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
Vvi1g401 . . . . . . Bma14g01581 . . Cmo18g00982 . Cma18g00978 . Car18g00897 . Cpe09g00339 . . . . . . . . . . . . . . . Cone13ag0778 Cone19ag0781 . . . . . . . . . . . . . . . . Cmo15g00991 . Cma15g00951 . Car15g00895 . . . . . . . . . . . . . . . . . . . .
Vvi1g402 . . . . . . . . Cmo04g01536 Cmo18g00981 . . Car04g01524 Car18g00896 . Cpe09g00340 Cpe01g01308 Bhi07g01235 . . . Hepe01g1135 . . Cla05g02253 Cam05g2419 Cec05g2436 Cco05g2481 Clacu05g2408 Cmu05g2274 Cre05g2392 Cone13ag0777 Cone19ag0780 . . Lsi04g00196 Csa05g02673 Chy10g01202 Cme10g00198 . Blo11g00741 Bda07g01446 . Bpe11g01615 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g403 . . . . . . . . . . . . . . . . Cpe01g01821 . . . . . . . Cla05g02250 Cam05g2416 Cec05g2433 Cco05g2478 Clacu05g2405 Cmu05g2271 Cre05g2389 Cone13ag0776 Cone19ag0779 . . Lsi04g00194 Csa05g02676 . Cme10g00194 . Blo11g00740 Bda07g01442 . Bpe11g01614 . . . . . Cmo15g00988 . Cma15g00948 . Car15g00892 . . . . . . . . . . . . . . . . . . . .
Vvi1g404 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g02033 . . . . Bda07g01441 . Bpe11g01613 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g405 . . . . . . . . Cmo04g01532 Cmo18g00980 . Cma18g00977 Car04g01520 . . Cpe09g00341 Cpe01g01305 . . . . . . . Cla05g02249 Cam05g2415 Cec05g2432 Cco05g2477 Clacu05g2404 Cmu05g2270 Cre05g2388 Cone13ag0775 Cone19ag0778 Cone6ag0404 . . Csa05g02677 Chy10g01205 Cme10g00193 . Blo11g00737 Bda07g01440 . Bpe11g01612 . . . . . Cmo15g00986 . Cma15g00947 . Car15g00891 Cpe13g00375 . . . . . . . . . . . . . . . . . . .
Vvi1g406 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone9ag0428 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy09g00865 .
Vvi1g407 . . . . . . . . . . . . . . . . Cpe01g01885 . . . . . . . . . . . . . . . Cone19ag0777 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g408 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo15g00985 . . . Car15g00890 . . . . . . . . . . . . . . . . . . . Cme09g01398
Vvi1g409 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g410 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo15g00985 . Cma15g00946 . Car15g00890 . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 26662863 26663633 - Bda028267.1 Bda07g01440 1440
7 26664633 26666297 - Bda028268.1 Bda07g01441 1441
7 26667303 26669897 - Bda028269.1 Bda07g01442 1442
7 26867070 26877531 - Bda028273.1 Bda07g01446 1446
7 38870287 38882062 + XM_039036211.1 Bhi07g01235 1235
11 9909086 9914021 - BLOR03613 Blo11g00737 737
11 9943021 9945854 - BLOR03616 Blo11g00740 740
11 9984689 9986760 + BLOR03617 Blo11g00741 741
14 32654334 32659489 - Bma012273.1 Bma14g01581 1581
11 12257801 12258641 - Bpe004929.1 Bpe11g01612 1612
11 12260535 12262199 - Bpe024851 Bpe11g01613 1613
11 12265171 12268113 - Bpe004930.1 Bpe11g01614 1614
11 12272042 12281252 + Bpe004931.1 Bpe11g01615 1615
5 32146395 32147272 - CaPI482276_05g024150.1 Cam05g2415 2415
5 32152205 32155503 - CaPI482276_05g024160.1 Cam05g2416 2416
5 32173441 32179459 + CaPI482276_05g024190.1 Cam05g2419 2419
4 8836614 8838209 - Carg01880-RA Car04g01520 1520
4 8847707 8853669 + Carg01876-RA Car04g01524 1524
15 5383216 5394198 - Carg26354-RA Car15g00890 890
15 5407998 5408749 - Carg26353-RA Car15g00891 891
15 5428262 5430752 + Carg26352-RA Car15g00892 892
15 5446529 5448844 + Carg26349-RA Car15g00895 895
18 9828508 9835718 + Carg19022-RA Car18g00896 896
18 9837540 9838985 + Carg19023-RA Car18g00897 897
5 33201737 33202602 - CcPI632755_05g024770.1 Cco05g2477 2477
5 33207497 33210794 - CcPI632755_05g024780.1 Cco05g2478 2478
5 33228156 33234079 + CcPI632755_05g024810.1 Cco05g2481 2481
5 35552088 35552958 - CePI673135_05g024320.1 Cec05g2432 2432
5 35557937 35561259 - CePI673135_05g024330.1 Cec05g2433 2433
5 35579406 35585401 + CePI673135_05g024360.1 Cec05g2436 2436
