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
Vvi3g436 . . . . . . . . Cmo19g00631 Cmo11g01352 . . . . Sed10g2040 Cpe04g00272 Cpe15g00496 Bhi05g01130 Tan02g0898 Cmetu01g1020 . Hepe02g0577 . . Cla02g00589 Cam02g0621 Cec02g0620 . Clacu02g0619 Cmu02g0614 . Cone12ag1102 . . . . Csa07g00770 . Cme01g00039 Blo04g00491 . . Bda14g00521 Bpe15g00893 . Bma03g00522 . . . . Cma11g01760 Cma19g00612 . Car19g00465 . . . . . . . . . . . . . . . . Lsi11g01018 . Chy01g00045 .
Vvi3g437 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g438 . . . . . . . Bma12g00465 . . . Cma20g00896 . . . . . . . . . . . . . . . . . . . . . . . Lsi10g00291 . Chy11g00446 . . . . . . . . . . . Cmo20g00903 . . . . . . Bhi10g02091 Tan05g1416 Cmetu11g2337 . Hepe08g1077 . . . . . . . . . . . . Cme11g00528
Vvi3g439 . . . . Bpe07g00393 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi10g00292 . . . . . . . . . . . Sed01g0355 . Cmo20g00902 . . . . . . Bhi10g02090 Tan05g1437 Cmetu11g1551 . Hepe08g1091 . . . . . . . . . . . . .
Vvi3g440 . . . Bda08g00850 . . . . . . Cma02g00445 Cma20g00895 . . . . . . . . . . . . . . . . . . . . . Cone3ag1108 . Lsi10g00295 . Chy11g00445 . . . . . . . . . . Cmo02g00454 Cmo20g00901 . . . . . . Bhi10g02089 Tan05g1411 . . Hepe08g1073 . . Cla09g01700 Cam09g1796 Cec09g1859 Cco09g1949 . . Cre01g0711 . . . Cme11g00519
Vvi3g441 Blo02g00823 . . . . . . . . . . Cma20g00894 . . . . . . . . . . . . . . . . . . . . . . . Lsi10g00298 . . . . . . . . . . . Sed01g0344 . . . . . . . . Bhi10g02088 Tan05g1409 Cmetu11g1661 . Hepe08g1072 . . Cla09g01701 Cam09g1797 Cec09g1860 Cco09g1950 . . Cre01g0710 . Csa02g01191 . .
Vvi3g442 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g443 . Blo15g00733 . Bda08g00848 . . . . . . Cma02g00444 Cma20g00893 Car02g00301 Car20g00770 . . . . . . . . . . . . . . . . . . . . . Lsi10g00302 . Chy11g00444 . . . . . . . . . . Cmo02g00453 Cmo20g00900 . . . . . . Bhi10g02087 . . . Hepe08g1071 . . Cla09g01703 Cam09g1798 Cec09g1861 Cco09g1952 . . Cre01g0708 . Csa02g01192 . Cme11g00518
Vvi3g444 Blo02g00821 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi10g00303 . . . . . . . . . . . . . . . . . . . Cpe05g01218 Bhi10g02086 . . . Hepe08g1070 . . Cla09g01704 Cam09g1801 Cec09g1862 Cco09g1954 . . Cre01g0706 . Csa02g01193 . .
