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
Vvi1g51 . . . . . . Bma14g01663 . Cmo04g01782 . . . . . . . Cpe01g01502 Bhi07g01500 . . . . . . Cla05g02397 . . Cco05g2645 Clacu05g2574 Cmu05g2430 Cre05g2547 . Cone19ag0905 . . Lsi04g00368 Csa05g02506 Chy10g01053 Cme10g00363 Blo06g00926 Blo11g00792 . . . . . . . . . Cma04g01697 . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g52 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01731 Chy09g00672 .
Vvi1g53 . . . . . . . Bma15g00135 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01732 Chy09g00673 Cme09g00691
Vvi1g54 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01742 Chy09g00680 Cme09g00683
Vvi1g55 . . . . . . . . . . . Cma18g00483 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g56 . . . . . Bpe10g00897 Bma14g01662 . Cmo04g01776 . . . . . . Cpe09g00936 Cpe01g01498 . . . . . . . . . . . . . . . . . . . . Chy10g01049 . . Blo11g00791 . . . . . . . . . Cma04g01693 . Car04g01730 . . . . . . . . . . . . . . . . . . . . .
Vvi1g57 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g58 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone19ag0907 Cone6ag0539 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g59 . . . . . . . . . . . . . . . . . . . . . . . . Cla05g02400 Cam05g2576 Cec05g2610 Cco05g2648 Clacu05g2579 Cmu05g2433 Cre05g2550 . Cone19ag0908 Cone6ag0540 Cone9ag0550 Lsi04g00370 . . Cme10g00366 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g60 Blo01g00448 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0914 Cone19ag0910 Cone6ag0541 Cone9ag0551 . . . . . . . . . . Bma01g00117 Bma06g00731 . . . . . . . . Cpe07g00080 . . . . . . . Cla01g01022 Cam01g1059 . Cco01g1115 Clacu01g1050 Cmu01g1004 Cre01g0946 . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 43595123 43598297 - XM_039037437.1 Bhi07g01500 1500
1 4939080 4941076 + BLOR00448 Blo01g00448 448
6 32496759 32502790 + BLOR17509 Blo06g00926 926
11 12037944 12039659 - BLOR03667 Blo11g00791 791
11 12063212 12065042 + BLOR03668 Blo11g00792 792
1 1178049 1180000 + Bma000281.2 Bma01g00117 117
6 38296601 38297871 + Bma023716.1 Bma06g00731 731
14 35239843 35241111 - Bma012393.1 Bma14g01662 1662
14 35272720 35274904 + Bma012395.1 Bma14g01663 1663
15 1459555 1462155 + Bma013114.1 Bma15g00135 135
10 14664655 14668739 - Bpe003201.1 Bpe10g00897 897
1 15353732 15361620 - CaPI482276_01g010590.1 Cam01g1059 1059
5 33477370 33478728 + CaPI482276_05g025760.1 Cam05g2576 2576
4 9914376 9916806 - Carg14375-RA Car04g01730 1730
1 15841871 15849869 - CcPI632755_01g011150.1 Cco01g1115 1115
5 34563465 34565911 - CcPI632755_05g026450.1 Cco05g2645 2645
5 34592514 34593869 + CcPI632755_05g026480.1 Cco05g2648 2648
5 36921281 36922639 + CePI673135_05g026100.1 Cec05g2610 2610
9 8783823 8785421 + Chy9G163880.1 Chy09g00672 672
9 8792127 8795510 - Chy9G163890.1 Chy09g00673 673
