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
Vvi19g294 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g295 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g296 . . . . . . . . . . . . . . . . . . . . . . . . Cla10g00608 Cam10g0601 Cec10g0628 Cco10g0604 Clacu10g0630 . Cre10g0842 . . . . . Csa03g00596 . . . . . . . . . . . . . . . . Car16g00819 . . . . . . . . . . . . . . . . Lsi05g00687 . . .
Vvi19g297 . . Bda07g00274 . . . . . . . . . . . . Cpe06g00718 Cpe02g00725 . . . . . . . Cla11g01804 Cam11g1870 Cec11g1894 Cco11g1900 Clacu11g2033 Cmu11g1838 Cre11g2245 Cone6ag0113 . Cone14ag1087 Cone15ag1098 Lsi04g01280 . . . . . . . Bpe11g00503 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g298 . . Bda07g00273 . . . . . Cmo16g00863 . . . . . . . . . . . . . . . Cla10g00607 Cam10g0600 Cec10g0627 Cco10g0603 Clacu10g0629 . Cre10g0841 Cone6ag0112 Cone9ag0132 . . . Csa03g00595 . . . . . . Bpe11g00504 . . . . . . Cma04g00918 . . . Cpe14g00702 . Bhi11g00737 . . . . . . . . . . . . . Lsi05g00685 . Chy06g01728 .
Vvi19g299 . . . . . . . . Cmo16g00864 . . . . . . . . . . . . . . . Cla10g00606 Cam10g0599 Cec10g0626 Cco10g0602 Clacu10g0628 . Cre10g0840 . . . Cone15ag1099 . Csa03g00594 . . . . . . . . . . . . . Cma04g00919 . Car04g00861 Car16g00820 Cpe14g00703 . . . . . . . . . . . . . . . . . Chy06g01729 .
Vvi19g300 . . . . . . . . . . . . . . . Cpe06g00719 . . . . . . . . Cla11g01805 Cam11g1871 . Cco11g1901 Clacu11g2035 Cmu11g1840 Cre11g2246 . . Cone14ag1088 Cone15ag1100 Lsi04g01279 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g301 . . . . . . . . Cmo16g00865 . . . . . . . . . . . . . . . Cla10g00605 Cam10g0598 Cec10g0625 Cco10g0601 Clacu10g0627 . Cre10g0839 . . Cone14ag1089 Cone15ag1101 . Csa03g00593 . . . . . . . . . . . . . . . . Car16g00821 Cpe14g00704 . . . . . . . . . . . . . . . Lsi05g00683 . Chy06g01730 .
Vvi19g302 . . Bda07g00271 . . . . . . . . . . . . Cpe06g00720 . . . . . . . . Cla11g01806 Cam11g1872 Cec11g1895 Cco11g1903 Clacu11g2036 Cmu11g1841 . Cone6ag0111 . Cone14ag1090 . Lsi04g01278 . . . . . . . Bpe11g00506 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g303 . . Bda07g00270 . . . . . . . . . . . . Cpe06g00721 Cpe02g00726 . . . . . . . Cla11g01807 Cam11g1873 Cec11g1896 Cco11g1904 Clacu11g2037 Cmu11g1842 Cre11g2247 . . Cone14ag1091 Cone15ag1102 Lsi04g01277 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 3876806 3878365 - Bda025352.1 Bda07g00270 270
7 3883239 3883694 + Bda025353.1 Bda07g00271 271
7 3895327 3896394 + Bda033833 Bda07g00273 273
7 3897299 3907324 - Bda025355.3 Bda07g00274 274
11 19236618 19238299 - XM_039050062.1 Bhi11g00737 737
11 3891843 3901836 + Bpe003874.1 Bpe11g00503 503
11 3902721 3903826 - Bpe024759 Bpe11g00504 504
11 3910909 3911361 - Bpe024760 Bpe11g00506 506
10 9172520 9178696 - CaPI482276_10g005980.1 Cam10g0598 598
10 9184760 9192148 - CaPI482276_10g005990.1 Cam10g0599 599
