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
Vvi18g910 Blo01g01554 . . Bda03g00254 . . Bma04g00203 Bma01g02309 . . Cma01g01892 Cma09g00171 Car01g01476 . . . . . . . . . . . . . . . . . . . . Cone17ag1330 Cone20ag0148 Lsi04g01644 Csa03g04189 Chy04g00530 . . . . . . . . . . Cmo01g01955 . . . . Car09g00150 . Cpe02g00140 . . . . . . . . . . . . . . . . . Cme04g00610
Vvi18g911 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla05g01958 Cam05g2106 Cec05g2116 Cco05g2170 Clacu05g2095 Cmu05g1972 Cre05g2091 . . . Cme04g00609
Vvi18g912 Blo01g01555 . . Bda03g00255 . . Bma04g00204 Bma01g02310 . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi04g01645 Csa03g04190 Chy04g00529 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme04g00607
Vvi18g913 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla05g01957 Cam05g2104 Cec05g2114 Cco05g2169 Clacu05g2094 Cmu05g1971 Cre05g2089 . . . .
Vvi18g914 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi04g01646 Csa03g04191 Chy04g00528 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme04g00606
Vvi18g915 . . . . Bpe02g00400 . . . . . . Cma09g00170 . . . Cpe06g00121 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo09g00166 . . . Car09g00149 . . . . . . . . . Cla05g01956 Cam05g2103 Cec05g2113 Cco05g2168 . Cmu05g1970 Cre05g2088 . . . .
Vvi18g916 . . Bda01g00540 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi04g01647 Csa03g04192 Chy04g00527 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme04g00603
Vvi18g917 . . . Bda03g00256 . Bpe04g00209 Bma04g00205 . . Cmo12g00430 Cma01g01894 Cma09g00169 Car01g01477 . Sed10g1335 . Cpe07g00434 Bhi04g00265 Tan02g1942 Cmetu03g1690 . Hepe10g0659 . Lcy13g2000 Cla08g01505 Cam08g1994 Cec08g1569 Cco08g1706 Clacu08g1684 . Cre08g1467 Cone4ag1898 Cone7ag1811 . . . . . Cme03g01971 . . . . . . . . . Cmo01g01957 Cmo09g00165 Cma12g00483 . . Car09g00148 . Cpe02g00139 . . . . . . . . . . . . . . Lsi08g01410 Csa02g02036 Chy03g01477 .
Vvi18g918 . . Bda01g00539 . Bpe02g00399 . . Bma01g02311 . . . Cma09g00167 . . . Cpe06g00120 . . . . . . . . . . . . . . . Cone4ag1899 Cone7ag1812 . . Lsi04g01648 Csa03g04193 Chy04g00526 . . . . . . . . . . . Cmo09g00164 . . . Car09g00147 . . . . . . . . . Cla05g01955 Cam05g2101 Cec05g2110 Cco05g2167 Clacu05g2093 Cmu05g1969 Cre05g2087 . . . Cme04g00602
Vvi18g919 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 32343965 32349492 + Bda002551.1 Bda01g00539 539
1 32352225 32359620 + Bda002552.1 Bda01g00540 540
3 2283379 2284810 - Bda016210.1 Bda03g00254 254
3 2285857 2287575 - Bda016211.1 Bda03g00255 255
3 2288639 2290763 - Bda016212.1 Bda03g00256 256
4 6358825 6362244 + XM_039030522.1 Bhi04g00265 265
1 55297652 55300581 - BLOR01554 Blo01g01554 1554
1 55304386 55306194 - BLOR01555 Blo01g01555 1555
1 80628361 80632131 - Bma003171.1 Bma01g02309 2309
1 80650793 80652542 - Bma003172.1 Bma01g02310 2310
1 80653790 80659261 - Bma003173.1 Bma01g02311 2311
4 1781591 1784029 - Bma018652.1 Bma04g00203 203
