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
Vvi4g1092 . . Bda04g00028 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag1674 Cone9ag1595 . . . . Blo05g00824 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1093 . . Bda04g00027 . . . Bma09g00102 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag1675 Cone9ag1596 . . . . . . . . . Bpe06g00025 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1094 Blo04g00890 Blo16g00075 . . Bpe15g00467 Bpe13g00422 . Bma15g00952 . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag1676 Cone9ag1597 . . . . . . Bda11g01842 . Bpe10g00148 . Bma03g00966 Bma06g00102 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1095 . . . . . . . Bma15g00949 . . Cma03g00697 Cma07g00438 Car03g00641 Car07g00386 . Cpe19g00848 Cpe10g00653 Bhi03g00882 . . . . . . Cla01g01966 Cam01g2058 Cec04g1716 Cco04g1782 Clacu01g2079 Cmu01g1956 Cre04g1630 . . . . Lsi01g00616 . . Cme08g00913 . . . . Bpe10g00150 . . . . Cmo03g00724 Cmo07g00436 . . . . . . . . . . . . . . . . . . . . . Csa06g03311 Chy02g00586 .
Vvi4g1096 . . Bda04g00026 . . . Bma09g00103 . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0840 . . . . . . . Blo05g00825 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1097 Blo04g00889 . . . Bpe15g00468 . . . . . Cma03g00696 Cma07g00437 Car03g00640 Car07g00385 Sed10g0984 Cpe19g00849 Cpe10g00654 Bhi03g00880 Tan03g2058 Cmetu04g1220 . Hepe04g1580 . . Cla01g01967 Cam01g2059 Cec04g1717 Cco04g1783 Clacu01g2080 Cmu01g1957 Cre04g1631 . . Cone6ag1677 Cone9ag1598 Lsi01g00615 . . Cme08g00914 . . . . . . Bma03g00965 . . Cmo03g00722 Cmo07g00435 . . . . . . . . . . . . . . . . . . . . . Csa06g03312 Chy02g00585 .
Vvi4g1098 . . . . Bpe15g00330 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1099 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1100 . . . . . . . . . . Cma03g00693 Cma07g00434 Car03g00638 Car07g00382 Sed14g1179 Cpe19g00852 Cpe10g00656 Bhi03g00877 Tan03g2062 Cmetu04g0248 . Hepe04g1583 . . Cla01g01969 Cam01g2062 Cec04g1720 Cco04g1787 Clacu01g2083 Cmu01g1960 Cre04g1634 Cone8ag0844 Cone12ag0722 . . Lsi01g00611 . . Cme08g00917 Blo05g00827 . . . . Bpe06g00024 . . . Cmo03g00719 Cmo07g00433 . . . . . . . . . . . . . . . . . . . . . Csa06g03315 Chy02g00583 .
Vvi4g1101 Blo04g00887 . . . Bpe15g00470 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma03g00963 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 435989 437289 + Bda018800.1 Bda04g00026 26
4 438045 439803 - Bda033561 Bda04g00027 27
4 440430 444682 + Bda018799.1 Bda04g00028 28
11 53616078 53617193 + Bda008779.1 Bda11g01842 1842
3 16330693 16332986 + XM_039025150.1 Bhi03g00877 877
3 16346170 16348697 + XM_039025388.1 Bhi03g00880 880
3 16357515 16361391 - XM_039027911.1 Bhi03g00882 882
4 10167532 10172542 + BLOR13799 Blo04g00887 887
4 10201814 10204451 + BLOR13801 Blo04g00889 889
4 10206183 10207286 + BLOR13802 Blo04g00890 890
