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
Vvi16g614 . Blo15g00159 . . . Bpe07g00948 . . Cmo16g00147 . . Cma15g01202 . Car15g01089 . . Cpe14g00119 . . . . . . . Cla01g00295 Cam01g0306 Cec01g0296 Cco01g0313 Clacu01g0306 Cmu01g0291 Cre09g2217 . . . . Lsi05g01251 Csa05g00318 Chy09g01190 Cme06g00976 . . Bda06g00673 Bda15g00736 . Bpe12g00418 . . . . . Cma16g00141 . . . . Cpe13g00173 Bhi12g00209 . . Lac11g2129 Hepe06g1577 . Lcy12g1689 Cla05g00860 Cam05g0946 Cec05g0951 Cco05g0951 Clacu05g0933 Cmu05g0891 Cre05g0976 . Csa03g01690 Chy06g00923 Cme09g01724
Vvi16g615 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g616 . . . . Bpe03g00296 . Bma10g01213 . Cmo16g00146 Cmo18g01257 . . . . . . Cpe14g00118 Bhi01g01347 . . . Hepe07g0176 Mch10g0172 . . . . . . . . . . . . Lsi05g01248 . . Cme06g00978 Blo07g00421 . . . . . . . . . . Cma16g00140 Cma18g01234 . Car18g01138 Cpe09g00102 . . . . . . . . Cla05g00862 Cam05g0949 Cec05g0954 Cco05g0954 Clacu05g0936 Cmu05g0894 Cre05g0978 . Csa03g01692 Chy06g00925 .
Vvi16g617 Blo06g01115 . . . . . . . . . Cma02g01040 . Car02g00785 . . Cpe05g00681 . . . . . . . . Cla01g00540 Cam01g0564 Cec01g0554 Cco01g0579 Clacu01g0560 Cmu01g0532 Cre09g1977 . . . . . Csa05g00574 Chy09g00931 . . . . Bda15g00735 . Bpe12g00419 Bma08g00340 . . Cmo02g01055 . . . . . . Cpe13g00045 . . . . . . . . . . . . . . Lsi09g00584 . . Cme09g01458
Vvi16g618 . . Bda05g00059 . Bpe03g00295 . Bma10g01214 . Cmo16g00145 . . . . . Sed07g1050 . Cpe14g00117 Bhi01g01345 Tan01g0271 Cmetu06g0928 . Hepe07g0175 Mch10g0171 . . . . . . . . . . . . Lsi05g01247 . . Cme06g00979 Blo07g00420 . . . . . . . . . . Cma16g00139 . Car16g00123 . . . . . . . . . . Cla05g00863 Cam05g0950 Cec05g0955 Cco05g0955 Clacu05g0937 Cmu05g0895 Cre05g0979 . Csa03g01693 Chy06g00927 .
Vvi16g619 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe09g00101 . . . . . . . . . . . . . . . . . Chy06g00929 .
Vvi16g620 . Blo15g00160 . . . Bpe07g00947 . . Cmo16g00141 Cmo18g01259 . Cma15g01203 . Car15g01090 Sed01g3914 . Cpe14g00115 Bhi01g01343 Tan01g0269 Cmetu06g2712 Lac11g2126 Hepe07g0173 Mch10g0169 . Cla01g00293 Cam01g0304 Cec01g0295 Cco01g0311 Clacu01g0304 Cmu01g0289 . . . . . . Csa05g00316 Chy09g01192 Cme06g00981 . . Bda06g00674 . . . . Bma12g01125 . . Cmo15g01268 Cma16g00136 Cma18g01236 Car16g00120 Car18g01140 Cpe09g00100 Cpe13g00172 Bhi12g00210 . . Lac11g2126 Hepe06g1576 . Lcy12g1687 . . . . . . . . Csa03g01695 Chy06g00930 Cme09g01727
Vvi16g621 . . . Bda07g01857 . . . . . Cmo18g01260 . . . . . . . Bhi01g01342 . . . Hepe07g0172 . . . . . . . . . . . . . Lsi05g01244 . . Cme06g00982 . . . . . . . . . . . . Cma18g01238 . Car18g01141 . . . . . . . . . Cla05g00865 Cam05g0952 Cec05g0957 Cco05g0957 Clacu05g0939 Cmu05g0897 Cre05g0981 . Csa03g01696 Chy06g00931 .
