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
Vvi1g1321 Blo01g00162 . . Bda11g00379 . . . . . . . . . . . . . . . . . . . . Cla06g00168 Cam06g0044 Cec06g0188 Cco06g0181 Clacu06g0183 Cmu06g0178 Cre06g0951 . . . . . . Chy11g01820 Cme11g02354 . Blo12g00290 . Bda11g00379 . . . . Sed07g0124 . . . . . . Cpe17g00933 . Bhi12g02405 Tan06g1460 . . . . . . . . . . . . Lsi09g01756 . . .
Vvi1g1322 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1323 Blo01g00161 . . . . . . . . . . . . . . . . . . . . . . . Cla06g00167 Cam06g0045 Cec06g0187 Cco06g0180 Clacu06g0182 Cmu06g0177 Cre06g0950 . . . . . . Chy11g01821 Cme11g02355 . . . . . . . . . . . . . . . Cpe17g00934 . Bhi12g02403 Tan06g1458 . . . . . . . . . . . . Lsi09g01757 . . .
Vvi1g1324 . . . . . . . . . . . . . . . . . . . . . . . . Cla06g00166 Cam06g0047 Cec06g0186 Cco06g0179 Clacu06g0181 Cmu06g0176 Cre06g0949 . . . . . . . Cme11g02356 . . . . . . . . Sed12g1621 . . . . . . . . Bhi12g02401 Tan06g1456 Cmetu11g1073 . . . . . . . . . . . . . . .
Vvi1g1325 . . Bda01g02111 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy11g01822 Cme11g02357 . . . . . . . . Sed08g1027 . . . . . . Cpe17g00935 . Bhi12g02400 Tan06g1455 Cmetu11g0835 . Hepe03g1159 . . . . . . . . . Lsi09g01758 . . .
Vvi1g1326 . . . Bda11g00378 Bpe13g00823 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00287 . . Blo02g00202 . . Bda11g00378 Bpe14g00807 . . Bma06g01334 . . . . . . . . Cpe03g01212 . . . . . . . . . . . . . . . . Chy07g01493 Cme07g01930
Vvi1g1327 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy11g01823 Cme11g02358 . . . . . . . . Sed07g0128 . . . . . . Cpe17g00936 . Bhi12g02399 Tan06g1453 Cmetu11g2573 . . . . . . . . . . . Lsi09g01760 . . .
Vvi1g1328 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1329 Blo01g00160 . . Bda11g00377 Bpe13g00824 . . . . . . . . . . . . . . . . . . . Cla06g00164 Cam06g0049 Cec06g0183 Cco06g0176 Clacu06g0177 Cmu06g0172 Cre06g0946 . . . . . . Chy11g01824 Cme11g02359 . Blo12g00291 . Bda11g00377 . . . Bma06g01333 Sed07g0129 . . . . . . Cpe17g00937 . Bhi12g02398 Tan06g1452 Cmetu11g1288 . . . . . . . . . . . Lsi09g01761 . Chy07g01527 Cme07g01971
Vvi1g1330 . . . Bda11g00376 Bpe13g00825 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00260 . . Blo02g00203 . . Bda11g00376 Bpe14g00808 . . Bma06g01332 . . . . . . . . Cpe03g01197 . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 57168550 57171315 + Bda004442.1 Bda01g02111 2111
11 4158221 4159181 + Bda005115.1 Bda11g00376 376
11 4161224 4162513 - Bda005116.1 Bda11g00377 377
11 4164682 4168282 + Bda005117.1 Bda11g00378 378
11 4168734 4172097 - Bda005118.1 Bda11g00379 379
12 75849751 75851213 - XM_039050910.1 Bhi12g02398 2398
12 75877493 75879570 + XM_039050517.1 Bhi12g02399 2399
