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
Vvi1g1101 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla01g00681 Cam01g0714 Cec01g0705 Cco01g0735 Clacu01g0700 . . . . . Cme09g01259
Vvi1g1102 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1103 . . . . . . Bma14g01735 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe11g01725 . . . . . . . . . . . . . . . . . . . Cla11g01360 Cam11g1416 Cec11g1445 Cco11g1441 Clacu11g1575 . Cre11g1816 . . . .
Vvi1g1104 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1105 . . . . . . . . Cmo04g01049 . Cma04g00972 . Car04g00914 . . . . . . . . . . . . . . . . . . . . . . . . Chy10g00019 Cme10g01341 . . . . Bpe11g01724 . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g00946 . .
Vvi1g1106 . . . . . . . . . . . . Car04g00912 . . . . . . . . . . . . . . . . . . Cone13ag0678 Cone19ag0668 . . . . . . . . . . Bpe11g01720 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1107 . . . . . . . . Cmo04g01048 . Cma04g00971 . . . . Cpe09g00622 . . . . . . . . . . . . . . . . . . . . . Chy10g00017 Cme10g01333 . . . . Bpe11g01719 . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g00943 . .
Vvi1g1108 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0679 Cone19ag0669 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1109 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1110 . . Bda01g01766 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe02g01940 . . . . Cmo15g00905 . Cma15g00870 . Car15g00817 . . Bhi12g01003 . . . . . Lcy10g1569 Cla01g00679 Cam01g0711 Cec01g0703 Cco01g0732 Clacu01g0697 Cmu01g0672 Cre09g1833 Lsi09g00736 Csa05g01314 Chy09g00454 Cme09g01260
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 53877506 53911464 + Bda004055.1 Bda01g01766 1766
12 30565178 30589706 - XM_039051253.1 Bhi12g01003 1003
14 37300713 37306801 + Bma012501.1 Bma14g01735 1735
2 21328737 21366766 + Bpe009765.3 Bpe02g01940 1940
11 13511914 13515713 + Bpe005034.1 Bpe11g01719 1719
11 13523139 13530301 - Bpe005035.1 Bpe11g01720 1720
11 13561454 13564351 - Bpe005039.1 Bpe11g01724 1724
11 13589513 13597677 + Bpe005040.1 Bpe11g01725 1725
1 7980907 7996832 - CaPI482276_01g007110.1 Cam01g0711 711
1 8015895 8016247 + CaPI482276_01g007140.1 Cam01g0714 714
11 26868099 26870222 - CaPI482276_11g014160.1 Cam11g1416 1416
4 5193744 5210964 + Carg00087-RA Car04g00912 912
4 5222006 5223952 - Carg00089-RA Car04g00914 914
15 4640760 4656381 + Carg01338-RA Car15g00817 817
1 7776451 7792474 - CcPI632755_01g007320.1 Cco01g0732 732
1 7810735 7811064 + CcPI632755_01g007350.1 Cco01g0735 735
11 27187139 27188976 - CcPI632755_11g014410.1 Cco11g1441 1441
1 7846995 7863866 - CePI673135_01g007030.1 Cec01g0703 703
1 7879294 7879644 + CePI673135_01g007050.1 Cec01g0705 705
11 28616789 28618878 - CePI673135_11g014450.1 Cec11g1445 1445
9 4022828 4037467 + Chy9G161700.1 Chy09g00454 454
10 579188 581730 - Chy10G172110.1 Chy10g00017 17
10 731682 736567 - Chy10G172130.1 Chy10g00019 19
1 7650688 7664418 - ClG42_01g0069700.10 Clacu01g0697 697
1 7683523 7683872 + ClG42_01g0070000.10 Clacu01g0700 700
11 26893534 26895682 - ClG42_11g0157500.10 Clacu11g1575 1575
1 8054694 8072851 - ClCG01G006950.2 Cla01g00679 679
1 8091757 8092591 + ClCG01G006965.1 Cla01g00681 681
11 27099022 27101499 - ClCG11G013880.1 Cla11g01360 1360
4 4993365 4995838 - CmaCh04G009710.1 Cma04g00971 971
4 4999755 5002308 - CmaCh04G009720.1 Cma04g00972 972
15 4385677 4402652 + CmaCh15G008700.1 Cma15g00870 870
9 17444839 17446017 - MELO3C005215.2.1 Cme09g01259 1259
9 17461734 17487963 + MELO3C005216.2.1 Cme09g01260 1260
10 15114723 15119464 - MELO3C022568.2.1 Cme10g01333 1333
10 15349540 15355587 - MELO3C022574.2.1 Cme10g01341 1341
4 5233890 5235765 - CmoCh04G010480.1 Cmo04g01048 1048
4 5241270 5243458 - CmoCh04G010490.1 Cmo04g01049 1049
15 4567382 4583685 + CmoCh15G009050.1 Cmo15g00905 905
1 7621962 7637785 - CmPI595203_01g006720.1 Cmu01g0672 672
13 6750545 6755750 + Conep13aG0070200.1 Cone13ag0678 678
13 6757015 6760638 + Conep13aG0070300.1 Cone13ag0679 679
19 5692050 5694248 + Conep19aG0068900.1 Cone19ag0668 668
19 5696424 5700582 + Conep19aG0069000.1 Cone19ag0669 669
9 4502966 4507170 + Cp4.1LG09g05600.1 Cpe09g00622 622
9 36694079 36710127 + CrPI670011_09g018330.1 Cre09g1833 1833
11 29766104 29768219 - CrPI670011_11g018160.1 Cre11g1816 1816
5 7821071 7826073 - CsaV3_5G012400.1 Csa05g00943 943
5 7900420 7905450 - CsaV3_5G012430.1 Csa05g00946 946
5 13931016 13960066 - CsaV3_5G017370.1 Csa05g01314 1314
10 40019129 40040963 + Maker00007006 Lcy10g1569 1569
9 8481272 8485810 - Lsi09G007360.1 Lsi09g00736 736
1 18696200 18697377 - Vvi1g1101 Vvi1g1101 1101
1 18751025 18752609 + Vvi1g1102 Vvi1g1102 1102
1 18753619 18764461 - Vvi1g1103 Vvi1g1103 1103
1 18797580 18798005 - Vvi1g1104 Vvi1g1104 1104
1 18906767 18909820 + Vvi1g1105 Vvi1g1105 1105
1 18955321 18986890 + Vvi1g1106 Vvi1g1106 1106
1 19016017 19020560 + Vvi1g1107 Vvi1g1107 1107
1 19042622 19048171 - Vvi1g1108 Vvi1g1108 1108
1 19095840 19096432 - Vvi1g1109 Vvi1g1109 1109
1 19097141 19129029 + Vvi1g1110 Vvi1g1110 1110
       

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