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
Vvi18g740 . . . Bda03g00207 . . . . . . Cma01g01829 . . . . Cpe06g00169 . . . . . . . . . . . . . . . . . . . Lsi04g01539 Csa04g02427 . . . . . . . . . . . Cmo01g01885 Cmo09g00239 . . . . . . Bhi09g03302 Tan01g4754 . . Hepe01g1783 Mch11g0310 . Cla05g02055 Cam05g2209 Cec05g2225 Cco05g2268 Clacu05g2201 Cmu05g2067 Cre05g2193 . . Chy07g00145 .
Vvi18g741 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone17ag0853 Cone20ag0199 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g742 . . . . . . . . . Cmo12g00503 . . . Car12g00516 . . Cpe07g00492 Bhi04g00371 Tan02g1796 . . Hepe08g1297 . Lcy13g2093 . . . . . . . . . . . . . . Cme03g02064 Blo17g00874 . . Bda01g01607 Bpe02g01796 . Bma01g00659 . . . . Cma12g00560 . . . . . . . . . . . . . . . . . . . . . Chy03g01557 .
Vvi18g743 . . . . . . . . Cmo05g00171 . . . . . Sed11g0938 . . Bhi04g00370 Tan02g1797 . . . . . Cla08g01584 Cam08g2081 Cec08g1664 Cco08g1793 Clacu08g1767 . Cre08g1552 Cone4ag1588 Cone7ag1361 Cone17ag0852 Cone20ag0198 . . . . . . . . . Bpe05g00370 . . . . . . Cma05g00173 Car05g00146 . Cpe11g00142 . . . . . . . . . . . . . . . Lsi08g01487 Csa02g01933 . .
Vvi18g744 . . . . . . . . Cmo05g00172 Cmo12g00502 . . . Car12g00514 Sed10g1234 . Cpe07g00491 Bhi04g00369 Tan02g1798 Cmetu03g0637 . Hepe08g1296 . Lcy13g2092 . . . . . . . Cone4ag1587 Cone7ag1362 . . . . . Cme03g02063 Blo17g00875 . . . . . . Bma05g00041 . . . Cma12g00559 Cma05g00174 Car05g00147 . Cpe11g00143 . . . . . . . . . . . . . . . . Csa02g01934 Chy03g01556 .
Vvi18g745 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g746 . . . . . . . . Cmo05g00173 . . . . . . . . Bhi04g00368 . . . . . Lcy13g2091 Cla08g01583 . . . . . . Cone4ag1586 Cone7ag1363 Cone17ag0849 . . . . Cme03g02062 Blo17g00877 Blo18g00689 . . . . . Bma05g00040 . . . . Cma05g00175 Car05g00148 . Cpe11g00144 . . . . . . . . . . . . . . . Lsi08g01486 Csa02g01935 Chy03g01555 .
Vvi18g747 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe05g00038 . Bma05g00049 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g748 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g749 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 51923084 51926529 - Bda003879.1 Bda01g01607 1607
3 1627721 1629118 + Bda016152.1 Bda03g00207 207
4 9070948 9074161 - XM_039029029.1 Bhi04g00368 368
4 9078245 9081692 - XM_039029030.1 Bhi04g00369 369
4 9098550 9102680 - XM_039029539.1 Bhi04g00370 370
4 9098902 9104771 - XM_039029536.1 Bhi04g00371 371
9 84392755 84394392 + XM_039042951.1 Bhi09g03302 3302
17 28800371 28806172 + BLOR08420 Blo17g00874 874
17 28856763 28858886 + BLOR08421 Blo17g00875 875
17 28915243 28917393 + BLOR08423 Blo17g00877 877
18 14827290 14830558 - BLOR09177 Blo18g00689 689
1 6000514 6003965 + Bma000868.2 Bma01g00659 659
5 2169428 2171580 - Bma020729.1 Bma05g00040 40
5 2179225 2181322 - Bma020730.1 Bma05g00041 41
5 2336507 2338801 - Bma020738.1 Bma05g00049 49
2 20219711 20223130 - Bpe009629.1 Bpe02g01796 1796
5 723973 726261 - Bpe017425.1 Bpe05g00038 38
5 17815934 17820807 - Bpe017784.1 Bpe05g00370 370
5 30417357 30418736 - CaPI482276_05g022090.1 Cam05g2209 2209
8 26361787 26365571 - CaPI482276_08g020810.1 Cam08g2081 2081
5 735660 740745 + Carg11858-RA Car05g00146 146
5 741778 743708 + Carg11857-RA Car05g00147 147
5 745968 748911 + Carg11856-RA Car05g00148 148
12 3405430 3408320 - Carg26159-RA Car12g00514 514
12 3414227 3417089 - Carg26161-RA Car12g00516 516
5 31425580 31426959 - CcPI632755_05g022680.1 Cco05g2268 2268
8 29060594 29064383 - CcPI632755_08g017930.1 Cco08g1793 1793
5 33787044 33788423 - CePI673135_05g022250.1 Cec05g2225 2225
8 27961351 27969752 - CePI673135_08g016640.1 Cec08g1664 1664
3 17717842 17720222 - Chy3G065350.1 Chy03g01555 1555
3 17723343 17725939 - Chy3G065360.1 Chy03g01556 1556
3 17728854 17732632 - Chy3G065370.1 Chy03g01557 1557
7 1246046 1247437 - Chy7G129750.1 Chy07g00145 145