12 75884689 75886494 + XM_039019949.1 Bhi12g02400 2400
12 75894651 75896656 + XM_039051120.1 Bhi12g02401 2401
12 75897195 75904710 - XM_039051118.1 Bhi12g02403 2403
12 75924984 75930365 - XM_039019554.1 Bhi12g02405 2405
1 2151686 2155489 - BLOR00160 Blo01g00160 160
1 2167347 2172752 - BLOR00161 Blo01g00161 161
1 2174932 2183967 - BLOR00162 Blo01g00162 162
2 1830592 1832862 - BLOR09932 Blo02g00202 202
2 1835004 1836110 - BLOR09933 Blo02g00203 203
12 17128144 17140042 + BLOR04309 Blo12g00290 290
12 17248543 17249173 + BLOR04310 Blo12g00291 291
6 50290092 50291238 + Bma024443.1 Bma06g01332 1332
6 50292143 50293043 - Bma024444.1 Bma06g01333 1333
6 50294261 50296913 + Bma024445.1 Bma06g01334 1334
13 14510438 14513069 - Bpe010514.3 Bpe13g00823 823
13 14518028 14518982 + Bpe010515.1 Bpe13g00824 824
13 14520272 14521424 - Bpe010516.1 Bpe13g00825 825
14 6077903 6080116 - Bpe014184.1 Bpe14g00807 807
14 6081037 6082021 - Bpe014185.1 Bpe14g00808 808
6 2291071 2297736 + CaPI482276_06g000440.1 Cam06g0044 44
6 2308384 2316160 + CaPI482276_06g000450.1 Cam06g0045 45
6 2325378 2328043 - CaPI482276_06g000470.1 Cam06g0047 47
6 2345722 2346923 + CaPI482276_06g000490.1 Cam06g0049 49
6 1829275 1830477 - CcPI632755_06g001760.1 Cco06g0176 176
6 1858421 1859996 + CcPI632755_06g001790.1 Cco06g0179 179
6 1860134 1867881 - CcPI632755_06g001800.1 Cco06g0180 180
6 1877859 1883849 - CcPI632755_06g001810.1 Cco06g0181 181
6 1855772 1856983 - CePI673135_06g001830.1 Cec06g0183 183
6 1884957 1886532 + CePI673135_06g001860.1 Cec06g0186 186
6 1886660 1894409 - CePI673135_06g001870.1 Cec06g0187 187
6 1904971 1910234 - CePI673135_06g001880.1 Cec06g0188 188
7 19217216 19219706 - Chy7G143230.1 Chy07g01493 1493
7 19537305 19538167 - Chy7G143570.1 Chy07g01527 1527
11 24568593 24573338 + Chy11G204000.1 Chy11g01820 1820
11 24579149 24585422 + Chy11G204010.1 Chy11g01821 1821
11 24586601 24594674 - Chy11G204020.1 Chy11g01822 1822
11 24596884 24598735 - Chy11G204030.1 Chy11g01823 1823
11 24602625 24603823 + Chy11G204040.1 Chy11g01824 1824
6 1998722 1999929 - ClG42_06g0017700.10 Clacu06g0177 177
6 2028666 2030239 + ClG42_06g0018100.10 Clacu06g0181 181
6 2030376 2038156 - ClG42_06g0018200.10 Clacu06g0182 182
6 2048745 2054025 - ClG42_06g0018300.10 Clacu06g0183 183
6 1872802 1874086 - ClCG06G001810.1 Cla06g00164 164
6 1892684 1905177 + ClCG06G001830.1 Cla06g00166 166
6 1905457 1912691 - ClCG06G001840.2 Cla06g00167 167
6 1924255 1929473 - ClCG06G001850.2 Cla06g00168 168
7 24509783 24512843 - MELO3C017755.2.1 Cme07g01930 1930
7 24850814 24852288 - MELO3C017796.2.1 Cme07g01971 1971
11 30552434 30558421 + MELO3C022343.2.1 Cme11g02354 2354
11 30563450 30570235 + MELO3C022344.2.1 Cme11g02355 2355
11 30570709 30572942 - MELO3C022345.2.1 Cme11g02356 2356
