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
Vvi4g1072 Blo04g00898 Blo16g00066 . . . . . . . . . Cma07g00445 . . . Cpe19g00843 . Bhi03g00891 . . . . . . Cla01g01960 . . . . . . Cone8ag0835 Cone12ag0732 . . Lsi01g00622 . Chy07g01271 Cme08g00907 . . . . . . Bma03g00973 . . . Cmo07g00442 . . . . . . . . . . . . . . . . . . . . . Csa06g03302 Chy02g00593 .
Vvi4g1073 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1074 . . . . . Bpe13g00426 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag0731 . . . . Chy07g01270 . . . . . . . . Bma06g00106 . . . . . . . . . . . . . . . . . . . . . . . Lsi07g00226 . . .
Vvi4g1075 . Blo16g00071 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00531 . .
Vvi4g1076 Blo04g00897 . . . Bpe15g00416 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0836 Cone12ag0730 . . . . Chy07g01269 . . . . . . . Bma03g00972 . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00532 . .
Vvi4g1077 Blo04g00896 Blo16g00072 . . Bpe15g00463 Bpe13g00425 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag1664 . . . Chy07g01268 . . . Bda11g01845 . . . Bma03g00971 Bma06g00105 . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00533 . .
Vvi4g1078 . . . . . . Bma09g00101 . . . . Cma07g00444 . Car07g00391 . Cpe19g00844 . Bhi03g00890 . . . . . . Cla01g01961 Cam01g2051 Cec04g1709 Cco04g1774 Clacu01g2072 Cmu01g1949 Cre04g1624 . . Cone6ag1665 Cone9ag1587 Lsi01g00621 . . Cme08g00908 Blo05g00822 . . . . . . . . . Cmo07g00441 . . . . . . . . . . . . . . . . . . . . . Csa06g03303 Chy02g00592 .
Vvi4g1079 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy07g01267 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00534 . .
Vvi4g1080 Blo04g00895 . . . Bpe15g00464 . . . Cmo04g00796 . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag1666 Cone9ag1588 . . Chy07g01230 . . . . . . . Bma03g00970 . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00579 . .
Vvi4g1081 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed01g0256 . . . Cma20g00807 . . . . Bhi10g01934 Tan05g1232 Cmetu09g0265 . Hepe08g0970 . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 53642575 53651857 + Bda008782.1 Bda11g01845 1845
3 16614887 16619296 - XM_039026930.1 Bhi03g00890 890
3 16722188 16743264 - XM_039027617.1 Bhi03g00891 891
10 48279807 48282540 - XM_039045463.1 Bhi10g01934 1934
4 10319596 10323543 - BLOR13807 Blo04g00895 895
4 10335718 10359394 + BLOR13808 Blo04g00896 896
4 10417997 10423109 + BLOR13809 Blo04g00897 897
4 10453477 10455436 - BLOR13810 Blo04g00898 898
5 29966668 29971084 + BLOR15784 Blo05g00822 822
16 1997519 2000294 + BLOR07314 Blo16g00066 66
16 2061418 2063972 - BLOR07319 Blo16g00071 71
16 2065051 2071276 - BLOR07320 Blo16g00072 72
3 10291990 10293828 - Bma017309.3 Bma03g00970 970
3 10303974 10310276 + Bma017310.1 Bma03g00971 971
3 10312849 10319417 + Bma017311.1 Bma03g00972 972
3 10326286 10328100 - Bma017312.1 Bma03g00973 973
6 1504564 1508532 + Bma022725.1 Bma06g00105 105
6 1509170 1511222 + Bma031265 Bma06g00106 106
9 2755558 2759410 + Bma028797.1 Bma09g00101 101
13 11869794 11876021 + Bpe006550.1 Bpe13g00425 425
13 11876813 11879083 + Bpe024941 Bpe13g00426 426
15 15670568 15681470 + Bpe001354.3 Bpe15g00416 416
15 16014176 16020472 - Bpe001397.1 Bpe15g00463 463
15 16023583 16024312 + Bpe001398.1 Bpe15g00464 464
