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
Vvi17g76 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g77 . . . . . . . . Cmo13g00852 Cmo18g00231 . . . . . . . . . . . . . . . . . . . . . . Cone16ag0003 . . Lsi02g00519 Csa01g00981 Chy12g01151 Cme12g01572 . . . Bda14g01347 . Bpe15g00229 . . . . . Cma13g00821 Cma18g00304 . . Cpe09g00950 . Bhi08g01521 Tan05g2995 Cmetu12g0843 Lac10g0601 . . . Cla03g00370 Cam03g0390 Cec03g0376 Cco03g0391 Clacu03g0389 Cmu03g0994 Cre03g0686 . . . .
Vvi17g78 . . . . . . . . Cmo13g00851 Cmo18g00230 . . . . . Cpe20g00296 . . . . . . . . . . . . . . . . . . . Lsi02g00518 Csa01g00980 Chy12g01152 Cme12g01573 . . . . . . Bma03g01242 . Sed08g2421 . . Cma13g00820 Cma18g00306 Car13g00664 Car18g00241 . . Bhi08g01520 Tan05g2993 Cmetu12g1667 Lac10g0600 . . . . . . . . . . . . . .
Vvi17g79 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g80 . . . . . Bpe13g00195 . . . . Cma10g00049 Cma11g00023 Car10g00038 . Sed08g0020 . . Bhi02g00663 Tan09g2392 Cmetu02g1141 . . . . Cla06g01756 Cam06g1948 Cec06g1997 Cco06g2003 Clacu06g1905 Cmu06g1845 Cre06g2659 . Cone16ag0005 . . . . . . . . . Bda14g01350 . Bpe15g00227 Bma03g01244 . . Cmo10g00044 . . . . . . Cpe18g00917 . . . . . . . . . . . . . . Lsi06g01655 Csa01g00041 Chy02g02677 Cme02g02081
Vvi17g81 . Blo16g00278 . . . . Bma06g00270 . Cmo13g00849 . . . . . . . . . . . . . . . . . . . . . . . Cone16ag0006 . . Lsi02g00516 Csa01g00979 . . . . . . . . . . . . . Cma13g00819 . Car13g00663 . . . . . . . . . . Cla03g00368 Cam03g0387 Cec03g0373 Cco03g0388 Clacu03g0386 Cmu03g0991 Cre03g0683 . . . .
Vvi17g82 . . . . . . . . . . . . . . . Cpe20g00297 . . . . . . . . . . . . . . . . . . . . . Chy12g01154 Cme12g01576 . . Bda11g01589 . . . . . Sed08g2423 . . . . . . . . Bhi08g01516 Tan05g2990 Cmetu12g0820 Lac10g0598 Hepe07g2122 . . . . . . . . . . . . .
Vvi17g83 . Blo16g00277 . . . . Bma06g00269 . Cmo13g00848 Cmo18g00228 Cma10g00050 Cma11g00024 Car10g00039 Car11g00024 Sed08g0021 Cpe20g00298 Cpe04g01624 Bhi02g00667 Tan09g2388 Cmetu02g1739 . Hepe09g0037 . . Cla06g01754 Cam06g1946 Cec06g1996 Cco06g2001 Clacu06g1903 Cmu06g1843 Cre06g2656 . Cone16ag0007 Cone13ag0233 Cone19ag0219 Lsi02g00515 Csa01g00978 Chy12g01155 Cme12g01577 . . Bda11g01590 Bda14g01351 . Bpe15g00226 Bma03g01247 . Sed08g2424 . Cmo11g00025 Cma13g00818 Cma18g00308 Car13g00662 Car18g00239 Cpe09g00951 Cpe18g00916 Bhi08g01515 Tan05g2989 Cmetu12g1119 Lac10g0597 Hepe07g2121 . . Cla03g00367 Cam03g0386 Cec03g0372 Cco03g0387 Clacu03g0385 Cmu03g0990 Cre03g0682 Lsi06g01653 Csa01g00043 Chy02g02675 Cme02g02079
Vvi17g84 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g85 . . . . . . . . . . . . . . . . . Bhi02g00523 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 49385243 49388150 + Bda008467.1 Bda11g01589 1589
