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
Vvi2g102 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g103 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g104 . . . . . . . Bma14g00625 . . Cma02g01397 Cma15g01268 Car02g01176 Car15g01143 . . Cpe05g00377 . . . . . . . . . . . . . . Cone8ag0256 . Cone6ag0836 . . Csa05g00217 Chy09g01282 . . Blo19g00360 . . . Bpe11g00643 . . . Cmo02g01432 Cmo15g01338 Cma06g01032 . . . . Cpe13g00120 Bhi12g00163 . . Lac11g2016 Hepe06g1491 . . Cla01g00200 Cam01g0206 Cec01g0200 Cco01g0205 Clacu01g0202 Cmu01g0198 Cre09g2309 Lsi09g00188 . . Cme09g01827
Vvi2g105 . . . . . . . Bma14g00626 . . Cma02g01396 Cma15g01269 Car02g01175 Car15g01144 . . Cpe05g00378 . . . . . . . . . . . . . . Cone8ag0255 Cone12ag0261 . . . Csa05g00216 Chy09g01283 . . . Bda07g00466 . . Bpe11g00642 . . . Cmo02g01431 Cmo15g01339 . . . . . Cpe13g00119 Bhi12g00161 . . Lac11g2015 Hepe06g1490 . Lcy12g1581 Cla01g00199 Cam01g0205 Cec01g0199 Cco01g0204 Clacu01g0201 Cmu01g0197 Cre09g2310 Lsi09g00187 . . Cme09g01828
Vvi2g106 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g107 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g108 . . Bda06g00139 Bda08g00482 . Bpe07g00078 . . . Cmo16g00608 . . . . . Cpe14g00472 . . . . . . . . Cla07g01412 Cam07g1514 Cec07g1610 Cco07g1570 Clacu07g1502 Cmu07g1472 Cre07g1849 . . Cone6ag0838 . . . . Cme07g01580 . . . . . . Bma05g00855 Bma12g00049 . . . . Cma16g00559 . . . . . . . . . . . . . . . . . . . Csa04g00641 Chy07g01168 .
Vvi2g109 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0839 Cone9ag0836 . . . . . . . . . . . . . . . Cma06g01029 . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g110 Blo02g01141 . . . Bpe05g00682 . . . Cmo06g01054 . . . . . . Cpe14g00471 . . . . . . . . Cla07g01414 Cam07g1515 Cec07g1611 Cco07g1571 Clacu07g1503 Cmu07g1473 Cre07g1850 . . Cone6ag0840 Cone9ag0837 . . . Cme07g01579 . . . . . . Bma05g00858 . . . . . Cma16g00555 Car06g00867 . . . . . . . . . . . . . . . . . . Csa04g00643 Chy07g01167 .
Vvi2g111 . . . . . . Bma07g01681 . . . Cma02g01395 Cma15g01270 Car02g01174 Car15g01145 . . Cpe05g00379 . . . . . . . . . . . . . . Cone8ag0253 . . . . Csa05g00214 Chy09g01285 . . . Bda07g00465 Bda09g00018 . Bpe11g00641 . . . Cmo02g01430 Cmo15g01340 . . . . . Cpe13g00118 Bhi12g00160 . . Lac11g2012 Hepe06g1489 . . Cla01g00198 Cam01g0204 Cec01g0198 Cco01g0203 Clacu01g0200 Cmu01g0196 Cre09g2311 Lsi09g00186 . . Cme09g01829
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 2108276 2110402 + Bda023338.1 Bda06g00139 139
7 5933093 5935025 - Bda025566.1 Bda07g00465 465
7 5936957 5942840 + Bda025567.1 Bda07g00466 466
8 4958573 4962571 - Bda024933.1 Bda08g00482 482
9 318283 319340 - Bda030536.4 Bda09g00018 18
12 4714982 4718542 - XM_039019401.1 Bhi12g00160 160
12 4723688 4731317 + XM_039019856.1 Bhi12g00161 161
12 4732318 4735507 - XM_039019859.1 Bhi12g00163 163
2 42830702 42842051 + BLOR10871 Blo02g01141 1141
19 23320066 23322747 + BLOR09703 Blo19g00360 360
5 46089400 46093166 + Bma021972.1 Bma05g00855 855
5 46129323 46130814 + Bma021977.1 Bma05g00858 858
7 52382576 52383730 + Bma026978.2 Bma07g01681 1681
12 1056308 1058706 - Bma006921.1 Bma12g00049 49
14 6750234 6752186 + Bma011067.1 Bma14g00625 625
