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
Vvi3g6 . . . Bda08g00947 . . Bma05g00433 . . . . . . . . . Cpe15g00552 . . . . . . . . . . . . . . . . Cone3ag1223 Cone10ag1108 . Csa07g00016 . Cme01g01366 . . . . . Bpe05g00327 . . . . . . . . Car19g00524 . . . . . . . . . . . . . . . . Lsi11g01124 . Chy01g00761 .
Vvi3g7 . . . . . . . . . . Cma02g00373 . Car02g00240 . . . . . . . . . . . . . . . . . . . . . . . . Chy11g00348 . . . . . . . . . Sed05g3535 . . . . . . . Cpe05g01282 Bhi10g01964 Tan05g1258 Cmetu11g0111 . Hepe08g0988 . . . . . . . . . . Csa02g01295 . Cme11g00156
Vvi3g8 . . . . . Bpe12g00087 . . Cmo19g00694 . . . . . Sed05g2305 Cpe04g00115 Cpe15g00553 Bhi05g01787 Tan02g0774 Cmetu01g1478 . Hepe02g0245 . . Cla02g00500 Cam02g0510 Cec02g0510 Cco02g0517 Clacu02g0512 Cmu02g0508 Cre02g0841 Cone12ag1172 Cone8ag1219 . . . Csa07g00017 . Cme01g01365 Blo04g00526 Blo13g00542 Bda15g01076 Bda14g00569 Bpe15g00854 . Bma03g00563 Bma08g00787 . . . . . . Car19g00525 . . . . . . . . . . . . . . . . Lsi11g01125 . Chy01g00760 .
Vvi3g9 . Blo15g00678 Bda06g00950 . . . . . . . . Cma20g00821 . Car20g00708 . . . . . . . . . . . . . . . . . . . Cone3ag1222 Cone10ag1107 Lsi10g00404 . Chy11g00347 . . . . . . . . . Sed05g3536 . Cmo20g00830 . . . . Cpe16g00266 . Bhi10g01963 Tan05g1257 Cmetu11g1123 . Hepe08g0987 . . . . . . . . . . Csa02g01296 . Cme11g00157
Vvi3g10 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag1174 Cone8ag1220 . . . Csa07g00018 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g11 . . . . . . . . . . . . . . . Cpe04g00114 . . . . . . . . Cla02g00499 Cam02g0509 Cec02g0509 Cco02g0515 Clacu02g0511 Cmu02g0507 Cre02g0840 . . . . . . . Cme01g01364 Blo04g00527 . . Bda14g00570 . . Bma03g00564 . . . . . . . . . . . . . . . . . . . . . . . . Lsi11g01126 . Chy01g00759 .
Vvi3g12 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g13 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g14 . . . . . Bpe12g00089 . . . . . . . . . Cpe04g00112 Cpe15g00555 . . . . . . . Cla02g00497 Cam02g0507 Cec02g0507 Cco02g0512 Clacu02g0509 Cmu02g0505 Cre02g0838 . . Cone3ag1221 Cone10ag1105 . Csa07g00020 . Cme01g01362 Blo04g00529 Blo13g00540 Bda15g01074 Bda14g00572 Bpe15g00852 . Bma03g00566 Bma08g00785 . . . . Cma19g00683 . Car19g00527 . . . . . . . . . . . . . . . . Lsi11g01128 . Chy01g00757 .
Vvi3g15 . . . . . . . . Cmo19g00696 . . . . . . Cpe04g00111 Cpe15g00556 . . . . . . . Cla02g00495 Cam02g0506 Cec02g0506 Cco02g0511 Clacu02g0508 Cmu02g0504 Cre02g0837 . . Cone3ag1220 . . Csa07g00021 . Cme01g01361 . . . . . . . . . . . . Cma19g00684 . Car19g00528 . . . . . . . . . . . . . . . . Lsi11g01129 . Chy01g00756 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 26313096 26322326 - Bda022584.1 Bda06g00950 950
8 17789171 17794262 + Bda029593.1 Bda08g00947 947
14 4339225 4341530 + Bda027320.1 Bda14g00569 569
14 4342318 4344579 - Bda027321.1 Bda14g00570 570
14 4347542 4371662 - Bda027323.2 Bda14g00572 572
15 19977149 19985501 + Bda013069.1 Bda15g01074 1074
15 19989195 19991625 - Bda013071.1 Bda15g01076 1076
5 56788190 56793062 + XM_039033111.1 Bhi05g01787 1787
10 48925341 48937425 + XM_039045415.1 Bhi10g01963 1963
10 48937626 48945289 - XM_039045979.1 Bhi10g01964 1964
4 4532435 4533527 + BLOR13438 Blo04g00526 526
4 4539168 4541745 - BLOR13439 Blo04g00527 527
