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
Vvi2g22 . . . . . . . Bma14g00603 . . Cma02g01433 Cma15g01243 Car02g01202 Car15g01121 . . Cpe05g00353 . . . . . . . . . . . . . . Cone8ag0286 Cone12ag0291 . . . Csa05g00259 Chy09g01248 . . . . . . Bpe11g00664 . . . Cmo02g01468 Cmo15g01309 . . . . . Cpe13g00141 Bhi12g00292 . . Lac11g2066 Hepe06g1523 . . Cla01g00244 Cam01g0248 Cec01g0241 Cco01g0254 Clacu01g0246 Cmu01g0236 Cre09g2272 Lsi09g00234 . . Cme09g01783
Vvi2g23 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g24 . . . . . . . . . . Cma02g01432 . Car02g01200 . . . Cpe05g00354 . . . . . . . . . . . . . . Cone8ag0285 . . . . Csa05g00257 Chy09g01250 . . . . . . . . . . Cmo02g01466 . . . . . . . Bhi12g00293 . . Lac11g2064 Hepe06g1522 . Lcy12g1626 Cla01g00242 Cam01g0247 Cec01g0240 Cco01g0253 Clacu01g0245 Cmu01g0235 . Lsi09g00233 . . Cme09g01785
Vvi2g25 . . . . . . . Bma14g00602 . . Cma02g01431 Cma15g01244 Car02g01199 Car15g01122 . . Cpe05g00355 . . . . . . . . . . . . . . Cone8ag0284 Cone12ag0290 Cone6ag0798 Cone9ag0798 . Csa05g00256 Chy09g01251 . . . . . . Bpe11g00665 . . . Cmo02g01465 Cmo15g01310 . . . . . Cpe13g00140 Bhi12g00295 . . . . . . Cla01g00239 Cam01g0245 Cec01g0238 Cco01g0252 Clacu01g0243 Cmu01g0234 Cre09g2275 Lsi09g00232 . . Cme09g01786
Vvi2g26 . . . . . . . . . Cmo16g00655 Cma02g01430 Cma15g01245 Car02g01198 Car15g01123 . Cpe14g00510 Cpe05g00356 . . . . . . . Cla07g00784 Cam07g0843 Cec07g0896 Cco07g0877 Clacu07g0819 Cmu07g0823 Cre07g1179 Cone8ag0283 Cone12ag0289 Cone6ag0799 . . Csa05g00255 Chy09g01252 Cme07g01637 . . . . Bpe08g01495 . . . . Cmo02g01464 Cmo15g01311 . Cma16g00600 . . . Cpe13g00139 Bhi12g00296 . . Lac11g2060 Hepe06g1520 . Lcy12g1624 Cla01g00238 Cam01g0244 Cec01g0237 Cco01g0251 Clacu01g0242 Cmu01g0233 Cre09g2276 Lsi09g00231 Csa04g00588 Chy07g01223 Cme09g01787
Vvi2g27 Blo02g01116 . . Bda08g00510 Bpe05g00653 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0800 . . . . . . . . . . . Bma05g00825 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g28 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g29 . . . . . . . Bma14g00601 . . . Cma15g01247 . Car15g01125 . . . . . . . . . . . . . . . . . . . Cone14ag0059 Cone15ag0063 . Csa05g00252 . . . . Bda07g01901 . . Bpe11g00666 . . . . Cmo15g01313 . . . . . Cpe13g00137 Bhi12g00298 . . . . . Lcy12g1621 Cla01g00235 . Cec01g0233 . . . Cre09g2279 Lsi09g00227 . . Cme09g01790
Vvi2g30 . . . . . . . . . . . . . . . . . . . . . . . . Cla07g00782 Cam07g0839 Cec07g0895 Cco07g0873 Clacu07g0816 Cmu07g0822 Cre07g1176 . . Cone6ag0801 . . . . Cme07g01636 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00589 Chy07g01222 .
