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
Vvi19g724 . Blo03g01486 Bda07g00425 Bda09g00443 . Bpe08g01085 . . . . Cma01g01059 . Car01g00933 Car09g00934 Sed04g3621 Cpe06g00838 Cpe02g00837 Bhi09g01813 Tan01g3230 Cmetu01g1660 . . Mch11g1309 . . . . . . . . Cone6ag0002 Cone9ag0004 . . Lsi02g01806 . . . . . . . Bpe11g00600 . Bma07g01239 . . Cmo01g01100 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g725 . . Bda07g00426 . . . . . . . . Cma09g01031 . Car09g00936 . . . Bhi09g01815 . . . . Mch11g1310 . . . . . . . . . . . . Lsi02g01803 Csa07g01065 . . . . . . . . . . . . Cmo09g01033 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g726 . . . Bda09g00446 . Bpe08g01083 . . . . . . . Car09g00938 Sed07g2766 Cpe06g00840 . Bhi09g01817 Tan01g3232 Cmetu01g0567 . . Mch11g1311 . . . . . . . . . . . . Lsi02g01802 Csa07g01063 . . . . . . . . Bma07g01238 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g727 Blo03g00494 . . . . . . . . . Cma01g01058 Cma09g01033 Car01g00932 Car09g00939 . Cpe06g00841 Cpe02g00838 Bhi09g01820 . . . . Mch11g1312 . . . . . . . . Cone6ag0001 Cone9ag0003 . . Lsi02g01801 Csa07g01062 . . . . . . Bpe11g00603 . . Bma14g00667 . Cmo01g01099 Cmo09g01035 . . . . . . . . . . . . . Cla09g02100 Cam09g2186 Cec09g2255 . . . . . . . .
Vvi19g728 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1268 Cone15ag1294 . Csa07g01043 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy01g01034 Cme01g01117
Vvi19g729 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g730 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g731 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g732 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy01g01179 .
Vvi19g733 . . . . . . . . . Cmo06g00674 . . . . . . . . . . . . . . Cla10g00428 Cam10g0426 Cec10g0448 Cco10g0438 Clacu10g0433 Cmu10g1264 Cre10g0681 . . . Cone15ag1293 . . . . Blo07g00859 . . . . Bpe03g00740 . . . . . . . . . . . . . . . . . . . . . . . . . Lsi05g00517 . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 5431503 5434604 + Bda025520.1 Bda07g00425 425
7 5445047 5447182 + Bda025521.1 Bda07g00426 426
9 5850521 5852609 + Bda031033.1 Bda09g00443 443
9 5867171 5881147 - Bda034097 Bda09g00446 446
9 49111160 49123491 + XM_039040489.1 Bhi09g01813 1813
9 49194676 49198287 + XM_039043484.1 Bhi09g01815 1815
9 49221672 49236190 - XM_039041608.1 Bhi09g01817 1817
9 49273605 49282903 - XM_039040970.1 Bhi09g01820 1820
3 17799350 17805650 + BLOR11675 Blo03g00494 494
3 41678469 41680655 + BLOR12667 Blo03g01486 1486
7 27030071 27031176 + BLOR18791 Blo07g00859 859
7 47326569 47341496 + Bma031404 Bma07g01238 1238
7 47341403 47343577 - Bma026491.1 Bma07g01239 1239
14 7234114 7240163 + Bma011116.1 Bma14g00667 667
3 27495272 27496395 + Bpe012648.1 Bpe03g00740 740
8 12941674 12950562 + Bpe026163 Bpe08g01083 1083
8 12962106 12964278 - Bpe023208.1 Bpe08g01085 1085
11 4568125 4570080 + Bpe003965.1 Bpe11g00600 600
11 4582905 4589036 - Bpe003968.1 Bpe11g00603 603
9 36372603 36380997 - CaPI482276_09g021860.1 Cam09g2186 2186
10 6609535 6612372 + CaPI482276_10g004260.1 Cam10g0426 426
1 9009409 9017531 + Carg23348-RA Car01g00932 932
1 9019233 9029980 - Carg23347-RA Car01g00933 933
9 5751598 5756126 + Carg24740-RA Car09g00934 934
9 5757751 5761097 + Carg24738-RA Car09g00936 936
9 5763200 5767045 - Carg24736-RA Car09g00938 938
