1 Bpe14g00826 826
6 2486141 2486893 - CaPI482276_06g000620.1 Cam06g0062 62
6 1684295 1684808 - CcPI632755_06g001630.1 Cco06g0163 163
6 1686876 1687612 + CcPI632755_06g001640.1 Cco06g0164 164
6 1710950 1711464 - CePI673135_06g001690.1 Cec06g0169 169
6 1713510 1714257 + CePI673135_06g001700.1 Cec06g0170 170
7 19777891 19780179 + Chy7G143840.1 Chy07g01554 1554
7 19784127 19792463 - Chy7G143850.1 Chy07g01555 1555
7 19803603 19805778 + Chy7G143860.1 Chy07g01556 1556
11 24709645 24710393 - Chy11G204150.1 Chy11g01835 1835
11 24711997 24713033 - Chy11G204160.1 Chy11g01836 1836
11 24716856 24717154 + Chy11G204180.1 Chy11g01838 1838
6 1852223 1857517 - ClG42_06g0016300.10 Clacu06g0163 163
6 1859304 1860048 + ClG42_06g0016400.10 Clacu06g0164 164
6 1725991 1726750 - ClCG06G001690.2 Cla06g00153 153
6 1728512 1729368 + ClCG06G001710.1 Cla06g00154 154
7 25081989 25084945 + MELO3C017823.2.1 Cme07g02001 2001
7 25087910 25096324 - MELO3C017824.2.1 Cme07g02002 2002
7 25108916 25111551 + MELO3C017825.2.1 Cme07g02003 2003
11 30702184 30703562 - MELO3C022360.2.1 Cme11g02371 2371
11 30704040 30706484 - MELO3C022361.2.1 Cme11g02372 2372
11 30710189 30711095 + MELO3C022363.2.1 Cme11g02374 2374
11 1339445 1340222 - PI0024822.1 Cmetu11g0098 98
11 1344321 1345531 + PI0008691.1 Cmetu11g1216 1216
6 1654618 1655362 + CmPI595203_06g001600.1 Cmu06g0160 160
14 3224844 3229988 - Conep14aG0065600.1 Cone14ag0642 642
15 3421829 3426637 - Conep15aG0066500.1 Cone15ag0652 652
3 9587849 9589979 - Cp4.1LG03g13280.1 Cpe03g01170 1170
3 9601552 9610203 + Cp4.1LG03g13370.1 Cpe03g01171 1171
17 7270571 7272002 + Cp4.1LG17g09510.1 Cpe17g00947 947
6 2753791 2754531 - CrPI670011_06g009350.1 Cre06g0935 935
6 2756615 2757354 + CrPI670011_06g009360.1 Cre06g0936 936
4 1252025 1254723 - CsaV3_4G002130.1 Csa04g00213 213
4 1266108 1275433 + CsaV3_4G002140.1 Csa04g00214 214
4 1277647 1280532 - CsaV3_4G002150.1 Csa04g00215 215
3 65507397 65508988 - Hsped.03g11780.1 Hepe03g1178 1178
9 26486101 26487333 - Lsi09G017720.1 Lsi09g01772 1772
9 26489893 26491232 + Lsi09G017730.1 Lsi09g01773 1773
9 3109317 3111043 - Sed0020506.1 Sed09g0343 343
9 3112075 3114359 + Sed0005297.1 Sed09g0344 344
6 18949702 18950833 - Tan0014559.1 Tan06g1432 1432
6 18956587 18957597 + Tan0015115.1 Tan06g1433 1433
1 22646708 22649537 - Vvi1g1361 Vvi1g1361 1361
1 22666633 22667976 + Vvi1g1362 Vvi1g1362 1362
1 22670467 22671235 + Vvi1g1363 Vvi1g1363 1363
1 22671238 22673946 + Vvi1g1364 Vvi1g1364 1364
1 22675675 22682448 - Vvi1g1365 Vvi1g1365 1365
1 22685708 22688351 - Vvi1g1366 Vvi1g1366 1366
1 22688381 22689371 - Vvi1g1367 Vvi1g1367 1367
1 22694140 22703040 - Vvi1g1368 Vvi1g1368 1368
1 22706569 22709016 - Vvi1g1369 Vvi1g1369 1369
1 22715105 22716003 + Vvi1g1370 Vvi1g1370 1370
       

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