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
Vvi4g522 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed05g1731 . . . . . . . Cpe02g00335 Bhi09g02984 Tan01g3583 Cmetu07g2204 . Hepe01g1978 Mch11g0514 . . . . . . . . . . . Cme07g00109
Vvi4g523 . . Bda01g00668 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed05g1730 . . . . . . . . Bhi09g02983 Tan01g3584 Cmetu02g1625 . Hepe01g1979 Mch11g0515 . . . . . . . . . . . Cme07g00108
Vvi4g524 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g525 . . Bda01g00760 . . Bpe02g00545 . . . . . . . . Sed11g1150 . . Bhi04g00040 Tan02g2755 Cmetu03g0839 . Hepe10g0223 . Lcy13g1820 . . . . . . . . . . . . . . . . . . . . . . . Sed06g2059 . . . . . . . . Bhi09g02982 Tan01g3585 Cmetu07g2142 . Hepe01g1980 Mch11g0516 . . . . . . . . . . . Cme07g00107
Vvi4g526 . Blo12g01059 . . . . . . . . Cma01g01648 . . . . . Cpe06g00307 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed13g1983 Cmo01g01700 . Cma09g00422 . . . . . Bhi09g02980 Tan01g3587 Cmetu07g1548 . Hepe01g1981 Mch11g0517 . . . . . . . . . . . Cme07g00106
Vvi4g527 . . Bda01g00759 . . . . . . . Cma01g01477 . Car09g00374 . Sed09g0886 . . Bhi04g00039 Tan02g2754 Cmetu02g2111 . Hepe10g0224 . Lcy13g1819 . . . . . . . . . . . . . . . . Blo18g00013 . . . . Bma01g01268 . Sed05g1728 Cmo01g01533 Cmo09g00429 . . . . . . Bhi09g02978 Tan01g3588 Cmetu07g0071 . Hepe01g1982 Mch11g0518 . . . . . . . . . . Chy03g01091 Cme07g00105
Vvi4g528 . . Bda01g00758 . . . . . . . Cma01g01478 . . . Sed11g1153 . . Bhi04g00038 Tan02g2753 Cmetu03g1994 . Hepe10g0225 . Lcy13g1818 . . . . . . . Cone10ag0690 . . . . . . Cme03g01587 . Blo18g00014 Bda01g01007 . . . . . Sed05g1726 Cmo01g01534 . . . . . . . Bhi09g02976 Tan01g3589 Cmetu07g2171 . Hepe01g1983 Mch11g0519 . . . . . . . . . . . Cme07g00104
Vvi4g529 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g530 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g531 . . . . Bpe02g01256 . . . Cmo05g00361 . Cma01g01479 Cma05g00357 . . Sed03g1636 . . Bhi04g00037 Tan02g2752 Cmetu03g1240 . Hepe10g0226 . Lcy13g1817 . . . . . . . Cone4ag1757 . . Cone20ag0337 . . . . . Blo18g00015 . Bda13g01247 . . . . . Cmo01g01535 . . . . Car05g00302 Cpe11g00306 . Bhi09g02975 Tan01g3590 Cmetu07g1351 . Hepe01g1984 Mch11g0520 . . . . . . . . Lsi08g01234 . . Cme07g00103
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 33698071 33701484 + Bda002696.1 Bda01g00668 668
1 34825210 34826265 + Bda002799.1 Bda01g00758 758
1 34827319 34828425 - Bda002800.1 Bda01g00759 759
1 34838893 34839741 - Bda002802.1 Bda01g00760 760
1 43657111 43658160 + Bda003166.2 Bda01g01007 1007
13 34905529 34906178 - Bda000055.1 Bda13g01247 1247
4 860884 861748 + XM_039030253.1 Bhi04g00037 37
4 901433 903339 + XM_039030740.1 Bhi04g00038 38
4 963855 965389 - XM_039029617.1 Bhi04g00039 39