14 6752897 6758636 - Bma011068.1 Bma14g00626 626
5 20451148 20465435 + Bpe018095.2 Bpe05g00682 682
7 574121 576397 - Bpe020891.1 Bpe07g00078 78
11 4943490 4945405 - Bpe003999.1 Bpe11g00641 641
11 4947340 4953192 + Bpe004000.1 Bpe11g00642 642
11 4953706 4955926 - Bpe024774 Bpe11g00643 643
1 2333995 2336579 - CaPI482276_01g002040.1 Cam01g0204 204
1 2348075 2354106 + CaPI482276_01g002050.1 Cam01g0205 205
1 2356533 2358740 - CaPI482276_01g002060.1 Cam01g0206 206
7 29756228 29761977 + CaPI482276_07g015140.1 Cam07g1514 1514
7 29764420 29768770 + CaPI482276_07g015150.1 Cam07g1515 1515
2 8003679 8007113 - Carg02574-RA Car02g01174 1174
2 8009126 8017291 + Carg02573-RA Car02g01175 1175
2 8016876 8019086 - Carg02572-RA Car02g01176 1176
6 6774265 6778580 - Carg20883-RA Car06g00867 867
15 9011946 9014499 + Carg21267-RA Car15g01143 1143
15 9015030 9022262 - Carg21268-RA Car15g01144 1144
15 9024807 9027048 + Carg21269-RA Car15g01145 1145
1 1925222 1927809 - CcPI632755_01g002030.1 Cco01g0203 203
1 1933291 1939438 + CcPI632755_01g002040.1 Cco01g0204 204
1 1941963 1944170 - CcPI632755_01g002050.1 Cco01g0205 205
7 29700469 29706258 + CcPI632755_07g015700.1 Cco07g1570 1570
7 29709158 29713041 + CcPI632755_07g015710.1 Cco07g1571 1571
1 1917709 1920298 - CePI673135_01g001980.1 Cec01g0198 198
1 1931756 1937851 + CePI673135_01g001990.1 Cec01g0199 199
1 1940394 1943497 - CePI673135_01g002000.1 Cec01g0200 200
7 31615180 31620956 + CePI673135_07g016100.1 Cec07g1610 1610
7 31623149 31627741 + CePI673135_07g016110.1 Cec07g1611 1611
7 16550660 16556209 - Chy7G139970.1 Chy07g01167 1167
7 16559411 16563885 - Chy7G139980.1 Chy07g01168 1168
9 14829160 14831384 + Chy9G169980.1 Chy09g01282 1282
9 14833412 14839233 - Chy9G169990.1 Chy09g01283 1283
9 14843662 14846005 + Chy9G170010.1 Chy09g01285 1285
1 1953394 1955979 - ClG42_01g0020000.10 Clacu01g0200 200
1 1967330 1973463 + ClG42_01g0020100.10 Clacu01g0201 201
1 1975997 1978204 - ClG42_01g0020200.10 Clacu01g0202 202
7 29614070 29619855 + ClG42_07g0150200.10 Clacu07g1502 1502
7 29621443 29626660 + ClG42_07g0150300.10 Clacu07g1503 1503
1 1966098 1969383 - ClCG01G002010.1 Cla01g00198 198
1 1980313 1986446 + ClCG01G002030.2 Cla01g00199 199
1 1988980 1991187 - ClCG01G002040.1 Cla01g00200 200
7 31311068 31314470 + ClCG07G014890.2 Cla07g01412 1412
7 31316259 31337457 + ClCG07G014895.1 Cla07g01414 1414
2 8099946 8103492 - CmaCh02G013950.1 Cma02g01395 1395
2 8104971 8112853 + CmaCh02G013960.1 Cma02g01396 1396
2 8113093 8115303 - CmaCh02G013970.1 Cma02g01397 1397
6 6931565 6937706 + CmaCh06G010290.1 Cma06g01029 1029
6 6945490 6945984 - CmaCh06G010320.1 Cma06g01032 1032
15 8052558 8054815 + CmaCh15G012680.1 Cma15g01268 1268
15 8055396 8062736 - CmaCh15G012690.1 Cma15g01269 1269
15 8064433 8067645 + CmaCh15G012700.1 Cma15g01270 1270
16 2852400 2855997 - CmaCh16G005550.1 Cma16g00555 555
16 2862694 2864572 - CmaCh16G005590.1 Cma16g00559 559
7 21600688 21606271 - MELO3C016307.2.1 Cme07g01579 1579
7 21606326 21614671 - MELO3C016308.2.1 Cme07g01580 1580
9 22567099 22571757 + MELO3C005737.2.1 Cme09g01827 1827
9 22571808 22577761 - MELO3C005738.2.1 Cme09g01828 1828
9 22581638 22584933 + MELO3C005739.2.1 Cme09g01829 1829
2 8445940 8448678 - CmoCh02G014300.1 Cmo02g01430 1430
