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
Vvi1g721 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g722 Blo01g00397 . Bda01g02223 . . Bpe10g00837 . Bma15g00187 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo06g00875 . . . . . Bma01g00051 . . . . . Cma05g00006 . Car05g00005 . . . . . . . . . . . . . . . . . . . .
Vvi1g723 . . . . . Bpe10g00836 Bma14g01790 Bma15g00188 . Cmo18g00805 . . . Car18g00732 Sed06g1635 Cpe09g00502 Cpe01g01528 Bhi07g01722 Tan04g1228 Cmetu10g1166 . Hepe10g1644 . . Cla05g02538 Cam05g2728 Cec05g2758 Cco05g2799 Clacu05g2729 Cmu05g2582 Cre05g2696 . . . Cone12ag0639 Lsi04g00546 Csa05g02340 Chy10g00907 Cme10g00519 Blo06g00874 Blo11g00912 Bda07g01599 . . . . . . . . Cma04g01729 . Car04g01761 . . . . . . . . . . . . . . . . . . . . .
Vvi1g724 . . Bda01g02224 . Bpe13g00495 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0658 . . . . . . . . . . . Bma01g00052 . . . . . Cma05g00005 . . . . . . . . . . . . . . . . . . . . . .
Vvi1g725 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g726 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g727 . . . . Bpe13g00494 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0657 . . . . . . . . . . . Bma01g00053 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g728 . . . . . . Bma14g01789 . . . . Cma18g00801 . . Sed04g0635 Cpe09g00501 Cpe01g01527 Bhi07g01721 Tan04g1227 Cmetu10g0164 Lac13g0205 Hepe10g1645 . . Cla05g02536 Cam05g2727 Cec05g2757 Cco05g2798 Clacu05g2728 Cmu05g2581 Cre05g2695 . . . . Lsi04g00545 Csa05g02341 Chy10g00908 Cme10g00518 . Blo11g00911 . . . . . . . . . Cma04g01728 . Car04g01760 . . . . . . . . . . . . . . . . . . . . .
Vvi1g729 . . . . . . . . . Cmo18g00806 . . . Car18g00733 . . . . . . . . . . . . . . . . . . . Cone8ag0656 Cone12ag0638 . . . . . . Bda07g01598 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g730 . . . . . . Bma14g01788 . . Cmo18g00807 . Cma18g00802 . Car18g00734 . Cpe09g00500 Cpe01g01526 Bhi07g01719 Tan04g1224 Cmetu10g0122 Lac13g0206 Hepe10g1646 . . Cla05g02535 Cam05g2726 Cec05g2756 Cco05g2797 Clacu05g2727 Cmu05g2580 Cre05g2694 Cone13ag1035 Cone19ag1026 . . Lsi04g00542 Csa05g02342 Chy10g00909 Cme10g00517 . Blo11g00910 Bda07g01597 . . . . . . . . Cma04g01727 . Car04g01759 . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 58061427 58062330 + Bda004563.2 Bda01g02223 2223
1 58064787 58066606 + Bda004564.1 Bda01g02224 2224
7 29650420 29655758 + Bda028466.3 Bda07g01597 1597
7 29662210 29672580 + Bda028467.1 Bda07g01598 1598
7 29678061 29679815 - Bda028468.1 Bda07g01599 1599
7 47582100 47588149 - XM_039037469.1 Bhi07g01719 1719
7 47661200 47679118 + XM_039036257.1 Bhi07g01721 1721
7 47680243 47683633 - XM_039037482.1 Bhi07g01722 1722
1 4497687 4505676 + BLOR00397 Blo01g00397 397
