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
Vvi19g244 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g245 . Blo03g01543 . Bda09g00501 . Bpe08g01028 . . . . Cma01g01205 . Car01g01029 Car09g00786 Sed04g3115 Cpe06g00696 Cpe02g00706 Bhi09g03404 Tan01g4406 Cmetu07g1213 . Hepe01g1378 Mch11g1078 . Cla11g01770 Cam11g1835 Cec11g1856 Cco11g1864 Clacu11g1996 Cmu11g1805 Cre11g2214 Cone6ag0138 Cone9ag0163 . . Lsi04g01327 Csa04g02352 . . . . . . . . . . . Cmo01g01257 Cmo09g00862 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g246 Blo03g00649 Blo03g01542 Bda07g00291 . . Bpe08g01029 . . . . Cma01g01204 Cma09g00875 Car01g01028 Car09g00788 Sed04g1597 Cpe06g00699 . Bhi09g03403 Tan01g0784 Cmetu04g0308 . . . . Cla11g01772 Cam11g1837 Cec11g1858 Cco11g1866 Clacu11g1998 Cmu11g1807 Cre11g2216 Cone6ag0137 Cone9ag0162 . . Lsi04g01324 Csa04g02353 Chy07g00085 . . . . . Bpe11g00487 . Bma07g01182 . . Cmo01g01256 Cmo09g00864 Cma04g00535 . Car04g00505 . . . . . . . . . . Cla05g01024 Cam05g1118 Cec05g1128 Cco05g1118 Clacu05g1109 Cmu05g1058 Cre05g1133 . . Chy06g01139 .
Vvi19g247 . Blo03g01541 . Bda09g00500 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0136 Cone9ag0161 . . . . . . . . . . . . Bma07g01183 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g248 . . . . . . . . Cmo16g00848 . . . . . . . . . . . . . . . Cla10g00639 Cam10g0637 Cec10g0657 Cco10g0633 Clacu10g0660 Cmu10g1485 Cre10g0867 . . Cone14ag1071 Cone15ag1064 . Csa03g00619 . . . . . . . . . . . . . . Cma16g00786 . . Cpe14g00684 . . . . . . . . . . . . . . . Lsi05g00710 . Chy06g01706 .
Vvi19g249 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g250 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g251 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g252 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g253 . Blo03g01540 . Bda09g00499 . . . . . . Cma01g01201 Cma09g00877 Car01g01026 Car09g00789 Sed04g3120 Cpe06g00700 Cpe02g00708 Bhi09g03400 Tan01g4411 Cmetu07g0621 . Hepe01g1375 Mch11g1083 . Cla11g01774 Cam11g1838 Cec11g1859 Cco11g1869 Clacu11g2000 Cmu11g1809 Cre11g2217 . . . . Lsi04g01323 Csa04g02357 Chy07g00086 . . . . . . . Bma07g01184 . . Cmo01g01255 Cmo09g00866 . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 4031223 4035792 + Bda025373.1 Bda07g00291 291
9 6628113 6631463 + Bda031097.1 Bda09g00499 499
9 6633177 6637417 + Bda031098.1 Bda09g00500 500
9 6649556 6653001 - Bda031099.1 Bda09g00501 501
9 86417547 86422476 - XM_039043344.1 Bhi09g03400 3400
9 86482716 86491465 + XM_039042636.1 Bhi09g03403 3403
9 86492824 86499802 - XM_039043177.1 Bhi09g03404 3404
3 27578258 27590788 + BLOR11830 Blo03g00649 649
3 42879122 42882799 + BLOR12721 Blo03g01540 1540
3 42884633 42899729 + BLOR12722 Blo03g01541 1541
3 42937782 42943121 + BLOR12723 Blo03g01542 1542
3 42945022 42949041 - BLOR12724 Blo03g01543 1543
7 46327967 46333052 - Bma026423.1 Bma07g01182 1182
7 46337172 46341438 - Bma026424.1 Bma07g01183 1183
7 46343003 46345999 - Bma026425.1 Bma07g01184 1184