4 4553860 4568936 - BLOR13441 Blo04g00529 529
13 27258802 27269488 + BLOR05821 Blo13g00540 540
13 27279434 27281687 - BLOR05823 Blo13g00542 542
15 20766204 20769132 + BLOR07072 Blo15g00678 678
3 4679396 4681481 + Bma016851.1 Bma03g00563 563
3 4682231 4684487 - Bma016852.2 Bma03g00564 564
3 4689080 4710676 - Bma016854.2 Bma03g00566 566
5 14331507 14338699 + Bma021281.1 Bma05g00433 433
8 45234372 45242738 + Bma028166.3 Bma08g00785 785
8 45246956 45249262 - Bma028168.1 Bma08g00787 787
5 17025906 17033077 - Bpe017742.1 Bpe05g00327 327
12 633750 636172 + Bpe005326.1 Bpe12g00087 87
12 639661 647429 - Bpe005328.1 Bpe12g00089 89
15 18514200 18534212 + Bpe001776.1 Bpe15g00852 852
15 18539502 18541752 - Bpe001778.1 Bpe15g00854 854
2 5717152 5722158 + CaPI482276_02g005060.1 Cam02g0506 506
2 5724712 5735802 + CaPI482276_02g005070.1 Cam02g0507 507
2 5751123 5754157 + CaPI482276_02g005090.1 Cam02g0509 509
2 5760503 5780489 - CaPI482276_02g005100.1 Cam02g0510 510
2 1619582 1625874 - Carg24144-RA Car02g00240 240
19 6847546 6856604 + Carg19396-RA Car19g00524 524
19 6857897 6861434 + Carg19395-RA Car19g00525 525
19 6865119 6874291 - Carg19393-RA Car19g00527 527
19 6875084 6880931 - Carg19392-RA Car19g00528 528
20 4063737 4077780 + Carg26796-RA Car20g00708 708
2 4762916 4767918 + CcPI632755_02g005110.1 Cco02g0511 511
2 4770590 4781595 + CcPI632755_02g005120.1 Cco02g0512 512
2 4794956 4797995 + CcPI632755_02g005150.1 Cco02g0515 515
2 4810019 4822332 - CcPI632755_02g005170.1 Cco02g0517 517
2 4723559 4733673 + CePI673135_02g005060.1 Cec02g0506 506
2 4736066 4747156 + CePI673135_02g005070.1 Cec02g0507 507
2 4761526 4764541 + CePI673135_02g005090.1 Cec02g0509 509
2 4770953 4790954 - CePI673135_02g005100.1 Cec02g0510 510
1 5647357 5652165 + Chy1G007560.1 Chy01g00756 756
1 5656055 5666743 + Chy1G007570.1 Chy01g00757 757
1 5672319 5675558 + Chy1G007590.1 Chy01g00759 759
1 5677548 5683096 - Chy1G007600.1 Chy01g00760 760
1 5692633 5705847 - Chy1G007610.1 Chy01g00761 761
11 3144722 3154397 + Chy11G189270.1 Chy11g00347 347
11 3155136 3165907 - Chy11G189280.1 Chy11g00348 348
2 4680515 4685500 + ClG42_02g0050800.10 Clacu02g0508 508
2 4691372 4702456 + ClG42_02g0050900.10 Clacu02g0509 509
2 4716374 4719397 + ClG42_02g0051100.10 Clacu02g0511 511
2 4722502 4746394 - ClG42_02g0051200.10 Clacu02g0512 512
2 4896804 4902122 + ClCG02G004700.1 Cla02g00495 495
2 4907715 4918799 + ClCG02G004720.2 Cla02g00497 497
2 4932405 4936016 + ClCG02G004740.1 Cla02g00499 499
2 4938454 4961771 - ClCG02G004750.2 Cla02g00500 500
2 1867382 1874955 - CmaCh02G003730.1 Cma02g00373 373
19 7079317 7092700 - CmaCh19G006830.1 Cma19g00683 683
19 7093951 7099507 - CmaCh19G006840.1 Cma19g00684 684
20 3888142 3904238 + CmaCh20G008210.1 Cma20g00821 821
1 16983976 16989012 + MELO3C013436.2.1 Cme01g01361 1361
1 16991930 17007849 + MELO3C013437.2.1 Cme01g01362 1362
1 17012690 17016059 + MELO3C013439.2.1 Cme01g01364 1364
1 17017010 17022639 - MELO3C013440.2.1 Cme01g01365 1365
1 17028692 17044779 - MELO3C013443.2.1 Cme01g01366 1366
11 1687346 1693847 + MELO3C023335.2.1 Cme11g00156 156
11 1694094 1704135 - MELO3C023337.2.1 Cme11g00157 157
1 5883247 5888416 - PI0020423.7 Cmetu01g1478 1478
11 27796441 27802054 + PI0024882.1 Cmetu11g0111 111
11 27803076 27813332 - PI0001558.1 Cmetu11g1123 1123
19 7322454 7338761 + CmoCh19G006940.1 Cmo19g00694 694