2 8450975 8458603 + CmoCh02G014310.1 Cmo02g01431 1431
2 8458781 8460991 - CmoCh02G014320.1 Cmo02g01432 1432
6 8195768 8200457 - CmoCh06G010540.1 Cmo06g01054 1054
15 9162567 9164884 + CmoCh15G013380.1 Cmo15g01338 1338
15 9165497 9173980 - CmoCh15G013390.1 Cmo15g01339 1339
15 9176673 9179323 + CmoCh15G013400.1 Cmo15g01340 1340
16 2969648 2971524 - CmoCh16G006080.1 Cmo16g00608 608
1 1906545 1909130 - CmPI595203_01g001960.1 Cmu01g0196 196
1 1920509 1926640 + CmPI595203_01g001970.1 Cmu01g0197 197
1 1929173 1931380 - CmPI595203_01g001980.1 Cmu01g0198 198
7 29865841 29871627 + CmPI595203_07g014720.1 Cmu07g1472 1472
7 29874502 29878442 + CmPI595203_07g014730.1 Cmu07g1473 1473
6 4271358 4274204 + Conep06aG0086200.1 Cone6ag0836 836
6 4280139 4286005 + Conep06aG0086400.1 Cone6ag0838 838
6 4286484 4290474 - Conep06aG0086500.1 Cone6ag0839 839
6 4294414 4297714 + Conep06aG0086600.1 Cone6ag0840 840
8 1446437 1449306 - Conep08aG0026300.1 Cone8ag0253 253
8 1460573 1469137 + Conep08aG0026600.1 Cone8ag0255 255
8 1469350 1471877 - Conep08aG0026700.1 Cone8ag0256 256
9 4096979 4102275 - Conep09aG0085600.1 Cone9ag0836 836
9 4105125 4110181 + Conep09aG0085700.1 Cone9ag0837 837
12 1376878 1382016 + Conep12aG0026700.1 Cone12ag0261 261
5 2137206 2139583 + Cp4.1LG05g03040.1 Cpe05g00377 377
5 2139864 2147174 - Cp4.1LG05g02960.1 Cpe05g00378 378
5 2149689 2153328 + Cp4.1LG05g03030.1 Cpe05g00379 379
13 836274 838897 - Cp4.1LG13g01160.1 Cpe13g00118 118
13 841312 848614 + Cp4.1LG13g01090.1 Cpe13g00119 119
13 849209 851538 - Cp4.1LG13g01200.1 Cpe13g00120 120
14 2962957 2966085 - Cp4.1LG14g02490.1 Cpe14g00471 471
14 2967919 2986102 - Cp4.1LG14g02470.1 Cpe14g00472 472
7 33862359 33868144 + CrPI670011_07g018490.1 Cre07g1849 1849
7 33871038 33874980 + CrPI670011_07g018500.1 Cre07g1850 1850
9 42375200 42377407 + CrPI670011_09g023090.1 Cre09g2309 2309
9 42379716 42385939 - CrPI670011_09g023100.1 Cre09g2310 2310
9 42400654 42403370 + CrPI670011_09g023110.1 Cre09g2311 2311
4 4284549 4289374 + CsaV3_4G006410.1 Csa04g00641 641
4 4300553 4305570 + CsaV3_4G006430.1 Csa04g00643 643
5 1286040 1289455 - CsaV3_5G002140.1 Csa05g00214 214
5 1292519 1298350 + CsaV3_5G002160.1 Csa05g00216 216
5 1299747 1302867 - CsaV3_5G002170.1 Csa05g00217 217
6 65457827 65461340 - Hsped.06g14890.1 Hepe06g1489 1489
6 65478360 65484482 + Hsped.06g14900.1 Hepe06g1490 1490
6 65487371 65489831 - Hsped.06g14910.1 Hepe06g1491 1491
11 35650032 35652748 - Lag0032650.1 Lac11g2012 2012
11 35679605 35685609 + Lag0032653.1 Lac11g2015 2015
11 35689678 35691893 - Lag0032654.1 Lac11g2016 2016
12 35902922 35908347 + Maker00029405 Lcy12g1581 1581
9 1935097 1938804 - Lsi09G001860.1 Lsi09g00186 186
9 1948413 1957806 + Lsi09G001870.1 Lsi09g00187 187
9 1957590 1959844 - Lsi09G001880.1 Lsi09g00188 188
2 1053712 1055575 - Vvi2g102 Vvi2g102 102
2 1058658 1059355 - Vvi2g103 Vvi2g103 103
2 1063752 1066521 + Vvi2g104 Vvi2g104 104
2 1066669 1090707 - Vvi2g105 Vvi2g105 105
2 1094698 1097114 - Vvi2g106 Vvi2g106 106
2 1105168 1112931 + Vvi2g107 Vvi2g107 107
2 1128685 1137285 + Vvi2g108 Vvi2g108 108
2 1137553 1144610 - Vvi2g109 Vvi2g109 109
2 1157540 1162045 + Vvi2g110 Vvi2g110 110
2 1164897 1168589 + Vvi2g111 Vvi2g111 111
       

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