9 5768759 5777947 - Carg24735-RA Car09g00939 939
10 5162307 5165247 + CcPI632755_10g004380.1 Cco10g0438 438
9 39404697 39412601 - CePI673135_09g022550.1 Cec09g2255 2255
10 5347158 5349998 + CePI673135_10g004480.1 Cec10g0448 448
1 11172128 11175748 + Chy1G010340.1 Chy01g01034 1034
1 13700370 13707074 + Chy1G011790.1 Chy01g01179 1179
10 5403702 5406549 + ClG42_10g0043300.10 Clacu10g0433 433
9 38534088 38549456 - ClCG09G021580.2 Cla09g02100 2100
10 5739986 5748197 + ClCG10G004530.2 Cla10g00428 428
1 7825331 7834849 + CmaCh01G010580.1 Cma01g01058 1058
1 7835254 7843830 - CmaCh01G010590.1 Cma01g01059 1059
9 5293924 5303276 + CmaCh09G010310.1 Cma09g01031 1031
9 5304606 5318093 - CmaCh09G010330.1 Cma09g01033 1033
1 14226295 14232921 + MELO3C013225.2.1 Cme01g01117 1117
1 9726572 9739059 - PI0017596.1 Cmetu01g0567 567
1 9619338 9640961 + PI0025173.1 Cmetu01g1660 1660
1 9145484 9156099 + CmoCh01G010990.1 Cmo01g01099 1099
1 9155880 9166649 - CmoCh01G011000.1 Cmo01g01100 1100
6 3401443 3403397 + CmoCh06G006740.1 Cmo06g00674 674
9 5521116 5530428 + CmoCh09G010330.1 Cmo09g01033 1033
9 5533200 5547917 - CmoCh09G010350.1 Cmo09g01035 1035
10 5540646 5543493 + CmPI595203_10g012640.1 Cmu10g1264 1264
6 14249 20380 + Conep06aG0000100.1 Cone6ag0001 1
6 21031 23494 - Conep06aG0000200.1 Cone6ag0002 2
9 24355 29577 + Conep09aG0000300.1 Cone9ag0003 3
9 29943 32590 - Conep09aG0000400.1 Cone9ag0004 4
14 10157359 10161902 + Conep14aG0130000.1 Cone14ag1268 1268
15 10126011 10128383 - Conep15aG0132200.1 Cone15ag1293 1293
15 10134437 10137786 + Conep15aG0132300.1 Cone15ag1294 1294
2 5360928 5372157 + Cp4.1LG02g00350.1 Cpe02g00837 837
2 5372414 5381148 - Cp4.1LG02g00300.1 Cpe02g00838 838
6 5379185 5384142 + Cp4.1LG06g08250.1 Cpe06g00838 838
6 5389940 5394699 - Cp4.1LG06g08160.1 Cpe06g00840 840
6 5396430 5405159 - Cp4.1LG06g08190.1 Cpe06g00841 841
10 6462204 6465037 + CrPI670011_10g006810.1 Cre10g0681 681
7 9815773 9822552 - CsaV3_7G021320.1 Csa07g01043 1043
7 10136430 10148470 + CsaV3_7G021510.1 Csa07g01062 1062
7 10159535 10179044 + CsaV3_7G021520.1 Csa07g01063 1063
7 10186707 10190769 - CsaV3_7G021540.1 Csa07g01065 1065
2 23822236 23831896 + Lsi02G018010.1 Lsi02g01801 1801
2 23832061 23838554 + Lsi02G018020.1 Lsi02g01802 1802
2 23838350 23841700 - Lsi02G018030.1 Lsi02g01803 1803
2 23844889 23851210 - Lsi02G018060.1 Lsi02g01806 1806
5 6473851 6487515 + Lsi05G005170.1 Lsi05g00517 517
11 9247584 9250307 + MC11g1084 Mch11g1309 1309
11 9263070 9267282 + MC11g1085 Mch11g1310 1310
11 9273039 9276378 - MC11g1086 Mch11g1311 1311
11 9279874 9288647 - MC11g1087 Mch11g1312 1312
4 45441164 45445606 - Sed0026837.1 Sed04g3621 3621
7 42690258 42694484 - Sed0007098.1 Sed07g2766 2766
1 86547790 86553555 + Tan0021689.1 Tan01g3230 3230
1 86577443 86581032 - Tan0022863.1 Tan01g3232 3232
19 9180441 9187446 + Vvi19g724 Vvi19g724 724
19 9194801 9198616 + Vvi19g725 Vvi19g725 725
19 9199157 9208791 - Vvi19g726 Vvi19g726 726
19 9229429 9239572 - Vvi19g727 Vvi19g727 727
19 9245111 9251543 - Vvi19g728 Vvi19g728 728
19 9268236 9268866 - Vvi19g729 Vvi19g729 729
19 9307510 9308113 - Vvi19g730 Vvi19g730 730
19 9346609 9346837 + Vvi19g731 Vvi19g731 731
19 9349178 9350972 - Vvi19g732 Vvi19g732 732
19 9373955 9376573 + Vvi19g733 Vvi19g733 733
       

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