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
Vvi1g931 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g932 Blo01g00431 . Bda01g02147 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0572 . . . . . . . . . . Bpe02g02336 Bma01g00104 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g933 Blo01g00432 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe02g02335 Bma01g00105 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g934 Blo01g00433 . Bda01g02145 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0571 Cone9ag0577 . . . . . . . . . Bpe02g02334 Bma01g00106 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g935 Blo01g00434 . Bda01g02144 . . . . . Cmo04g01750 . . . . . . . Cpe01g01477 Bhi07g01539 . . . . . . Cla05g02427 . . . . . . . . . . Lsi04g00401 Csa05g02474 . Cme10g00397 Blo06g00912 Blo11g00783 Bda07g01475 . Bpe11g01650 Bpe02g02333 . . . . . Cma04g01671 . Car04g01709 . . . . . . . . . . . . . . . . . . . Chy09g00234 .
Vvi1g936 . Blo16g01111 . . Bpe13g01405 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0569 Cone9ag0575 . . . . . . . . . . . Bma06g00700 . . . . . . . . Cpe07g00648 . . . . . . . . . . . . . . . . . .
Vvi1g937 . Blo16g01110 . Bda11g01210 Bpe13g01404 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0944 Cone19ag0936 . . . . . . . . . Bda11g01210 . . . Bma06g00701 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g938 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g939 . . . . . . Bma14g01655 . Cmo04g01752 . . . . . Sed07g1949 . Cpe01g01479 Bhi07g01537 Tan04g1057 Cmetu10g0340 Lac13g0337 Hepe10g1763 . . Cla05g02425 Cam05g2607 Cec05g2641 Cco05g2679 Clacu05g2609 Cmu05g2462 Cre05g2578 . . Cone6ag0567 . Lsi04g00400 Csa05g02475 Chy10g01023 Cme10g00395 . Blo11g00784 Bda07g01476 . . . . . . . . Cma04g01673 . Car04g01711 . . Cpe07g00162 . . . . . . . . . . . . . . . . . .
Vvi1g940 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo04g02905 . . . . Car15g00259 . . . . . . . . . . . . . . . . . . Chy09g00231 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 57386654 57387636 + Bda004476.1 Bda01g02144 2144
1 57388044 57390363 + Bda004477.1 Bda01g02145 2145
1 57405014 57405720 + Bda004479.1 Bda01g02147 2147
7 27467861 27468854 - Bda028312.2 Bda07g01475 1475
7 27481974 27483929 + Bda028315.1 Bda07g01476 1476
11 12452977 12459138 + Bda007715.1 Bda11g01210 1210
7 44379084 44380872 - XM_039036646.1 Bhi07g01537 1537
7 44393494 44394911 + XM_039035510.1 Bhi07g01539 1539
1 4863302 4864021 - BLOR00431 Blo01g00431 431
1 4864397 4865870 + BLOR00432 Blo01g00432 432
1 4866491 4868533 - BLOR00433 Blo01g00433 433
1 4868907 4870160 - BLOR00434 Blo01g00434 434
6 32404876 32405790 - BLOR17495 Blo06g00912 912
11 11631978 11640136 - BLOR03659 Blo11g00783 783
11 11746904 11755495 + BLOR03660 Blo11g00784 784
16 39564527 39570618 + BLOR21897 Blo16g01110 1110
16 39571986 39580018 - BLOR21898 Blo16g01111 1111
1 1107364 1108083 - Bma000269.1 Bma01g00104 104
1 1108518 1109622 + Bma030171 Bma01g00105 105
1 1110007 1112172 - Bma000270.3 Bma01g00106 106
6 37232415 37241146 + Bma023680.1 Bma06g00700 700
6 37241939 37248176 - Bma023681.1 Bma06g00701 701
14 35157701 35159654 + Bma012386.1 Bma14g01655 1655