9 11395389 11397146 + Chy9G165810.1 Chy09g00865 865
10 16759877 16765704 - Chy10G183960.1 Chy10g01202 1202
10 16777985 16786616 + Chy10G183990.1 Chy10g01205 1205
5 32358874 32359764 - ClG42_05g0240400.10 Clacu05g2404 2404
5 32364592 32367847 - ClG42_05g0240500.10 Clacu05g2405 2405
5 32385685 32391926 + ClG42_05g0240800.10 Clacu05g2408 2408
5 34146572 34147588 - ClCG05G022160.1 Cla05g02249 2249
5 34152330 34155585 - ClCG05G022170.1 Cla05g02250 2250
5 34175088 34184939 + ClCG05G022200.2 Cla05g02253 2253
15 5061115 5070466 - CmaCh15G009460.1 Cma15g00946 946
15 5075320 5076218 - CmaCh15G009470.1 Cma15g00947 947
15 5090271 5093628 + CmaCh15G009480.1 Cma15g00948 948
15 5108392 5109756 + CmaCh15G009510.1 Cma15g00951 951
18 8259127 8260478 - CmaCh18G009770.1 Cma18g00977 977
18 8264911 8277066 + CmaCh18G009780.1 Cma18g00978 978
9 19171753 19176433 + MELO3C005317.2.1 Cme09g01398 1398
10 1309721 1311355 - MELO3C012307.2.1 Cme10g00193 193
10 1314602 1318781 - MELO3C012306.2.1 Cme10g00194 194
10 1330266 1340619 + MELO3C012302.2.1 Cme10g00198 198
4 7844135 7844917 - CmoCh04G015320.1 Cmo04g01532 1532
4 7855576 7862049 + CmoCh04G015360.1 Cmo04g01536 1536
15 5255085 5256424 - CmoCh15G009850.1 Cmo15g00985 985
15 5271291 5272222 - CmoCh15G009860.1 Cmo15g00986 986
15 5304685 5307227 + CmoCh15G009880.1 Cmo15g00988 988
15 5324205 5325690 + CmoCh15G009910.1 Cmo15g00991 991
18 10794699 10795977 - CmoCh18G009800.1 Cmo18g00980 980
18 10800948 10807659 + CmoCh18G009810.1 Cmo18g00981 981
18 10809296 10810699 + CmoCh18G009820.1 Cmo18g00982 982
5 32096538 32097428 - CmPI595203_05g022700.1 Cmu05g2270 2270
5 32102252 32105507 - CmPI595203_05g022710.1 Cmu05g2271 2271
5 32123573 32129740 + CmPI595203_05g022740.1 Cmu05g2274 2274
6 1941942 1943331 + Conep06aG0041400.1 Cone6ag0404 404
9 1973026 1974840 + Conep09aG0043800.1 Cone9ag0428 428
13 7294628 7296131 - Conep13aG0080000.1 Cone13ag0775 775
13 7299074 7302296 - Conep13aG0080100.1 Cone13ag0776 776
13 7304261 7308510 + Conep13aG0080200.1 Cone13ag0777 777
13 7308804 7310773 + Conep13aG0080300.1 Cone13ag0778 778
19 6330536 6333323 - Conep19aG0079900.1 Cone19ag0777 777
19 6339703 6340005 - Conep19aG0080000.1 Cone19ag0778 778
19 6347072 6350092 - Conep19aG0080100.1 Cone19ag0779 779
19 6351561 6355756 + Conep19aG0080200.1 Cone19ag0780 780
19 6356076 6358188 + Conep19aG0080300.1 Cone19ag0781 781
1 7851557 7855492 - Cp4.1LG01g13980.1 Cpe01g01305 1305
1 7862486 7872925 + Cp4.1LG01g14010.1 Cpe01g01308 1308
1 15424846 15430711 - Cp4.1LG01g18220.1 Cpe01g01821 1821
1 16143714 16145831 - Cp4.1LG01g18900.1 Cpe01g01885 1885
9 2052467 2054642 - Cp4.1LG09g03360.1 Cpe09g00339 339
9 2055648 2062643 - Cp4.1LG09g03400.1 Cpe09g00340 340
9 2067650 2069365 + Cp4.1LG09g03290.1 Cpe09g00341 341
13 4064732 4065659 + Cp4.1LG13g03670.1 Cpe13g00375 375
5 35421848 35422730 - CrPI670011_05g023880.1 Cre05g2388 2388
5 35427690 35431011 - CrPI670011_05g023890.1 Cre05g2389 2389
5 35449016 35457357 + CrPI670011_05g023920.1 Cre05g2392 2392
5 23670184 23672853 + CsaV3_5G028520.1 Csa05g02033 2033
5 27671428 27678230 - CsaV3_5G034920.1 Csa05g02673 2673
5 27689261 27693802 + CsaV3_5G034950.1 Csa05g02676 2676
5 27696903 27704277 + CsaV3_5G034960.1 Csa05g02677 2677
1 76497907 76504466 + Hsped.01g11350.1 Hepe01g1135 1135
4 2054818 2064773 - Lsi04G001940.1 Lsi04g00194 194
4 2068678 2089134 + Lsi04G001960.1 Lsi04g00196 196
1 4174792 4176857 - Vvi1g401 Vvi1g401 401
1 4194982 4204540 - Vvi1g402 Vvi1g402 402
1 4209010 4214620 + Vvi1g403 Vvi1g403 403
1 4214634 4217647 + Vvi1g404 Vvi1g404 404
1 4233086 4235221 + Vvi1g405 Vvi1g405 405
1 4242906 4245730 + Vvi1g406 Vvi1g406 406
1 4259393 4264674 + Vvi1g407 Vvi1g407 407
1 4265496 4268723 + Vvi1g408 Vvi1g408 408
1 4273740 4277143 + Vvi1g409 Vvi1g409 409
1 4278408 4287349 + Vvi1g410 Vvi1g410 410
       

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