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
Vvi18g200 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g201 . Blo12g01116 . . . . . . . Cmo15g00656 . . . . Sed03g0441 . . Bhi04g01857 Tan11g1227 Cmetu03g1243 . Hepe02g2733 . Lcy10g1268 Cla08g00630 Cam08g1048 Cec08g0634 Cco08g0746 Clacu08g0755 . Cre08g0564 . . Cone17ag0811 . . . . Cme03g00478 . . . . . . . . . . . . . . Car15g00592 . . . . . . . . . . . . . . . . Lsi08g00475 . Chy03g00745 .
Vvi18g202 Blo01g01312 . Bda01g00681 . Bpe02g00624 . . Bma01g02095 . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1438 . . Cone20ag0418 . . . . . . . . . . . . . . . . . . . . Cpe02g00868 Bhi09g01871 . . . . . . . . . . . . . . . . .
Vvi18g203 Blo01g01311 . Bda01g00680 . Bpe02g00625 . . Bma01g02094 . . Cma01g01033 . Car01g00908 . . . . . . . . . . . . . . . . . . . . Cone17ag0814 Cone20ag0419 . . . . . . . . . . . . . Cmo01g01072 . . . . . . Cpe02g00858 . . . . . . . . . . . . . . . . . .
Vvi18g204 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone17ag1294 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g205 Blo01g01310 Blo12g01117 Bda01g00679 Bda03g00024 Bpe02g00626 . Bma04g00020 Bma01g02093 Cmo04g02509 . . . . . Sed01g3096 . . Bhi04g01859 Tan11g1232 Cmetu03g0430 . Hepe02g2207 . Lcy10g1261 Cla08g00628 Cam08g1046 Cec08g0632 Cco08g0744 Clacu08g0753 . Cre08g0562 . . Cone17ag0816 Cone20ag0421 . . . Cme03g00485 . . . . . . . . . . . . . Car04g02317 . Cpe01g02078 . . . . . . . . . . . . . . . Lsi08g00468 . Chy03g00748 .
Vvi18g206 . . . . . . . . . . Cma01g01034 . Car01g00909 . . . . . . . . . . . . . . . . . . Cone4ag1437 . . . . . . . . . . . . . . . . Cmo01g01073 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g207 . . Bda01g00678 . Bpe02g00627 . . Bma01g02092 . . Cma01g01035 . Car01g00910 . . . . . . . . . . . . . . . . . . Cone4ag1436 Cone7ag1499 . . . . . . . . . . . . . . . Cmo01g01074 . . . . . . Cpe02g00856 Bhi09g01861 . . . . . . . . . . . . . . . . .
Vvi18g208 . . . . . . . . . . Cma01g01036 . Car01g00911 . . . . . . . . . . . . . . . . . . Cone4ag1435 Cone7ag1500 . . . . . . Blo17g00165 . . . . Bpe14g00400 . Bma02g00201 . Cmo01g01075 . . . . . . Cpe02g00855 . . . . . . . . . . . . . . . . . .
Vvi18g209 . . . . . . . . Cmo04g02508 Cmo15g00658 . . . . . . . Bhi04g01860 . . . . . Lcy10g1259 Cla08g00627 . . . . . . . . Cone17ag0817 Cone20ag0422 . Csa04g01957 . Cme03g00489 Blo17g00166 Blo18g00172 . Bda13g01465 Bpe02g01658 . Bma01g00797 . . . . . . Car04g02316 Car15g00595 Cpe01g02077 . . . . . . . . . . . . . . . Lsi08g00467 . Chy03g00749 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 33957236 33958173 + Bda032911 Bda01g00678 678
1 33965109 33973209 + Bda002715.4 Bda01g00679 679
1 33974031 33975035 - Bda002716.1 Bda01g00680 680
1 33975725 33979173 + Bda002717.1 Bda01g00681 681
3 408724 414048 + Bda015956.1 Bda03g00024 24
13 37551055 37554557 - Bda000307.1 Bda13g01465 1465
4 46827844 46831628 + XM_039028261.1 Bhi04g01857 1857