8 12528587 12531997 + Bpe023152.2 Bpe08g01028 1028
8 12534011 12538629 - Bpe023153.1 Bpe08g01029 1029
11 3759537 3764081 - Bpe003858.1 Bpe11g00487 487
5 10325147 10331772 + CaPI482276_05g011180.1 Cam05g1118 1118
10 9930247 9937335 - CaPI482276_10g006370.1 Cam10g0637 637
11 30886924 30898322 + CaPI482276_11g018350.1 Cam11g1835 1835
11 30900329 30907202 - CaPI482276_11g018370.1 Cam11g1837 1837
11 30907797 30918121 + CaPI482276_11g018380.1 Cam11g1838 1838
1 9754099 9758766 - Carg14690-RA Car01g01026 1026
1 9763379 9771206 + Carg14692-RA Car01g01028 1028
1 9772927 9779040 - Carg14693-RA Car01g01029 1029
4 2849214 2856346 - Carg13203-RA Car04g00505 505
9 4627631 4634760 + Carg17108-RA Car09g00786 786
9 4638469 4644462 - Carg17110-RA Car09g00788 788
9 4646347 4651922 + Carg17111-RA Car09g00789 789
5 10163969 10170591 + CcPI632755_05g011180.1 Cco05g1118 1118
10 8665472 8681782 - CcPI632755_10g006330.1 Cco10g0633 633
11 31324795 31330927 + CcPI632755_11g018640.1 Cco11g1864 1864
11 31332921 31339799 - CcPI632755_11g018660.1 Cco11g1866 1866
11 31347697 31350972 + CcPI632755_11g018690.1 Cco11g1869 1869
5 10107270 10113856 + CePI673135_05g011280.1 Cec05g1128 1128
10 9108965 9124757 - CePI673135_10g006570.1 Cec10g0657 657
11 32755407 32766955 + CePI673135_11g018560.1 Cec11g1856 1856
11 32768974 32775860 - CePI673135_11g018580.1 Cec11g1858 1858
11 32783623 32786842 + CePI673135_11g018590.1 Cec11g1859 1859
6 9921706 9928706 - Chy6G116670.1 Chy06g01139 1139
6 19710558 19723153 + Chy6G122340.1 Chy06g01706 1706
7 767985 774515 - Chy7G129150.1 Chy07g00085 85
7 784317 787632 + Chy7G129160.1 Chy07g00086 86
5 10064844 10071466 + ClG42_05g0110900.10 Clacu05g1109 1109
10 9184034 9203619 - ClG42_10g0066000.10 Clacu10g0660 660
11 30924650 30936172 + ClG42_11g0199600.10 Clacu11g1996 1996
11 30938180 30945064 - ClG42_11g0199800.10 Clacu11g1998 1998
11 30952698 30955967 + ClG42_11g0200000.10 Clacu11g2000 2000
5 10455482 10463035 + ClCG05G009500.1 Cla05g01024 1024
10 9705244 9726750 - ClCG10G006832.1 Cla10g00639 639
11 31309556 31316272 + ClCG11G018140.2 Cla11g01770 1770
11 31317987 31324880 - ClCG11G018160.1 Cla11g01772 1772
11 31330699 31335977 + ClCG11G018180.1 Cla11g01774 1774
1 8713586 8718062 - CmaCh01G012010.1 Cma01g01201 1201
1 8723068 8730135 + CmaCh01G012040.1 Cma01g01204 1204
1 8731471 8740042 - CmaCh01G012050.1 Cma01g01205 1205
4 2720460 2726383 - CmaCh04G005350.1 Cma04g00535 535
9 4293452 4300954 - CmaCh09G008750.1 Cma09g00875 875
9 4304049 4307737 + CmaCh09G008770.1 Cma09g00877 877
16 4313624 4324147 + CmaCh16G007860.1 Cma16g00786 786
4 12518715 12520526 + PI0025947.1 Cmetu04g0308 308
7 22110117 22115366 + PI0012640.1 Cmetu07g0621 621
7 22091955 22098174 + PI0024471.1 Cmetu07g1213 1213
1 10064276 10070084 - CmoCh01G012550.1 Cmo01g01255 1255
1 10073076 10081301 + CmoCh01G012560.1 Cmo01g01256 1256
1 10084519 10091132 - CmoCh01G012570.1 Cmo01g01257 1257
9 4448952 4455863 + CmoCh09G008620.1 Cmo09g00862 862