2 23915621 23916603 + Bpe010149.1 Bpe02g02333 2333
2 23917019 23919285 + Bpe010150.1 Bpe02g02334 2334
2 23919775 23920909 - Bpe010151.1 Bpe02g02335 2335
2 23921342 23922062 + Bpe010152.1 Bpe02g02336 2336
11 12645478 12646484 - Bpe004963.1 Bpe11g01650 1650
13 19271428 19277643 + Bpe011066.1 Bpe13g01404 1404
13 19278471 19279230 - Bpe025294 Bpe13g01405 1405
5 33670359 33671696 - CaPI482276_05g026070.1 Cam05g2607 2607
4 9806389 9807472 - Carg14396-RA Car04g01709 1709
4 9813251 9814609 + Carg14394-RA Car04g01711 1711
15 1417884 1419811 - Carg02240-RA Car15g00259 259
5 34787843 34789180 - CcPI632755_05g026790.1 Cco05g2679 2679
5 37117694 37119032 - CePI673135_05g026410.1 Cec05g2641 2641
9 1908981 1911291 - Chy9G159470.1 Chy09g00231 231
9 1925772 1926969 - Chy9G159500.1 Chy09g00234 234
10 15557977 15559455 + Chy10G182170.1 Chy10g01023 1023
5 33880631 33881968 - ClG42_05g0260900.10 Clacu05g2609 2609
5 35761365 35762702 - ClCG05G024090.2 Cla05g02425 2425
5 35771366 35772516 + ClCG05G024110.1 Cla05g02427 2427
4 8403973 8405927 - CmaCh04G016710.1 Cma04g01671 1671
4 8412730 8414231 + CmaCh04G016730.1 Cma04g01673 1673
10 2537253 2539026 - MELO3C012116.2.1 Cme10g00395 395
10 2545773 2547503 + MELO3C012114.2.1 Cme10g00397 397
10 19487994 19489526 + PI0019163.1 Cmetu10g0340 340
4 8840370 8841993 - CmoCh04G017500.1 Cmo04g01750 1750
4 8847344 8848860 + CmoCh04G017520.1 Cmo04g01752 1752
4 20646001 20652055 + CmoCh04G029050.1 Cmo04g02905 2905
5 33618345 33619682 - CmPI595203_05g024620.1 Cmu05g2462 2462
6 2780157 2780540 - Conep06aG0058000.1 Cone6ag0567 567
6 2781792 2790177 - Conep06aG0058200.1 Cone6ag0569 569
6 2796642 2798706 + Conep06aG0058400.1 Cone6ag0571 571
6 2799017 2800536 + Conep06aG0058500.1 Cone6ag0572 572
9 2705408 2713847 - Conep09aG0058500.1 Cone9ag0575 575
9 2720495 2722512 + Conep09aG0058700.1 Cone9ag0577 577
13 8129275 8134322 + Conep13aG0097200.1 Cone13ag0944 944
19 7169848 7178312 + Conep19aG0096400.1 Cone19ag0936 936
1 8822705 8824480 - Cp4.1LG01g12370.1 Cpe01g01477 1477
1 8831350 8832798 + Cp4.1LG01g12530.1 Cpe01g01479 1479
7 963681 964646 + Cp4.1LG07g01530.1 Cpe07g00162 162
7 4645329 4658611 + Cp4.1LG07g06540.1 Cpe07g00648 648
5 36978437 36979774 - CrPI670011_05g025780.1 Cre05g2578 2578
5 26500810 26502723 - CsaV3_5G032930.1 Csa05g02474 2474
5 26506099 26510727 + CsaV3_5G032940.1 Csa05g02475 2475
10 54404216 54406112 + Hsped.10g17630.1 Hepe10g1763 1763
13 2408799 2410224 + Lag0040133.1 Lac13g0337 337
4 3914743 3916477 - Lsi04G004000.1 Lsi04g00400 400
4 3924024 3925544 + Lsi04G004010.1 Lsi04g00401 401
7 34025449 34027471 + Sed0021515.2 Sed07g1949 1949
4 9423364 9425160 - Tan0007452.1 Tan04g1057 1057
1 12404355 12404707 + Vvi1g931 Vvi1g931 931
1 12408984 12410170 - Vvi1g932 Vvi1g932 932
1 12434638 12437491 + Vvi1g933 Vvi1g933 933
1 12438064 12440478 - Vvi1g934 Vvi1g934 934
1 12441951 12443272 - Vvi1g935 Vvi1g935 935
1 12478584 12504600 + Vvi1g936 Vvi1g936 936
1 12552046 12562188 - Vvi1g937 Vvi1g937 937
1 12600855 12602313 - Vvi1g938 Vvi1g938 938
1 12603603 12606875 + Vvi1g939 Vvi1g939 939
1 12652934 12655438 + Vvi1g940 Vvi1g940 940
       

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