11 49396673 49398034 - Bda008468.1 Bda11g01590 1590
14 15669825 15671218 - Bda011042.1 Bda14g01347 1347
14 15737290 15738078 - Bda011046.1 Bda14g01350 1350
14 15763415 15764901 - Bda011047.1 Bda14g01351 1351
2 10022921 10028253 - XM_039023067.1 Bhi02g00523 523
2 12779213 12780438 - XM_039023542.1 Bhi02g00663 663
2 12879321 12881508 - XM_039022684.1 Bhi02g00667 667
8 43574929 43576907 + XM_039040132.1 Bhi08g01515 1515
8 43591937 43594223 - XM_039039566.1 Bhi08g01516 1516
8 43634016 43636734 + XM_039039465.1 Bhi08g01520 1520
8 43638211 43648309 + XM_039039965.1 Bhi08g01521 1521
16 6586860 6590348 + BLOR07525 Blo16g00277 277
16 6615216 6617688 - BLOR07526 Blo16g00278 278
3 20521796 20530930 - Bma017697.1 Bma03g01242 1242
3 20534865 20535656 - Bma017699.1 Bma03g01244 1244
3 20641015 20642502 - Bma017707.1 Bma03g01247 1247
6 3716494 3717840 + Bma022902.1 Bma06g00269 269
6 3730808 3733455 - Bma022903.1 Bma06g00270 270
13 9903884 9922744 - Bpe006316.2 Bpe13g00195 195
15 13398686 13400188 + Bpe001161.2 Bpe15g00226 226
15 13425195 13425841 + Bpe001162.2 Bpe15g00227 227
15 13447314 13448694 + Bpe001164.2 Bpe15g00229 229
3 4952772 4954272 + CaPI482276_03g003860.1 Cam03g0386 386
3 4966156 4969283 - CaPI482276_03g003870.1 Cam03g0387 387
3 4992690 4995105 + CaPI482276_03g003900.1 Cam03g0390 390
6 30362543 30364076 + CaPI482276_06g019460.1 Cam06g1946 1946
6 30371765 30372715 + CaPI482276_06g019480.1 Cam06g1948 1948
10 167686 168814 - Carg10270-RA Car10g00038 38
10 169491 171149 - Carg10271-RA Car10g00039 39
11 108102 109240 - Carg24544-RA Car11g00024 24
13 8126036 8127745 + Carg07612-RA Car13g00662 662
13 8130290 8132812 - Carg07613-RA Car13g00663 663
13 8134396 8140616 + Carg07614-RA Car13g00664 664
18 1370932 1372674 + Carg06806-RA Car18g00239 239
18 1380779 1386241 + Carg06808-RA Car18g00241 241
3 4180736 4182213 + CcPI632755_03g003870.1 Cco03g0387 387
3 4195800 4198949 - CcPI632755_03g003880.1 Cco03g0388 388
3 4221561 4223958 + CcPI632755_03g003910.1 Cco03g0391 391
6 30106086 30107604 + CcPI632755_06g020010.1 Cco06g2001 2001
6 30115314 30116268 + CcPI632755_06g020030.1 Cco06g2003 2003
3 4130247 4131725 + CePI673135_03g003720.1 Cec03g0372 372
3 4144236 4147368 - CePI673135_03g003730.1 Cec03g0373 373
3 4170328 4172796 + CePI673135_03g003760.1 Cec03g0376 376
6 33187180 33193416 + CePI673135_06g019960.1 Cec06g1996 1996
6 33196368 33197320 + CePI673135_06g019970.1 Cec06g1997 1997
2 29700986 29707048 + Chy2G049420.1 Chy02g02675 2675
2 29713269 29714003 + Chy2G049440.1 Chy02g02677 2677
12 16452544 16457552 - Chy12G217510.1 Chy12g01151 1151
12 16458561 16460024 - Chy12G217520.1 Chy12g01152 1152
12 16468776 16470694 + Chy12G217540.1 Chy12g01154 1154
12 16478499 16479789 - Chy12G217550.1 Chy12g01155 1155
3 4269092 4270578 + ClG42_03g0038500.10 Clacu03g0385 385
