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
Vvi19g264 . Blo03g01535 . Bda09g00491 . Bpe08g01035 . . . . Cma01g01195 Cma09g00882 Car01g01020 Car09g00800 Sed04g3168 Cpe06g00706 Cpe02g00714 Bhi09g03391 Tan01g4426 Cmetu07g0553 . Hepe01g1368 Mch11g1091 . Cla11g01780 Cam11g1844 Cec11g1865 Cco11g1875 Clacu11g2006 Cmu11g1815 Cre11g2223 Cone6ag0128 Cone9ag0152 . . . Csa04g02365 Chy07g00094 . . . . . . . Bma07g01191 . . Cmo01g01249 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g265 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g266 . . . . . . . . Cmo16g00850 . . . . . . . . . . . . . . . . . . . . . . Cone6ag0126 Cone9ag0151 . . . Csa03g00615 . . . . . . . Bpe01g00410 . . . . . Cma04g00910 . Car04g00855 . Cpe14g00686 . . . . . . . . . . . . . . . Lsi05g00707 . Chy06g01710 .
Vvi19g267 . . . . . . . . . . . . . . Sed04g3164 . . Bhi09g02021 Tan01g4428 Cmetu04g2674 . . Mch11g1092 . . . . . . . . . . . . Lsi04g01303 Csa04g02366 Chy07g00095 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g268 Blo03g00640 . Bda07g00284 . . . . . . . . Cma09g00883 . Car09g00801 . Cpe06g00707 . Bhi09g02020 Tan01g4429 Cmetu04g2876 . Hepe01g1367 Mch11g1093 . . . . . . . . . . . . . . . . . . . . Bpe11g00493 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g269 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g270 . . . . . . . . Cmo16g00851 . . . . . . . . . . . . . . . Cla10g00629 Cam10g0620 Cec10g0650 Cco10g0625 Clacu10g0651 Cmu10g1474 Cre10g0861 . . Cone14ag1077 . . Csa03g00613 . . . . . . . . . . . . . . . . . Cpe14g00687 . . . . . . . . . . . . . . . Lsi05g00704 . Chy06g01711 .
Vvi19g271 Blo03g00639 Blo03g01534 Bda07g00283 Bda09g00490 . Bpe08g01037 . . Cmo16g00852 . Cma01g01194 . Car01g01019 . . . Cpe02g00715 Bhi09g02019 . . . . Mch11g1095 . Cla11g01785 . . . . . . Cone6ag0125 Cone9ag0150 Cone14ag1078 Cone15ag1070 Lsi04g01302 Csa03g00612 . . . . . Bda12g00861 Bpe11g00494 Bpe01g00409 . . . Cmo01g01248 . Cma04g00911 . Car04g00856 . Cpe14g00689 . Bhi11g00760 . . . . . . . . . . . . . Lsi05g00703 . . .
Vvi19g272 . . . . . . . . Cmo16g00853 . . Cma09g00885 Car01g01018 Car09g00802 . Cpe06g00708 Cpe02g00716 Bhi09g02017 . . . . Mch11g1098 . Cla11g01786 . . . . . . Cone6ag0124 Cone9ag0149 Cone14ag1079 Cone15ag1071 Lsi04g01300 Csa03g00609 . . . . . Bda12g00860 . . . . . Cmo01g01247 . Cma04g00913 . Car04g00857 Car16g00807 Cpe14g00690 . Bhi11g00759 . . . . . . . . . . . . . Lsi05g00702 . . .