4 46891276 46901476 - XM_039029318.1 Bhi04g01859 1859
4 46930876 46934648 - XM_039029490.1 Bhi04g01860 1860
9 51270932 51273227 - XM_039043261.1 Bhi09g01861 1861
9 51736452 51756176 + XM_039041930.1 Bhi09g01871 1871
1 50239779 50248477 + BLOR01310 Blo01g01310 1310
1 50249303 50250345 - BLOR01311 Blo01g01311 1311
1 50251077 50253171 + BLOR01312 Blo01g01312 1312
12 28814106 28818814 + BLOR05135 Blo12g01116 1116
12 28819648 28829998 - BLOR05136 Blo12g01117 1117
17 1666085 1674761 - BLOR15986 Blo17g00165 165
17 1676419 1679603 - BLOR15987 Blo17g00166 166
18 1660993 1664370 - BLOR08660 Blo18g00172 172
1 7486709 7489913 - Bma001015.1 Bma01g00797 797
1 76985121 76986201 + Bma002914.3 Bma01g02092 2092
1 77002808 77011789 + Bma002915.1 Bma01g02093 2093
1 77013770 77014773 - Bma002916.1 Bma01g02094 2094
1 77017734 77019788 + Bma002917.1 Bma01g02095 2095
2 2179879 2187958 - Bma014659.1 Bma02g00201 201
4 256657 262440 + Bma018468.1 Bma04g00020 20
2 4059475 4061542 - Bpe008465.1 Bpe02g00624 624
2 4063655 4064656 + Bpe008466.1 Bpe02g00625 625
2 4065537 4073694 - Bpe008467.1 Bpe02g00626 626
2 4080653 4081590 - Bpe025089 Bpe02g00627 627
2 19285046 19288075 + Bpe009499.1 Bpe02g01658 1658
14 3743962 3752113 + Bpe007053.1 Bpe14g00400 400
8 16742870 16755729 + CaPI482276_08g010460.1 Cam08g1046 1046
8 16762141 16766481 - CaPI482276_08g010480.1 Cam08g1048 1048
1 8814664 8822812 + Carg23374-RA Car01g00908 908
1 8823701 8826571 + Carg23373-RA Car01g00909 909
1 8827126 8827901 - Carg23372-RA Car01g00910 910
1 8828262 8838992 - Carg23371-RA Car01g00911 911
4 18659144 18662593 + Carg15750-RA Car04g02316 2316
4 18663979 18670906 + Carg15751-RA Car04g02317 2317
15 3279124 3282503 + Carg01563-RA Car15g00592 592
15 3287405 3289571 - Carg01560-RA Car15g00595 595
8 19105118 19118003 + CcPI632755_08g007440.1 Cco08g0744 744
8 19126403 19130175 - CcPI632755_08g007460.1 Cco08g0746 746
8 17928965 17945428 + CePI673135_08g006320.1 Cec08g0632 632
8 17953769 17957525 - CePI673135_08g006340.1 Cec08g0634 634
3 9930530 9936305 + Chy3G057250.1 Chy03g00745 745
3 9954826 9964754 - Chy3G057280.1 Chy03g00748 748
3 10012602 10015754 - Chy3G057290.1 Chy03g00749 749
8 17481550 17494399 + ClG42_08g0075300.10 Clacu08g0753 753
8 17500884 17504684 - ClG42_08g0075500.10 Clacu08g0755 755
8 18303997 18307916 + ClCG08G006040.1 Cla08g00627 627
8 18319298 18335915 + ClCG08G006050.2 Cla08g00628 628
8 18341956 18345970 - ClCG08G006070.2 Cla08g00630 630
1 7641845 7650279 + CmaCh01G010330.1 Cma01g01033 1033
1 7651436 7654765 + CmaCh01G010340.1 Cma01g01034 1034
1 7654867 7655955 - CmaCh01G010350.1 Cma01g01035 1035
1 7656463 7667614 - CmaCh01G010360.1 Cma01g01036 1036
3 6926570 6930488 + MELO3C008461.2.1 Cme03g00478 478
3 7091731 7102599 - MELO3C008467.2.1 Cme03g00485 485
3 7136649 7140608 - MELO3C008469.2.1 Cme03g00489 489
3 11770171 11780954 - PI0002437.1 Cmetu03g0430 430
3 11691819 11695772 + PI0009746.1 Cmetu03g1243 1243
