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
Vvi17g266 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g267 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g268 . . . . . . . . . . . Cma11g00294 . Car11g00269 Sed08g0380 . Cpe04g01388 Bhi02g00109 Tan09g1859 Cmetu02g1486 . Hepe09g0367 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo11g00299 . . . . . . . . . . . . . . . . . . . . Lsi06g01307 Csa01g00408 Chy02g02336 Cme02g01710
Vvi17g269 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g270 Blo04g00834 . . . . . . . Cmo13g01043 . . . . . . Cpe20g00138 . . . . . . . . . . . . . . . . . . . Lsi02g00215 Csa01g00698 Chy12g01415 Cme12g01849 . . . . . Bpe15g00533 Bma03g00902 . . . . Cma13g01005 . Car13g00840 Car18g00050 Cpe09g01126 . Bhi08g01267 Tan05g2221 . Lac10g0269 Hepe07g2369 . . Cla04g01067 Cam04g1110 Cec01g1624 Cco01g1671 Clacu04g1136 Cmu04g1119 Cre01g1420 . . . .
Vvi17g271 . . . Bda15g00501 Bpe12g00706 . . . Cmo13g01044 . Cma10g00314 . Car10g00297 . . . . Bhi02g00107 . . . Hepe09g0366 . . . . . . . . . Cone2ag0743 . . . Lsi02g00214 Csa01g00697 . Cme12g01850 Blo13g00182 . . . . . . Bma08g00044 Sed01g1749 Cmo10g00337 . Cma13g01006 Cma18g00055 Car13g00841 Car18g00049 . . Bhi08g01265 Tan05g2224 Cmetu12g0059 Lac10g0268 . . . . . . . . . . Lsi06g01308 Csa01g00407 Chy02g02337 Cme02g01711
Vvi17g272 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g273 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g274 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g275 . . . . . . . . . . Cma10g00310 . Car10g00295 Car11g00266 . . Cpe04g01389 . . . . . . . Cla06g01447 Cam06g1600 Cec06g1662 Cco06g1656 Clacu06g1565 Cmu06g1518 Cre06g2329 . Cone16ag0553 Cone13ag0315 . . . . . . . . . . . . . . Cmo10g00335 Cmo11g00297 . . . . . . . . . . . . . . . . . . . . Lsi06g01313 Csa01g00403 Chy02g02346 Cme02g01723
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
15 8113621 8115263 - Bda012331.1 Bda15g00501 501
2 1989185 1992688 - XM_039024052.1 Bhi02g00107 107
2 2017130 2024515 + XM_039023739.1 Bhi02g00109 109
8 38962129 38963969 - XM_039039407.1 Bhi08g01265 1265
8 38964235 38971312 - XM_039038352.1 Bhi08g01267 1267
4 8953881 8958838 - BLOR13746 Blo04g00834 834
13 7081474 7082786 + BLOR05463 Blo13g00182 182
3 8954377 8963770 - Bma017227.1 Bma03g00902 902
8 640396 641839 - Bma027039.1 Bma08g00044 44
12 12620248 12621906 + Bpe005966.1 Bpe12g00706 706
15 16483590 16489470 - Bpe001468.1 Bpe15g00533 533
4 25235458 25242452 + CaPI482276_04g011100.1 Cam04g1110 1110
6 27493223 27495713 + CaPI482276_06g016000.1 Cam06g1600 1600
10 1421983 1424359 - Carg15162-RA Car10g00295 295
10 1437009 1439086 - Carg15164-RA Car10g00297 297
11 1457835 1460133 - Carg09123-RA Car11g00266 266
11 1476101 1483286 + Carg09120-RA Car11g00269 269
13 9049544 9055343 + Carg04832-RA Car13g00840 840
13 9055664 9057250 + Carg04831-RA Car13g00841 841
18 217235 219133 - Carg22737-RA Car18g00049 49
18 219608 226247 - Carg22736-RA Car18g00050 50
1 29452549 29459540 + CcPI632755_01g016710.1 Cco01g1671 1671
6 27163686 27166175 + CcPI632755_06g016560.1 Cco06g1656 1656
1 30889328 30896321 + CePI673135_01g016240.1 Cec01g1624 1624
6 30236843 30239333 + CePI673135_06g016620.1 Cec06g1662 1662
2 27308917 27314323 - Chy2G046030.1 Chy02g02336 2336
2 27315867 27318262 + Chy2G046040.1 Chy02g02337 2337
2 27360315 27362735 + Chy2G046130.1 Chy02g02346 2346
12 18232153 18244816 + Chy12G220150.1 Chy12g01415 1415
