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
Vvi1g601 . . . . . . . . . . . . . . . . . . . . . . . . Cla05g02617 . . . . . . . Cone19ag1084 . . Lsi04g00630 Csa05g02257 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g602 . . . . . . Bma14g01832 . . Cmo18g00721 . Cma18g00732 . Car18g00682 Sed06g1708 . . Bhi07g01834 Tan04g0134 Cmetu10g0004 Lac13g0117 Hepe10g1568 . . Cla05g02616 Cam05g2804 Cec05g2840 Cco05g2872 Clacu05g2808 Cmu05g2656 Cre05g2772 . Cone19ag1083 . . . Csa05g02258 Chy10g00828 . Blo06g00839 Blo11g01035 Bda07g01648 . . . . . . . Cmo15g00862 Cma04g01790 Cma15g00831 . . . . . . . . . . . . . . . . . . . . . .
Vvi1g603 . . . Bda11g01298 Bpe13g01492 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g01298 . . . Bma06g00593 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g604 . . . Bda11g01297 Bpe13g01491 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g01297 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g605 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma06g00594 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g606 . Blo16g01177 . Bda11g01296 Bpe13g01490 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g01296 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g607 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g608 . . . . . . Bma14g01831 . . . . . . . Sed01g3841 . Cpe01g01578 Bhi07g01832 Tan04g0135 Cmetu01g1934 Lac13g0118 Hepe10g1569 . . Cla05g02615 Cam05g2803 Cec05g2839 Cco05g2871 Clacu05g2806 Cmu05g2655 Cre05g2771 . . Cone8ag0705 . Lsi04g00629 Csa05g02259 Chy10g00829 Cme10g00603 . Blo11g01038 Bda07g01647 . . . . . . . . Cma04g01789 . Car04g01805 . . . . . . . . . . . . . . . . . . . . .
Vvi1g609 . . . Bda11g01294 . . . . . . . . . . . . Cpe01g01577 Bhi07g01829 . . . . . . Cla05g02614 Cam05g2802 Cec05g2838 Cco05g2870 Clacu05g2805 Cmu05g2653 Cre05g2770 . . . Cone12ag0684 Lsi04g00628 Csa05g02261 Chy10g00831 Cme10g00601 . . . Bda11g01294 . . . Bma06g00595 . . . Cma04g01788 . Car04g01804 . . . . . . . . . . . . . . . . . . . . .
Vvi1g610 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 30688192 30690726 + Bda028528.1 Bda07g01647 1647
7 30699517 30700794 - Bda028529.1 Bda07g01648 1648
11 13641825 13648929 - Bda007816.1 Bda11g01294 1294
11 13676325 13677887 - Bda007818.1 Bda11g01296 1296
11 13679573 13681699 + Bda007819.1 Bda11g01297 1297
11 13683219 13685354 + Bda007820.1 Bda11g01298 1298
7 49635115 49646577 - XM_039036226.1 Bhi07g01829 1829
7 49719659 49724117 + XM_039037460.1 Bhi07g01832 1832
7 49745524 49747143 - XM_039037318.1 Bhi07g01834 1834
6 31636837 31647419 + BLOR17422 Blo06g00839 839
11 27867057 27868334 + BLOR03911 Blo11g01035 1035
11 27955589 27958023 - BLOR03914 Blo11g01038 1038
16 40319427 40320989 - BLOR21964 Blo16g01177 1177
6 31685543 31688121 - Bma023520.1 Bma06g00593 593
6 31689322 31691328 - Bma023521.1 Bma06g00594 594
6 31700632 31737215 + Bma023522.2 Bma06g00595 595
14 39208579 39210785 + Bma012610.1 Bma14g01831 1831
14 39231395 39232672 - Bma012611.1 Bma14g01832 1832
13 20281788 20283221 - Bpe011157.1 Bpe13g01490 1490
13 20284658 20287183 + Bpe011158.2 Bpe13g01491 1491
13 20288944 20291079 + Bpe011159.1 Bpe13g01492 1492
5 35152328 35163934 - CaPI482276_05g028020.1 Cam05g2802 2802
5 35167170 35170746 + CaPI482276_05g028030.1 Cam05g2803 2803
5 35178777 35180117 - CaPI482276_05g028040.1 Cam05g2804 2804
4 10457272 10467306 - Carg14301-RA Car04g01804 1804
4 10467423 10470229 + Carg14300-RA Car04g01805 1805
18 7990836 7992199 + Carg27648-RA Car18g00682 682