6 32038772 32042258 - BLOR17457 Blo06g00874 874
6 32044726 32046725 - BLOR17458 Blo06g00875 875
11 18794410 18800180 - BLOR03786 Blo11g00910 910
11 18832141 18843630 + BLOR03787 Blo11g00911 911
11 18859564 18860814 - BLOR03788 Blo11g00912 912
1 560939 561881 + Bma000219.1 Bma01g00051 51
1 563149 566146 + Bma000220.2 Bma01g00052 52
1 568658 571015 + Bma000221.1 Bma01g00053 53
14 38477781 38483128 - Bma012559.2 Bma14g01788 1788
14 38485184 38493629 + Bma012560.1 Bma14g01789 1789
14 38496182 38497930 - Bma012561.1 Bma14g01790 1790
15 1937806 1939790 + Bma013169.1 Bma15g00187 187
15 1940254 1942002 + Bma013170.1 Bma15g00188 188
10 14344143 14345891 - Bpe003140.1 Bpe10g00836 836
10 14346375 14348512 - Bpe003141.1 Bpe10g00837 837
13 12340319 12342220 - Bpe010205.1 Bpe13g00494 494
13 12345070 12346902 - Bpe010206.2 Bpe13g00495 495
5 34572225 34578053 - CaPI482276_05g027260.1 Cam05g2726 2726
5 34583002 34596307 + CaPI482276_05g027270.1 Cam05g2727 2727
5 34598313 34602713 - CaPI482276_05g027280.1 Cam05g2728 2728
4 10077347 10082011 - Carg14346-RA Car04g01759 1759
4 10083565 10093330 + Carg14345-RA Car04g01760 1760
4 10095113 10097308 - Carg14344-RA Car04g01761 1761
5 23814 29118 - Carg21805-RA Car05g00005 5
18 8442110 8445799 + Carg14466-RA Car18g00732 732
18 8446608 8457159 - Carg14465-RA Car18g00733 733
18 8459238 8465431 + Carg14464-RA Car18g00734 734
5 35717437 35724831 - CcPI632755_05g027970.1 Cco05g2797 2797
5 35726583 35738290 + CcPI632755_05g027980.1 Cco05g2798 2798
5 35740231 35744880 - CcPI632755_05g027990.1 Cco05g2799 2799
5 38030258 38036089 - CePI673135_05g027560.1 Cec05g2756 2756
5 38040910 38052818 + CePI673135_05g027570.1 Cec05g2757 2757
5 38054776 38057557 - CePI673135_05g027580.1 Cec05g2758 2758
10 14762874 14764649 + Chy10G181010.1 Chy10g00907 907
10 14767197 14776131 - Chy10G181020.1 Chy10g00908 908
10 14778369 14784159 + Chy10G181030.1 Chy10g00909 909
5 34781417 34787248 - ClG42_05g0272700.10 Clacu05g2727 2727
5 34792235 34803984 + ClG42_05g0272800.10 Clacu05g2728 2728
5 34805935 34808712 - ClG42_05g0272900.10 Clacu05g2729 2729
5 36717294 36723505 - ClCG05G025280.2 Cla05g02535 2535
5 36728385 36741479 + ClCG05G025290.1 Cla05g02536 2536
5 36742187 36745597 - ClCG05G025310.1 Cla05g02538 2538
4 8678384 8684961 - CmaCh04G017270.1 Cma04g01727 1727
4 8685705 8695142 + CmaCh04G017280.1 Cma04g01728 1728
4 8696133 8699499 - CmaCh04G017290.1 Cma04g01729 1729
5 22824 26090 - CmaCh05G000050.1 Cma05g00005 5
5 26292 28681 - CmaCh05G000060.1 Cma05g00006 6
18 7039539 7049174 - CmaCh18G008010.1 Cma18g00801 801
18 7050544 7056765 + CmaCh18G008020.1 Cma18g00802 802
10 3334131 3340485 - MELO3C012001.2.1 Cme10g00517 517
10 3342494 3350700 + MELO3C012000.2.1 Cme10g00518 518
10 3351016 3354464 - MELO3C011999.2.1 Cme10g00519 519
