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
Vvi1g221 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g222 . . . . . . . . Cmo04g01622 . . . Car04g01601 . Sed06g1847 . . Bhi07g01387 Tan04g0921 Cmetu10g1685 . Hepe10g1854 . . Cla05g02347 . . Cco05g2587 . . . . . . . . Csa05g02562 Chy10g01102 Cme10g00308 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g223 Blo01g00437 . . . . . Bma14g01687 . Cmo04g01621 Cmo18g01077 . Cma18g01055 Car04g01600 Car18g00979 Sed02g1420 Cpe09g00260 Cpe01g01377 Bhi07g01386 Tan04g0919 Cmetu10g1688 Lac13g0442 Hepe10g1855 . . Cla05g02345 . . Cco05g2586 Clacu05g2513 . Cre05g2491 Cone13ag0869 Cone19ag0870 Cone6ag0482 Cone9ag0494 Lsi04g00305 Csa05g02563 Chy10g01103 Cme10g00307 . Blo11g00822 Bda07g01518 . Bpe11g01680 . . . . . . . . . Car15g00855 . . . . . . . . . . . . . . . . . . Chy09g00646 .
Vvi1g224 . . Bda01g02106 . . . . . Cmo04g01620 . . . Car04g01599 . Sed06g1851 . Cpe01g01376 Bhi07g01385 Tan04g0917 Cmetu10g1102 Lac13g0443 Hepe10g1857 . . Cla05g02344 Cam05g2517 Cec05g2543 Cco05g2584 Clacu05g2511 Cmu05g2373 Cre05g2490 . Cone19ag0869 Cone6ag0481 Cone9ag0493 Lsi04g00304 Csa05g02564 Chy10g01104 Cme10g00306 . . . . . Bpe02g02295 Bma01g00145 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g225 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g226 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g227 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g228 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g229 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g230 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 57133788 57137219 - Bda004434.1 Bda01g02106 2106
7 28226724 28227291 - Bda028369.1 Bda07g01518 1518
7 41774737 41779451 - XM_039035481.1 Bhi07g01385 1385
7 41837695 41842806 + XM_039035843.1 Bhi07g01386 1386
7 41844525 41846910 + XM_039035875.1 Bhi07g01387 1387
1 4878194 4881973 - BLOR00437 Blo01g00437 437
11 13598070 13602269 - BLOR03698 Blo11g00822 822
1 1380488 1383869 + Bma000311.1 Bma01g00145 145
14 35918041 35922239 - Bma012431.1 Bma14g01687 1687
2 23682990 23686353 - Bpe010112.1 Bpe02g02295 2295
11 13083556 13087760 - Bpe004993.2 Bpe11g01680 1680
5 32992084 32995296 - CaPI482276_05g025170.1 Cam05g2517 2517
4 9241746 9246838 - Carg01801-RA Car04g01599 1599
4 9254705 9259347 + Carg01800-RA Car04g01600 1600
4 9260022 9261912 + Carg01799-RA Car04g01601 1601
15 4963551 4965725 + Carg26882-RA Car15g00855 855
18 10330363 10332995 + Carg21551-RA Car18g00979 979
5 34091092 34094293 - CcPI632755_05g025840.1 Cco05g2584 2584
5 34114391 34119074 + CcPI632755_05g025860.1 Cco05g2586 2586
5 34120657 34122707 + CcPI632755_05g025870.1 Cco05g2587 2587
5 36425981 36429136 - CePI673135_05g025430.1 Cec05g2543 2543
9 8316031 8319691 + Chy9G163620.1 Chy09g00646 646
10 16066548 16067757 - Chy10G182960.1 Chy10g01102 1102
10 16067804 16073379 - Chy10G182970.1 Chy10g01103 1103
10 16086835 16090739 + Chy10G182980.1 Chy10g01104 1104
