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
Vvi1g1351 . . . . . . . . . . . . . . . . . . . . . . . . Cla06g00156 Cam06g0060 Cec06g0172 Cco06g0167 Clacu06g0166 Cmu06g0162 Cre06g0938 . . . . . . Chy11g01833 Cme11g02369 Blo02g00209 . . . Bpe14g00816 . . . Sed09g0340 . . . . . . . . Bhi12g02385 Tan06g1437 Cmetu11g1306 . Hepe03g1176 . . . . . . . . . Lsi09g01770 . . .
Vvi1g1352 . . . . . . . . . . . . . . . . . . . . . . . . Cla06g00155 Cam06g0061 Cec06g0171 Cco06g0165 Clacu06g0165 Cmu06g0161 Cre06g0937 Cone14ag0646 . . . . . Chy11g01834 Cme11g02370 . . . . . . . . Sed09g0342 . . . . . . Cpe17g00946 . Bhi12g02383 Tan06g1436 Cmetu11g1074 . Hepe03g1177 . . . . . . . . . Lsi09g01771 . . .
Vvi1g1353 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0268 Cone19ag0252 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1354 . . . . Bpe13g00830 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe14g00817 . . Bma06g01327 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1355 . . . . Bpe13g00831 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo02g00210 . . . Bpe14g00818 . . Bma06g01326 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1356 . . . . Bpe13g00832 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo02g00211 . . . Bpe14g00819 . . Bma06g01325 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1357 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0645 Cone15ag0655 . . . Csa04g00220 . . . . . . Bpe14g00820 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1358 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0644 Cone15ag0654 . . . . . . Blo02g00212 . . . Bpe14g00821 . . . . . . . . . . . Cpe03g01174 . . . . . . . . . . . . . . . . Chy07g01548 Cme07g01994
Vvi1g1359 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1360 . . . Bda11g00372 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0643 Cone15ag0653 . . . . . . Blo02g00213 . . Bda11g00372 Bpe14g00822 . . Bma06g01324 . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 4062034 4063727 + Bda005109.1 Bda11g00372 372
12 75241897 75250872 - XM_039018723.1 Bhi12g02383 2383
12 75383594 75394542 - XM_039019185.1 Bhi12g02385 2385
2 1961999 1965435 + BLOR09939 Blo02g00209 209
2 1972470 1980416 + BLOR09940 Blo02g00210 210
2 1981216 1983259 - BLOR09941 Blo02g00211 211
2 1989010 1998128 + BLOR09942 Blo02g00212 212
2 1998558 2000561 - BLOR09943 Blo02g00213 213
6 50202929 50205103 + Bma024433.1 Bma06g01324 1324
6 50217117 50218921 + Bma024434.1 Bma06g01325 1325
6 50219671 50220273 - Bma024435.1 Bma06g01326 1326
6 50223038 50231973 - Bma024436.1 Bma06g01327 1327
13 14578055 14582100 + Bpe010521.1 Bpe13g00830 830
13 14584741 14585427 + Bpe010522.1 Bpe13g00831 831
13 14586203 14588164 - Bpe025250 Bpe13g00832 832
14 6177253 6177789 + Bpe014193.1 Bpe14g00816 816
14 6185508 6189522 + Bpe014194.1 Bpe14g00817 817
14 6192324 6192968 + Bpe014195.1 Bpe14g00818 818
14 6193762 6195704 - Bpe014196.1 Bpe14g00819 819
14 6199200 6201698 + Bpe014197.2 Bpe14g00820 820