Vvi2g31 Blo02g01117 . . Bda08g00507 Bpe05g00655 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma05g00827 . . Cmo02g01097 Cmo15g01129 . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 36392314 36409909 - Bda028874.1 Bda07g01901 1901
8 5143849 5145901 - Bda024959.1 Bda08g00507 507
8 5167068 5168939 - Bda024964.1 Bda08g00510 510
12 8498463 8502259 + XM_039018444.1 Bhi12g00292 292
12 8502786 8505269 - XM_039018446.1 Bhi12g00293 293
12 8561478 8565967 + XM_039018343.1 Bhi12g00295 295
12 8603295 8606441 - XM_039020301.1 Bhi12g00296 296
12 8628042 8631754 - XM_039051225.1 Bhi12g00298 298
2 42333697 42336135 + BLOR10846 Blo02g01116 1116
2 42336941 42354825 + BLOR10847 Blo02g01117 1117
5 45611562 45614000 + Bma021934.1 Bma05g00825 825
5 45652560 45656345 + Bma021936.2 Bma05g00827 827
14 6518582 6523974 + Bma011038.1 Bma14g00601 601
14 6539299 6542135 - Bma011040.1 Bma14g00602 602
14 6554775 6556854 - Bma011041.1 Bma14g00603 603
5 20305326 20307764 + Bpe018068.1 Bpe05g00653 653
5 20316390 20318416 + Bpe018070.1 Bpe05g00655 655
8 15641306 15643482 + Bpe023607.1 Bpe08g01495 1495
11 5097930 5100033 + Bpe004021.1 Bpe11g00664 664
11 5111635 5114449 + Bpe004022.1 Bpe11g00665 665
11 5122226 5123662 - Bpe004023.1 Bpe11g00666 666
1 2737332 2740075 + CaPI482276_01g002440.1 Cam01g0244 244
1 2746669 2749688 - CaPI482276_01g002450.1 Cam01g0245 245
1 2772446 2775536 + CaPI482276_01g002470.1 Cam01g0247 247
1 2777526 2779713 - CaPI482276_01g002480.1 Cam01g0248 248
7 21020303 21030097 + CaPI482276_07g008390.1 Cam07g0839 839
7 21118840 21125619 + CaPI482276_07g008430.1 Cam07g0843 843
2 8151851 8154020 + Carg02550-RA Car02g01198 1198
2 8154919 8157784 - Carg02549-RA Car02g01199 1199
2 8161091 8162463 + Carg02548-RA Car02g01200 1200
2 8163386 8165780 - Carg02546-RA Car02g01202 1202
15 8851318 8853338 + Carg16621-RA Car15g01121 1121
15 8861237 8863457 + Carg16620-RA Car15g01122 1122
15 8865195 8868836 - Carg16619-RA Car15g01123 1123
15 8874636 8876871 - Carg16617-RA Car15g01125 1125
1 2361424 2364160 + CcPI632755_01g002510.1 Cco01g0251 251
1 2370519 2373591 - CcPI632755_01g002520.1 Cco01g0252 252
1 2396672 2399701 + CcPI632755_01g002530.1 Cco01g0253 253
1 2401635 2403833 - CcPI632755_01g002540.1 Cco01g0254 254
7 20246863 20251198 + CcPI632755_07g008730.1 Cco07g0873 873
7 20436485 20443492 + CcPI632755_07g008770.1 Cco07g0877 877
1 2323954 2326990 + CePI673135_01g002330.1 Cec01g0233 233
1 2340417 2343152 + CePI673135_01g002370.1 Cec01g0237 237
1 2349830 2352926 - CePI673135_01g002380.1 Cec01g0238 238
1 2375709 2378809 + CePI673135_01g002400.1 Cec01g0240 240
1 2380725 2382909 - CePI673135_01g002410.1 Cec01g0241 241
7 22161900 22167113 + CePI673135_07g008950.1 Cec07g0895 895
7 22253849 22260696 + CePI673135_07g008960.1 Cec07g0896 896
7 17019859 17020290 + Chy7G140520.1 Chy07g01222 1222
7 17027570 17031320 + Chy7G140530.1 Chy07g01223 1223
9 14538533 14540701 + Chy9G169640.1 Chy09g01248 1248