4 1785399 1787138 - Bma018653.1 Bma04g00204 204
4 1788132 1790269 - Bma018654.1 Bma04g00205 205
2 2592579 2598051 + Bpe008240.1 Bpe02g00399 399
2 2599965 2608134 + Bpe008241.1 Bpe02g00400 400
4 1434848 1436716 - Bpe014927.1 Bpe04g00209 209
5 29529458 29539552 + CaPI482276_05g021010.1 Cam05g2101 2101
5 29554734 29555964 + CaPI482276_05g021030.1 Cam05g2103 2103
5 29558630 29560492 + CaPI482276_05g021040.1 Cam05g2104 2104
5 29567975 29569837 + CaPI482276_05g021060.1 Cam05g2106 2106
8 25730325 25733172 + CaPI482276_08g019940.1 Cam08g1994 1994
1 12605502 12611314 - Carg17131-RA Car01g01476 1476
1 12613645 12617196 - Carg17132-RA Car01g01477 1477
9 708738 716281 + Carg08731-RA Car09g00147 147
9 719274 721480 + Carg08732-RA Car09g00148 148
9 722058 724238 + Carg08733-RA Car09g00149 149
9 725177 729136 + Carg08734-RA Car09g00150 150
5 30495758 30505941 + CcPI632755_05g021670.1 Cco05g2167 2167
5 30519172 30522453 + CcPI632755_05g021680.1 Cco05g2168 2168
5 30525184 30527275 + CcPI632755_05g021690.1 Cco05g2169 2169
5 30534743 30536608 + CcPI632755_05g021700.1 Cco05g2170 2170
8 28416846 28419695 + CcPI632755_08g017060.1 Cco08g1706 1706
5 32871623 32881277 + CePI673135_05g021100.1 Cec05g2110 2110
5 32896142 32896486 + CePI673135_05g021130.1 Cec05g2113 2113
5 32898890 32900799 + CePI673135_05g021140.1 Cec05g2114 2114
5 32908232 32910139 + CePI673135_05g021160.1 Cec05g2116 2116
8 27281530 27284239 + CePI673135_08g015690.1 Cec08g1569 1569
3 17237665 17240358 + Chy3G064570.1 Chy03g01477 1477
4 5207772 5214922 + Chy4G072440.1 Chy04g00526 526
4 5246948 5248818 + Chy4G072450.1 Chy04g00527 527
4 5255009 5257754 + Chy4G072460.1 Chy04g00528 528
4 5281153 5284057 + Chy4G072470.1 Chy04g00529 529
4 5286550 5289738 + Chy4G072480.1 Chy04g00530 530
5 29741557 29751833 + ClG42_05g0209300.10 Clacu05g2093 2093
5 29764392 29766835 + ClG42_05g0209400.10 Clacu05g2094 2094
5 29769619 29780751 + ClG42_05g0209500.10 Clacu05g2095 2095
8 26474575 26477430 + ClG42_08g0168400.10 Clacu08g1684 1684
5 31356972 31367602 + ClCG05G019150.1 Cla05g01955 1955
5 31380569 31383012 + ClCG05G019152.1 Cla05g01956 1956
5 31385796 31387688 + ClCG05G019154.1 Cla05g01957 1957
5 31393896 31395931 + ClCG05G019156.1 Cla05g01958 1958
8 27861370 27864221 + ClCG08G015260.2 Cla08g01505 1505
1 12388132 12393844 - CmaCh01G018920.1 Cma01g01892 1892
1 12396752 12399146 - CmaCh01G018940.1 Cma01g01894 1894
9 709495 716217 + CmaCh09G001670.1 Cma09g00167 167
9 719687 721995 + CmaCh09G001690.1 Cma09g00169 169
9 722558 725250 + CmaCh09G001700.1 Cma09g00170 170
9 725867 730222 + CmaCh09G001710.1 Cma09g00171 171
12 2520186 2522639 + CmaCh12G004830.1 Cma12g00483 483
3 27590275 27593743 + MELO3C010929.2.1 Cme03g01971 1971
4 5696100 5713694 + MELO3C003867.2.1 Cme04g00602 602
4 5740251 5742192 + MELO3C003868.2.1 Cme04g00603 603
4 5825061 5826986 + MELO3C030409.2.1 Cme04g00606 606
4 5831833 5834696 + MELO3C003872.2.1 Cme04g00607 607
4 5866560 5869532 + MELO3C003874.2.1 Cme04g00609 609