9 4457635 4465689 - CmoCh09G008640.1 Cmo09g00864 864
9 4469302 4473000 + CmoCh09G008660.1 Cmo09g00866 866
16 4472682 4484858 + CmoCh16G008480.1 Cmo16g00848 848
5 9906301 9912914 + CmPI595203_05g010580.1 Cmu05g1058 1058
10 9806238 9815631 - CmPI595203_10g014850.1 Cmu10g1485 1485
11 30180176 30191693 + CmPI595203_11g018050.1 Cmu11g1805 1805
11 30193701 30200584 - CmPI595203_11g018070.1 Cmu11g1807 1807
11 30208200 30211469 + CmPI595203_11g018090.1 Cmu11g1809 1809
6 662270 665879 + Conep06aG0013700.1 Cone6ag0136 136
6 668377 673252 + Conep06aG0013800.1 Cone6ag0137 137
6 673618 676985 - Conep06aG0013900.1 Cone6ag0138 138
9 707963 711537 + Conep09aG0016300.1 Cone9ag0161 161
9 713974 717359 + Conep09aG0016400.1 Cone9ag0162 162
9 718929 723029 - Conep09aG0016500.1 Cone9ag0163 163
14 8997902 9003268 + Conep14aG0109200.1 Cone14ag1071 1071
15 8796099 8800619 + Conep15aG0108700.1 Cone15ag1064 1064
2 4454219 4463291 + Cp4.1LG02g01640.1 Cpe02g00706 706
2 4473847 4479540 + Cp4.1LG02g01670.1 Cpe02g00708 708
6 4329871 4336871 + Cp4.1LG06g06940.1 Cpe06g00696 696
6 4338901 4347851 - Cp4.1LG06g07040.1 Cpe06g00699 699
6 4349341 4353716 + Cp4.1LG06g06920.1 Cpe06g00700 700
14 4488459 4499202 + Cp4.1LG14g00350.1 Cpe14g00684 684
5 10792689 10799276 + CrPI670011_05g011330.1 Cre05g1133 1133
10 9788612 9804389 - CrPI670011_10g008670.1 Cre10g0867 867
11 33860659 33866778 + CrPI670011_11g022140.1 Cre11g2214 2214
11 33868779 33875681 - CrPI670011_11g022160.1 Cre11g2216 2216
11 33883736 33887007 + CrPI670011_11g022170.1 Cre11g2217 2217
3 5392437 5405882 - CsaV3_3G006190.1 Csa03g00619 619
4 23937829 23944412 + CsaV3_4G033780.1 Csa04g02352 2352
4 23944644 23954167 - CsaV3_4G033790.1 Csa04g02353 2353
4 23961775 23967588 + CsaV3_4G033830.1 Csa04g02357 2357
1 78979307 78982914 - Hsped.01g13750.1 Hepe01g1375 1375
1 79001804 79008369 - Hsped.01g13780.1 Hepe01g1378 1378
4 21028025 21033795 - Lsi04G013230.1 Lsi04g01323 1323
4 21042641 21050456 + Lsi04G013240.1 Lsi04g01324 1324
4 21051947 21058565 - Lsi04G013270.1 Lsi04g01327 1327
5 9575682 9586625 - Lsi05G007100.1 Lsi05g00710 710
11 7505103 7512258 + MC11g0884 Mch11g1078 1078
11 7526186 7532525 + MC11g0888 Mch11g1083 1083
4 30737466 30743462 + Sed0012752.1 Sed04g1597 1597
4 42011999 42017211 + Sed0005873.2 Sed04g3115 3115
4 42032814 42038886 + Sed0004906.2 Sed04g3120 3120
1 7484329 7489559 - Tan0014735.1 Tan01g0784 784
1 109227294 109234213 + Tan0007505.1 Tan01g4406 4406
1 109257354 109264259 + Tan0010700.2 Tan01g4411 4411
19 3038730 3047932 + Vvi19g244 Vvi19g244 244
19 3056792 3068794 + Vvi19g245 Vvi19g245 245
19 3076913 3091784 - Vvi19g246 Vvi19g246 246
19 3098249 3107821 - Vvi19g247 Vvi19g247 247
19 3110459 3131353 + Vvi19g248 Vvi19g248 248
19 3167257 3183140 - Vvi19g249 Vvi19g249 249
19 3220029 3220137 - Vvi19g250 Vvi19g250 250
19 3246770 3250280 - Vvi19g251 Vvi19g251 251
19 3253144 3253999 - Vvi19g252 Vvi19g252 252
19 3256083 3262753 + Vvi19g253 Vvi19g253 253
       

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