9 14542682 14544481 - Chy9G169660.1 Chy09g01250 1250
9 14557463 14560299 + Chy9G169670.1 Chy09g01251 1251
9 14562600 14565666 - Chy9G169680.1 Chy09g01252 1252
1 2354236 2356933 + ClG42_01g0024200.10 Clacu01g0242 242
1 2363460 2366496 - ClG42_01g0024300.10 Clacu01g0243 243
1 2389194 2392284 + ClG42_01g0024500.10 Clacu01g0245 245
1 2394271 2396461 - ClG42_01g0024600.10 Clacu01g0246 246
7 20745353 20745837 + ClG42_07g0081600.10 Clacu07g0816 816
7 20828163 20835005 + ClG42_07g0081900.10 Clacu07g0819 819
1 2378718 2386915 + ClCG01G002410.2 Cla01g00235 235
1 2393991 2397901 + ClCG01G002440.1 Cla01g00238 238
1 2404412 2409333 - ClCG01G002450.1 Cla01g00239 239
1 2434756 2437846 + ClCG01G002470.1 Cla01g00242 242
1 2439833 2442023 - ClCG01G002490.1 Cla01g00244 244
7 21869281 21870502 + ClCG07G008200.1 Cla07g00782 782
7 21957369 21964195 + ClCG07G008220.1 Cla07g00784 784
2 8243896 8246382 + CmaCh02G014300.1 Cma02g01430 1430
2 8246912 8250913 - CmaCh02G014310.1 Cma02g01431 1431
2 8253859 8255336 + CmaCh02G014320.1 Cma02g01432 1432
2 8255557 8258808 - CmaCh02G014330.1 Cma02g01433 1433
15 7900517 7903108 + CmaCh15G012430.1 Cma15g01243 1243
15 7909711 7911923 + CmaCh15G012440.1 Cma15g01244 1244
15 7913965 7917047 - CmaCh15G012450.1 Cma15g01245 1245
15 7922649 7924937 - CmaCh15G012470.1 Cma15g01247 1247
16 3101425 3103295 + CmaCh16G006000.1 Cma16g00600 600
7 22121102 22122076 + MELO3C016359.2.1 Cme07g01636 1636
7 22126657 22129389 + MELO3C016360.2.1 Cme07g01637 1637
9 22281746 22285616 + MELO3C005697.2.1 Cme09g01783 1783
9 22286458 22288437 - MELO3C005698.2.1 Cme09g01785 1785
9 22302206 22306415 + MELO3C005699.2.1 Cme09g01786 1786
9 22309126 22312361 - MELO3C005701.2.1 Cme09g01787 1787
9 22323835 22327134 - MELO3C005704.2.1 Cme09g01790 1790
2 6654766 6657837 + CmoCh02G010970.1 Cmo02g01097 1097
2 8603746 8606933 + CmoCh02G014640.1 Cmo02g01464 1464
2 8606548 8610022 - CmoCh02G014650.1 Cmo02g01465 1465
2 8612897 8614386 + CmoCh02G014660.1 Cmo02g01466 1466
2 8615213 8617764 - CmoCh02G014680.1 Cmo02g01468 1468
15 7845877 7847813 - CmoCh15G011290.1 Cmo15g01129 1129
15 8995923 8999196 + CmoCh15G013090.1 Cmo15g01309 1309
15 9005443 9007994 + CmoCh15G013100.1 Cmo15g01310 1310
15 9009345 9013734 - CmoCh15G013110.1 Cmo15g01311 1311
15 9019551 9021806 - CmoCh15G013130.1 Cmo15g01313 1313
16 3235276 3237672 + CmoCh16G006550.1 Cmo16g00655 655
1 2307275 2309972 + CmPI595203_01g002330.1 Cmu01g0233 233
1 2316473 2319545 - CmPI595203_01g002340.1 Cmu01g0234 234
1 2342128 2345198 + CmPI595203_01g002350.1 Cmu01g0235 235
1 2347188 2349375 - CmPI595203_01g002360.1 Cmu01g0236 236
7 20959197 20959681 + CmPI595203_07g008220.1 Cmu07g0822 822
7 21041929 21048766 + CmPI595203_07g008230.1 Cmu07g0823 823
6 4056769 4059649 + Conep06aG0082200.1 Cone6ag0798 798
6 4062711 4065278 - Conep06aG0082300.1 Cone6ag0799 799
6 4067642 4071004 + Conep06aG0082400.1 Cone6ag0800 800
6 4079036 4079695 + Conep06aG0082500.1 Cone6ag0801 801