3 4282601 4285682 - ClG42_03g0038600.10 Clacu03g0386 386
3 4309056 4311550 + ClG42_03g0038900.10 Clacu03g0389 389
6 29413278 29414811 + ClG42_06g0190300.10 Clacu06g1903 1903
6 29422500 29423450 + ClG42_06g0190500.10 Clacu06g1905 1905
3 4218961 4220678 + ClCG03G003900.1 Cla03g00367 367
3 4235474 4238555 - ClCG03G003910.2 Cla03g00368 368
3 4246531 4265265 + ClCG03G003930.1 Cla03g00370 370
6 31061136 31072131 + ClCG06G018040.2 Cla06g01754 1754
6 31079390 31080808 + ClCG06G018060.1 Cla06g01756 1756
10 180893 182957 - CmaCh10G000490.1 Cma10g00049 49
10 183213 185105 - CmaCh10G000500.1 Cma10g00050 50
11 109580 112477 - CmaCh11G000230.1 Cma11g00023 23
11 114385 115623 - CmaCh11G000240.1 Cma11g00024 24
13 6882631 6884481 + CmaCh13G008180.1 Cma13g00818 818
13 6886064 6888995 - CmaCh13G008190.1 Cma13g00819 819
13 6889787 6892306 + CmaCh13G008200.1 Cma13g00820 820
13 6893304 6895783 + CmaCh13G008210.1 Cma13g00821 821
18 1625454 1628355 - CmaCh18G003040.1 Cma18g00304 304
18 1629870 1631280 - CmaCh18G003060.1 Cma18g00306 306
18 1639268 1640832 - CmaCh18G003080.1 Cma18g00308 308
2 26699224 26701418 + MELO3C026194.2.1 Cme02g02079 2079
2 26707002 26708715 + MELO3C026192.2.1 Cme02g02081 2081
12 23099694 23101518 - MELO3C002376.2.1 Cme12g01572 1572
12 23102482 23104520 - MELO3C002375.2.1 Cme12g01573 1573
12 23114008 23116318 + MELO3C002373.2.1 Cme12g01576 1576
12 23123894 23126363 - MELO3C002372.2.1 Cme12g01577 1577
2 25024669 25025980 + PI0001403.1 Cmetu02g1141 1141
2 25015992 25018677 + PI0010698.1 Cmetu02g1739 1739
12 3264121 3267179 - PI0021033.1 Cmetu12g0820 820
12 3281677 3283329 + PI0003733.1 Cmetu12g0843 843
12 3253101 3255034 + PI0002393.1 Cmetu12g1119 1119
12 3278532 3279996 + PI0017298.1 Cmetu12g1667 1667
10 212985 216097 - CmoCh10G000440.1 Cmo10g00044 44
11 107890 109286 - CmoCh11G000250.1 Cmo11g00025 25
13 7815071 7816918 + CmoCh13G008480.1 Cmo13g00848 848
13 7819263 7821932 - CmoCh13G008490.1 Cmo13g00849 849
13 7823790 7825846 + CmoCh13G008510.1 Cmo13g00851 851
13 7827057 7831495 + CmoCh13G008520.1 Cmo13g00852 852
18 1491157 1492856 + CmoCh18G002280.1 Cmo18g00228 228
18 1505401 1507816 + CmoCh18G002300.1 Cmo18g00230 230
18 1508349 1511164 + CmoCh18G002310.1 Cmo18g00231 231
3 4483022 4484516 + CmPI595203_03g009900.1 Cmu03g0990 990
3 4496602 4499686 - CmPI595203_03g009910.1 Cmu03g0991 991
3 4523134 4525646 + CmPI595203_03g009940.1 Cmu03g0994 994
6 29316111 29317632 + CmPI595203_06g018430.1 Cmu06g1843 1843
6 29325321 29326273 + CmPI595203_06g018450.1 Cmu06g1845 1845
13 1527152 1528659 + Conep13aG0024300.1 Cone13ag0233 233
16 53465 55100 - Conep16aG0000300.1 Cone16ag0003 3
16 63493 64687 - Conep16aG0000500.1 Cone16ag0005 5
16 65960 67532 + Conep16aG0000600.1 Cone16ag0006 6
16 74119 75374 - Conep16aG0000700.1 Cone16ag0007 7