4 25609721 25616716 + ClG42_04g0113600.10 Clacu04g1136 1136
6 26550843 26553333 + ClG42_06g0156500.10 Clacu06g1565 1565
4 25834925 25842238 + ClCG04G010850.2 Cla04g01067 1067
6 28054994 28059441 + ClCG06G014590.2 Cla06g01447 1447
10 1407510 1410056 - CmaCh10G003100.1 Cma10g00310 310
10 1425284 1427197 - CmaCh10G003140.1 Cma10g00314 314
11 1455272 1463937 + CmaCh11G002940.1 Cma11g00294 294
13 7757694 7763814 + CmaCh13G010050.1 Cma13g01005 1005
13 7764047 7765810 + CmaCh13G010060.1 Cma13g01006 1006
18 229486 238691 - CmaCh18G000550.1 Cma18g00055 55
2 24149666 24156236 - MELO3C029743.2.1 Cme02g01710 1710
2 24157069 24162182 + MELO3C017333.2.1 Cme02g01711 1711
2 24248287 24250949 + MELO3C017326.2.1 Cme02g01723 1723
12 24805322 24810511 + MELO3C002115.2.1 Cme12g01849 1849
12 24810848 24813198 + MELO3C002114.2.1 Cme12g01850 1850
2 22563394 22569891 - PI0026360.1 Cmetu02g1486 1486
12 1417872 1420101 - PI0026368.1 Cmetu12g0059 59
10 1498289 1500703 - CmoCh10G003350.1 Cmo10g00335 335
10 1513690 1515798 - CmoCh10G003370.1 Cmo10g00337 337
11 1424050 1426352 - CmoCh11G002970.1 Cmo11g00297 297
11 1438182 1445971 + CmoCh11G002990.1 Cmo11g00299 299
13 8751643 8753735 + CmoCh13G010430.1 Cmo13g01043 1043
13 8755688 8757227 + CmoCh13G010440.1 Cmo13g01044 1044
4 25790821 25797816 + CmPI595203_04g011190.1 Cmu04g1119 1119
6 26454065 26456555 + CmPI595203_06g015180.1 Cmu06g1518 1518
2 33182809 33189498 + Conep02aG0175600.1 Cone2ag0743 743
13 2530558 2533235 - Conep13aG0033400.1 Cone13ag0315 315
16 7464492 7466498 + Conep16aG0291400.1 Cone16ag0553 553
4 11226445 11235021 - Cp4.1LG04g13920.1 Cpe04g01388 1388
4 11247395 11249947 + Cp4.1LG04g13760.1 Cpe04g01389 1389
9 9672902 9682352 + Cp4.1LG09g11290.1 Cpe09g01126 1126
20 764870 773828 - Cp4.1LG20g01360.1 Cpe20g00138 138
1 27442324 27449309 + CrPI670011_01g014200.1 Cre01g1420 1420
6 31239816 31243656 + CrPI670011_06g023290.1 Cre06g2329 2329
1 2512675 2515423 - CsaV3_1G004030.1 Csa01g00403 403
1 2551308 2554963 - CsaV3_1G004070.1 Csa01g00407 407
1 2556187 2562245 + CsaV3_1G004080.1 Csa01g00408 408
1 4415106 4416799 - CsaV3_1G006970.1 Csa01g00697 697
1 4417551 4422352 - CsaV3_1G006980.1 Csa01g00698 698
7 68062066 68068423 + Hsped.07g23690.1 Hepe07g2369 2369
9 3231071 3236022 - Hsped.09g03660.1 Hepe09g0366 366
9 3237816 3246284 + Hsped.09g03670.1 Hepe09g0367 367
10 2040695 2042467 - Lag0024313.1 Lac10g0268 268
10 2043266 2050481 - Lag0024314.1 Lac10g0269 269
2 1768875 1777224 - Lsi02G002140.1 Lsi02g00214 214
2 1777983 1785605 - Lsi02G002150.1 Lsi02g00215 215
6 23630470 23637747 - Lsi06G013070.1 Lsi06g01307 1307
6 23639476 23642348 + Lsi06G013080.1 Lsi06g01308 1308
6 23710920 23713330 + Lsi06G013130.1 Lsi06g01313 1313
1 12708472 12710603 - Sed0019630.1 Sed01g1749 1749
8 2294221 2300930 + Sed0009882.1 Sed08g0380 380
5 73194194 73199856 + Tan0012950.3 Tan05g2221 2221
5 73203218 73204328 + Tan0013432.2 Tan05g2224 2224
9 69870193 69879249 - Tan0003890.1 Tan09g1859 1859
17 2900281 2907002 + Vvi17g266 Vvi17g266 266
17 2907491 2909885 + Vvi17g267 Vvi17g267 267
17 2913009 2945668 + Vvi17g268 Vvi17g268 268
17 2947347 3002451 + Vvi17g269 Vvi17g269 269
17 3007994 3020353 + Vvi17g270 Vvi17g270 270
17 3021896 3034010 + Vvi17g271 Vvi17g271 271
17 3045924 3046839 - Vvi17g272 Vvi17g272 272
17 3056030 3059184 - Vvi17g273 Vvi17g273 273
17 3063848 3066558 - Vvi17g274 Vvi17g274 274
17 3071406 3074093 + Vvi17g275 Vvi17g275 275
       

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