14 6202974 6205633 + Bpe014198.1 Bpe14g00821 821
14 6208878 6210830 - Bpe014199.3 Bpe14g00822 822
6 2471612 2472160 + CaPI482276_06g000600.1 Cam06g0060 60
6 2479823 2485814 + CaPI482276_06g000610.1 Cam06g0061 61
6 1687933 1693924 - CcPI632755_06g001650.1 Cco06g0165 165
6 1704022 1704196 - CcPI632755_06g001670.1 Cco06g0167 167
6 1714584 1720602 - CePI673135_06g001710.1 Cec06g0171 171
6 1728157 1731060 - CePI673135_06g001720.1 Cec06g0172 172
7 19719167 19721953 - Chy7G143780.1 Chy07g01548 1548
11 24696536 24699255 + Chy11G204130.1 Chy11g01833 1833
11 24705067 24709316 + Chy11G204140.1 Chy11g01834 1834
6 1860374 1866360 - ClG42_06g0016500.10 Clacu06g0165 165
6 1874034 1878037 - ClG42_06g0016600.10 Clacu06g0166 166
6 1729582 1735569 - ClCG06G001700.2 Cla06g00155 155
6 1743252 1751268 - ClCG06G001720.2 Cla06g00156 156
7 25038850 25042577 - MELO3C017817.2.1 Cme07g01994 1994
11 30691737 30692270 + MELO3C022358.2.1 Cme11g02369 2369
11 30698860 30703562 + MELO3C022359.2.1 Cme11g02370 2370
11 1348214 1352492 - PI0027306.1 Cmetu11g1074 1074
11 1358404 1361393 - PI0016568.1 Cmetu11g1306 1306
6 1655688 1661675 - CmPI595203_06g001610.1 Cmu06g0161 161
6 1669394 1669942 - CmPI595203_06g001620.1 Cmu06g0162 162
13 1878840 1883317 - Conep13aG0027900.1 Cone13ag0268 268
14 3232322 3234505 + Conep14aG0065700.1 Cone14ag0643 643
14 3235123 3237880 - Conep14aG0065800.1 Cone14ag0644 644
14 3238788 3240551 - Conep14aG0065900.1 Cone14ag0645 645
14 3241739 3244048 - Conep14aG0066000.1 Cone14ag0646 646
15 3429770 3431974 + Conep15aG0066600.1 Cone15ag0653 653
15 3432657 3435439 - Conep15aG0066700.1 Cone15ag0654 654
15 3436316 3437802 - Conep15aG0066800.1 Cone15ag0655 655
19 1667868 1672361 - Conep19aG0025900.1 Cone19ag0252 252
3 9623005 9626179 + Cp4.1LG03g13350.1 Cpe03g01174 1174
17 7266026 7270235 + Cp4.1LG17g09500.1 Cpe17g00946 946
6 2757687 2763630 - CrPI670011_06g009370.1 Cre06g0937 937
6 2771490 2774392 - CrPI670011_06g009380.1 Cre06g0938 938
4 1314688 1317941 + CsaV3_4G002200.1 Csa04g00220 220
3 65457065 65457592 + Hsped.03g11760.1 Hepe03g1176 1176
3 65502343 65507267 + Hsped.03g11770.1 Hepe03g1177 1177
9 26473043 26474152 + Lsi09G017700.1 Lsi09g01770 1770
9 26480869 26487461 + Lsi09G017710.1 Lsi09g01771 1771
9 3089837 3091074 + Sed0001349.1 Sed09g0340 340
9 3102212 3107615 + Sed0005763.2 Sed09g0342 342
6 19031439 19035082 - Tan0021539.1 Tan06g1436 1436
6 19171204 19173038 - Tan0021301.1 Tan06g1437 1437
1 22567822 22570236 + Vvi1g1351 Vvi1g1351 1351
1 22579760 22585456 + Vvi1g1352 Vvi1g1352 1352
1 22586177 22593857 - Vvi1g1353 Vvi1g1353 1353
1 22596662 22602230 + Vvi1g1354 Vvi1g1354 1354
1 22603168 22607807 + Vvi1g1355 Vvi1g1355 1355
1 22609280 22613729 - Vvi1g1356 Vvi1g1356 1356
1 22621560 22626108 + Vvi1g1357 Vvi1g1357 1357
1 22628855 22634048 + Vvi1g1358 Vvi1g1358 1358
1 22634727 22637919 + Vvi1g1359 Vvi1g1359 1359
1 22640305 22644443 - Vvi1g1360 Vvi1g1360 1360
       

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