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
Vvi1g321 . . . . . . . . . . . . . . . Cpe09g00310 . Bhi07g01313 . . . . . . . . . . . . . . Cone19ag0829 . . . . . Cme10g00247 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g322 . . . . . . . . . . . . . . . . . Bhi07g01312 . . Lac13g0509 . . . . . . . . . . . . . . . Csa05g02624 Chy10g01159 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g323 . . . Bda11g00190 . . . . . . . . . . . Cpe09g00312 . . . . . . . . . . . . . . . . . . . . Csa05g02625 Chy10g01161 Cme10g00246 . . . Bda11g00190 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g324 . . . . . . . . . Cmo18g01020 . . . Car18g00933 . . . Bhi07g01308 . . . . . . Cla05g02288 Cam05g2461 Cec05g2481 Cco05g2524 Clacu05g2456 Cmu05g2317 Cre05g2435 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g325 . . . . . . . . . Cmo18g01019 . Cma18g01010 . Car18g00931 . Cpe09g00313 . Bhi07g01306 . . Lac13g0512 Hepe01g1177 . . Cla05g02287 Cam05g2460 Cec05g2480 . Clacu05g2455 Cmu05g2316 Cre05g2434 Cone13ag0822 Cone19ag0828 . . Lsi04g00242 . . Cme10g00245 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g326 . . . . . Bpe10g01021 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0437 . . . . . . . . . . . . . . . Cmo15g00954 . Cma15g00915 . Car15g00796 Cpe13g00466 Cpe04g01400 . . . . . . . . . . . . . . . . . .
Vvi1g327 Blo01g00501 . Bda01g02071 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0821 Cone19ag0827 . . . . . . . . . . . Bpe02g02262 Bma01g00174 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g328 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0820 Cone19ag0826 . . . . . . . . . . . . . . . . Cmo15g00955 . Cma15g00916 . Car15g00859 Cpe13g00403 . . . . . . . . . . . . . . . . . . .
Vvi1g329 Blo01g00502 . Bda01g02070 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe02g02261 . . . Cmo04g02163 Cmo15g00956 Cma04g02066 Cma15g00917 Car04g02006 Car15g00860 Cpe13g00402 . . . . . . . . . . . . . . . . . . .
Vvi1g330 . . Bda01g02068 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0819 Cone19ag0825 . Cone9ag0452 . . . . . . . . . Bpe02g02259 . . . . Cmo15g00959 . Cma15g00920 . Car15g00862 Cpe13g00400 . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 56877836 56878820 + Bda004394.1 Bda01g02068 2068
1 56883576 56891092 + Bda004396.1 Bda01g02070 2070
1 56893323 56894385 - Bda004397.1 Bda01g02071 2071
11 2421797 2423796 + Bda004907.1 Bda11g00190 190
7 40075649 40076699 + XM_039037132.1 Bhi07g01306 1306
7 40159805 40162684 + XM_039036929.1 Bhi07g01308 1308
7 40159811 40162649 + XM_039036927.1 Bhi07g01312 1312
7 40159814 40162684 + XM_039036925.1 Bhi07g01313 1313
1 5575725 5576774 + BLOR00501 Blo01g00501 501
1 5579828 5582435 - BLOR00502 Blo01g00502 502
1 1631694 1632771 + Bma000339.1 Bma01g00174 174
2 23477407 23478455 + Bpe010076.1 Bpe02g02259 2259
2 23483434 23485166 + Bpe010078.1 Bpe02g02261 2261
2 23486232 23487297 - Bpe010079.1 Bpe02g02262 2262
10 15649727 15650413 + Bpe003327.1 Bpe10g01021 1021
5 32486446 32490962 + CaPI482276_05g024600.1 Cam05g2460 2460
5 32494211 32496154 + CaPI482276_05g024610.1 Cam05g2461 2461
4 15691950 15695813 - Carg28089-RA Car04g02006 2006
15 4524480 4527747 + Carg01359-RA Car15g00796 796
15 4995439 5008598 - Carg26886-RA Car15g00859 859
15 5026030 5030086 - Carg24934-RA Car15g00860 860
15 5054941 5056419 + Carg24932-RA Car15g00862 862
18 10034889 10037745 + Carg19057-RA Car18g00931 931
18 10040475 10043365 + Carg19059-RA Car18g00933 933
