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
Vvi1g1301 . . . . . . . . . . . . . . . . . . . . . . . . Cla06g00179 Cam06g0032 Cec06g0198 Cco06g0193 Clacu06g0195 Cmu06g0189 Cre06g0961 . . . . . Csa04g00296 Chy11g01810 Cme11g02343 . Blo12g00284 . . . . . . Sed12g0612 . . . . . . Cpe17g00924 Cpe03g01219 Bhi12g02421 Tan06g1481 Cmetu07g0215 . . . . . . . . . . . Lsi09g01746 . Chy07g01484 Cme07g01921
Vvi1g1302 . . . . . . . Bma15g00278 . . . . . . . . . . . . . . . . Cla06g00178 Cam06g0033 Cec06g0197 Cco06g0192 Clacu06g0194 Cmu06g0188 Cre06g0960 . . . . Lsi04g00730 . Chy11g01811 Cme11g02344 Blo06g00788 Blo12g00285 . . . . . . Sed09g0360 . . . . . . . . Bhi12g02419 Tan06g1479 Cmetu11g1517 . Hepe03g1142 . . . . . . . . . Lsi09g01747 . . .
Vvi1g1303 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00294 . . . . . . . . . . . . . . . . . . Cpe03g01218 . . . . . . . . . . . . . . . . Chy07g01485 Cme07g01922
Vvi1g1304 . . . . Bpe13g00818 . . . . . . . . . . . . . . . . . . . Cla06g00177 Cam06g0034 Cec06g0196 Cco06g0191 Clacu06g0193 Cmu06g0187 Cre06g0959 . . . . . . . . Blo02g00198 . . . Bpe14g00803 . . . . . . . . . . . . Bhi12g02418 . . . Hepe03g1143 . . . . . . . . . . . . .
Vvi1g1305 . . . Bda11g00384 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy11g01812 Cme11g02345 . . . Bda11g00384 . . . Bma06g01339 Sed09g0359 . . . . . . Cpe17g00925 . Bhi12g02417 Tan06g1477 Cmetu11g1068 . . . . . . . . . . . Lsi09g01748 . . .
Vvi1g1306 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1307 . . . . . . . Bma15g00313 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00293 . . Blo06g00756 Blo12g00287 . . . . . . . . . . . . . . Cpe03g01216 . . . . . . . . . . . . . . . . . .
Vvi1g1308 . . . Bda11g00382 Bpe13g00820 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00292 . . . . . Bda11g00382 . . . Bma06g01337 . . . . . . . . Cpe03g01215 . . . . . . . . . . . . . . . . Chy07g01487 Cme07g01925
Vvi1g1309 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1310 . . . . . . . . . . . . . . . . . . . . . . . . Cla06g00176 Cam06g0035 Cec06g0195 Cco06g0190 Clacu06g0192 Cmu06g0186 Cre06g0958 . . . . . . Chy11g01813 Cme11g02346 . . . . . . . . Sed07g0116 . . . . . . Cpe17g00927 . Bhi12g02416 Tan06g1476 Cmetu11g1752 . Hepe03g1149 . . . . . . . . . Lsi09g01749 . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 4183705 4187774 + Bda005121.1 Bda11g00382 382
11 4190887 4199495 + Bda005123.1 Bda11g00384 384
12 76198896 76199998 + XM_039018895.1 Bhi12g02416 2416
12 76319508 76328688 + XM_039019579.1 Bhi12g02417 2417
12 76319508 76328688 + XM_039019580.1 Bhi12g02418 2418