1 8943517 8943954 + CmoCh01G010720.1 Cmo01g01072 1072
1 8944883 8947780 + CmoCh01G010730.1 Cmo01g01073 1073
1 8948129 8949175 - CmoCh01G010740.1 Cmo01g01074 1074
1 8949855 8960061 - CmoCh01G010750.1 Cmo01g01075 1075
4 18481789 18485223 + CmoCh04G025080.1 Cmo04g02508 2508
4 18486720 18494752 + CmoCh04G025090.1 Cmo04g02509 2509
15 3172600 3181912 + CmoCh15G006560.1 Cmo15g00656 656
15 3185027 3188672 - CmoCh15G006580.1 Cmo15g00658 658
4 11406661 11414504 + Conep04aG0148700.1 Cone4ag1435 1435
4 11414612 11415738 + Conep04aG0148800.1 Cone4ag1436 1436
4 11415874 11418550 - Conep04aG0148900.1 Cone4ag1437 1437
4 11418715 11422443 + Conep04aG0149000.1 Cone4ag1438 1438
7 10479208 10479842 - Conep07aG0154200.1 Cone7ag1499 1499
7 10480308 10487829 - Conep07aG0154300.1 Cone7ag1500 1500
17 6443159 6446246 + Conep17aG0083000.1 Cone17ag0811 811
17 6491411 6493009 + Conep17aG0083300.1 Cone17ag0814 814
17 6496905 6506363 - Conep17aG0083500.1 Cone17ag0816 816
17 6507785 6511598 - Conep17aG0083600.1 Cone17ag0817 817
17 9262358 9265673 + Conep17aG0132600.1 Cone17ag1294 1294
20 2042396 2045838 - Conep20aG0043200.1 Cone20ag0418 418
20 2047439 2048927 + Conep20aG0043300.1 Cone20ag0419 419
20 2054263 2063271 - Conep20aG0043500.1 Cone20ag0421 421
20 2066692 2070412 - Conep20aG0043600.1 Cone20ag0422 422
1 17624119 17627579 + Cp4.1LG01g20790.1 Cpe01g02077 2077
1 17628898 17635993 + Cp4.1LG01g20780.1 Cpe01g02078 2078
2 5570415 5580917 + Cp4.1LG02g00180.1 Cpe02g00855 855
2 5581801 5582927 + Cp4.1LG02g00190.1 Cpe02g00856 856
2 5586937 5592285 - Cp4.1LG02g00150.1 Cpe02g00858 858
2 5824985 5834583 + Cp4.1LG02g00120.1 Cpe02g00868 868
8 18393931 18406799 + CrPI670011_08g005620.1 Cre08g0562 562
8 18414931 18418718 - CrPI670011_08g005640.1 Cre08g0564 564
4 19553603 19565399 + CsaV3_4G029830.1 Csa04g01957 1957
2 62391690 62400622 - Hsped.02g22070.1 Hepe02g2207 2207
2 75763430 75767092 - Hsped.02g27330.1 Hepe02g2733 2733
10 35286296 35290197 + Maker00008449 Lcy10g1259 1259
10 35307086 35311864 + Maker00008741 Lcy10g1261 1261
10 35416911 35420792 - Maker00008618 Lcy10g1268 1268
8 12398614 12402738 + Lsi08G004670.1 Lsi08g00467 467
8 12408640 12420515 + Lsi08G004680.1 Lsi08g00468 468
8 12490012 12497987 - Lsi08G004750.1 Lsi08g00475 475
1 41627973 41629452 + Sed0012376.1 Sed01g3096 3096
3 2640741 2644328 - Sed0020251.1 Sed03g0441 441
11 10392393 10395983 + Tan0019291.1 Tan11g1227 1227
11 10453672 10463006 - Tan0001724.1 Tan11g1232 1232
18 2113194 2127909 + Vvi18g200 Vvi18g200 200
18 2130879 2138950 + Vvi18g201 Vvi18g201 201
18 2150108 2166350 - Vvi18g202 Vvi18g202 202
18 2174947 2177102 + Vvi18g203 Vvi18g203 203
18 2177336 2196765 - Vvi18g204 Vvi18g204 204
18 2203012 2218030 - Vvi18g205 Vvi18g205 205
18 2222530 2227556 + Vvi18g206 Vvi18g206 206
18 2227631 2229602 - Vvi18g207 Vvi18g207 207
18 2231116 2244484 - Vvi18g208 Vvi18g208 208
18 2245946 2250187 - Vvi18g209 Vvi18g209 209
       

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