Vvi19g273 Blo03g00638 . Bda07g00282 . . . . . Cmo16g00855 . . . . . . . . . . . . . . . Cla10g00622 Cam10g0615 Cec10g0644 Cco10g0619 Clacu10g0645 Cmu10g1466 Cre10g0857 Cone6ag0123 Cone9ag0147 Cone14ag1080 . . Csa03g00608 . . . . . . Bpe11g00495 . . . . . . . . . . Cpe14g00692 . . . . . . . . . . . . . . . Lsi05g00700 . Chy06g01715 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 3974069 3977674 + Bda025363.1 Bda07g00282 282
7 3981745 3982918 - Bda025364.1 Bda07g00283 283
7 3985933 3989599 + Bda025365.1 Bda07g00284 284
9 6399884 6401073 - Bda031086.1 Bda09g00490 490
9 6412906 6418158 + Bda031087.2 Bda09g00491 491
12 38872190 38873390 - Bda009385.1 Bda12g00860 860
12 38894972 38896178 - Bda009387.1 Bda12g00861 861
9 56527274 56529311 + XM_039040457.1 Bhi09g02017 2017
9 56646874 56648355 - XM_039041097.1 Bhi09g02019 2019
9 56724862 56733266 + XM_039042579.1 Bhi09g02020 2020
9 56741562 56765621 + XM_039040626.1 Bhi09g02021 2021
9 86283369 86289204 + XM_039044092.1 Bhi09g03391 3391
11 20201937 20203624 - XM_039050340.1 Bhi11g00759 759
11 20284364 20286241 + XM_039049710.1 Bhi11g00760 760
3 27345678 27348588 + BLOR11819 Blo03g00638 638
3 27355385 27356548 - BLOR11820 Blo03g00639 639
3 27381006 27391270 + BLOR11821 Blo03g00640 640
3 42344066 42345251 - BLOR12715 Blo03g01534 1534
3 42349715 42361818 + BLOR12716 Blo03g01535 1535
7 46673486 46678359 - Bma026441.1 Bma07g01191 1191
1 2509309 2510544 - Bpe000395.1 Bpe01g00409 409
1 2514496 2515002 - Bpe000396.1 Bpe01g00410 410
8 12583431 12588485 - Bpe023159.1 Bpe08g01035 1035
8 12599122 12600312 + Bpe023161.1 Bpe08g01037 1037
11 3805016 3808633 - Bpe003864.1 Bpe11g00493 493
11 3811332 3812181 + Bpe003865.1 Bpe11g00494 494
11 3816003 3819140 - Bpe003866.1 Bpe11g00495 495
10 9396854 9399634 + CaPI482276_10g006150.1 Cam10g0615 615
10 9628816 9632084 - CaPI482276_10g006200.1 Cam10g0620 620
11 30980665 30986386 - CaPI482276_11g018440.1 Cam11g1844 1844
1 9703481 9704600 + Carg14682-RA Car01g01018 1018
1 9708265 9709533 - Carg14683-RA Car01g01019 1019
1 9714954 9720992 + Carg14684-RA Car01g01020 1020
4 4949814 4950567 + Carg00030-RA Car04g00855 855
4 4952607 4953978 + Carg00031-RA Car04g00856 856
4 4958711 4962434 + Carg00032-RA Car04g00857 857
9 4836322 4843144 - Carg12754-RA Car09g00800 800
9 4846117 4852011 - Carg12755-RA Car09g00801 801
9 4856049 4857262 - Carg12756-RA Car09g00802 802
16 5309870 5320659 + Carg24063-RA Car16g00807 807
10 8246293 8246696 + CcPI632755_10g006190.1 Cco10g0619 619
10 8537331 8540597 - CcPI632755_10g006250.1 Cco10g0625 625
11 31413222 31418946 - CcPI632755_11g018750.1 Cco11g1875 1875
10 8617793 8618265 + CePI673135_10g006440.1 Cec10g0644 644
10 8932789 8936060 - CePI673135_10g006500.1 Cec10g0650 650
11 32858957 32864687 - CePI673135_11g018650.1 Cec11g1865 1865