12 76329313 76335403 + XM_039020007.1 Bhi12g02419 2419
12 76341001 76343871 - XM_039020158.1 Bhi12g02421 2421
2 1796365 1806889 - BLOR09928 Blo02g00198 198
6 30796856 30798682 - BLOR17339 Blo06g00756 756
6 31181427 31183365 + BLOR17371 Blo06g00788 788
12 16957300 16964334 + BLOR04303 Blo12g00284 284
12 16962520 16975376 - BLOR04304 Blo12g00285 285
12 17082422 17084359 - BLOR04306 Blo12g00287 287
6 50310609 50319008 + Bma024448.2 Bma06g01337 1337
6 50323965 50331277 + Bma024450.1 Bma06g01339 1339
15 2726632 2727720 - Bma030780 Bma15g00278 278
15 3022118 3023941 + Bma013289.1 Bma15g00313 313
13 14481327 14489607 - Bpe025248 Bpe13g00818 818
13 14493010 14496622 - Bpe010511.1 Bpe13g00820 820
14 6051424 6059789 - Bpe014180.2 Bpe14g00803 803
6 2155442 2157795 + CaPI482276_06g000320.1 Cam06g0032 32
6 2161442 2167232 - CaPI482276_06g000330.1 Cam06g0033 33
6 2168636 2177206 - CaPI482276_06g000340.1 Cam06g0034 34
6 2184359 2184886 - CaPI482276_06g000350.1 Cam06g0035 35
6 1993427 1993954 + CcPI632755_06g001900.1 Cco06g0190 190
6 2001097 2009711 + CcPI632755_06g001910.1 Cco06g0191 191
6 2011036 2016868 + CcPI632755_06g001920.1 Cco06g0192 192
6 2020881 2023237 - CcPI632755_06g001930.1 Cco06g0193 193
6 2023150 2023677 + CePI673135_06g001950.1 Cec06g0195 195
6 2030391 2038995 + CePI673135_06g001960.1 Cec06g0196 196
6 2040375 2046121 + CePI673135_06g001970.1 Cec06g0197 197
6 2049856 2052204 - CePI673135_06g001980.1 Cec06g0198 198
7 19165589 19168145 + Chy7G143140.1 Chy07g01484 1484
7 19171480 19174408 + Chy7G143150.1 Chy07g01485 1485
7 19178996 19185276 - Chy7G143170.1 Chy07g01487 1487
11 24434723 24447011 + Chy11G203900.1 Chy11g01810 1810
11 24451805 24456267 - Chy11G203910.1 Chy11g01811 1811
11 24457203 24464691 - Chy11G203920.1 Chy11g01812 1812
11 24477798 24482566 - Chy11G203930.1 Chy11g01813 1813
6 2173638 2174165 + ClG42_06g0019200.10 Clacu06g0192 192
6 2181288 2189953 + ClG42_06g0019300.10 Clacu06g0193 193
6 2191347 2197141 + ClG42_06g0019400.10 Clacu06g0194 194
6 2200785 2203136 - ClG42_06g0019500.10 Clacu06g0195 195
6 2059456 2059983 + ClCG06G001920.1 Cla06g00176 176
6 2067356 2076591 + ClCG06G001930.1 Cla06g00177 177
6 2077707 2083749 + ClCG06G001940.2 Cla06g00178 178
6 2086841 2089540 - ClCG06G001950.2 Cla06g00179 179
7 24424930 24427938 + MELO3C017747.2.1 Cme07g01921 1921
7 24432655 24438706 + MELO3C017748.2.1 Cme07g01922 1922
7 24471528 24477609 - MELO3C017750.2.1 Cme07g01925 1925
11 30456839 30459639 + MELO3C022334.2.1 Cme11g02343 2343
11 30463098 30468677 - MELO3C022335.2.1 Cme11g02344 2344
11 30469128 30478265 - MELO3C022336.2.1 Cme11g02345 2345
11 30481662 30482590 - MELO3C022337.2.1 Cme11g02346 2346