4 986932 987874 - XM_039030216.1 Bhi04g00040 40
9 77308288 77309365 + XM_039043635.1 Bhi09g02975 2975
9 77341660 77343305 + XM_039040914.1 Bhi09g02976 2976
9 77346375 77349299 - XM_039040524.1 Bhi09g02978 2978
9 77378318 77381857 + XM_039041068.1 Bhi09g02980 2980
9 77386712 77387557 - XM_039043530.1 Bhi09g02982 2982
9 77402042 77407048 + XM_039042555.1 Bhi09g02983 2983
9 77407239 77413550 - XM_039042556.1 Bhi09g02984 2984
12 28391310 28392469 - BLOR05078 Blo12g01059 1059
18 140448 143627 + BLOR08501 Blo18g00013 13
18 144483 145526 - BLOR08502 Blo18g00014 14
18 147452 148407 - BLOR08503 Blo18g00015 15
1 17151759 17152620 + Bma001583.1 Bma01g01268 1268
2 3536132 3536992 + Bpe008384.1 Bpe02g00545 545
2 16047004 16047634 + Bpe009112.1 Bpe02g01256 1256
5 1680751 1681361 - Carg09357-RA Car05g00302 302
9 2052280 2055042 + Carg02854-RA Car09g00374 374
3 14319508 14320635 + Chy3G060710.1 Chy03g01091 1091
1 10410792 10412969 + CmaCh01G014770.1 Cma01g01477 1477
1 10414482 10415432 - CmaCh01G014780.1 Cma01g01478 1478
1 10416824 10417624 - CmaCh01G014790.1 Cma01g01479 1479
1 11282949 11285093 + CmaCh01G016480.1 Cma01g01648 1648
5 1600464 1601349 - CmaCh05G003570.1 Cma05g00357 357
9 1833532 1836986 - CmaCh09G004220.1 Cma09g00422 422
3 24885321 24886219 - MELO3C011288.2.1 Cme03g01587 1587
7 640263 641102 + MELO3C016980.2.1 Cme07g00103 103
7 646316 647908 + MELO3C016979.2.1 Cme07g00104 104
7 649752 652428 - MELO3C016978.2.1 Cme07g00105 105
7 656666 658917 + MELO3C016977.2.1 Cme07g00106 106
7 662882 663746 - MELO3C016976.2.1 Cme07g00107 107
7 673597 678483 + MELO3C016975.2.1 Cme07g00108 108
7 678531 681959 - MELO3C016974.2.1 Cme07g00109 109
2 21521691 21523414 + PI0013565.1 Cmetu02g1625 1625
2 18368838 18371387 - PI0023363.1 Cmetu02g2111 2111
3 4543946 4544821 - PI0012661.1 Cmetu03g0839 839
3 4515943 4517007 + PI0019865.1 Cmetu03g1240 1240
3 4529195 4531103 + PI0026389.1 Cmetu03g1994 1994
7 24125506 24127165 + PI0027036.1 Cmetu07g0071 71
7 24137195 24137818 - PI0028156.1 Cmetu07g1351 1351
7 24119466 24121301 - PI0013271.1 Cmetu07g1548 1548
7 24113618 24114260 + PI0027052.1 Cmetu07g2142 2142
7 24130859 24131904 - PI0025715.1 Cmetu07g2171 2171
7 24095732 24099722 + PI0017590.1 Cmetu07g2204 2204
1 11834754 11836579 + CmoCh01G015330.1 Cmo01g01533 1533
1 11837913 11838532 - CmoCh01G015340.1 Cmo01g01534 1534
1 11839451 11840104 - CmoCh01G015350.1 Cmo01g01535 1535
1 12758825 12761739 + CmoCh01G017000.1 Cmo01g01700 1700
5 1637315 1637932 - CmoCh05G003610.1 Cmo05g00361 361
9 1917384 1919710 + CmoCh09G004290.1 Cmo09g00429 429
4 12906148 12906943 - Conep04aG0181400.1 Cone4ag1757 1757
10 3361752 3362696 - Conep10aG0071000.1 Cone10ag0690 690
20 1511034 1511858 - Conep20aG0035100.1 Cone20ag0337 337
2 1801808 1804332 + Cp4.1LG02g05420.1 Cpe02g00335 335
6 1698627 1702321 - Cp4.1LG06g03140.1 Cpe06g00307 307