10 9201747 9203438 + CaPI482276_10g006000.1 Cam10g0600 600
10 9205708 9207914 + CaPI482276_10g006010.1 Cam10g0601 601
11 31259887 31270429 + CaPI482276_11g018700.1 Cam11g1870 1870
11 31272763 31280582 - CaPI482276_11g018710.1 Cam11g1871 1871
11 31283843 31284519 - CaPI482276_11g018720.1 Cam11g1872 1872
11 31292398 31294344 + CaPI482276_11g018730.1 Cam11g1873 1873
4 4971351 4974583 + Carg00036-RA Car04g00861 861
16 5388038 5390296 - Carg24075-RA Car16g00819 819
16 5397127 5399650 + Carg24076-RA Car16g00820 820
16 5402498 5406145 + Carg24077-RA Car16g00821 821
10 8019795 8025979 - CcPI632755_10g006010.1 Cco10g0601 601
10 8038263 8041378 - CcPI632755_10g006020.1 Cco10g0602 602
10 8051347 8053066 + CcPI632755_10g006030.1 Cco10g0603 603
10 8055361 8057539 + CcPI632755_10g006040.1 Cco10g0604 604
11 31701923 31713533 + CcPI632755_11g019000.1 Cco11g1900 1900
11 31713833 31723527 - CcPI632755_11g019010.1 Cco11g1901 1901
11 31740636 31741778 - CcPI632755_11g019030.1 Cco11g1903 1903
11 31749778 31751802 + CcPI632755_11g019040.1 Cco11g1904 1904
10 8379962 8386180 - CePI673135_10g006250.1 Cec10g0625 625
10 8391965 8398070 - CePI673135_10g006260.1 Cec10g0626 626
10 8406037 8407721 + CePI673135_10g006270.1 Cec10g0627 627
10 8409782 8411978 + CePI673135_10g006280.1 Cec10g0628 628
11 33162329 33172825 + CePI673135_11g018940.1 Cec11g1894 1894
11 33173055 33187001 - CePI673135_11g018950.1 Cec11g1895 1895
11 33194813 33196810 + CePI673135_11g018960.1 Cec11g1896 1896
6 20138010 20139333 - Chy6G122560.1 Chy06g01728 1728
6 20147894 20155265 + Chy6G122570.1 Chy06g01729 1729
6 20155535 20160798 + Chy6G122580.1 Chy06g01730 1730
10 8510796 8516888 - ClG42_10g0062700.10 Clacu10g0627 627
10 8522745 8530067 - ClG42_10g0062800.10 Clacu10g0628 628
10 8539886 8541581 + ClG42_10g0062900.10 Clacu10g0629 629
10 8543876 8545971 + ClG42_10g0063000.10 Clacu10g0630 630
11 31301357 31312404 + ClG42_11g0203300.10 Clacu11g2033 2033
11 31314230 31322140 - ClG42_11g0203500.10 Clacu11g2035 2035
11 31325408 31326108 - ClG42_11g0203600.10 Clacu11g2036 2036
11 31333906 31335851 + ClG42_11g0203700.10 Clacu11g2037 2037
10 9002173 9008720 - ClCG10G006450.1 Cla10g00605 605
10 9018252 9021944 - ClCG10G006460.2 Cla10g00606 606
10 9031527 9033477 + ClCG10G006490.1 Cla10g00607 607
10 9037628 9039915 + ClCG10G006500.1 Cla10g00608 608
11 31704159 31715312 + ClCG11G018470.1 Cla11g01804 1804
11 31713290 31725797 - ClCG11G018480.1 Cla11g01805 1805
11 31728863 31729760 - ClCG11G018540.2 Cla11g01806 1806
11 31737535 31739793 + ClCG11G018550.1 Cla11g01807 1807
4 4748020 4749246 - CmaCh04G009180.1 Cma04g00918 918
4 4750609 4754604 + CmaCh04G009190.1 Cma04g00919 919
16 4590539 4600415 - CmoCh16G008630.1 Cmo16g00863 863
16 4604088 4606492 + CmoCh16G008640.1 Cmo16g00864 864
16 4610071 4613857 + CmoCh16G008650.1 Cmo16g00865 865
11 30550965 30561496 + CmPI595203_11g018380.1 Cmu11g1838 1838
11 30564039 30572056 - CmPI595203_11g018400.1 Cmu11g1840 1840