19 7351871 7367860 - CmoCh19G006960.1 Cmo19g00696 696
20 4122204 4137562 + CmoCh20G008300.1 Cmo20g00830 830
2 4619130 4624115 + CmPI595203_02g005040.1 Cmu02g0504 504
2 4629973 4641061 + CmPI595203_02g005050.1 Cmu02g0505 505
2 4654970 4657993 + CmPI595203_02g005070.1 Cmu02g0507 507
2 4661100 4683569 - CmPI595203_02g005080.1 Cmu02g0508 508
3 30947681 30952979 + Conep03aG0172700.1 Cone3ag1220 1220
3 30955706 30971215 + Conep03aG0172800.1 Cone3ag1221 1221
3 30974236 30986139 + Conep03aG0172900.1 Cone3ag1222 1222
3 30993176 31009778 + Conep03aG0173000.1 Cone3ag1223 1223
8 10319175 10321017 + Conep08aG0125600.1 Cone8ag1219 1219
8 10324613 10327194 - Conep08aG0125700.1 Cone8ag1220 1220
10 7840508 7850310 + Conep10aG0113400.1 Cone10ag1105 1105
10 7862574 7869709 + Conep10aG0113600.1 Cone10ag1107 1107
10 7874223 7883200 + Conep10aG0113800.1 Cone10ag1108 1108
12 9290024 9292299 + Conep12aG0121100.1 Cone12ag1172 1172
12 9296505 9298716 - Conep12aG0121300.1 Cone12ag1174 1174
4 991728 996980 + Cp4.1LG04g01090.1 Cpe04g00111 111
4 997971 1014106 + Cp4.1LG04g01070.1 Cpe04g00112 112
4 1019418 1023512 + Cp4.1LG04g00990.1 Cpe04g00114 114
4 1024404 1028130 - Cp4.1LG04g00940.1 Cpe04g00115 115
5 8947114 8954493 + Cp4.1LG05g12770.1 Cpe05g01282 1282
15 6369847 6379323 + Cp4.1LG15g05540.1 Cpe15g00552 552
15 6380322 6384187 + Cp4.1LG15g05530.1 Cpe15g00553 553
15 6387031 6397072 - Cp4.1LG15g05610.1 Cpe15g00555 555
15 6397771 6403636 - Cp4.1LG15g05620.1 Cpe15g00556 556
16 4661352 4676579 - Cp4.1LG16g02690.1 Cpe16g00266 266
2 5159468 5164496 + CrPI670011_02g008370.1 Cre02g0837 837
2 5167116 5178213 + CrPI670011_02g008380.1 Cre02g0838 838
2 5191692 5194712 + CrPI670011_02g008400.1 Cre02g0840 840
2 5197937 5218983 - CrPI670011_02g008410.1 Cre02g0841 841
2 12597777 12603702 + CsaV3_2G015110.1 Csa02g01295 1295
2 12604165 12614634 - CsaV3_2G015120.1 Csa02g01296 1296
7 309072 324987 + CsaV3_7G000160.1 Csa07g00016 16
7 330803 336925 + CsaV3_7G000170.1 Csa07g00017 17
7 338015 341834 - CsaV3_7G000180.1 Csa07g00018 18
7 346023 357462 - CsaV3_7G000200.1 Csa07g00020 20
7 360064 365832 - CsaV3_7G000210.1 Csa07g00021 21
2 2456592 2460979 + Hsped.02g02450.1 Hepe02g0245 245
8 9334998 9348733 + Hsped.08g09870.1 Hepe08g0987 987
8 9349152 9349706 - Hsped.08g09880.1 Hepe08g0988 988
10 6138079 6149110 - Lsi10G004040.1 Lsi10g00404 404
11 19665521 19675509 + Lsi11G011240.1 Lsi11g01124 1124
11 19679215 19684307 + Lsi11G011250.1 Lsi11g01125 1125
11 19691751 19695535 - Lsi11G011260.1 Lsi11g01126 1126
11 19704107 19719537 - Lsi11G011280.1 Lsi11g01128 1128
11 19722511 19727950 - Lsi11G011290.1 Lsi11g01129 1129
5 35542698 35547324 - Sed0017186.2 Sed05g2305 2305
5 43980023 43985157 + Sed0020390.1 Sed05g3535 3535
5 43985812 43993507 - Sed0016950.1 Sed05g3536 3536
2 7384793 7389410 - Tan0008604.1 Tan02g0774 774
5 13380711 13415511 + Tan0010373.1 Tan05g1257 1257
5 13420690 13426326 - Tan0003627.1 Tan05g1258 1258
3 78494 94105 + Vvi3g6 Vvi3g6 6
3 110952 117181 + Vvi3g7 Vvi3g7 7
3 120121 125179 + Vvi3g8 Vvi3g8 8
3 126115 137455 - Vvi3g9 Vvi3g9 9
3 155823 159081 - Vvi3g10 Vvi3g10 10
3 173839 177946 - Vvi3g11 Vvi3g11 11
3 205525 209603 - Vvi3g12 Vvi3g12 12
3 256876 259331 + Vvi3g13 Vvi3g13 13
3 260947 276256 - Vvi3g14 Vvi3g14 14
3 277283 284427 - Vvi3g15 Vvi3g15 15
       

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