5 36307099 36318755 - CcPI632755_05g028700.1 Cco05g2870 2870
5 36322032 36325657 + CcPI632755_05g028710.1 Cco05g2871 2871
5 36333758 36335098 - CcPI632755_05g028720.1 Cco05g2872 2872
5 38623253 38637396 - CePI673135_05g028380.1 Cec05g2838 2838
5 38637724 38641330 + CePI673135_05g028390.1 Cec05g2839 2839
5 38648967 38650295 - CePI673135_05g028400.1 Cec05g2840 2840
10 14229026 14230363 + Chy10G180220.1 Chy10g00828 828
10 14239125 14241224 - Chy10G180230.1 Chy10g00829 829
10 14244344 14255399 + Chy10G180250.1 Chy10g00831 831
5 35370749 35389344 - ClG42_05g0280500.10 Clacu05g2805 2805
5 35391041 35394616 + ClG42_05g0280600.10 Clacu05g2806 2806
5 35402684 35404024 - ClG42_05g0280800.10 Clacu05g2808 2808
5 37342594 37353976 - ClCG05G026050.2 Cla05g02614 2614
5 37365072 37373531 + ClCG05G026060.2 Cla05g02615 2615
5 37377138 37378478 - ClCG05G026080.1 Cla05g02616 2616
5 37385108 37389978 - ClCG05G026090.1 Cla05g02617 2617
4 9016196 9025248 - CmaCh04G017880.1 Cma04g01788 1788
4 9026796 9029657 + CmaCh04G017890.1 Cma04g01789 1789
4 9033323 9034627 - CmaCh04G017900.1 Cma04g01790 1790
15 4195566 4196804 - CmaCh15G008310.1 Cma15g00831 831
18 6615935 6617200 + CmaCh18G007320.1 Cma18g00732 732
10 3828777 3839987 - MELO3C011924.2.1 Cme10g00601 601
10 3841787 3844840 + MELO3C011922.2.1 Cme10g00603 603
1 18987571 18989419 + PI0028520.1 Cmetu01g1934 1934
10 18081056 18082602 + PI0012559.1 Cmetu10g0004 4
15 4365133 4366371 - CmoCh15G008620.1 Cmo15g00862 862
18 9005162 9006418 + CmoCh18G007210.1 Cmo18g00721 721
5 35109049 35118217 - CmPI595203_05g026530.1 Cmu05g2653 2653
5 35128704 35132916 + CmPI595203_05g026550.1 Cmu05g2655 2655
5 35140986 35142326 - CmPI595203_05g026560.1 Cmu05g2656 2656
8 7097976 7103448 + Conep08aG0072800.1 Cone8ag0705 705
12 6246706 6254594 - Conep12aG0070700.1 Cone12ag0684 684
19 7884280 7885934 - Conep19aG0111700.1 Cone19ag1083 1083
19 7890099 7894390 - Conep19aG0111800.1 Cone19ag1084 1084
1 9622329 9631600 - Cp4.1LG01g15780.1 Cpe01g01577 1577
1 9632659 9635920 + Cp4.1LG01g15760.1 Cpe01g01578 1578
5 38478022 38489755 - CrPI670011_05g027700.1 Cre05g2770 2770
5 38492981 38496603 + CrPI670011_05g027710.1 Cre05g2771 2771
5 38504718 38506058 - CrPI670011_05g027720.1 Cre05g2772 2772
5 25216771 25221398 + CsaV3_5G030760.1 Csa05g02257 2257
5 25225144 25227550 + CsaV3_5G030770.1 Csa05g02258 2258
5 25234163 25237013 - CsaV3_5G030780.1 Csa05g02259 2259
5 25238987 25249516 + CsaV3_5G030790.1 Csa05g02261 2261
10 52386074 52387622 + Hsped.10g15680.1 Hepe10g1568 1568
10 52399320 52405063 - Hsped.10g15690.1 Hepe10g1569 1569
13 817893 819209 + Lag0039913.1 Lac13g0117 117
13 826114 829735 - Lag0039914.1 Lac13g0118 118
4 5741156 5756633 - Lsi04G006280.1 Lsi04g00628 628
4 5756806 5760099 + Lsi04G006290.1 Lsi04g00629 629
4 5775644 5783492 - Lsi04G006300.1 Lsi04g00630 630
1 67668778 67677231 - Sed0012306.1 Sed01g3841 3841
6 41800481 41801922 - Sed0004425.1 Sed06g1708 1708
4 875071 876796 + Tan0000503.1 Tan04g0134 134
4 885074 888888 - Tan0013948.1 Tan04g0135 135
1 6877618 6883938 + Vvi1g601 Vvi1g601 601
1 6886456 6888175 + Vvi1g602 Vvi1g602 602
1 6907732 6911179 - Vvi1g603 Vvi1g603 603
1 6911854 6915565 - Vvi1g604 Vvi1g604 604
1 6925462 6929045 - Vvi1g605 Vvi1g605 605
1 6936327 6938135 + Vvi1g606 Vvi1g606 606
1 6948086 6954828 + Vvi1g607 Vvi1g607 607
1 6955273 6958016 - Vvi1g608 Vvi1g608 608
1 6964072 6976804 + Vvi1g609 Vvi1g609 609
1 6976807 6977762 - Vvi1g610 Vvi1g610 610
       

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