11 30575308 30575971 - CmPI595203_11g018410.1 Cmu11g1841 1841
11 30583770 30585721 + CmPI595203_11g018420.1 Cmu11g1842 1842
6 538488 539197 + Conep06aG0011100.1 Cone6ag0111 111
6 539985 541366 + Conep06aG0011200.1 Cone6ag0112 112
6 541407 549670 - Conep06aG0011300.1 Cone6ag0113 113
9 578039 579402 + Conep09aG0013300.1 Cone9ag0132 132
14 9103051 9110193 + Conep14aG0110900.1 Cone14ag1087 1087
14 9131965 9136875 - Conep14aG0111000.1 Cone14ag1088 1088
14 9139951 9144499 + Conep14aG0111100.1 Cone14ag1089 1089
14 9144552 9145547 - Conep14aG0111200.1 Cone14ag1090 1090
14 9146697 9148717 + Conep14aG0111300.1 Cone14ag1091 1091
15 9008926 9015270 + Conep15aG0112400.1 Cone15ag1098 1098
15 9023467 9025451 + Conep15aG0112500.1 Cone15ag1099 1099
15 9025613 9030087 - Conep15aG0112600.1 Cone15ag1100 1100
15 9035099 9039506 + Conep15aG0112700.1 Cone15ag1101 1101
15 9041680 9042988 + Conep15aG0112800.1 Cone15ag1102 1102
2 4617228 4627158 + Cp4.1LG02g01530.1 Cpe02g00725 725
2 4629509 4630992 + Cp4.1LG02g01510.1 Cpe02g00726 726
6 4471672 4479670 + Cp4.1LG06g07090.1 Cpe06g00718 718
6 4479755 4487867 - Cp4.1LG06g07160.1 Cpe06g00719 719
6 4488573 4489528 - Cp4.1LG06g07190.1 Cpe06g00720 720
6 4494299 4495667 + Cp4.1LG06g07220.1 Cpe06g00721 721
14 4610792 4612397 - Cp4.1LG14g00150.1 Cpe14g00702 702
14 4616207 4619563 + Cp4.1LG14g00230.1 Cpe14g00703 703
14 4622628 4626735 + Cp4.1LG14g00210.1 Cpe14g00704 704
10 9147254 9153487 - CrPI670011_10g008390.1 Cre10g0839 839
10 9159346 9166566 - CrPI670011_10g008400.1 Cre10g0840 840
10 9175870 9177561 + CrPI670011_10g008410.1 Cre10g0841 841
10 9179860 9182037 + CrPI670011_10g008420.1 Cre10g0842 842
11 34221993 34233204 + CrPI670011_11g022450.1 Cre11g2245 2245
11 34235031 34242845 - CrPI670011_11g022460.1 Cre11g2246 2246
11 34255209 34257269 + CrPI670011_11g022470.1 Cre11g2247 2247
3 5111379 5117032 - CsaV3_3G005930.1 Csa03g00593 593
3 5121395 5125115 - CsaV3_3G005940.1 Csa03g00594 594
3 5129160 5131051 + CsaV3_3G005950.1 Csa03g00595 595
3 5131730 5134136 + CsaV3_3G005960.1 Csa03g00596 596
4 20153211 20155699 - Lsi04G012770.1 Lsi04g01277 1277
4 20165609 20166304 + Lsi04G012780.1 Lsi04g01278 1278
4 20175104 20188153 + Lsi04G012790.1 Lsi04g01279 1279
4 20201696 20214669 - Lsi04G012800.1 Lsi04g01280 1280
5 9081344 9090742 - Lsi05G006830.1 Lsi05g00683 683
5 9123085 9125173 + Lsi05G006850.1 Lsi05g00685 685
5 9150084 9152476 + Lsi05G006870.1 Lsi05g00687 687
19 3676944 3687513 - Vvi19g294 Vvi19g294 294
19 3721385 3724388 - Vvi19g295 Vvi19g295 295
19 3738257 3741107 - Vvi19g296 Vvi19g296 296
19 3749994 3776743 + Vvi19g297 Vvi19g297 297
19 3777345 3779258 - Vvi19g298 Vvi19g298 298
19 3780455 3784385 + Vvi19g299 Vvi19g299 299
19 3785443 3802981 - Vvi19g300 Vvi19g300 300
19 3814609 3826987 + Vvi19g301 Vvi19g301 301
19 3837562 3838138 - Vvi19g302 Vvi19g302 302
19 3843833 3846216 + Vvi19g303 Vvi19g303 303
       

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