Vvi3g445 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 14058656 14061711 + Bda029417.1 Bda08g00848 848
8 14187661 14188620 + Bda029419.1 Bda08g00850 850
14 3764226 3772510 - Bda027266.1 Bda14g00521 521
5 40688002 40708386 - XM_039031685.1 Bhi05g01130 1130
10 52280021 52292536 - XM_039044557.1 Bhi10g02086 2086
10 52280021 52292536 - XM_039044559.1 Bhi10g02087 2087
10 52280973 52292536 - XM_039044558.1 Bhi10g02088 2088
10 52280973 52292536 - XM_039044556.1 Bhi10g02089 2089
10 52289459 52292536 - XM_039044562.1 Bhi10g02090 2090
10 52289479 52292536 - XM_039044560.1 Bhi10g02091 2091
2 29254266 29255180 + BLOR10551 Blo02g00821 821
2 29492198 29493142 + BLOR10553 Blo02g00823 823
4 4062940 4070962 - BLOR13403 Blo04g00491 491
15 24549902 24550819 + BLOR07127 Blo15g00733 733
3 4033539 4041790 - Bma016804.1 Bma03g00522 522
12 12339762 12340202 - Bma007482.1 Bma12g00465 465
7 3605594 3606511 + Bpe021211.1 Bpe07g00393 393
15 18836736 18846228 + Bpe001814.1 Bpe15g00893 893
2 7123383 7138419 + CaPI482276_02g006210.1 Cam02g0621 621
9 32269997 32270953 - CaPI482276_09g017960.1 Cam09g1796 1796
9 32282023 32285106 - CaPI482276_09g017970.1 Cam09g1797 1797
9 32299785 32300717 - CaPI482276_09g017980.1 Cam09g1798 1798
9 32324750 32326035 - CaPI482276_09g018010.1 Cam09g1801 1801
2 2018906 2020465 + Carg24056-RA Car02g00301 301
19 6327132 6339317 - Carg22059-RA Car19g00465 465
20 4538328 4540237 + Carg23613-RA Car20g00770 770
9 33454740 33455696 - CcPI632755_09g019490.1 Cco09g1949 1949
9 33468402 33471815 - CcPI632755_09g019500.1 Cco09g1950 1950
9 33487937 33488863 - CcPI632755_09g019520.1 Cco09g1952 1952
9 33512148 33513431 - CcPI632755_09g019540.1 Cco09g1954 1954
2 6196979 6212088 + CePI673135_02g006200.1 Cec02g0620 620
9 35168140 35169096 - CePI673135_09g018590.1 Cec09g1859 1859
9 35183266 35186305 - CePI673135_09g018600.1 Cec09g1860 1860
9 35198446 35199372 - CePI673135_09g018610.1 Cec09g1861 1861
9 35222761 35224072 - CePI673135_09g018620.1 Cec09g1862 1862
1 323910 334839 + Chy1G000450.1 Chy01g00045 45
11 4374742 4382289 + Chy11G190240.1 Chy11g00444 444
11 4410525 4411481 + Chy11G190250.1 Chy11g00445 445
11 4438312 4439268 + Chy11G190260.1 Chy11g00446 446
2 6114230 6128379 + ClG42_02g0061900.10 Clacu02g0619 619
2 6400506 6415161 + ClCG02G005810.1 Cla02g00589 589
9 34069613 34071157 - ClCG09G017340.2 Cla09g01700 1700
9 34104424 34121836 - ClCG09G017350.2 Cla09g01701 1701
9 34138090 34139016 - ClCG09G017390.1 Cla09g01703 1703
9 34157804 34166930 - ClCG09G017410.1 Cla09g01704 1704
2 2273180 2274097 + CmaCh02G004440.1 Cma02g00444 444
2 2275085 2276053 + CmaCh02G004450.1 Cma02g00445 445
11 11729326 11747147 - CmaCh11G017600.1 Cma11g01760 1760
19 6663413 6675705 - CmaCh19G006120.1 Cma19g00612 612
20 4298988 4300243 + CmaCh20G008930.1 Cma20g00893 893
20 4303143 4304114 + CmaCh20G008940.1 Cma20g00894 894
20 4313622 4314005 + CmaCh20G008950.1 Cma20g00895 895
20 4314016 4314527 + CmaCh20G008960.1 Cma20g00896 896
1 316418 328594 + MELO3C018441.2.1 Cme01g00039 39
11 5340349 5344770 + MELO3C021904.2.1 Cme11g00518 518
11 5380593 5381698 + MELO3C021903.2.1 Cme11g00519 519
