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
Vvi16g954 . . . . . . . . Cmo16g00016 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma16g00014 . Car16g00013 . . . . . . . . . . . . . . . . . . . . .
Vvi16g955 . . Bda05g00145 . . . Bma10g01323 . . Cmo18g01376 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo07g00311 . . . . . . . . . . . Cma18g01342 . . . . . . . . . . . . . . . . . . . . . .
Vvi16g956 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo07g00312 . . . . . . . . . . . . . Car18g01255 Cpe09g00009 . . . . . . . . . . . . . . . . . . .
Vvi16g957 . . . . . . . Bma14g02030 Cmo16g00018 . . . . . . . . . . . . . . . . . . . . . . Cone1ag1024 Cone5ag0731 . . . . . . . Blo09g00001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g958 . . Bda05g00144 . . . Bma10g01322 . Cmo16g00019 . . . . . . . Cpe14g00015 . . . . . . . . . . . . . . Cone1ag1023 Cone5ag0730 . . . . . . Blo07g00313 . . . . . . . . . . Cma16g00016 . Car16g00016 . . . . . . . . . . . . . . . . . . . . .
Vvi16g959 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g960 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g961 . . Bda05g00143 Bda07g01959 Bpe03g00223 . Bma10g01321 Bma14g02030 . . . Cma15g00995 Car02g00951 . . Cpe05g00576 . . . . . . . . Cla01g00007 Cam01g0007 Cec01g0006 Cco01g0008 Clacu01g0008 Cmu01g0008 Cre09g2497 Cone1ag1021 Cone5ag0728 . . . Csa05g00009 Chy09g01471 . Blo07g00314 . . . . . . . . Cmo02g01182 Cmo15g01055 . . . . . Cpe13g00339 Bhi12g00702 . . . Hepe06g0835 . . . . . . . . . . . . Cme09g02020
Vvi16g962 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g963 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 6231346 6231978 + Bda020769.1 Bda05g00143 143
5 6232726 6233655 - Bda020770.1 Bda05g00144 144
5 6234137 6235685 - Bda020771.1 Bda05g00145 145
7 36961945 36965549 + Bda028938.2 Bda07g01959 1959
12 20438060 20443227 + XM_039018864.1 Bhi12g00702 702
7 3975906 3977875 + BLOR18243 Blo07g00311 311
7 3982542 3984197 + BLOR18244 Blo07g00312 312
7 3984604 3985608 + BLOR18245 Blo07g00313 313
7 3986264 3986896 - BLOR18246 Blo07g00314 314
9 15981 29340 - BLOR20916 Blo09g00001 1
10 46839282 46839914 + Bma005437.1 Bma10g01321 1321
10 46840681 46841688 - Bma005438.1 Bma10g01322 1322
10 46866691 46868378 - Bma005439.1 Bma10g01323 1323
14 43603874 43606213 + Bma012838.1 Bma14g02030 2030
3 2925854 2926486 - Bpe012078.1 Bpe03g00223 223
1 546702 547337 - CaPI482276_01g000070.1 Cam01g0007 7
2 6706772 6711192 + Carg13990-RA Car02g00951 951
16 193228 194246 - Carg15032-RA Car16g00013 13
16 200732 201751 + Carg15035-RA Car16g00016 16
18 11913618 11915808 - Carg20314-RA Car18g01255 1255
1 57922 58557 - CcPI632755_01g000080.1 Cco01g0008 8
1 78507 79142 - CePI673135_01g000060.1 Cec01g0006 6
9 16140996 16141634 - Chy9G171870.1 Chy09g01471 1471
1 149001 149636 - ClG42_01g0000800.10 Clacu01g0008 8
1 65047 65682 - ClCG01G000070.1 Cla01g00007 7
15 5988212 6001662 - CmaCh15G009950.1 Cma15g00995 995
16 85013 85784 - CmaCh16G000140.1 Cma16g00014 14
16 92428 100881 + CmaCh16G000160.1 Cma16g00016 16
18 10209866 10212157 - CmaCh18G013420.1 Cma18g01342 1342
9 23888243 23889178 - MELO3C005920.2.1 Cme09g02020 2020
2 7085038 7091096 + CmoCh02G011820.1 Cmo02g01182 1182
15 6845235 6850248 - CmoCh15G010550.1 Cmo15g01055 1055
16 99282 100177 - CmoCh16G000160.1 Cmo16g00016 16
16 101453 104373 - CmoCh16G000180.1 Cmo16g00018 18
16 107077 108096 + CmoCh16G000190.1 Cmo16g00019 19
18 12845400 12847758 - CmoCh18G013760.1 Cmo18g01376 1376
1 93976 94611 - CmPI595203_01g000080.1 Cmu01g0008 8
1 55118294 55122107 + Conep01aG0106900.1 Cone1ag1021 1021
1 55126303 55127737 - Conep01aG0107100.1 Cone1ag1023 1023
1 55132884 55137105 + Conep01aG0107200.1 Cone1ag1024 1024
5 3135786 3139743 + Conep05aG0075300.1 Cone5ag0728 728
5 3143475 3145487 - Conep05aG0075500.1 Cone5ag0730 730
5 3151061 3154523 + Conep05aG0075600.1 Cone5ag0731 731
5 3487535 3496211 - Cp4.1LG05g05750.1 Cpe05g00576 576
9 41343 43723 + Cp4.1LG09g00040.1 Cpe09g00009 9
13 3053370 3059278 + Cp4.1LG13g03380.1 Cpe13g00339 339
14 91558 92577 + Cp4.1LG14g07030.1 Cpe14g00015 15
9 44227828 44228463 + CrPI670011_09g024970.1 Cre09g2497 2497
5 54545 59025 + CsaV3_5G000090.1 Csa05g00009 9
6 55125390 55129213 + Hsped.06g08350.1 Hepe06g0835 835
16 21159329 21160238 - Vvi16g954 Vvi16g954 954
16 21165377 21168368 + Vvi16g955 Vvi16g955 955
16 21175294 21178118 + Vvi16g956 Vvi16g956 956
16 21183001 21188853 - Vvi16g957 Vvi16g957 957
16 21201380 21203927 + Vvi16g958 Vvi16g958 958
16 21215730 21223306 - Vvi16g959 Vvi16g959 959
16 21223311 21223523 + Vvi16g960 Vvi16g960 960
16 21228110 21238026 - Vvi16g961 Vvi16g961 961
16 21243054 21243315 - Vvi16g962 Vvi16g962 962
16 21243319 21244892 + Vvi16g963 Vvi16g963 963
       

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