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
Vvi1g781 Blo01g00406 . . . . . . . . . . . . . . . . Bhi07g01709 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g782 . . . . . . . . . . . . . . . . . Bhi07g01706 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g783 . . . . . . . . . . . . . . . . . Bhi07g01704 . . . . . . . . . . . . . . . . . . . . . . . Bda07g01566 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g784 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g785 . . . . . . Bma14g01775 . . . . . . . . . . Bhi07g01703 . . . . . . . . . . . . . . . . . . . . . . Blo11g00898 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g786 . . . . . . . . . . . . . . Sed06g1602 . . Bhi07g01672 Tan04g1177 Cmetu10g1745 Lac13g0238 Hepe10g1675 . . Cla05g02511 Cam05g2695 Cec05g2729 Cco05g2763 Clacu05g2698 Cmu05g2552 Cre05g2667 . . . . Lsi04g00510 Csa05g02371 Chy10g00935 Cme10g00490 . . Bda07g01569 . Bpe11g01737 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g787 Blo01g00407 Blo16g01146 Bda01g02237 . Bpe13g00480 . . . . Cmo18g01213 . Cma18g01231 . Car18g01100 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma01g00067 . . . . . . . . . Cpe07g00640 . . . . . . . . . . . . . . . Csa05g01687 Chy09g00629 .
Vvi1g788 . . Bda01g02238 . Bpe13g00479 . . . Cmo04g01671 . . . . . Sed08g1992 . Cpe01g01413 Bhi07g01671 Tan04g1173 Cmetu04g1975 Lac13g0239 Hepe10g1677 . . Cla05g02510 Cam05g2694 Cec05g2728 Cco05g2762 Clacu05g2697 Cmu05g2551 Cre05g2666 . . . . Lsi04g00509 Csa05g02372 Chy10g00937 . . . . . . . Bma01g00068 Bma06g00635 . . . Cma04g01597 . Car04g01643 . . . . . . . . . . . . . . . . . . . . .
Vvi1g789 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0641 . . . . . . . Bda07g01570 . Bpe11g01738 . . . . Cmo04g02857 . . . . . Cpe13g00922 Cpe07g00639 . . . . . . . . . . . . . . . Csa05g01723 Chy09g00662 .
Vvi1g790 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 58192977 58196774 - Bda004582.1 Bda01g02237 2237
1 58207514 58208110 - Bda004584.1 Bda01g02238 2238
7 29090609 29092748 + Bda028429.2 Bda07g01566 1566
7 29140431 29142768 - Bda028433.1 Bda07g01569 1569
7 29147540 29149714 - Bda028434.1 Bda07g01570 1570
7 46767435 46768325 + XM_039037136.1 Bhi07g01671 1671
7 46789671 46793039 + XM_039037472.1 Bhi07g01672 1672
7 47334244 47336106 - XM_039035565.1 Bhi07g01703 1703
7 47373109 47375715 + XM_039036305.1 Bhi07g01704 1704
7 47376676 47380894 + XM_039036300.1 Bhi07g01706 1706
7 47394384 47395594 + XM_039035609.1 Bhi07g01709 1709
1 4579092 4579976 + BLOR00406 Blo01g00406 406
1 4594416 4606233 - BLOR00407 Blo01g00407 407
11 17999876 18001692 + BLOR03774 Blo11g00898 898
16 39990618 39994259 + BLOR21933 Blo16g01146 1146
1 685103 688532 - Bma000234.1 Bma01g00067 67
1 691204 691839 - Bma000235.1 Bma01g00068 68
6 33727565 33728173 - Bma023582.1 Bma06g00635 635
14 38150475 38151572 + Bma012545.1 Bma14g01775 1775
11 13759798 13761930 - Bpe005054.1 Bpe11g01737 1737
11 13766132 13769978 - Bpe005055.1 Bpe11g01738 1738
13 12248680 12249297 + Bpe010190.1 Bpe13g00479 479
13 12252204 12256078 + Bpe010191.1 Bpe13g00480 480