19 1384542 1386202 + Conep19aG0022500.1 Cone19ag0219 219
4 12587805 12589420 + Cp4.1LG04g16310.1 Cpe04g01624 1624
9 8511387 8517588 - Cp4.1LG09g09540.1 Cpe09g00950 950
9 8524932 8527043 - Cp4.1LG09g09520.1 Cpe09g00951 951
18 8158347 8160349 + Cp4.1LG18g09120.1 Cpe18g00916 916
18 8160632 8162046 + Cp4.1LG18g09130.1 Cpe18g00917 917
20 1657742 1663218 - Cp4.1LG20g02990.1 Cpe20g00296 296
20 1663608 1667830 + Cp4.1LG20g02890.1 Cpe20g00297 297
20 1672651 1674564 - Cp4.1LG20g02970.1 Cpe20g00298 298
3 5693854 5695342 + CrPI670011_03g006820.1 Cre03g0682 682
3 5707907 5711116 - CrPI670011_03g006830.1 Cre03g0683 683
3 5736511 5738931 + CrPI670011_03g006860.1 Cre03g0686 686
6 34147987 34149525 + CrPI670011_06g026560.1 Cre06g2656 2656
6 34157136 34158089 + CrPI670011_06g026590.1 Cre06g2659 2659
1 245887 246608 - CsaV3_1G000410.1 Csa01g00041 41
1 252445 255087 - CsaV3_1G000430.1 Csa01g00043 43
1 6067074 6069903 + CsaV3_1G009780.1 Csa01g00978 978
1 6077196 6079670 - CsaV3_1G009790.1 Csa01g00979 979
1 6082302 6084932 + CsaV3_1G009800.1 Csa01g00980 980
1 6086469 6087947 + CsaV3_1G009810.1 Csa01g00981 981
7 65551951 65553275 + Hsped.07g21210.1 Hepe07g2121 2121
7 65572025 65575410 - Hsped.07g21220.1 Hepe07g2122 2122
9 306223 320927 - Hsped.09g00370.1 Hepe09g0037 37
10 4587426 4588911 + Lag0024642.1 Lac10g0597 597
10 4596166 4597863 - Lag0024643.1 Lac10g0598 598
10 4607190 4608637 + Lag0024645.1 Lac10g0600 600
10 4610213 4611695 + Lag0024646.1 Lac10g0601 601
2 4407000 4408904 + Lsi02G005150.1 Lsi02g00515 515
2 4424845 4431138 - Lsi02G005160.1 Lsi02g00516 516
2 4437983 4442517 + Lsi02G005180.1 Lsi02g00518 518
2 4444267 4446328 + Lsi02G005190.1 Lsi02g00519 519
6 26810108 26812314 + Lsi06G016530.1 Lsi06g01653 1653
6 26819731 26821470 + Lsi06G016550.1 Lsi06g01655 1655
8 68336 71633 - Sed0011464.1 Sed08g0020 20
8 74554 76106 - Sed0024741.1 Sed08g0021 21
8 37290475 37293586 - Sed0005087.1 Sed08g2421 2421
8 37300887 37303517 + Sed0022142.1 Sed08g2423 2423
8 37318621 37320242 - Sed0018440.1 Sed08g2424 2424
5 81841632 81843695 + Tan0009336.2 Tan05g2989 2989
5 81855770 81859271 - Tan0012266.1 Tan05g2990 2990
5 81874371 81875829 + Tan0014184.1 Tan05g2993 2993
5 81888461 81890692 + Tan0011883.1 Tan05g2995 2995
9 73569414 73571563 + Tan0000608.1 Tan09g2388 2388
9 73579261 73580775 + Tan0000039.2 Tan09g2392 2392
17 743852 744203 - Vvi17g76 Vvi17g76 76
17 744204 746348 - Vvi17g77 Vvi17g77 77
17 746759 748821 - Vvi17g78 Vvi17g78 78
17 751112 752057 - Vvi17g79 Vvi17g79 79
17 756549 757963 - Vvi17g80 Vvi17g80 80
17 759889 762017 + Vvi17g81 Vvi17g81 81
17 769341 770298 + Vvi17g82 Vvi17g82 82
17 784244 786076 - Vvi17g83 Vvi17g83 83
17 797554 799083 + Vvi17g84 Vvi17g84 84
17 802903 807282 - Vvi17g85 Vvi17g85 85
       

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