7 2454958 2457948 - PI0005003.1 Cmetu07g0215 215
11 1593502 1602443 + PI0012086.1 Cmetu11g1068 1068
11 1602987 1606617 + PI0004496.1 Cmetu11g1517 1517
11 1587297 1588593 + PI0019600.1 Cmetu11g1752 1752
6 1969094 1969621 + CmPI595203_06g001860.1 Cmu06g0186 186
6 1976738 1985396 + CmPI595203_06g001870.1 Cmu06g0187 187
6 1986759 1992553 + CmPI595203_06g001880.1 Cmu06g0188 188
6 1996203 1998555 - CmPI595203_06g001890.1 Cmu06g0189 189
3 9914438 9923323 + Cp4.1LG03g12930.1 Cpe03g01215 1215
3 9914479 9916512 - Cp4.1LG03g12840.1 Cpe03g01216 1216
3 9927503 9931889 - Cp4.1LG03g12860.1 Cpe03g01218 1218
3 9932567 9935927 - Cp4.1LG03g12870.1 Cpe03g01219 1219
17 7144786 7147291 + Cp4.1LG17g09270.1 Cpe17g00924 924
17 7147450 7156183 - Cp4.1LG17g09320.1 Cpe17g00925 925
17 7159705 7162337 - Cp4.1LG17g09370.1 Cpe17g00927 927
6 3059616 3060143 + CrPI670011_06g009580.1 Cre06g0958 958
6 3067173 3075825 + CrPI670011_06g009590.1 Cre06g0959 959
6 3077146 3083042 + CrPI670011_06g009600.1 Cre06g0960 960
6 3087006 3089359 - CrPI670011_06g009610.1 Cre06g0961 961
4 1818065 1827873 + CsaV3_4G002920.1 Csa04g00292 292
4 1818166 1820190 - CsaV3_4G002930.1 Csa04g00293 293
4 1828700 1835110 - CsaV3_4G002940.1 Csa04g00294 294
4 1836767 1839989 - CsaV3_4G002960.1 Csa04g00296 296
3 64658632 64665285 - Hsped.03g11420.1 Hepe03g1142 1142
3 64669961 64678699 - Hsped.03g11430.1 Hepe03g1143 1143
3 64877401 64878537 - Hsped.03g11490.1 Hepe03g1149 1149
4 6731941 6736889 + Lsi04G007300.1 Lsi04g00730 730
9 26116300 26119174 + Lsi09G017460.1 Lsi09g01746 1746
9 26124029 26131834 - Lsi09G017470.1 Lsi09g01747 1747
9 26132221 26141100 - Lsi09G017480.1 Lsi09g01748 1748
9 26150155 26150682 - Lsi09G017490.1 Lsi09g01749 1749
7 1054921 1055893 - Sed0008200.1 Sed07g0116 116
9 3233500 3243597 + Sed0008887.1 Sed09g0359 359
9 3245618 3254623 + Sed0001951.1 Sed09g0360 360
12 3621147 3623860 - Sed0023729.2 Sed12g0612 612
6 20046061 20047240 + Tan0005832.1 Tan06g1476 1476
6 20163127 20172798 + Tan0012713.1 Tan06g1477 1477
6 20175122 20179271 + Tan0002511.2 Tan06g1479 1479
6 20192687 20195581 - Tan0005399.2 Tan06g1481 1481
1 21888058 21891236 + Vvi1g1301 Vvi1g1301 1301
1 21897412 21913235 - Vvi1g1302 Vvi1g1302 1302
1 21915489 21919833 + Vvi1g1303 Vvi1g1303 1303
1 21920559 21924350 - Vvi1g1304 Vvi1g1304 1304
1 21924402 21931626 - Vvi1g1305 Vvi1g1305 1305
1 21937511 21939486 - Vvi1g1306 Vvi1g1306 1306
1 21941246 21943211 - Vvi1g1307 Vvi1g1307 1307
1 21945722 21956866 - Vvi1g1308 Vvi1g1308 1308
1 21992964 21995256 + Vvi1g1309 Vvi1g1309 1309
1 22022631 22023096 + Vvi1g1310 Vvi1g1310 1310
       

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