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
Vvi17g6 . . . . . . . . Cmo13g00861 Cmo18g00240 . . . . . Cpe20g00287 . . . . . . . . . . . . . . . . . Cone13ag0271 Cone19ag0255 Lsi02g00530 Csa01g00993 Chy12g01141 Cme12g01559 . . . . . . . . Sed08g2406 . . Cma13g00832 . Car13g00675 Car18g00252 Cpe09g00940 . Bhi08g01543 Tan05g3015 Cmetu12g0056 Lac10g0616 Hepe07g2079 . . Cla03g00382 Cam03g0401 Cec03g0387 Cco03g0402 Clacu03g0400 Cmu03g1005 Cre03g0697 . . . .
Vvi17g7 . . . Bda15g00701 Bpe12g00454 . . . . . . . . . . . . . . . . . . . Cla06g01790 Cam06g1989 Cec06g2039 Cco06g2049 Clacu06g1946 Cmu06g1886 Cre06g2697 . . Cone13ag0270 Cone19ag0254 . . . . . . . . . . . Bma08g00284 . . . . . . . . . . . . . . . . . . . . . . . Lsi06g01689 . Chy02g02709 Cme02g02119
Vvi17g8 . Blo16g00315 Bda06g00703 . . Bpe13g00160 . Bma12g01101 . . . Cma11g00002 . Car11g00002 . . Cpe04g01642 . . . . . . . Cla06g01790 Cam06g1989 Cec06g2039 Cco06g2049 Clacu06g1946 Cmu06g1886 Cre06g2697 . . Cone13ag0269 Cone19ag0253 . . . . . . . . Bpe07g00913 . . . . . Cmo11g00002 . . . . . . . . . . . . . . . . . . . . Lsi06g01689 Csa01g00004 Chy02g02709 Cme02g02119
Vvi17g9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g10 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g11 . . Bda06g00704 . . . . Bma12g01100 . . Cma10g00008 . Car10g00005 . . . . . . . . . . . Cla06g01789 . . . . . . . . . . . . . . . . . . Bpe07g00912 . . . . Cmo10g00006 . . . . . . Cpe18g00944 . . . . . . . . . . . . . . . . . .
Vvi17g12 . . . . . . . . . . Cma10g00009 Cma11g00003 Car10g00006 Car11g00003 . . Cpe04g01641 . . . . . . . Cla06g01788 Cam06g1986 Cec06g2036 Cco06g2044 Clacu06g1943 Cmu06g1883 Cre06g2694 . . . . . . . . . . . . . . . . . Cmo10g00007 Cmo11g00003 . . . . . Cpe18g00943 . . . . . . . . . . . . . . Lsi06g01688 Csa01g00005 Chy02g02708 Cme02g02117
Vvi17g13 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g14 . . Bda06g00705 Bda15g00700 Bpe12g00455 . . Bma12g01099 . . . Cma11g00004 . Car11g00004 . . Cpe04g01640 . . . . . . . . . . . . . . . . . . . . . . . Blo15g00186 . . Bpe07g00911 . . Bma08g00283 . . Cmo11g00004 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g15 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 9689215 9690652 - Bda024001.1 Bda06g00703 703
6 9693504 9694802 - Bda024002.1 Bda06g00704 704
6 9727526 9733274 + Bda024005.2 Bda06g00705 705
15 10433153 10438858 - Bda012554.1 Bda15g00700 700
15 10443069 10446948 + Bda033308 Bda15g00701 701
8 44276751 44279943 - XM_039039535.1 Bhi08g01543 1543
15 1947080 1951118 + BLOR06580 Blo15g00186 186
16 7968021 7972188 - BLOR07563 Blo16g00315 315
8 3871694 3887374 - Bma027305.1 Bma08g00283 283
8 3884415 3885207 + Bma031432 Bma08g00284 284
12 43253364 43258356 - Bma008443.1 Bma12g01099 1099
12 43273215 43274513 + Bma008444.1 Bma12g01100 1100
12 43276202 43277766 + Bma008445.1 Bma12g01101 1101
7 15082699 15088459 - Bpe021752.1 Bpe07g00911 911
7 15089611 15090840 + Bpe021753.1 Bpe07g00912 912
7 15093334 15094894 + Bpe021754.1 Bpe07g00913 913
12 10271752 10273445 - Bpe005712.1 Bpe12g00454 454
12 10277793 10283498 + Bpe005713.2 Bpe12g00455 455
13 9375425 9382831 + Bpe006279.1 Bpe13g00160 160
3 5133415 5136536 - CaPI482276_03g004010.1 Cam03g0401 401
6 30599082 30601669 - CaPI482276_06g019860.1 Cam06g1986 1986
6 30615534 30618521 + CaPI482276_06g019890.1 Cam06g1989 1989
10 25666 27704 - Carg10237-RA Car10g00005 5
10 29840 31757 + Carg10238-RA Car10g00006 6
11 6950 13387 - Carg24566-RA Car11g00002 2
11 14837 16670 + Carg24565-RA Car11g00003 3
11 19736 26518 + Carg24564-RA Car11g00004 4
13 8198174 8201670 - Carg07625-RA Car13g00675 675
18 1461304 1465988 - Carg06819-RA Car18g00252 252
3 4360027 4363272 - CcPI632755_03g004020.1 Cco03g0402 402