9 8897754 8900104 - Chy9G163960.1 Chy09g00680 680
10 15703284 15704841 - Chy10G182430.1 Chy10g01049 1049
10 15730984 15733990 + Chy10G182470.1 Chy10g01053 1053
1 14924837 14932671 - ClG42_01g0105000.10 Clacu01g1050 1050
5 33656379 33659277 - ClG42_05g0257400.10 Clacu05g2574 2574
5 33685457 33686809 + ClG42_05g0257900.10 Clacu05g2579 2579
1 15649121 15657403 - ClCG01G010320.1 Cla01g01022 1022
5 35521249 35524046 - ClCG05G023760.1 Cla05g02397 2397
5 35558176 35559528 + ClCG05G023790.1 Cla05g02400 2400
4 8513095 8516739 - CmaCh04G016930.1 Cma04g01693 1693
4 8531498 8534298 + CmaCh04G016970.1 Cma04g01697 1697
18 2743703 2745880 - CmaCh18G004830.1 Cma18g00483 483
9 7676779 7679874 + MELO3C002922.2.1 Cme09g00683 683
9 7824311 7827938 + MELO3C002928.2.1 Cme09g00691 691
10 2337132 2340006 - MELO3C012146.2.1 Cme10g00363 363
10 2353046 2355797 + MELO3C012144.2.1 Cme10g00366 366
4 8950322 8952826 - CmoCh04G017760.1 Cmo04g01776 1776
4 8966872 8969150 + CmoCh04G017820.1 Cmo04g01782 1782
1 14915365 14923205 - CmPI595203_01g010040.1 Cmu01g1004 1004
5 33394200 33397097 - CmPI595203_05g024300.1 Cmu05g2430 2430
5 33423257 33424609 + CmPI595203_05g024330.1 Cmu05g2433 2433
6 2660483 2660974 + Conep06aG0055200.1 Cone6ag0539 539
6 2662307 2665544 + Conep06aG0055300.1 Cone6ag0540 540
6 2670377 2672222 - Conep06aG0055400.1 Cone6ag0541 541
9 2618445 2620050 + Conep09aG0056000.1 Cone9ag0550 550
9 2624393 2626734 - Conep09aG0056100.1 Cone9ag0551 551
13 8023565 8026212 - Conep13aG0094200.1 Cone13ag0914 914
19 7049179 7050970 - Conep19aG0093100.1 Cone19ag0905 905
19 7060375 7062518 + Conep19aG0093300.1 Cone19ag0907 907
19 7062956 7065057 + Conep19aG0093400.1 Cone19ag0908 908
19 7071382 7074020 - Conep19aG0093600.1 Cone19ag0910 910
1 8937991 8942417 - Cp4.1LG01g12180.1 Cpe01g01498 1498
1 8963226 8965985 + Cp4.1LG01g12070.1 Cpe01g01502 1502
7 389969 391304 - Cp4.1LG07g00870.1 Cpe07g00080 80
9 8403972 8405791 + Cp4.1LG09g09350.1 Cpe09g00936 936
1 14082712 14090726 - CrPI670011_01g009460.1 Cre01g0946 946
5 36747386 36749837 - CrPI670011_05g025470.1 Cre05g2547 2547
5 36775958 36777316 + CrPI670011_05g025500.1 Cre05g2550 2550
5 20634737 20636997 + CsaV3_5G025500.1 Csa05g01731 1731
5 20638434 20642507 - CsaV3_5G025510.1 Csa05g01732 1732
5 20707088 20710096 - CsaV3_5G025610.1 Csa05g01742 1742
5 26677086 26681017 + CsaV3_5G033250.1 Csa05g02506 2506
4 3674392 3676541 - Lsi04G003680.1 Lsi04g00368 368
4 3694697 3696052 + Lsi04G003700.1 Lsi04g00370 370
1 563210 566736 - Vvi1g51 Vvi1g51 51
1 572046 573055 + Vvi1g52 Vvi1g52 52
1 573525 579404 - Vvi1g53 Vvi1g53 53
1 586452 588903 + Vvi1g54 Vvi1g54 54
1 590868 593407 + Vvi1g55 Vvi1g55 55
1 593577 596330 - Vvi1g56 Vvi1g56 56
1 599212 602915 + Vvi1g57 Vvi1g57 57
1 605266 607892 + Vvi1g58 Vvi1g58 58
1 609374 618213 + Vvi1g59 Vvi1g59 59
1 628681 633595 - Vvi1g60 Vvi1g60 60
       

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