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
Vvi4g542 Blo01g01397 . Bda01g00754 . . . . . . . . . . . Sed01g1388 . . Bhi04g00025 Tan02g2741 Cmetu03g2008 . Hepe10g0236 . Lcy13g1806 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g543 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g544 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g545 . . . . . . . . . . . . . . Sed08g1803 . . Bhi04g00024 Tan02g2740 Cmetu03g1584 . Hepe10g0237 . Lcy13g1805 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g546 . . . . . . . . . Cmo12g00299 . . . Car12g00331 Sed08g1556 . . Bhi04g00023 Tan02g2738 Cmetu03g1685 . . . Lcy13g1804 . . . . . . . . . . . . . . . . . . Bda13g01250 Bpe14g00593 . . . . . . . Cma12g00348 . . . . . . . . . . . . . . . . . . . . . .
Vvi4g547 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed01g2452 . . . . . . . . Bhi09g02931 Tan01g5081 Cmetu07g1738 . . Mch11g0072 . . . . . . . . . . . Cme07g00072
Vvi4g548 . . . . . . . . . . . . . . . . . . . . . . . . Cla05g01713 Cam05g1828 Cec05g1840 Cco05g1898 Clacu05g1814 Cmu05g1699 Cre05g1828 . . . . Lsi04g02106 . . . . . . . . . . . . Cmo01g01572 . . . . . . Cpe02g00437 Bhi09g02945 . . . . . . . . . . . . . . . . Cme07g00086
Vvi4g549 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g550 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g551 . . . . . . . . . . . . . . . . . . . . . . . . Cla05g01711 Cam05g1826 Cec05g1838 Cco05g1896 Clacu05g1811 Cmu05g1697 Cre05g1826 . . . . Lsi04g02104 . . . . . . . . . . . . . . . . . . . . Bhi09g02958 . . . . Mch11g0529 . . . . . . . . . . . Cme07g00089
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 34786717 34789034 - Bda002794.1 Bda01g00754 754
13 34933771 34935053 - Bda032806 Bda13g01250 1250
4 499703 501628 + XM_039028337.1 Bhi04g00023 23
4 508564 510351 + XM_039029288.1 Bhi04g00024 24
4 535472 538818 - XM_039029289.1 Bhi04g00025 25
9 76449940 76459823 + XM_039042101.1 Bhi09g02931 2931
9 76863545 76867978 + XM_039041249.1 Bhi09g02945 2945
9 76996240 77000722 + XM_039042795.1 Bhi09g02958 2958
1 52377294 52389757 - BLOR01397 Blo01g01397 1397
14 4948274 4949628 + Bpe007242.1 Bpe14g00593 593
5 27188782 27192462 - CaPI482276_05g018260.1 Cam05g1826 1826
5 27221759 27226060 - CaPI482276_05g018280.1 Cam05g1828 1828
12 2105267 2107647 + Carg03938-RA Car12g00331 331
5 28040072 28043736 - CcPI632755_05g018960.1 Cco05g1896 1896
5 28072672 28076978 - CcPI632755_05g018980.1 Cco05g1898 1898
5 30413729 30417391 - CePI673135_05g018380.1 Cec05g1838 1838
5 30440940 30445226 - CePI673135_05g018400.1 Cec05g1840 1840
5 27397575 27401289 - ClG42_05g0181100.10 Clacu05g1811 1811
5 27423057 27427349 - ClG42_05g0181400.10 Clacu05g1814 1814
5 28933703 28938925 - ClCG05G016640.1 Cla05g01711 1711
5 28962139 28966555 - ClCG05G016660.2 Cla05g01713 1713
12 1770612 1772885 + CmaCh12G003480.1 Cma12g00348 348
7 448572 460494 + MELO3C017008.2.1 Cme07g00072 72
7 534228 538523 + MELO3C016996.2.1 Cme07g00086 86
7 547704 551366 + MELO3C016993.2.1 Cme07g00089 89
3 4441741 4443599 + PI0024159.1 Cmetu03g1584 1584
3 4434735 4437020 + PI0008603.1 Cmetu03g1685 1685
3 4446710 4449837 - PI0005730.1 Cmetu03g2008 2008
7 24332844 24342980 - PI0016715.1 Cmetu07g1738 1738
1 12085912 12091931 + CmoCh01G015720.1 Cmo01g01572 1572
12 1877196 1880319 + CmoCh12G002990.1 Cmo12g00299 299
5 27116630 27120303 - CmPI595203_05g016970.1 Cmu05g1697 1697
5 27142097 27146390 - CmPI595203_05g016990.1 Cmu05g1699 1699
2 2457940 2466223 - Cp4.1LG02g04320.1 Cpe02g00437 437
5 30420610 30424322 - CrPI670011_05g018260.1 Cre05g1826 1826
5 30451476 30455764 - CrPI670011_05g018280.1 Cre05g1828 1828
10 2498733 2501611 + Hsped.10g02360.1 Hepe10g0236 236
10 2504337 2506003 - Hsped.10g02370.1 Hepe10g0237 237
13 37013224 37018422 + Maker00033888 Lcy13g1804 1804
13 37024349 37026264 + Maker00033860 Lcy13g1805 1805
13 37027393 37031972 - Maker00034161 Lcy13g1806 1806
4 28196302 28199268 - Lsi04G021040.1 Lsi04g02104 2104
4 28213845 28218314 - Lsi04G021060.1 Lsi04g02106 2106
11 456475 466388 + MC11g0066 Mch11g0072 72
11 3404314 3407874 - MC11g0432 Mch11g0529 529
1 10291833 10294636 - Sed0020768.1 Sed01g1388 1388
1 18282403 18293232 + Sed0000145.1 Sed01g2452 2452
8 30635360 30637761 - Sed0011082.1 Sed08g1556 1556
8 32749223 32751644 - Sed0019233.1 Sed08g1803 1803
1 116292330 116305249 - Tan0020866.1 Tan01g5081 5081
2 95645709 95647696 + Tan0005894.1 Tan02g2738 2738
2 95656113 95657672 + Tan0019428.1 Tan02g2740 2740
2 95657782 95660809 - Tan0008244.1 Tan02g2741 2741
4 5932037 5936741 + Vvi4g542 Vvi4g542 542
4 5937870 5970124 - Vvi4g543 Vvi4g543 543
4 5980583 5997956 - Vvi4g544 Vvi4g544 544
4 6021155 6034187 - Vvi4g545 Vvi4g545 545
4 6037924 6041003 - Vvi4g546 Vvi4g546 546
4 6044777 6059248 - Vvi4g547 Vvi4g547 547
4 6067868 6071553 + Vvi4g548 Vvi4g548 548
4 6089264 6096741 - Vvi4g549 Vvi4g549 549
4 6098326 6100296 - Vvi4g550 Vvi4g550 550
4 6104684 6128186 + Vvi4g551 Vvi4g551 551
       

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