5 29987304 29992565 - BLOR15786 Blo05g00824 824
5 29995374 29996910 - BLOR15787 Blo05g00825 825
5 30004363 30005937 - BLOR15789 Blo05g00827 827
16 2115161 2116276 - BLOR07323 Blo16g00075 75
3 10246169 10247912 + Bma017302.1 Bma03g00963 963
3 10251389 10253967 + Bma017304.1 Bma03g00965 965
3 10255735 10256841 + Bma017305.1 Bma03g00966 966
6 1461079 1462194 + Bma022719.4 Bma06g00102 102
9 2765692 2767442 + Bma028798.1 Bma09g00102 102
9 2768079 2769735 - Bma028799.1 Bma09g00103 103
15 35476066 35479543 + Bma014205.1 Bma15g00949 949
15 35918943 35920052 + Bma014212.1 Bma15g00952 952
6 268324 274987 + Bpe019468.1 Bpe06g00024 24
6 283358 285094 - Bpe025920 Bpe06g00025 25
10 3375040 3376149 - Bpe002456.1 Bpe10g00148 148
10 3534625 3538204 - Bpe002459.1 Bpe10g00150 150
13 11851705 11852820 + Bpe006547.1 Bpe13g00422 422
15 14826830 14830960 + Bpe001267.1 Bpe15g00330 330
15 16049876 16050982 - Bpe001401.1 Bpe15g00467 467
15 16051673 16054277 - Bpe001402.1 Bpe15g00468 468
15 16057014 16058724 - Bpe001404.1 Bpe15g00470 470
1 33671921 33675229 + CaPI482276_01g020580.1 Cam01g2058 2058
1 33678899 33680849 - CaPI482276_01g020590.1 Cam01g2059 2059
1 33691352 33695509 - CaPI482276_01g020620.1 Cam01g2062 2062
3 5794528 5797395 + Carg00598-RA Car03g00638 638
3 5804078 5806435 + Carg00600-RA Car03g00640 640
3 5807137 5810959 - Carg00601-RA Car03g00641 641
7 1931521 1933208 + Carg07962-RA Car07g00382 382
7 1941973 1944103 + Carg07965-RA Car07g00385 385
7 1946596 1949539 - Carg07966-RA Car07g00386 386
4 32740434 32743746 + CcPI632755_04g017820.1 Cco04g1782 1782
4 32747347 32749303 - CcPI632755_04g017830.1 Cco04g1783 1783
4 32760702 32762638 - CcPI632755_04g017870.1 Cco04g1787 1787
4 36229077 36232384 + CePI673135_04g017160.1 Cec04g1716 1716
4 36236033 36237986 - CePI673135_04g017170.1 Cec04g1717 1717
4 36248311 36252439 - CePI673135_04g017200.1 Cec04g1720 1720
2 3534882 3538346 + Chy2G028500.1 Chy02g00583 583
2 3546401 3551020 + Chy2G028520.1 Chy02g00585 585
2 3553639 3556627 - Chy2G028530.1 Chy02g00586 586
1 32528337 32531650 + ClG42_01g0207900.10 Clacu01g2079 2079
1 32535251 32537194 - ClG42_01g0208000.10 Clacu01g2080 2080
1 32547581 32551650 - ClG42_01g0208300.10 Clacu01g2083 2083
1 34313882 34316173 + ClCG01G020170.2 Cla01g01966 1966
1 34319101 34321421 - ClCG01G020180.2 Cla01g01967 1967
1 34329877 34336067 - ClCG01G020200.2 Cla01g01969 1969
3 5704452 5707532 + CmaCh03G006930.1 Cma03g00693 693
3 5713662 5716345 + CmaCh03G006960.1 Cma03g00696 696
3 5716957 5720545 - CmaCh03G006970.1 Cma03g00697 697
7 1895442 1898575 + CmaCh07G004340.1 Cma07g00434 434
7 1907552 1909770 + CmaCh07G004370.1 Cma07g00437 437
7 1911458 1914533 - CmaCh07G004380.1 Cma07g00438 438
8 6020906 6024568 + MELO3C007890.2.1 Cme08g00913 913
8 6026419 6029049 - MELO3C007891.2.1 Cme08g00914 914
8 6038789 6041888 - MELO3C007894.2.1 Cme08g00917 917
4 3803195 3807287 + PI0016404.1 Cmetu04g0248 248