6 19807022 19809009 + Chy6G122380.1 Chy06g01710 1710
6 19854977 19864477 + Chy6G122390.1 Chy06g01711 1711
6 19999515 20002411 - Chy6G122430.1 Chy06g01715 1715
7 840950 846346 - Chy7G129240.1 Chy07g00094 94
7 851772 857539 - Chy7G129250.1 Chy07g00095 95
10 8737419 8746439 + ClG42_10g0064500.10 Clacu10g0645 645
10 9003864 9007110 - ClG42_10g0065100.10 Clacu10g0651 651
11 31018138 31023862 - ClG42_11g0200600.10 Clacu11g2006 2006
10 9244472 9248013 + ClCG10G006690.2 Cla10g00622 622
10 9523012 9526258 - ClCG10G006770.1 Cla10g00629 629
11 31400713 31407122 - ClCG11G018250.1 Cla11g01780 1780
11 31503654 31504916 + ClCG11G018280.1 Cla11g01785 1785
11 31527445 31529444 - ClCG11G018290.1 Cla11g01786 1786
1 8666662 8667915 - CmaCh01G011940.1 Cma01g01194 1194
1 8674025 8680191 + CmaCh01G011950.1 Cma01g01195 1195
4 4729153 4729995 + CmaCh04G009100.1 Cma04g00910 910
4 4731268 4733240 + CmaCh04G009110.1 Cma04g00911 911
4 4736437 4738358 + CmaCh04G009130.1 Cma04g00913 913
9 4340783 4347063 - CmaCh09G008820.1 Cma09g00882 882
9 4350170 4355965 - CmaCh09G008830.1 Cma09g00883 883
9 4359823 4361312 - CmaCh09G008850.1 Cma09g00885 885
4 26980435 26998059 + PI0029138.2 Cmetu04g2674 2674
4 26927251 26937141 + PI0017923.1 Cmetu04g2876 2876
7 22173111 22177921 - PI0008132.1 Cmetu07g0553 553
1 10013336 10014468 + CmoCh01G012470.1 Cmo01g01247 1247
1 10019230 10020511 - CmoCh01G012480.1 Cmo01g01248 1248
1 10026086 10031967 + CmoCh01G012490.1 Cmo01g01249 1249
16 4500234 4500861 + CmoCh16G008500.1 Cmo16g00850 850
16 4504237 4506500 + CmoCh16G008510.1 Cmo16g00851 851
16 4511166 4512303 + CmoCh16G008520.1 Cmo16g00852 852
16 4521438 4523204 + CmoCh16G008530.1 Cmo16g00853 853
16 4533927 4537228 + CmoCh16G008550.1 Cmo16g00855 855
10 9318726 9319186 + CmPI595203_10g014660.1 Cmu10g1466 1466
10 9582393 9585635 - CmPI595203_10g014740.1 Cmu10g1474 1474
11 30273627 30279354 - CmPI595203_11g018150.1 Cmu11g1815 1815
6 594908 597247 + Conep06aG0012400.1 Cone6ag0123 123
6 602368 603718 - Conep06aG0012500.1 Cone6ag0124 124
6 610458 611885 - Conep06aG0012600.1 Cone6ag0125 125
6 618878 619463 - Conep06aG0012700.1 Cone6ag0126 126
6 626570 631612 + Conep06aG0012900.1 Cone6ag0128 128
9 646036 648801 + Conep09aG0014900.1 Cone9ag0147 147
9 653173 654527 - Conep09aG0015100.1 Cone9ag0149 149
9 661549 663086 - Conep09aG0015200.1 Cone9ag0150 150
9 667332 668030 - Conep09aG0015300.1 Cone9ag0151 151
9 672480 677337 + Conep09aG0015400.1 Cone9ag0152 152
14 9027083 9029704 + Conep14aG0109800.1 Cone14ag1077 1077
14 9038127 9039559 + Conep14aG0109900.1 Cone14ag1078 1078
14 9048358 9050056 + Conep14aG0110000.1 Cone14ag1079 1079
14 9052524 9054861 - Conep14aG0110100.1 Cone14ag1080 1080
15 8839796 8841176 + Conep15aG0109300.1 Cone15ag1070 1070