6 30357425 30359722 - CcPI632755_06g020440.1 Cco06g2044 2044
6 30377684 30383243 + CcPI632755_06g020490.1 Cco06g2049 2049
3 4317627 4320899 - CePI673135_03g003870.1 Cec03g0387 387
6 33441541 33444135 - CePI673135_06g020360.1 Cec06g2036 2036
6 33458103 33460787 + CePI673135_06g020390.1 Cec06g2039 2039
2 29911665 29913472 - Chy2G049750.1 Chy02g02708 2708
2 29918018 29922339 + Chy2G049760.1 Chy02g02709 2709
12 16352460 16355273 + Chy12G217410.1 Chy12g01141 1141
3 4448849 4452182 - ClG42_03g0040000.10 Clacu03g0400 400
6 29633994 29636572 - ClG42_06g0194300.10 Clacu06g1943 1943
6 29650626 29653297 + ClG42_06g0194600.10 Clacu06g1946 1946
3 4410543 4414558 - ClCG03G004050.2 Cla03g00382 382
6 31300936 31303216 - ClCG06G018380.2 Cla06g01788 1788
6 31307664 31309963 + ClCG06G018390.1 Cla06g01789 1789
6 31311409 31327887 + ClCG06G018400.1 Cla06g01790 1790
10 25625 27921 - CmaCh10G000080.1 Cma10g00008 8
10 30790 33412 + CmaCh10G000090.1 Cma10g00009 9
11 3180 9961 - CmaCh11G000020.1 Cma11g00002 2
11 11395 18321 + CmaCh11G000030.1 Cma11g00003 3
11 21237 28132 + CmaCh11G000040.1 Cma11g00004 4
13 6955499 6959277 - CmaCh13G008320.1 Cma13g00832 832
2 26911408 26914635 - MELO3C026157.2.1 Cme02g02117 2117
2 26919956 26925335 + MELO3C026156.2.1 Cme02g02119 2119
12 23000093 23003977 + MELO3C002387.2.1 Cme12g01559 1559
12 3390242 3394265 - PI0005711.3 Cmetu12g0056 56
10 65335 67373 - CmoCh10G000060.1 Cmo10g00006 6
10 69447 71489 + CmoCh10G000070.1 Cmo10g00007 7
11 3386 10300 - CmoCh11G000020.1 Cmo11g00002 2
11 11592 13757 + CmoCh11G000030.1 Cmo11g00003 3
11 16697 23713 + CmoCh11G000040.1 Cmo11g00004 4
13 7886705 7892613 - CmoCh13G008610.1 Cmo13g00861 861
18 1586990 1592025 - CmoCh18G002400.1 Cmo18g00240 240
3 4662832 4666165 - CmPI595203_03g010050.1 Cmu03g1005 1005
6 29544586 29547164 - CmPI595203_06g018830.1 Cmu06g1883 1883
6 29560911 29563896 + CmPI595203_06g018860.1 Cmu06g1886 1886
13 1889324 1892489 + Conep13aG0028000.1 Cone13ag0269 269
13 1892938 1894722 + Conep13aG0028100.1 Cone13ag0270 270
13 1893832 1897540 - Conep13aG0028200.1 Cone13ag0271 271
19 1681669 1684669 + Conep19aG0026000.1 Cone19ag0253 253
19 1684981 1686682 + Conep19aG0026100.1 Cone19ag0254 254
19 1686658 1689725 - Conep19aG0026200.1 Cone19ag0255 255
4 12672072 12679264 - Cp4.1LG04g16360.1 Cpe04g01640 1640
4 12681987 12684934 - Cp4.1LG04g16340.1 Cpe04g01641 1641
4 12685619 12696753 + Cp4.1LG04g16300.1 Cpe04g01642 1642
9 8424009 8429064 + Cp4.1LG09g09310.1 Cpe09g00940 940
18 8306325 8308760 - Cp4.1LG18g09380.1 Cpe18g00943 943
18 8309400 8313508 + Cp4.1LG18g09360.1 Cpe18g00944 944
20 1590006 1594223 + Cp4.1LG20g02880.1 Cpe20g00287 287
3 5877321 5880582 - CrPI670011_03g006970.1 Cre03g0697 697
6 34386483 34388673 - CrPI670011_06g026940.1 Cre06g2694 2694
6 34403316 34406008 + CrPI670011_06g026970.1 Cre06g2697 2697
1 42320 47225 - CsaV3_1G000040.1 Csa01g00004 4
1 49628 52342 + CsaV3_1G000050.1 Csa01g00005 5
1 6188087 6190927 - CsaV3_1G009930.1 Csa01g00993 993
7 65061406 65065428 + Hsped.07g20790.1 Hepe07g2079 2079
10 4738888 4742654 - Lag0024661.1 Lac10g0616 616
2 4598760 4602745 - Lsi02G005300.1 Lsi02g00530 530
6 27082938 27085937 - Lsi06G016880.1 Lsi06g01688 1688
6 27086085 27105714 + Lsi06G016890.1 Lsi06g01689 1689
8 37173615 37177962 + Sed0019000.2 Sed08g2406 2406
5 82050638 82054516 - Tan0000185.2 Tan05g3015 3015
17 39226 44383 + Vvi17g6 Vvi17g6 6
17 44410 46742 - Vvi17g7 Vvi17g7 7
17 47470 51961 - Vvi17g8 Vvi17g8 8
17 52746 54869 + Vvi17g9 Vvi17g9 9
17 55860 62009 + Vvi17g10 Vvi17g10 10
17 68009 69620 - Vvi17g11 Vvi17g11 11
17 71717 73739 + Vvi17g12 Vvi17g12 12
17 74093 79126 - Vvi17g13 Vvi17g13 13
17 88281 90652 + Vvi17g14 Vvi17g14 14
17 100533 102042 - Vvi17g15 Vvi17g15 15
       

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