11 1659772 1660609 - Cp4.1LG11g03060.1 Cpe11g00306 306
1 84598495 84602517 + Hsped.01g19780.1 Hepe01g1978 1978
1 84601864 84607837 - Hsped.01g19790.1 Hepe01g1979 1979
1 84618310 84618912 + Hsped.01g19800.1 Hepe01g1980 1980
1 84623009 84626530 - Hsped.01g19810.1 Hepe01g1981 1981
1 84632313 84634578 + Hsped.01g19820.1 Hepe01g1982 1982
1 84637960 84639325 - Hsped.01g19830.1 Hepe01g1983 1983
1 84647565 84648425 - Hsped.01g19840.1 Hepe01g1984 1984
10 2361055 2361750 + Hsped.10g02230.1 Hepe10g0223 223
10 2373369 2375735 + Hsped.10g02240.1 Hepe10g0224 224
10 2380230 2381731 - Hsped.10g02250.1 Hepe10g0225 225
10 2400040 2400718 - Hsped.10g02260.1 Hepe10g0226 226
13 37127558 37128416 + Maker00033941 Lcy13g1817 1817
13 37144654 37145646 + Maker00034234 Lcy13g1818 1818
13 37152646 37154535 - Maker00034101 Lcy13g1819 1819
13 37165673 37166392 - Maker00033950 Lcy13g1820 1820
8 20802008 20802626 + Lsi08G012340.1 Lsi08g01234 1234
11 3303560 3310347 + MC11g0418 Mch11g0514 514
11 3306819 3313016 - MC11g0419 Mch11g0515 515
11 3321759 3322286 + MC11g0420 Mch11g0516 516
11 3325245 3327234 - MC11g0421 Mch11g0517 517
11 3331946 3334206 + MC11g0422 Mch11g0518 518
11 3337123 3339045 - MC11g0423 Mch11g0519 519
11 3342964 3344298 - MC11g0424 Mch11g0520 520
3 10430156 10431110 + Sed0027877.1 Sed03g1636 1636
5 31049048 31051807 + Sed0003032.1 Sed05g1726 1726
5 31056991 31060190 - Sed0002218.2 Sed05g1728 1728
5 31101267 31106089 + Sed0003022.1 Sed05g1730 1730
5 31106591 31110196 - Sed0006294.1 Sed05g1731 1731
6 44664678 44665824 + Sed0007138.1 Sed06g2059 2059
9 29009769 29013827 + Sed0020546.2 Sed09g0886 886
11 27405509 27406314 + Sed0003295.1 Sed11g1150 1150
11 27435840 27437469 - Sed0005390.1 Sed11g1153 1153
13 24711070 24716453 - Sed0018913.1 Sed13g1983 1983
1 100884065 100890514 + Tan0005722.1 Tan01g3583 3583
1 100891063 100895522 - Tan0016345.1 Tan01g3584 3584
1 100910655 100911398 + Tan0009317.1 Tan01g3585 3585
1 100917229 100918944 - Tan0006613.2 Tan01g3587 3587
1 100925863 100928281 + Tan0021423.1 Tan01g3588 3588
1 100931010 100932656 - Tan0007399.1 Tan01g3589 3589
1 100944558 100945344 - Tan0009070.1 Tan01g3590 3590
2 95774936 95775921 + Tan0000968.1 Tan02g2752 2752
2 95795559 95797120 + Tan0019797.1 Tan02g2753 2753
2 95804706 95806629 - Tan0021446.1 Tan02g2754 2754
2 95820018 95821091 - Tan0021903.1 Tan02g2755 2755
4 5596165 5598770 + Vvi4g522 Vvi4g522 522
4 5599591 5606765 - Vvi4g523 Vvi4g523 523
4 5614239 5625665 + Vvi4g524 Vvi4g524 524
4 5625724 5635064 + Vvi4g525 Vvi4g525 525
4 5636702 5639632 - Vvi4g526 Vvi4g526 526
4 5652934 5655912 + Vvi4g527 Vvi4g527 527
4 5662464 5663800 - Vvi4g528 Vvi4g528 528
4 5676521 5681319 - Vvi4g529 Vvi4g529 529
4 5682267 5696450 + Vvi4g530 Vvi4g530 530
4 5696450 5697730 - Vvi4g531 Vvi4g531 531
       

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