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
Vvi4g662 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g663 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g664 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g665 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0211 Cone9ag0239 Cone14ag1019 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g666 . . . . . Bpe02g00222 . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1863 Cone7ag1768 . . . Csa03g04410 Chy04g00290 . . . . . . . . . Sed13g2098 . . Cma09g00532 . . . . . Bhi09g02378 Tan01g3741 Cmetu04g0136 . Hepe01g2094 Mch11g0632 . . . . . . . . . . . Cme04g00332
Vvi4g667 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed13g2097 . . Cma09g00531 . . . . . Bhi09g02377 Tan01g3740 Cmetu04g3258 . Hepe01g2093 Mch11g0631 . . . . . . . . . . . .
Vvi4g668 . . . . . . . . . . Cma01g01576 . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g04409 Chy04g00291 . . . . . . . . . . . . . . . . . . Bhi09g02376 . . . . . . . . . . . . . . . . Cme04g00333
Vvi4g669 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g670 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g671 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
9 64831545 64843717 + XM_039041917.1 Bhi09g02376 2376
9 64833149 64843717 + XM_039041918.1 Bhi09g02377 2377
9 64844315 64845867 - XM_039040837.1 Bhi09g02378 2378
2 1538040 1539266 - Bpe008068.1 Bpe02g00222 222
4 2619024 2620253 + Chy4G070080.1 Chy04g00290 290
4 2621684 2631410 - Chy4G070090.1 Chy04g00291 291
1 10889715 10901960 + CmaCh01G015760.1 Cma01g01576 1576
9 2363083 2374186 + CmaCh09G005310.1 Cma09g00531 531
9 2374439 2375836 - CmaCh09G005320.1 Cma09g00532 532
4 2636298 2637760 + MELO3C003620.2.1 Cme04g00332 332
4 2637956 2648521 - MELO3C003621.2.1 Cme04g00333 333
4 30731623 30733216 - PI0028314.1 Cmetu04g0136 136
4 30720206 30731417 + PI0019317.1 Cmetu04g3258 3258
4 13359157 13360593 - Conep04aG0192200.1 Cone4ag1863 1863
6 998981 1002370 - Conep06aG0021300.1 Cone6ag0211 211
7 11659527 11660179 - Conep07aG0182100.1 Cone7ag1768 1768
9 1021249 1024616 - Conep09aG0024200.1 Cone9ag0239 239
14 8516548 8519328 + Conep14aG0103900.1 Cone14ag1019 1019
3 38446753 38458131 + CsaV3_3G047150.1 Csa03g04409 4409
3 38458226 38460187 - CsaV3_3G047160.1 Csa03g04410 4410
1 85546273 85557868 + Hsped.01g20930.1 Hepe01g2093 2093
1 85558375 85559889 - Hsped.01g20940.1 Hepe01g2094 2094
11 4066488 4077081 + MC11g0525 Mch11g0631 631
11 4077472 4079569 - MC11g0526 Mch11g0632 632
13 25675562 25687492 + Sed0008947.3 Sed13g2097 2097
13 25688601 25689853 - Sed0023873.1 Sed13g2098 2098
1 102196636 102207933 + Tan0006407.1 Tan01g3740 3740
1 102209939 102211573 - Tan0012334.1 Tan01g3741 3741
4 8913224 8913872 - Vvi4g662 Vvi4g662 662
4 8920372 8921014 + Vvi4g663 Vvi4g663 663
4 8940023 8941073 - Vvi4g664 Vvi4g664 664
4 8941127 8966253 + Vvi4g665 Vvi4g665 665
4 8999308 9004276 + Vvi4g666 Vvi4g666 666
4 9011203 9019599 - Vvi4g667 Vvi4g667 667
4 9019649 9026026 - Vvi4g668 Vvi4g668 668
4 9035777 9036847 - Vvi4g669 Vvi4g669 669
4 9060433 9112245 + Vvi4g670 Vvi4g670 670
4 9132359 9153875 + Vvi4g671 Vvi4g671 671
       

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