5 33204319 33207525 - ClG42_05g0251100.10 Clacu05g2511 2511
5 33226914 33230957 + ClG42_05g0251300.10 Clacu05g2513 2513
5 35026993 35030863 - ClCG05G023180.1 Cla05g02344 2344
5 35050198 35056382 + ClCG05G023190.2 Cla05g02345 2345
5 35060060 35062160 + ClCG05G023210.1 Cla05g02347 2347
18 8776107 8781253 + CmaCh18G010550.1 Cma18g01055 1055
10 1995500 2000098 - MELO3C012201.2.1 Cme10g00306 306
10 2012708 2017736 + MELO3C012200.2.1 Cme10g00307 307
10 2018802 2020578 + MELO3C012198.2.1 Cme10g00308 308
10 20066653 20071073 + PI0010393.1 Cmetu10g1102 1102
10 20044769 20045961 - PI0020520.1 Cmetu10g1685 1685
10 20046523 20051629 - PI0001370.1 Cmetu10g1688 1688
4 8262141 8267330 - CmoCh04G016200.1 Cmo04g01620 1620
4 8275358 8280680 + CmoCh04G016210.1 Cmo04g01621 1621
4 8281122 8282938 + CmoCh04G016220.1 Cmo04g01622 1622
18 11346562 11351921 + CmoCh18G010770.1 Cmo18g01077 1077
5 32942393 32945600 - CmPI595203_05g023730.1 Cmu05g2373 2373
6 2385093 2388492 - Conep06aG0049100.1 Cone6ag0481 481
6 2405094 2409381 + Conep06aG0049200.1 Cone6ag0482 482
9 2361622 2365192 - Conep09aG0050300.1 Cone9ag0493 493
9 2372521 2376827 + Conep09aG0050400.1 Cone9ag0494 494
13 7748105 7752952 + Conep13aG0089600.1 Cone13ag0869 869
19 6807475 6810262 - Conep19aG0089300.1 Cone19ag0869 869
19 6817557 6822239 + Conep19aG0089400.1 Cone19ag0870 870
1 8266632 8271844 - Cp4.1LG01g13340.1 Cpe01g01376 1376
1 8279352 8284248 + Cp4.1LG01g13420.1 Cpe01g01377 1377
9 1521352 1527396 - Cp4.1LG09g02720.1 Cpe09g00260 260
5 36278616 36282218 - CrPI670011_05g024900.1 Cre05g2490 2490
5 36302457 36310997 + CrPI670011_05g024910.1 Cre05g2491 2491
5 26997426 27000989 - CsaV3_5G033810.1 Csa05g02562 2562
5 27001449 27006958 - CsaV3_5G033820.1 Csa05g02563 2563
5 27018138 27024067 + CsaV3_5G033830.1 Csa05g02564 2564
10 55267315 55271804 - Hsped.10g18540.1 Hepe10g1854 1854
10 55272748 55277378 - Hsped.10g18550.1 Hepe10g1855 1855
10 55314267 55318949 + Hsped.10g18570.1 Hepe10g1857 1857
13 3138162 3142884 - Lag0040238.1 Lac13g0442 442
13 3163935 3167220 + Lag0040239.1 Lac13g0443 443
4 3067657 3072298 - Lsi04G003040.1 Lsi04g00304 304
4 3097530 3102697 + Lsi04G003050.1 Lsi04g00305 305
2 50343986 50352196 - Sed0014746.1 Sed02g1420 1420
6 42863960 42867353 - Sed0005065.1 Sed06g1847 1847
6 42899732 42905225 + Sed0007827.2 Sed06g1851 1851
4 7948985 7952866 - Tan0003054.2 Tan04g0917 917
4 7993231 7998411 + Tan0001746.2 Tan04g0919 919
4 7998979 8002074 + Tan0017959.1 Tan04g0921 921
1 2281186 2282306 + Vvi1g221 Vvi1g221 221
1 2282306 2285389 - Vvi1g222 Vvi1g222 222
1 2286638 2292078 - Vvi1g223 Vvi1g223 223
1 2301128 2308453 + Vvi1g224 Vvi1g224 224
1 2312371 2313431 + Vvi1g225 Vvi1g225 225
1 2324671 2327945 - Vvi1g226 Vvi1g226 226
1 2339821 2340254 + Vvi1g227 Vvi1g227 227
1 2344271 2344630 + Vvi1g228 Vvi1g228 228
1 2352040 2356540 + Vvi1g229 Vvi1g229 229
1 2365382 2365923 - Vvi1g230 Vvi1g230 230
       

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