1 33619396 33623312 + CaPI482276_01g020510.1 Cam01g2051 2051
7 1974039 1975725 - Carg07971-RA Car07g00391 391
4 32687123 32691018 + CcPI632755_04g017740.1 Cco04g1774 1774
4 36177530 36181431 + CePI673135_04g017090.1 Cec04g1709 1709
2 3598342 3602533 - Chy2G028590.1 Chy02g00592 592
2 3608005 3611268 - Chy2G028600.1 Chy02g00593 593
7 17097355 17099796 - Chy7G140600.1 Chy07g01230 1230
7 17393411 17405314 + Chy7G140970.1 Chy07g01267 1267
7 17408028 17415404 + Chy7G140980.1 Chy07g01268 1268
7 17417094 17423499 + Chy7G140990.1 Chy07g01269 1269
7 17426426 17429140 + Chy7G141000.1 Chy07g01270 1270
7 17432213 17434965 - Chy7G141010.1 Chy07g01271 1271
1 32473568 32477486 + ClG42_01g0207200.10 Clacu01g2072 2072
1 34243021 34246746 + ClCG01G020110.2 Cla01g01960 1960
1 34249624 34257130 + ClCG01G020120.2 Cla01g01961 1961
7 1942634 1947005 - CmaCh07G004440.1 Cma07g00444 444
7 1948968 1950806 - CmaCh07G004450.1 Cma07g00445 445
20 3796753 3799549 - CmaCh20G008070.1 Cma20g00807 807
8 5961591 5965184 + MELO3C007884.2.1 Cme08g00907 907
8 5971929 5976109 + MELO3C007885.2.1 Cme08g00908 908
9 4861909 4866040 + PI0023233.1 Cmetu09g0265 265
4 3988809 3991662 - CmoCh04G007960.1 Cmo04g00796 796
7 2027464 2033314 - CmoCh07G004410.1 Cmo07g00441 441
7 2035379 2037256 - CmoCh07G004420.1 Cmo07g00442 442
1 32810754 32814679 + CmPI595203_01g019490.1 Cmu01g1949 1949
6 12672959 12678548 - Conep06aG0172900.1 Cone6ag1664 1664
6 12679992 12683658 + Conep06aG0173000.1 Cone6ag1665 1665
6 12683850 12685843 + Conep06aG0173100.1 Cone6ag1666 1666
8 8371094 8372891 + Conep08aG0086100.1 Cone8ag0835 835
8 8380024 8386525 - Conep08aG0086200.1 Cone8ag0836 836
9 11398360 11401760 + Conep09aG0163700.1 Cone9ag1587 1587
9 11402363 11404366 + Conep09aG0163800.1 Cone9ag1588 1588
12 6697225 6713572 + Conep12aG0075300.1 Cone12ag0730 730
12 6713875 6715385 + Conep12aG0075400.1 Cone12ag0731 731
12 6720642 6722522 - Conep12aG0075500.1 Cone12ag0732 732
19 6246842 6248518 + Cp4.1LG19g09140.1 Cpe19g00843 843
19 6251126 6256838 + Cp4.1LG19g09120.1 Cpe19g00844 844
4 34658472 34662389 + CrPI670011_04g016240.1 Cre04g1624 1624
4 3494715 3498678 - CsaV3_4G005310.1 Csa04g00531 531
4 3500065 3507259 - CsaV3_4G005320.1 Csa04g00532 532
4 3507369 3516485 - CsaV3_4G005330.1 Csa04g00533 533
4 3525509 3528884 - CsaV3_4G005340.1 Csa04g00534 534
4 3805645 3809595 + CsaV3_4G005790.1 Csa04g00579 579
6 27665594 27668783 + CsaV3_6G046880.1 Csa06g03302 3302
6 27673838 27677726 + CsaV3_6G046890.1 Csa06g03303 3303
8 9099266 9101714 - Hsped.08g09700.1 Hepe08g0970 970
1 4988487 4995259 - Lsi01G006210.1 Lsi01g00621 621
1 5002931 5004585 - Lsi01G006220.1 Lsi01g00622 622
7 2450825 2454537 - Lsi07G002260.1 Lsi07g00226 226
1 2002147 2005285 - Sed0002284.1 Sed01g0256 256
5 12740968 12743455 - Tan0021141.1 Tan05g1232 1232
4 19492611 19494687 + Vvi4g1072 Vvi4g1072 1072
4 19495078 19495418 + Vvi4g1073 Vvi4g1073 1073
4 19496678 19502630 - Vvi4g1074 Vvi4g1074 1074
4 19502781 19506001 - Vvi4g1075 Vvi4g1075 1075
4 19508699 19523351 - Vvi4g1076 Vvi4g1076 1076
4 19524045 19544727 - Vvi4g1077 Vvi4g1077 1077
4 19579518 19585872 + Vvi4g1078 Vvi4g1078 1078
4 19585928 19587433 - Vvi4g1079 Vvi4g1079 1079
4 19589674 19597480 + Vvi4g1080 Vvi4g1080 1080
4 19605005 19607076 + Vvi4g1081 Vvi4g1081 1081
       

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