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
Vvi19g304 . . . . . . . . . . . . . . . Cpe06g00722 Cpe02g00727 . . . . . . . Cla11g01808 Cam11g1874 Cec11g1897 Cco11g1905 Clacu11g2038 Cmu11g1843 Cre11g2248 . . Cone14ag1092 Cone15ag1103 Lsi04g01276 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g305 . . Bda07g00269 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0109 Cone9ag0129 Cone14ag1094 Cone15ag1104 . . . . . . . . Bpe11g00507 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g306 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g307 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g308 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma14g00165 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g309 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g310 . . . . . . . . Cmo16g00867 . . . . . . . . . . . . . . . Cla10g00601 Cam10g0594 Cec10g0620 Cco10g0596 Clacu10g0623 Cmu10g1434 Cre10g0835 . . Cone14ag1095 . . Csa03g00586 . . . . . . . . . . . . . . . . Car16g00823 Cpe14g00706 . . . . . . . . . . . . . . . Lsi05g00677 . Chy06g01736 .
Vvi19g311 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone7ag0234 Cone4ag0224 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g312 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g313 . . . . . Bpe02g01923 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe01g00389 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 3875520 3875792 + Bda025351.1 Bda07g00269 269
14 2223990 2226179 + Bma010572.1 Bma14g00165 165
1 2417708 2418925 - Bpe000377.1 Bpe01g00389 389
2 21199867 21201064 + Bpe009749.1 Bpe02g01923 1923
11 3919749 3920015 - Bpe003876.1 Bpe11g00507 507
10 9106129 9116537 + CaPI482276_10g005940.1 Cam10g0594 594
11 31297425 31300178 - CaPI482276_11g018740.1 Cam11g1874 1874
16 5413378 5417536 - Carg24079-RA Car16g00823 823
10 7957343 7964019 + CcPI632755_10g005960.1 Cco10g0596 596
11 31755424 31758667 - CcPI632755_11g019050.1 Cco11g1905 1905
10 8307577 8314424 + CePI673135_10g006200.1 Cec10g0620 620
11 33200552 33203246 - CePI673135_11g018970.1 Cec11g1897 1897
6 20206700 20217532 - Chy6G122640.1 Chy06g01736 1736
10 8449789 8456356 + ClG42_10g0062300.10 Clacu10g0623 623
11 31337319 31341650 - ClG42_11g0203800.10 Clacu11g2038 2038
10 8940086 8945678 + ClCG10G006400.2 Cla10g00601 601
11 31742242 31745464 - ClCG11G018560.1 Cla11g01808 1808
16 4621618 4627850 - CmoCh16G008670.1 Cmo16g00867 867
10 8569201 8575775 + CmPI595203_10g014340.1 Cmu10g1434 1434
11 30588825 30591519 - CmPI595203_11g018430.1 Cmu11g1843 1843
4 1023815 1026564 - Conep04aG0023300.1 Cone4ag0224 224
6 535336 535713 + Conep06aG0010900.1 Cone6ag0109 109
7 992943 994750 - Conep07aG0023900.1 Cone7ag0234 234
9 573177 573642 + Conep09aG0012900.1 Cone9ag0129 129
14 9148868 9150718 - Conep14aG0111400.1 Cone14ag1092 1092
14 9160374 9160688 - Conep14aG0111600.1 Cone14ag1094 1094
14 9161407 9164812 - Conep14aG0111700.1 Cone14ag1095 1095
15 9043368 9045314 - Conep15aG0112900.1 Cone15ag1103 1103
15 9048457 9048735 - Conep15aG0113000.1 Cone15ag1104 1104
2 4631576 4634732 - Cp4.1LG02g01500.1 Cpe02g00727 727
6 4497701 4501742 - Cp4.1LG06g07410.1 Cpe06g00722 722
14 4634912 4641182 - Cp4.1LG14g00170.1 Cpe14g00706 706
10 9082751 9092148 + CrPI670011_10g008350.1 Cre10g0835 835
11 34260525 34263234 - CrPI670011_11g022480.1 Cre11g2248 2248
3 5068061 5075238 + CsaV3_3G005860.1 Csa03g00586 586
4 20136103 20139840 + Lsi04G012760.1 Lsi04g01276 1276
5 8971652 8989533 + Lsi05G006770.1 Lsi05g00677 677
19 3850728 3854891 - Vvi19g304 Vvi19g304 304
19 3858391 3858658 + Vvi19g305 Vvi19g305 305
19 3859501 3860403 - Vvi19g306 Vvi19g306 306
19 3860467 3862735 - Vvi19g307 Vvi19g307 307
19 3863615 3864196 - Vvi19g308 Vvi19g308 308
19 3864264 3865832 - Vvi19g309 Vvi19g309 309
19 3867294 3892849 - Vvi19g310 Vvi19g310 310
19 3894330 3896647 - Vvi19g311 Vvi19g311 311
19 3904134 3904689 + Vvi19g312 Vvi19g312 312
19 3913822 3915339 + Vvi19g313 Vvi19g313 313
       

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