4 3817321 3819635 + PI0020397.1 Cmetu04g1220 1220
3 6201437 6203892 + CmoCh03G007190.1 Cmo03g00719 719
3 6210999 6213487 + CmoCh03G007220.1 Cmo03g00722 722
3 6214141 6217884 - CmoCh03G007240.1 Cmo03g00724 724
7 1988935 1989942 + CmoCh07G004330.1 Cmo07g00433 433
7 1999288 2001382 + CmoCh07G004350.1 Cmo07g00435 435
7 2002523 2005359 - CmoCh07G004360.1 Cmo07g00436 436
1 32864323 32867636 + CmPI595203_01g019560.1 Cmu01g1956 1956
1 32871246 32873190 - CmPI595203_01g019570.1 Cmu01g1957 1957
1 32883490 32887648 - CmPI595203_01g019600.1 Cmu01g1960 1960
6 12719781 12725634 - Conep06aG0173900.1 Cone6ag1674 1674
6 12725826 12726925 + Conep06aG0174000.1 Cone6ag1675 1675
6 12726700 12728648 - Conep06aG0174100.1 Cone6ag1676 1676
6 12733496 12734703 - Conep06aG0174200.1 Cone6ag1677 1677
8 8422273 8424651 - Conep08aG0086600.1 Cone8ag0840 840
8 8433252 8436249 - Conep08aG0087000.1 Cone8ag0844 844
9 11435870 11445021 - Conep09aG0164500.1 Cone9ag1595 1595
9 11445181 11447942 + Conep09aG0164600.1 Cone9ag1596 1596
9 11446730 11447860 - Conep09aG0164700.1 Cone9ag1597 1597
9 11452032 11453469 - Conep09aG0164800.1 Cone9ag1598 1598
12 6651892 6654866 + Conep12aG0074500.1 Cone12ag0722 722
10 3759928 3764003 + Cp4.1LG10g00430.1 Cpe10g00653 653
10 3764412 3768499 - Cp4.1LG10g00370.1 Cpe10g00654 654
10 3771704 3776420 - Cp4.1LG10g00180.1 Cpe10g00656 656
19 6277665 6280887 + Cp4.1LG19g08900.1 Cpe19g00848 848
19 6281429 6283690 - Cp4.1LG19g08830.1 Cpe19g00849 849
19 6292768 6295752 - Cp4.1LG19g08880.1 Cpe19g00852 852
4 34711788 34715111 + CrPI670011_04g016300.1 Cre04g1630 1630
4 34718746 34720710 - CrPI670011_04g016310.1 Cre04g1631 1631
4 34731106 34735290 - CrPI670011_04g016340.1 Cre04g1634 1634
6 27719713 27723506 + CsaV3_6G046970.1 Csa06g03311 3311
6 27725203 27728012 - CsaV3_6G046980.1 Csa06g03312 3312
6 27739005 27740975 - CsaV3_6G047010.1 Csa06g03315 3315
4 71300594 71304816 - Hsped.04g15800.1 Hepe04g1580 1580
4 71319277 71321139 - Hsped.04g15830.1 Hepe04g1583 1583
1 4912442 4914428 + Lsi01G006110.1 Lsi01g00611 611
1 4929025 4931413 + Lsi01G006150.1 Lsi01g00615 615
1 4933946 4937945 - Lsi01G006160.1 Lsi01g00616 616
10 8330729 8336361 - Sed0020033.1 Sed10g0984 984
14 21133359 21136688 - Sed0007682.2 Sed14g1179 1179
3 75580921 75584146 - Tan0012633.1 Tan03g2058 2058
3 75600095 75602307 - Tan0005873.1 Tan03g2062 2062
4 19714346 19719359 - Vvi4g1092 Vvi4g1092 1092
4 19719713 19723663 + Vvi4g1093 Vvi4g1093 1093
4 19724026 19725390 - Vvi4g1094 Vvi4g1094 1094
4 19732142 19742086 + Vvi4g1095 Vvi4g1095 1095
4 19742617 19746072 - Vvi4g1096 Vvi4g1096 1096
4 19753118 19761316 - Vvi4g1097 Vvi4g1097 1097
4 19772672 19782459 + Vvi4g1098 Vvi4g1098 1098
4 19784090 19787612 + Vvi4g1099 Vvi4g1099 1099
4 19792528 19795338 - Vvi4g1100 Vvi4g1100 1100
4 19796273 19802419 - Vvi4g1101 Vvi4g1101 1101
       

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