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
Vvi5g1429 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1430 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1431 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1432 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1433 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1434 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1435 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi6g1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi6g2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi6g3 . . . . Bpe01g00409 . Bma14g00744 . . . . . . . . Cpe05g00576 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe08g00340 . . Bma11g00387 Sed01g3430 . . . . . . . . Bhi10g00491 Tan07g0561 Cmetu05g1769 . Hepe08g0006 . . Cla03g01411 Cam03g1491 Cec03g1529 Cco03g1523 Clacu03g1514 Cmu03g2071 Cre03g1743 . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
10 11056258 11095895 + XM_039045881.1 Bhi10g00491 491
11 4144194 4145774 - Bma005845.1 Bma11g00387 387
14 8232195 8235181 + Bma011212.1 Bma14g00744 744
1 2509309 2510544 - Bpe000395.1 Bpe01g00409 409
8 2024600 2025407 - Bpe022434.1 Bpe08g00340 340
3 29827888 29832801 + CaPI482276_03g014910.1 Cam03g1491 1491
3 29836722 29841525 + CcPI632755_03g015230.1 Cco03g1523 1523
3 33382807 33387722 + CePI673135_03g015290.1 Cec03g1529 1529
3 28706465 28711363 + ClG42_03g0151400.10 Clacu03g1514 1514
3 29616560 29622549 + ClCG03G014680.2 Cla03g01411 1411
5 23055057 23074331 + PI0013592.2 Cmetu05g1769 1769
3 29101357 29106257 + CmPI595203_03g020710.1 Cmu03g2071 2071
5 3487535 3496211 - Cp4.1LG05g05750.1 Cpe05g00576 576
3 34232829 34237734 + CrPI670011_03g017430.1 Cre03g1743 1743
8 91376 105630 + Hsped.08g00060.1 Hepe08g0006 6
1 63355970 63363618 - Sed0012812.2 Sed01g3430 3430
7 9199713 9220446 + Tan0018817.3 Tan07g0561 561
5 24942991 24946222 + Vvi5g1429 Vvi5g1429 1429
5 24946234 24947803 + Vvi5g1430 Vvi5g1430 1430
5 24968751 24969352 - Vvi5g1431 Vvi5g1431 1431
5 24978595 24980036 - Vvi5g1432 Vvi5g1432 1432
5 24985106 24985426 - Vvi5g1433 Vvi5g1433 1433
5 24999067 24999172 - Vvi5g1434 Vvi5g1434 1434
5 25018223 25021287 + Vvi5g1435 Vvi5g1435 1435
6 5644 7247 - Vvi6g1 Vvi6g1 1
6 7305 8123 - Vvi6g2 Vvi6g2 2
6 96178 97337 - Vvi6g3 Vvi6g3 3
       

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