10 18674567 18681008 + PI0000171.4 Cmetu10g0122 122
10 18662177 18672309 - PI0020973.1 Cmetu10g0164 164
10 18658271 18661715 + PI0011165.1 Cmetu10g1166 1166
18 9496254 9500846 + CmoCh18G008050.1 Cmo18g00805 805
18 9501803 9512101 - CmoCh18G008060.1 Cmo18g00806 806
18 9514285 9520531 + CmoCh18G008070.1 Cmo18g00807 807
5 34519425 34525256 - CmPI595203_05g025800.1 Cmu05g2580 2580
5 34530244 34542093 + CmPI595203_05g025810.1 Cmu05g2581 2581
5 34543928 34546705 - CmPI595203_05g025820.1 Cmu05g2582 2582
8 6530341 6536094 + Conep08aG0067900.1 Cone8ag0656 656
8 6539519 6544506 - Conep08aG0068000.1 Cone8ag0657 657
8 6546136 6549414 - Conep08aG0068100.1 Cone8ag0658 658
12 5779602 5787264 + Conep12aG0066100.1 Cone12ag0638 638
12 5793465 5797027 + Conep12aG0066200.1 Cone12ag0639 639
13 8598925 8604582 - Conep13aG0106600.1 Cone13ag1035 1035
19 7651304 7656878 - Conep19aG0105800.1 Cone19ag1026 1026
1 9140562 9146161 - Cp4.1LG01g15320.1 Cpe01g01526 1526
1 9146961 9157089 + Cp4.1LG01g15240.1 Cpe01g01527 1527
1 9157421 9160634 - Cp4.1LG01g15330.1 Cpe01g01528 1528
9 3315065 3321826 - Cp4.1LG09g05040.1 Cpe09g00500 500
9 3323901 3334831 + Cp4.1LG09g04960.1 Cpe09g00501 501
9 3338145 3339887 - Cp4.1LG09g05060.1 Cpe09g00502 502
5 37874714 37882214 - CrPI670011_05g026940.1 Cre05g2694 2694
5 37883977 37896557 + CrPI670011_05g026950.1 Cre05g2695 2695
5 37897758 37900515 - CrPI670011_05g026960.1 Cre05g2696 2696
5 25757193 25760728 + CsaV3_5G031590.1 Csa05g02340 2340
5 25760937 25771034 - CsaV3_5G031600.1 Csa05g02341 2341
5 25772700 25779090 + CsaV3_5G031610.1 Csa05g02342 2342
10 53130622 53134280 + Hsped.10g16440.1 Hepe10g1644 1644
10 53135166 53148316 - Hsped.10g16450.1 Hepe10g1645 1645
10 53150725 53156361 + Hsped.10g16460.1 Hepe10g1646 1646
13 1411233 1423032 - Lag0040001.1 Lac13g0205 205
13 1424828 1430654 + Lag0040002.1 Lac13g0206 206
4 4990777 4997440 - Lsi04G005420.1 Lsi04g00542 542
4 5004405 5017841 + Lsi04G005450.1 Lsi04g00545 545
4 5019179 5022007 - Lsi04G005460.1 Lsi04g00546 546
4 4878601 4905420 - Sed0021630.1 Sed04g0635 635
6 41121285 41124405 - Sed0003805.1 Sed06g1635 1635
4 11593366 11600478 - Tan0008853.5 Tan04g1224 1224
4 11628938 11661977 + Tan0020931.3 Tan04g1227 1227
4 11663385 11667526 - Tan0017257.1 Tan04g1228 1228
1 8304389 8331824 + Vvi1g721 Vvi1g721 721
1 8666040 8668402 + Vvi1g722 Vvi1g722 722
1 8670275 8675422 + Vvi1g723 Vvi1g723 723
1 8677830 8680798 + Vvi1g724 Vvi1g724 724
1 8694649 8695830 - Vvi1g725 Vvi1g725 725
1 8695846 8697185 - Vvi1g726 Vvi1g726 726
1 8704046 8710652 + Vvi1g727 Vvi1g727 727
1 8712007 8728580 - Vvi1g728 Vvi1g728 728
1 8738933 8766205 - Vvi1g729 Vvi1g729 729
1 8775790 8787091 + Vvi1g730 Vvi1g730 730
       

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