15 8854299 8855925 + Conep15aG0109400.1 Cone15ag1071 1071
2 4513077 4519310 - Cp4.1LG02g01600.1 Cpe02g00714 714
2 4524572 4526400 + Cp4.1LG02g01650.1 Cpe02g00715 715
2 4530967 4531557 - Cp4.1LG02g01620.1 Cpe02g00716 716
6 4386889 4393003 - Cp4.1LG06g07170.1 Cpe06g00706 706
6 4395801 4402364 - Cp4.1LG06g07180.1 Cpe06g00707 707
6 4405815 4407294 - Cp4.1LG06g07150.1 Cpe06g00708 708
14 4508505 4508999 + Cp4.1LG14g00280.1 Cpe14g00686 686
14 4512022 4514367 + Cp4.1LG14g00300.1 Cpe14g00687 687
14 4520834 4522542 + Cp4.1LG14g00370.1 Cpe14g00689 689
14 4530718 4532656 + Cp4.1LG14g00360.1 Cpe14g00690 690
14 4543771 4547945 + Cp4.1LG14g00310.1 Cpe14g00692 692
10 9397747 9398207 + CrPI670011_10g008570.1 Cre10g0857 857
10 9668691 9671963 - CrPI670011_10g008610.1 Cre10g0861 861
11 33949576 33955472 - CrPI670011_11g022230.1 Cre11g2223 2223
3 5234231 5238218 + CsaV3_3G006080.1 Csa03g00608 608
3 5243303 5245652 - CsaV3_3G006090.1 Csa03g00609 609
3 5292534 5293999 + CsaV3_3G006120.1 Csa03g00612 612
3 5307037 5310430 - CsaV3_3G006130.1 Csa03g00613 613
3 5343164 5347102 - CsaV3_3G006150.1 Csa03g00615 615
4 24021808 24028883 - CsaV3_4G033910.1 Csa04g02365 2365
4 24032885 24038702 - CsaV3_4G033920.1 Csa04g02366 2366
1 78877419 78886219 + Hsped.01g13670.1 Hepe01g1367 1367
1 78899907 78905684 + Hsped.01g13680.1 Hepe01g1368 1368
4 20550978 20553225 + Lsi04G013000.1 Lsi04g01300 1300
4 20642716 20644782 - Lsi04G013020.1 Lsi04g01302 1302
4 20702644 20719960 + Lsi04G013030.1 Lsi04g01303 1303
5 9328006 9331512 + Lsi05G007000.1 Lsi05g00700 700
5 9357737 9358423 - Lsi05G007020.1 Lsi05g00702 702
5 9412373 9414184 + Lsi05G007030.1 Lsi05g00703 703
5 9436452 9439254 - Lsi05G007040.1 Lsi05g00704 704
5 9496434 9499405 - Lsi05G007070.1 Lsi05g00707 707
11 7605517 7612174 - MC11g0896 Mch11g1091 1091
11 7616578 7624378 - MC11g0897 Mch11g1092 1092
11 7626351 7634492 + MC11g0898 Mch11g1093 1093
11 7645514 7647203 + MC11g0899 Mch11g1095 1095
11 7665499 7670131 - MC11g0902 Mch11g1098 1098
4 42408656 42420572 + Sed0010700.1 Sed04g3164 3164
4 42428062 42434701 + Sed0003515.4 Sed04g3168 3168
1 109411737 109418595 - Tan0001169.2 Tan01g4426 4426
1 109425296 109438919 - Tan0014688.1 Tan01g4428 4428
1 109444251 109461364 - Tan0007609.1 Tan01g4429 4429
19 3339943 3347539 - Vvi19g264 Vvi19g264 264
19 3355216 3356111 + Vvi19g265 Vvi19g265 265
19 3357592 3358448 + Vvi19g266 Vvi19g266 266
19 3368203 3375246 - Vvi19g267 Vvi19g267 267
19 3377436 3381785 - Vvi19g268 Vvi19g268 268
19 3385515 3387819 + Vvi19g269 Vvi19g269 269
19 3404281 3407783 + Vvi19g270 Vvi19g270 270
19 3412513 3414239 + Vvi19g271 Vvi19g271 271
19 3429277 3430978 + Vvi19g272 Vvi19g272 272
19 3436084 3441137 - Vvi19g273 Vvi19g273 273
       

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