Vvi16g622 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g623 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 3469025 3473691 - Bda020648.1 Bda05g00059 59
6 9371756 9373606 - Bda023964.1 Bda06g00673 673
6 9382498 9383588 - Bda023966.1 Bda06g00674 674
7 35957916 35959250 - Bda028825.1 Bda07g01857 1857
15 10831044 10833983 - Bda012591.1 Bda15g00735 735
15 10836669 10837723 + Bda012592.1 Bda15g00736 736
1 27000729 27002605 + XM_039026731.1 Bhi01g01342 1342
1 27006458 27007981 + XM_039036075.1 Bhi01g01343 1343
1 27095990 27097611 + XM_039047830.1 Bhi01g01345 1345
1 27104562 27110259 - XM_039030007.1 Bhi01g01347 1347
12 6721599 6724305 - XM_039018763.1 Bhi12g00209 209
12 6830332 6832750 - XM_039019662.1 Bhi12g00210 210
6 34567345 34570504 + BLOR17698 Blo06g01115 1115
7 7927066 7927976 + BLOR18352 Blo07g00420 420
7 7981329 7996243 - BLOR18353 Blo07g00421 421
15 1625866 1627569 - BLOR06553 Blo15g00159 159
15 1640142 1641231 - BLOR06554 Blo15g00160 160
8 6103613 6106546 - Bma027383.1 Bma08g00340 340
10 42937910 42939540 + Bma005283.1 Bma10g01213 1213
10 42991148 42992020 - Bma030401 Bma10g01214 1214
12 43568516 43569523 + Bma008473.1 Bma12g01125 1125
3 4016732 4017600 + Bpe012147.2 Bpe03g00295 295
3 4039526 4042446 - Bpe012148.1 Bpe03g00296 296
7 15302916 15304003 + Bpe021789.1 Bpe07g00947 947
7 15306969 15309003 + Bpe021790.1 Bpe07g00948 948
12 9773585 9775382 - Bpe005674.1 Bpe12g00418 418
12 9803376 9806329 + Bpe005675.1 Bpe12g00419 419
1 3384797 3386828 + CaPI482276_01g003040.1 Cam01g0304 304
1 3397656 3399956 + CaPI482276_01g003060.1 Cam01g0306 306
1 5984413 5989322 - CaPI482276_01g005640.1 Cam01g0564 564
5 8554070 8556412 - CaPI482276_05g009460.1 Cam05g0946 946
5 8569244 8573786 + CaPI482276_05g009490.1 Cam05g0949 949
5 8578235 8579286 - CaPI482276_05g009500.1 Cam05g0950 950
5 8611974 8617338 - CaPI482276_05g009520.1 Cam05g0952 952
2 5709595 5715347 - Carg08436-RA Car02g00785 785
15 8544874 8546491 - Carg16653-RA Car15g01089 1089
15 8548467 8550051 - Carg16652-RA Car15g01090 1090
16 707776 708977 + Carg15142-RA Car16g00120 120
16 719140 720203 + Carg15145-RA Car16g00123 123
18 11310355 11314194 + Carg22086-RA Car18g01138 1138
18 11323494 11325059 - Carg22088-RA Car18g01140 1140
18 11326694 11328103 - Carg22089-RA Car18g01141 1141
1 3023119 3024286 + CcPI632755_01g003110.1 Cco01g0311 311
1 3034928 3037205 + CcPI632755_01g003130.1 Cco01g0313 313
1 5708294 5713254 - CcPI632755_01g005790.1 Cco01g0579 579
5 8320017 8323414 - CcPI632755_05g009510.1 Cco05g0951 951
5 8334654 8339179 + CcPI632755_05g009540.1 Cco05g0954 954
5 8343914 8344957 - CcPI632755_05g009550.1 Cco05g0955 955
5 8378730 8383994 - CcPI632755_05g009570.1 Cco05g0957 957
1 2984746 2992175 + CePI673135_01g002950.1 Cec01g0295 295
1 3002754 3005057 + CePI673135_01g002960.1 Cec01g0296 296
1 5749176 5754092 - CePI673135_01g005540.1 Cec01g0554 554
5 8301659 8303999 - CePI673135_05g009510.1 Cec05g0951 951
5 8315235 8321492 + CePI673135_05g009540.1 Cec05g0954 954
5 8326587 8327620 - CePI673135_05g009550.1 Cec05g0955 955
5 8360924 8366319 - CePI673135_05g009570.1 Cec05g0957 957