8 1631346 1634657 + Conep08aG0029800.1 Cone8ag0283 283
8 1635714 1639800 - Conep08aG0029900.1 Cone8ag0284 284
8 1649757 1654770 + Conep08aG0030000.1 Cone8ag0285 285
8 1651543 1654764 - Conep08aG0030100.1 Cone8ag0286 286
9 3829853 3832011 + Conep09aG0081600.1 Cone9ag0798 798
12 1557580 1562967 + Conep12aG0030100.1 Cone12ag0289 289
12 1567141 1570092 - Conep12aG0030200.1 Cone12ag0290 290
12 1578695 1580637 - Conep12aG0030300.1 Cone12ag0291 291
14 340150 341867 + Conep14aG0006100.1 Cone14ag0059 59
15 360134 362416 + Conep15aG0006500.1 Cone15ag0063 63
5 1974990 1979782 + Cp4.1LG05g03180.1 Cpe05g00353 353
5 1976587 1980131 - Cp4.1LG05g03110.1 Cpe05g00354 354
5 1984026 1986329 + Cp4.1LG05g03190.1 Cpe05g00355 355
5 1985697 1989735 - Cp4.1LG05g03160.1 Cpe05g00356 356
13 994536 997442 + Cp4.1LG13g01380.1 Cpe13g00137 137
13 1002694 1006074 + Cp4.1LG13g01420.1 Cpe13g00139 139
13 1007021 1010396 - Cp4.1LG13g01460.1 Cpe13g00140 140
13 1016204 1019190 - Cp4.1LG13g01450.1 Cpe13g00141 141
14 3231452 3232328 + Cp4.1LG14g02200.1 Cpe14g00510 510
7 24282834 24283318 - CrPI670011_07g011760.1 Cre07g1176 1176
7 24525187 24532164 + CrPI670011_07g011790.1 Cre07g1179 1179
9 41939596 41941783 + CrPI670011_09g022720.1 Cre09g2272 2272
9 41969914 41973042 + CrPI670011_09g022750.1 Cre09g2275 2275
9 41979808 41982554 - CrPI670011_09g022760.1 Cre09g2276 2276
9 41993938 41998196 - CrPI670011_09g022790.1 Cre09g2279 2279
4 3870183 3874134 - CsaV3_4G005880.1 Csa04g00588 588
4 3879098 3880212 - CsaV3_4G005890.1 Csa04g00589 589
5 1528968 1532711 + CsaV3_5G002520.1 Csa05g00252 252
5 1543743 1547597 + CsaV3_5G002550.1 Csa05g00255 255
5 1549371 1554061 - CsaV3_5G002560.1 Csa05g00256 256
5 1564694 1566740 + CsaV3_5G002570.1 Csa05g00257 257
5 1568639 1570804 - CsaV3_5G002590.1 Csa05g00259 259
6 65855512 65859319 + Hsped.06g15200.1 Hepe06g1520 1520
6 65900674 65903864 + Hsped.06g15220.1 Hepe06g1522 1522
6 65904576 65908283 - Hsped.06g15230.1 Hepe06g1523 1523
11 36412012 36414535 + Lag0032698.1 Lac11g2060 2060
11 36479677 36481184 + Lag0032702.1 Lac11g2064 2064
11 36483792 36485950 - Lag0032704.1 Lac11g2066 2066
12 36508051 36511668 + Maker00029174 Lcy12g1621 1621
12 36528097 36531414 + Maker00029342 Lcy12g1624 1624
12 36574054 36576039 + Maker00029372 Lcy12g1626 1626
9 2375121 2378233 + Lsi09G002270.1 Lsi09g00227 227
9 2400061 2403577 + Lsi09G002310.1 Lsi09g00231 231
9 2405783 2409877 - Lsi09G002320.1 Lsi09g00232 232
9 2444597 2447409 + Lsi09G002330.1 Lsi09g00233 233
9 2448711 2452354 - Lsi09G002340.1 Lsi09g00234 234
2 303718 306660 + Vvi2g22 Vvi2g22 22
2 308881 315609 + Vvi2g23 Vvi2g23 23
2 317022 321160 - Vvi2g24 Vvi2g24 24
2 330475 334581 + Vvi2g25 Vvi2g25 25
2 343028 346156 - Vvi2g26 Vvi2g26 26
2 349465 353491 + Vvi2g27 Vvi2g27 27
2 357128 358775 - Vvi2g28 Vvi2g28 28
2 359999 362037 - Vvi2g29 Vvi2g29 29
2 371213 372075 + Vvi2g30 Vvi2g30 30
2 377927 380101 + Vvi2g31 Vvi2g31 31
       

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