5 34350142 34350843 + CaPI482276_05g026940.1 Cam05g2694 2694
5 34360758 34363285 + CaPI482276_05g026950.1 Cam05g2695 2695
4 9461557 9462201 - Carg01757-RA Car04g01643 1643
18 11032806 11035843 + Carg17230-RA Car18g01100 1100
5 35477520 35478221 + CcPI632755_05g027620.1 Cco05g2762 2762
5 35488101 35490614 + CcPI632755_05g027630.1 Cco05g2763 2763
5 37799230 37799931 + CePI673135_05g027280.1 Cec05g2728 2728
5 37810024 37812523 + CePI673135_05g027290.1 Cec05g2729 2729
9 7899439 7904688 - Chy9G163450.1 Chy09g00629 629
9 8657806 8661416 - Chy9G163780.1 Chy09g00662 662
10 14962435 14964777 - Chy10G181290.1 Chy10g00935 935
10 14970026 14970793 - Chy10G181310.1 Chy10g00937 937
5 34557563 34558264 + ClG42_05g0269700.10 Clacu05g2697 2697
5 34568135 34570598 + ClG42_05g0269800.10 Clacu05g2698 2698
5 36479397 36480251 + ClCG05G024980.2 Cla05g02510 2510
5 36490094 36492557 + ClCG05G024990.1 Cla05g02511 2511
4 8069785 8070450 - CmaCh04G015970.1 Cma04g01597 1597
18 9683488 9687410 + CmaCh18G012310.1 Cma18g01231 1231
10 3157118 3159667 + MELO3C012027.2.1 Cme10g00490 490
4 21978156 21978617 + PI0024564.1 Cmetu04g1975 1975
10 18866955 18869985 - PI0008124.1 Cmetu10g1745 1745
4 8487185 8487826 - CmoCh04G016710.1 Cmo04g01671 1671
4 20363066 20366486 - CmoCh04G028570.1 Cmo04g02857 2857
18 12062536 12066017 + CmoCh18G012130.1 Cmo18g01213 1213
5 34295378 34296079 + CmPI595203_05g025510.1 Cmu05g2551 2551
5 34305963 34308426 + CmPI595203_05g025520.1 Cmu05g2552 2552
8 6301495 6305680 + Conep08aG0066200.1 Cone8ag0641 641
1 8493067 8493723 - Cp4.1LG01g12960.1 Cpe01g01413 1413
7 4543529 4550847 + Cp4.1LG07g06480.1 Cpe07g00639 639
7 4559190 4565225 + Cp4.1LG07g06530.1 Cpe07g00640 640
13 7817945 7828752 - Cp4.1LG13g08810.1 Cpe13g00922 922
5 37650592 37651293 + CrPI670011_05g026660.1 Cre05g2666 2666
5 37659955 37662467 + CrPI670011_05g026670.1 Cre05g2667 2667
5 20072544 20077846 - CsaV3_5G025060.1 Csa05g01687 1687
5 20535180 20550537 - CsaV3_5G025420.1 Csa05g01723 1723
5 25946033 25948949 - CsaV3_5G031900.1 Csa05g02371 2371
5 25953607 25955002 - CsaV3_5G031910.1 Csa05g02372 2372
10 53434890 53442322 - Hsped.10g16750.1 Hepe10g1675 1675
10 53457385 53458038 - Hsped.10g16770.1 Hepe10g1677 1677
13 1685327 1687550 - Lag0040034.1 Lac13g0238 238
13 1697328 1699355 - Lag0040035.1 Lac13g0239 239
4 4739377 4740087 + Lsi04G005090.1 Lsi04g00509 509
4 4748600 4751807 + Lsi04G005100.1 Lsi04g00510 510
6 40846767 40849953 + Sed0015146.2 Sed06g1602 1602
8 34284648 34285046 + Sed0020245.1 Sed08g1992 1992
4 10995598 10996590 + Tan0000121.1 Tan04g1173 1173
4 11027226 11030175 + Tan0005969.1 Tan04g1177 1177
1 9518209 9519608 - Vvi1g781 Vvi1g781 781
1 9525062 9530545 - Vvi1g782 Vvi1g782 782
1 9542889 9555896 - Vvi1g783 Vvi1g783 783
1 9565249 9637417 + Vvi1g784 Vvi1g784 784
1 9655499 9657867 + Vvi1g785 Vvi1g785 785
1 9674650 9688246 - Vvi1g786 Vvi1g786 786
1 9697619 9711615 - Vvi1g787 Vvi1g787 787
1 9724650 9730239 - Vvi1g788 Vvi1g788 788
1 9730772 9735394 - Vvi1g789 Vvi1g789 789
1 9764039 9764869 - Vvi1g790 Vvi1g790 790
       

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