6 6784141 6786404 - Chy6G114510.1 Chy06g00923 923
6 6797959 6802779 + Chy6G114530.1 Chy06g00925 925
6 6807202 6807662 - Chy6G114540.1 Chy06g00927 927
6 6834654 6838556 + Chy6G114570.1 Chy06g00929 929
6 6839586 6840560 - Chy6G114580.1 Chy06g00930 930
6 6843188 6844591 - Chy6G114590.1 Chy06g00931 931
9 12080070 12083827 + Chy9G166470.1 Chy09g00931 931
9 14107107 14109820 - Chy9G169060.1 Chy09g01190 1190
9 14116864 14118037 - Chy9G169080.1 Chy09g01192 1192
1 3000734 3002775 + ClG42_01g0030400.10 Clacu01g0304 304
1 3013553 3015852 + ClG42_01g0030600.10 Clacu01g0306 306
1 5617793 5622708 - ClG42_01g0056000.10 Clacu01g0560 560
5 8264053 8268830 - ClG42_05g0093300.10 Clacu05g0933 933
5 8281525 8286065 + ClG42_05g0093600.10 Clacu05g0936 936
5 8290553 8291607 - ClG42_05g0093700.10 Clacu05g0937 937
5 8320755 8326180 - ClG42_05g0093900.10 Clacu05g0939 939
1 3074578 3077457 + ClCG01G003040.1 Cla01g00293 293
1 3087903 3090356 + ClCG01G003060.1 Cla01g00295 295
1 5895482 5901435 - ClCG01G005510.2 Cla01g00540 540
5 8515037 8517379 - ClCG05G007890.2 Cla05g00860 860
5 8530092 8534632 + ClCG05G007900.1 Cla05g00862 862
5 8542409 8543546 - ClCG05G007910.1 Cla05g00863 863
5 8574780 8580558 - ClCG05G007930.1 Cla05g00865 865
2 6191825 6196144 - CmaCh02G010400.1 Cma02g01040 1040
15 7617391 7619284 - CmaCh15G012020.1 Cma15g01202 1202
15 7620776 7622819 - CmaCh15G012030.1 Cma15g01203 1203
16 599420 602376 + CmaCh16G001360.1 Cma16g00136 136
16 610396 611313 + CmaCh16G001390.1 Cma16g00139 139
16 612841 617178 - CmaCh16G001400.1 Cma16g00140 140
16 619181 623638 + CmaCh16G001410.1 Cma16g00141 141
18 9694311 9698287 + CmaCh18G012340.1 Cma18g01234 1234
18 9707338 9708594 - CmaCh18G012360.1 Cma18g01236 1236
18 9710564 9714600 - CmaCh18G012380.1 Cma18g01238 1238
6 6929843 6935458 - MELO3C006885.2.1 Cme06g00976 976
6 6946483 6952624 + MELO3C006887.2.1 Cme06g00978 978
6 6955905 6957126 - MELO3C006888.2.1 Cme06g00979 979
6 6987551 6989801 - MELO3C006891.2.1 Cme06g00981 981
6 6991345 6993501 - MELO3C006892.2.1 Cme06g00982 982
9 19805360 19810229 + MELO3C005379.2.1 Cme09g01458 1458
9 21865209 21871812 - MELO3C005637.2.1 Cme09g01724 1724
9 21878183 21880407 - MELO3C005639.2.1 Cme09g01727 1727
6 7009443 7010222 - PI0007812.1 Cmetu06g0928 928
6 7038388 7040454 - PI0027790.1 Cmetu06g2712 2712
2 6423880 6428560 - CmoCh02G010550.1 Cmo02g01055 1055
15 8690633 8692333 - CmoCh15G012680.1 Cmo15g01268 1268
16 644769 646828 + CmoCh16G001410.1 Cmo16g00141 141
16 661491 662614 + CmoCh16G001450.1 Cmo16g00145 145
16 664145 668610 - CmoCh16G001460.1 Cmo16g00146 146
16 670500 673190 + CmoCh16G001470.1 Cmo16g00147 147
18 12311482 12315772 + CmoCh18G012570.1 Cmo18g01257 1257
18 12324683 12328013 - CmoCh18G012590.1 Cmo18g01259 1259
18 12328143 12329552 - CmoCh18G012600.1 Cmo18g01260 1260
1 2956740 2958780 + CmPI595203_01g002890.1 Cmu01g0289 289
1 2969608 2971906 + CmPI595203_01g002910.1 Cmu01g0291 291
1 5574456 5579365 - CmPI595203_01g005320.1 Cmu01g0532 532
5 8112977 8117754 - CmPI595203_05g008910.1 Cmu05g0891 891
5 8130458 8134998 + CmPI595203_05g008940.1 Cmu05g0894 894
5 8139449 8140499 - CmPI595203_05g008950.1 Cmu05g0895 895