11 5468292 5469465 + MELO3C021901.2.1 Cme11g00528 528
1 372530 383767 + PI0009148.1 Cmetu01g1020 1020
11 26220513 26221535 - PI0026620.1 Cmetu11g1551 1551
11 26655470 26659187 - PI0018553.1 Cmetu11g1661 1661
11 26560526 26561482 - PI0010812.1 Cmetu11g2337 2337
2 2368848 2370338 + CmoCh02G004530.1 Cmo02g00453 453
2 2371070 2372038 + CmoCh02G004540.1 Cmo02g00454 454
11 9403378 9420155 + CmoCh11G013520.1 Cmo11g01352 1352
19 6866829 6879406 - CmoCh19G006310.1 Cmo19g00631 631
20 4570846 4572831 + CmoCh20G009000.1 Cmo20g00900 900
20 4574894 4575859 + CmoCh20G009010.1 Cmo20g00901 901
20 4580724 4581683 + CmoCh20G009020.1 Cmo20g00902 902
20 4584176 4585135 + CmoCh20G009030.1 Cmo20g00903 903
2 6021004 6035152 + CmPI595203_02g006140.1 Cmu02g0614 614
3 29659549 29660712 - Conep03aG0161200.1 Cone3ag1108 1108
12 8965718 8973193 - Conep12aG0113800.1 Cone12ag1102 1102
4 3387610 3400687 + Cp4.1LG04g08120.1 Cpe04g00272 272
5 8532978 8536321 - Cp4.1LG05g12180.1 Cpe05g01218 1218
15 5908618 5921061 - Cp4.1LG15g05010.1 Cpe15g00496 496
1 6774166 6774879 + CrPI670011_01g007060.1 Cre01g0706 706
1 6790162 6793234 + CrPI670011_01g007080.1 Cre01g0708 708
1 6803557 6804513 + CrPI670011_01g007100.1 Cre01g0710 710
1 6866492 6867448 + CrPI670011_01g007110.1 Cre01g0711 711
2 11712303 11713867 - CsaV3_2G014070.1 Csa02g01191 1191
2 11722276 11724452 - CsaV3_2G014080.1 Csa02g01192 1192
2 11726236 11732631 - CsaV3_2G014090.1 Csa02g01193 1193
7 5398376 5410474 - CsaV3_7G008690.1 Csa07g00770 770
2 5853557 5866294 + Hsped.02g05770.1 Hepe02g0577 577
8 10425535 10426928 + Hsped.08g10700.1 Hepe08g1070 1070
8 10433906 10434932 - Hsped.08g10710.1 Hepe08g1071 1071
8 10438752 10439759 - Hsped.08g10720.1 Hepe08g1072 1072
8 10452831 10453986 - Hsped.08g10730.1 Hepe08g1073 1073
8 10496888 10498230 + Hsped.08g10770.1 Hepe08g1077 1077
8 10754119 10755357 + Hsped.08g10910.1 Hepe08g1091 1091
10 4723396 4724352 - Lsi10G002910.1 Lsi10g00291 291
10 4755578 4760305 - Lsi10G002920.1 Lsi10g00292 292
10 4791596 4792516 - Lsi10G002950.1 Lsi10g00295 295
10 4798764 4799318 - Lsi10G002980.1 Lsi10g00298 298
10 4830252 4831175 - Lsi10G003020.1 Lsi10g00302 302
10 4844272 4845195 - Lsi10G003030.1 Lsi10g00303 303
11 17250106 17261967 - Lsi11G010180.1 Lsi11g01018 1018
1 2589958 2593553 + Sed0022633.1 Sed01g0344 344
1 2713703 2719963 + Sed0009822.1 Sed01g0355 355
10 36904838 36920820 - Sed0020763.1 Sed10g2040 2040
2 10227056 10240030 + Tan0002940.1 Tan02g0898 898
5 20722164 20723653 + Tan0012108.1 Tan05g1409 1409
5 21010352 21011706 + Tan0022869.1 Tan05g1411 1411
5 22180227 22181604 + Tan0000342.1 Tan05g1416 1416
5 23606327 23607554 + Tan0015118.1 Tan05g1437 1437
3 4216319 4236204 - Vvi3g436 Vvi3g436 436
3 4238892 4239063 + Vvi3g437 Vvi3g437 437
3 4252222 4254466 + Vvi3g438 Vvi3g438 438
3 4254509 4260217 + Vvi3g439 Vvi3g439 439
3 4261887 4262850 + Vvi3g440 Vvi3g440 440
3 4262853 4270341 - Vvi3g441 Vvi3g441 441
3 4270838 4271231 + Vvi3g442 Vvi3g442 442
3 4272692 4276413 - Vvi3g443 Vvi3g443 443
3 4277142 4282861 - Vvi3g444 Vvi3g444 444
3 4282871 4285254 + Vvi3g445 Vvi3g445 445
       

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