5 30607758 30609137 - ClG42_05g0220100.10 Clacu05g2201 2201
8 27106345 27110132 - ClG42_08g0176700.10 Clacu08g1767 1767
5 32277049 32281942 + ClCG05G020040.2 Cla05g02055 2055
8 28504183 28513983 - ClCG08G016080.2 Cla08g01583 1583
8 28519472 28523259 - ClCG08G016100.2 Cla08g01584 1584
1 12109556 12110917 + CmaCh01G018290.1 Cma01g01829 1829
5 732376 736078 + CmaCh05G001730.1 Cma05g00173 173
5 736528 739493 + CmaCh05G001740.1 Cma05g00174 174
5 740818 743380 + CmaCh05G001750.1 Cma05g00175 175
12 2912007 2915857 - CmaCh12G005590.1 Cma12g00559 559
12 2921491 2924877 - CmaCh12G005600.1 Cma12g00560 560
3 28105142 28108567 - MELO3C010844.2.1 Cme03g02062 2062
3 28110755 28114219 - MELO3C010843.2.1 Cme03g02063 2063
3 28116565 28122840 - MELO3C010842.2.1 Cme03g02064 2064
3 1234709 1238130 + PI0019522.1 Cmetu03g0637 637
1 13609205 13610590 + CmoCh01G018850.1 Cmo01g01885 1885
5 738564 742311 + CmoCh05G001710.1 Cmo05g00171 171
5 742861 745681 + CmoCh05G001720.1 Cmo05g00172 172
5 747084 750338 + CmoCh05G001730.1 Cmo05g00173 173
9 1081175 1082572 - CmoCh09G002390.1 Cmo09g00239 239
12 3086885 3094356 - CmoCh12G005020.1 Cmo12g00502 502
12 3099713 3102982 - CmoCh12G005030.1 Cmo12g00503 503
5 30342168 30343547 - CmPI595203_05g020670.1 Cmu05g2067 2067
4 12122766 12125324 - Conep04aG0163800.1 Cone4ag1586 1586
4 12126308 12128422 - Conep04aG0163900.1 Cone4ag1587 1587
4 12129337 12132298 - Conep04aG0164000.1 Cone4ag1588 1588
7 9875390 9879759 + Conep07aG0140200.1 Cone7ag1361 1361
7 9880700 9882803 + Conep07aG0140300.1 Cone7ag1362 1362
7 9883587 9886144 + Conep07aG0140400.1 Cone7ag1363 1363
17 6756706 6758827 - Conep17aG0086800.1 Cone17ag0849 849
17 6762013 6766269 - Conep17aG0087100.1 Cone17ag0852 852
17 6767561 6769585 - Conep17aG0087300.1 Cone17ag0853 853
20 851450 855380 - Conep20aG0020600.1 Cone20ag0198 198
20 856873 858619 - Conep20aG0020800.1 Cone20ag0199 199
6 916107 917504 - Cp4.1LG06g01710.1 Cpe06g00169 169
7 3203688 3207120 - Cp4.1LG07g05090.1 Cpe07g00491 491
7 3214700 3220305 - Cp4.1LG07g05100.1 Cpe07g00492 492
11 775512 781250 + Cp4.1LG11g01310.1 Cpe11g00142 142
11 781658 784790 + Cp4.1LG11g01260.1 Cpe11g00143 143
11 786439 789172 + Cp4.1LG11g01500.1 Cpe11g00144 144
5 33678043 33679422 - CrPI670011_05g021930.1 Cre05g2193 2193
8 28171192 28174981 - CrPI670011_08g015520.1 Cre08g1552 1552
2 18146642 18153254 + CsaV3_2G026530.1 Csa02g01933 1933
2 18154564 18158701 + CsaV3_2G026540.1 Csa02g01934 1934
2 18160240 18163780 + CsaV3_2G026550.1 Csa02g01935 1935
4 24447376 24451392 - CsaV3_4G034530.1 Csa04g02427 2427
1 82913753 82915872 - Hsped.01g17830.1 Hepe01g1783 1783
8 14495901 14499669 - Hsped.08g12960.1 Hepe08g1296 1296
8 14505475 14510736 - Hsped.08g12970.1 Hepe08g1297 1297
13 39893780 39897065 - Maker00025147 Lcy13g2091 2091
13 39899103 39903215 - Maker00025167 Lcy13g2092 2092
13 39907952 39912012 - Maker00025319 Lcy13g2093 2093
4 22998820 23000250 + Lsi04G015390.1 Lsi04g01539 1539
8 23012388 23022464 - Lsi08G014860.1 Lsi08g01486 1486
8 23031183 23037299 - Lsi08G014870.1 Lsi08g01487 1487
11 1936246 1938231 - MC11g_new0069 Mch11g0310 310
10 26434715 26437784 + Sed0000279.3 Sed10g1234 1234
11 23591214 23597614 + Sed0004383.4 Sed11g0938 938
1 113367583 113368798 + Tan0000444.1 Tan01g4754 4754
2 83299809 83306310 + Tan0009559.5 Tan02g1796 1796
2 83299809 83306310 + Tan0009559.6 Tan02g1797 1797
2 83355997 83359849 + Tan0008030.1 Tan02g1798 1798
18 8563883 8564847 + Vvi18g740 Vvi18g740 740
18 8591120 8596300 + Vvi18g741 Vvi18g741 741
18 8597931 8600974 + Vvi18g742 Vvi18g742 742
18 8600988 8605039 + Vvi18g743 Vvi18g743 743
18 8609030 8612826 + Vvi18g744 Vvi18g744 744
18 8624952 8627945 + Vvi18g745 Vvi18g745 745
18 8633938 8637255 + Vvi18g746 Vvi18g746 746
18 8641103 8643404 - Vvi18g747 Vvi18g747 747
18 8645811 8672088 + Vvi18g748 Vvi18g748 748
18 8676603 8677284 + Vvi18g749 Vvi18g749 749
       

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