5 8167680 8173101 - CmPI595203_05g008970.1 Cmu05g0897 897
5 4158761 4164122 + Cp4.1LG05g06810.1 Cpe05g00681 681
9 554986 560286 + Cp4.1LG09g00900.1 Cpe09g00100 100
9 560966 564880 - Cp4.1LG09g00950.1 Cpe09g00101 101
9 569079 573212 - Cp4.1LG09g00910.1 Cpe09g00102 102
13 334159 340949 + Cp4.1LG13g00390.1 Cpe13g00045 45
13 1360913 1362930 + Cp4.1LG13g01710.1 Cpe13g00172 172
13 1364685 1367578 + Cp4.1LG13g01720.1 Cpe13g00173 173
14 621995 629995 + Cp4.1LG14g06030.1 Cpe14g00115 115
14 635199 635560 + Cp4.1LG14g06110.1 Cpe14g00117 117
14 638199 640239 - Cp4.1LG14g05990.1 Cpe14g00118 118
14 643272 646837 + Cp4.1LG14g06040.1 Cpe14g00119 119
5 8993382 8995724 - CrPI670011_05g009760.1 Cre05g0976 976
5 9008584 9013107 + CrPI670011_05g009780.1 Cre05g0978 978
5 9017659 9018756 - CrPI670011_05g009790.1 Cre05g0979 979
5 9052955 9058290 - CrPI670011_05g009810.1 Cre05g0981 981
9 38752250 38757219 + CrPI670011_09g019770.1 Cre09g1977 1977
9 41341001 41343297 - CrPI670011_09g022170.1 Cre09g2217 2217
3 12665476 12668413 - CsaV3_3G016900.1 Csa03g01690 1690
3 12676781 12682846 + CsaV3_3G016920.1 Csa03g01692 1692
3 12686165 12687225 - CsaV3_3G016930.1 Csa03g01693 1693
3 12743761 12744742 - CsaV3_3G016950.1 Csa03g01695 1695
3 12747377 12748780 - CsaV3_3G016960.1 Csa03g01696 1696
5 1968211 1972957 + CsaV3_5G003160.1 Csa05g00316 316
5 1979521 1982356 + CsaV3_5G003180.1 Csa05g00318 318
5 3777803 3782491 - CsaV3_5G005740.1 Csa05g00574 574
6 66507717 66510642 + Hsped.06g15760.1 Hepe06g1576 1576
6 66521449 66523943 + Hsped.06g15770.1 Hepe06g1577 1577
7 1541583 1543367 + Hsped.07g01720.1 Hepe07g0172 172
7 1546114 1547038 + Hsped.07g01730.1 Hepe07g0173 173
7 1570128 1571624 + Hsped.07g01750.1 Hepe07g0175 175
7 1574301 1579398 - Hsped.07g01760.1 Hepe07g0176 176
11 37285583 37287711 + Lag0032764.1 Lac11g2126 2126
11 37329767 37332075 + Lag0032767.1 Lac11g2129 2129
12 37335374 37337573 + Maker00029189 Lcy12g1687 1687
12 37373106 37375549 + Maker00003084 Lcy12g1689 1689
5 20250709 20256496 + Lsi05G012440.1 Lsi05g01244 1244
5 20283046 20283851 + Lsi05G012470.1 Lsi05g01247 1247
5 20287533 20292248 - Lsi05G012480.1 Lsi05g01248 1248
5 20306257 20310415 + Lsi05G012510.1 Lsi05g01251 1251
9 6280251 6285756 - Lsi09G005840.1 Lsi09g00584 584
10 1008818 1018360 + MC10g0140 Mch10g0169 169
10 1027058 1028212 + MC10g0142 Mch10g0171 171
10 1029677 1035369 - MC10g_new0030 Mch10g0172 172
1 68338162 68340089 + Sed0000996.2 Sed01g3914 3914
7 7588056 7589212 + Sed0012908.1 Sed07g1050 1050
1 2272734 2278557 + Tan0002235.1 Tan01g0269 269
1 2308519 2310214 + Tan0017068.1 Tan01g0271 271
16 16123090 16126399 - Vvi16g614 Vvi16g614 614
16 16131008 16138470 - Vvi16g615 Vvi16g615 615
16 16145021 16162952 + Vvi16g616 Vvi16g616 616
16 16163503 16171880 + Vvi16g617 Vvi16g617 617
16 16172928 16174043 - Vvi16g618 Vvi16g618 618
16 16185825 16189731 + Vvi16g619 Vvi16g619 619
16 16193300 16199121 - Vvi16g620 Vvi16g620 620
16 16208717 16210275 - Vvi16g621 Vvi16g621 621
16 16225501 16227189 + Vvi16g622 Vvi16g622 622
16 16227282 16227553 + Vvi16g623 Vvi16g623 623
       

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