11 30578540 30579486 - MELO3C035241.2.1 Cme11g02357 2357
11 30581299 30583699 - MELO3C022346.2.1 Cme11g02358 2358
11 30587578 30589219 + MELO3C022347.2.1 Cme11g02359 2359
11 1486027 1487725 + PI0020091.1 Cmetu11g0835 835
11 1477423 1479178 + PI0013107.1 Cmetu11g1073 1073
11 1466211 1467929 - PI0011346.1 Cmetu11g1288 1288
11 1471904 1474750 + PI0023974.1 Cmetu11g2573 2573
6 1794077 1795284 - CmPI595203_06g001720.1 Cmu06g0172 172
6 1824000 1825573 + CmPI595203_06g001760.1 Cmu06g0176 176
6 1825710 1833494 - CmPI595203_06g001770.1 Cmu06g0177 177
6 1844059 1849341 - CmPI595203_06g001780.1 Cmu06g0178 178
3 9799414 9801411 + Cp4.1LG03g13070.1 Cpe03g01197 1197
3 9897821 9900787 + Cp4.1LG03g12900.1 Cpe03g01212 1212
17 7189177 7195078 + Cp4.1LG17g09290.1 Cpe17g00933 933
17 7196922 7204467 + Cp4.1LG17g09280.1 Cpe17g00934 934
17 7205562 7206345 - Cp4.1LG17g09350.1 Cpe17g00935 935
17 7207483 7210305 - Cp4.1LG17g09340.1 Cpe17g00936 936
17 7210496 7212339 + Cp4.1LG17g09230.1 Cpe17g00937 937
6 2896384 2897587 - CrPI670011_06g009460.1 Cre06g0946 946
6 2926019 2927592 + CrPI670011_06g009490.1 Cre06g0949 949
6 2927730 2935625 - CrPI670011_06g009500.1 Cre06g0950 950
6 2946339 2951587 - CrPI670011_06g009510.1 Cre06g0951 951
4 1608365 1609831 + CsaV3_4G002600.1 Csa04g00260 260
4 1790472 1794059 + CsaV3_4G002870.1 Csa04g00287 287
3 65129447 65132038 - Hsped.03g11590.1 Hepe03g1159 1159
9 26282769 26294417 + Lsi09G017560.1 Lsi09g01756 1756
9 26303257 26310794 + Lsi09G017570.1 Lsi09g01757 1757
9 26311232 26323645 - Lsi09G017580.1 Lsi09g01758 1758
9 26328623 26330719 - Lsi09G017600.1 Lsi09g01760 1760
9 26339501 26341326 + Lsi09G017610.1 Lsi09g01761 1761
7 1141880 1150664 + Sed0002747.1 Sed07g0124 124
7 1174915 1178359 - Sed0021477.1 Sed07g0128 128
7 1194718 1196634 + Sed0012192.1 Sed07g0129 129
8 11392135 11395463 - Sed0025827.1 Sed08g1027 1027
12 27216621 27222152 - Sed0003842.2 Sed12g1621 1621
6 19506935 19508633 - Tan0010201.1 Tan06g1452 1452
6 19538518 19541411 + Tan0006482.1 Tan06g1453 1453
6 19562965 19565309 + Tan0018929.1 Tan06g1455 1455
6 19562965 19565309 + Tan0018929.2 Tan06g1456 1456
6 19565768 19573061 - Tan0013229.1 Tan06g1458 1458
6 19583748 19590006 - Tan0001946.2 Tan06g1460 1460
1 22122604 22131879 + Vvi1g1321 Vvi1g1321 1321
1 22164907 22165280 - Vvi1g1322 Vvi1g1322 1322
1 22185831 22196323 + Vvi1g1323 Vvi1g1323 1323
1 22200552 22202463 - Vvi1g1324 Vvi1g1324 1324
1 22202980 22211903 - Vvi1g1325 Vvi1g1325 1325
1 22216360 22221088 - Vvi1g1326 Vvi1g1326 1326
1 22235755 22240368 - Vvi1g1327 Vvi1g1327 1327
1 22258689 22259169 + Vvi1g1328 Vvi1g1328 1328
1 22268128 22269638 + Vvi1g1329 Vvi1g1329 1329
1 22277020 22278198 - Vvi1g1330 Vvi1g1330 1330
       

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