4 5872885 5877119 + MELO3C003875.2.1 Cme04g00610 610
3 1753496 1756829 - PI0020719.1 Cmetu03g1690 1690
1 13903738 13909360 - CmoCh01G019550.1 Cmo01g01955 1955
1 13912614 13915005 - CmoCh01G019570.1 Cmo01g01957 1957
9 731223 739891 + CmoCh09G001640.1 Cmo09g00164 164
9 741745 744025 + CmoCh09G001650.1 Cmo09g00165 165
9 744605 755147 + CmoCh09G001660.1 Cmo09g00166 166
12 2652002 2659204 + CmoCh12G004300.1 Cmo12g00430 430
5 29468637 29478887 + CmPI595203_05g019690.1 Cmu05g1969 1969
5 29491401 29493858 + CmPI595203_05g019700.1 Cmu05g1970 1970
5 29496629 29498521 + CmPI595203_05g019710.1 Cmu05g1971 1971
5 29503155 29507757 + CmPI595203_05g019720.1 Cmu05g1972 1972
4 13515979 13518942 - Conep04aG0195900.1 Cone4ag1898 1898
4 13524480 13529421 - Conep04aG0196000.1 Cone4ag1899 1899
7 11826012 11829316 - Conep07aG0186500.1 Cone7ag1811 1811
7 11831380 11836709 - Conep07aG0186600.1 Cone7ag1812 1812
17 9375941 9378587 - Conep17aG0136200.1 Cone17ag1330 1330
20 657669 659475 + Conep20aG0015600.1 Cone20ag0148 148
2 691915 695518 + Cp4.1LG02g07320.1 Cpe02g00139 139
2 696942 701040 + Cp4.1LG02g07310.1 Cpe02g00140 140
6 588127 595419 + Cp4.1LG06g01230.1 Cpe06g00120 120
6 601142 615337 + Cp4.1LG06g01260.1 Cpe06g00121 121
7 2791390 2794366 + Cp4.1LG07g04270.1 Cpe07g00434 434
5 32782627 32792732 + CrPI670011_05g020870.1 Cre05g2087 2087
5 32805577 32808052 + CrPI670011_05g020880.1 Cre05g2088 2088
5 32810828 32812732 + CrPI670011_05g020890.1 Cre05g2089 2089
5 32820222 32822137 + CrPI670011_05g020910.1 Cre05g2091 2091
8 27543014 27545965 + CrPI670011_08g014670.1 Cre08g1467 1467
2 18764907 18768335 - CsaV3_2G028550.1 Csa02g02036 2036
3 36737678 36742516 - CsaV3_3G044950.1 Csa03g04189 4189
3 36743086 36746485 - CsaV3_3G044960.1 Csa03g04190 4190
3 36748734 36750652 - CsaV3_3G044970.1 Csa03g04191 4191
3 36758169 36760262 - CsaV3_3G044980.1 Csa03g04192 4192
3 36771671 36782163 - CsaV3_3G044990.1 Csa03g04193 4193
10 8737679 8740558 + Hsped.10g06590.1 Hepe10g0659 659
13 38981648 38984475 + Maker00033688 Lcy13g2000 2000
4 23907254 23911969 - Lsi04G016440.1 Lsi04g01644 1644
4 23913684 23916752 - Lsi04G016450.1 Lsi04g01645 1645
4 23929052 23941378 - Lsi04G016460.1 Lsi04g01646 1646
4 23946285 23948961 - Lsi04G016470.1 Lsi04g01647 1647
4 23958901 23966514 - Lsi04G016480.1 Lsi04g01648 1648
8 22345397 22350650 + Lsi08G014100.1 Lsi08g01410 1410
10 28982201 28986751 - Sed0007834.1 Sed10g1335 1335
2 88019556 88022723 - Tan0013342.1 Tan02g1942 1942
18 10334341 10341089 - Vvi18g910 Vvi18g910 910
18 10346530 10348895 - Vvi18g911 Vvi18g911 911
18 10356444 10357646 - Vvi18g912 Vvi18g912 912
18 10357646 10358778 - Vvi18g913 Vvi18g913 913
18 10363406 10370119 - Vvi18g914 Vvi18g914 914
18 10370552 10376406 - Vvi18g915 Vvi18g915 915
18 10381790 10384308 - Vvi18g916 Vvi18g916 916
18 10395349 10398504 - Vvi18g917 Vvi18g917 917
18 10403900 10426931 - Vvi18g918 Vvi18g918 918
18 10428995 10432146 + Vvi18g919 Vvi18g919 919
       

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