5 33555588 33565276 + CcPI632755_05g025240.1 Cco05g2524 2524
5 35888978 35896260 + CePI673135_05g024800.1 Cec05g2480 2480
5 35899930 35901874 + CePI673135_05g024810.1 Cec05g2481 2481
10 16465795 16466575 - Chy10G183530.1 Chy10g01159 1159
10 16467587 16475150 - Chy10G183550.1 Chy10g01161 1161
5 32698263 32702742 + ClG42_05g0245500.10 Clacu05g2455 2455
5 32705984 32707963 + ClG42_05g0245600.10 Clacu05g2456 2456
5 34491327 34495764 + ClCG05G022600.2 Cla05g02287 2287
5 34499008 34500165 + ClCG05G022610.2 Cla05g02288 2288
4 13864585 13868434 - CmaCh04G020660.1 Cma04g02066 2066
15 4738386 4740362 - CmaCh15G009150.1 Cma15g00915 915
15 4743571 4756254 - CmaCh15G009160.1 Cma15g00916 916
15 4778408 4782896 - CmaCh15G009170.1 Cma15g00917 917
15 4804219 4806184 + CmaCh15G009200.1 Cma15g00920 920
18 8461548 8473468 + CmaCh18G010100.1 Cma18g01010 1010
10 1618081 1620474 + MELO3C012260.2.1 Cme10g00245 245
10 1621625 1622807 + MELO3C012259.2.1 Cme10g00246 246
10 1623290 1627069 + MELO3C012258.2.1 Cme10g00247 247
4 15515150 15519011 - CmoCh04G021630.1 Cmo04g02163 2163
15 4914492 4917036 - CmoCh15G009540.1 Cmo15g00954 954
15 4919312 4932400 - CmoCh15G009550.1 Cmo15g00955 955
15 4947591 4951982 - CmoCh15G009560.1 Cmo15g00956 956
15 4979790 4982739 + CmoCh15G009590.1 Cmo15g00959 959
18 11019043 11026804 + CmoCh18G010190.1 Cmo18g01019 1019
18 11027572 11032458 + CmoCh18G010200.1 Cmo18g01020 1020
5 32436703 32441204 + CmPI595203_05g023160.1 Cmu05g2316 2316
5 32444431 32446410 + CmPI595203_05g023170.1 Cmu05g2317 2317
6 2134965 2136484 + Conep06aG0044700.1 Cone6ag0437 437
9 2108300 2110344 + Conep09aG0046200.1 Cone9ag0452 452
13 7493077 7494813 + Conep13aG0084500.1 Cone13ag0819 819
13 7495351 7501429 + Conep13aG0084600.1 Cone13ag0820 820
13 7502174 7503390 - Conep13aG0084700.1 Cone13ag0821 821
13 7506960 7508275 + Conep13aG0084800.1 Cone13ag0822 822
19 6544300 6545444 + Conep19aG0084800.1 Cone19ag0825 825
19 6546525 6552376 + Conep19aG0084900.1 Cone19ag0826 826
19 6553864 6555136 - Conep19aG0085000.1 Cone19ag0827 827
19 6559747 6561387 + Conep19aG0085100.1 Cone19ag0828 828
19 6562336 6563348 + Conep19aG0085200.1 Cone19ag0829 829
4 11301856 11303413 + Cp4.1LG04g13990.1 Cpe04g01400 1400
9 1836326 1841542 - Cp4.1LG09g03120.1 Cpe09g00310 310
9 1841944 1843052 - Cp4.1LG09g03170.1 Cpe09g00312 312
9 1844255 1850446 - Cp4.1LG09g03160.1 Cpe09g00313 313
13 4358769 4360659 - Cp4.1LG13g06740.1 Cpe13g00400 400
13 4387505 4391856 + Cp4.1LG13g06820.1 Cpe13g00402 402
13 4400254 4413356 + Cp4.1LG13g06840.1 Cpe13g00403 403
13 4893153 4897199 - Cp4.1LG13g06110.1 Cpe13g00466 466
5 35761375 35765940 + CrPI670011_05g024340.1 Cre05g2434 2434
5 35769232 35771179 + CrPI670011_05g024350.1 Cre05g2435 2435
5 27382048 27383070 - CsaV3_5G034430.1 Csa05g02624 2624
5 27383770 27390989 - CsaV3_5G034440.1 Csa05g02625 2625
1 76933040 76935971 + Hsped.01g11770.1 Hepe01g1177 1177
13 3726226 3733737 - Lag0040305.1 Lac13g0509 509
13 3754288 3755289 - Lag0040308.1 Lac13g0512 512
4 2467457 2475202 + Lsi04G002420.1 Lsi04g00242 242
1 3332312 3333709 - Vvi1g321 Vvi1g321 321
1 3338924 3340709 - Vvi1g322 Vvi1g322 322
1 3341191 3354024 - Vvi1g323 Vvi1g323 323
1 3356427 3358218 - Vvi1g324 Vvi1g324 324
1 3358783 3365292 - Vvi1g325 Vvi1g325 325
1 3368551 3370256 - Vvi1g326 Vvi1g326 326
1 3375070 3376413 + Vvi1g327 Vvi1g327 327
1 3379862 3395733 - Vvi1g328 Vvi1g328 328
1 3396141 3407109 - Vvi1g329 Vvi1g329 329
1 3407114 3417751 - Vvi1g330 Vvi1g330 330
       

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