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
Vvi16g644 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g645 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g646 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g647 . Blo15g00161 . . . Bpe07g00945 . . Cmo16g00138 Cmo18g01262 . . . . Sed13g0158 . Cpe14g00114 Bhi01g01338 Tan01g0267 Cmetu06g0672 . Hepe07g0170 Mch10g0167 . . . . . . . . . . Cone14ag0097 Cone15ag0103 Lsi05g01242 . . Cme06g00984 . . Bda06g00676 . . . . . . . . . Cma18g01239 . Car18g01143 Cpe09g00098 . . . . . . . . Cla05g00867 Cam05g0954 Cec05g0959 Cco05g0959 Clacu05g0941 Cmu05g0899 Cre05g0983 . Csa03g01698 Chy06g00934 .
Vvi16g648 . Blo15g00162 . . . Bpe07g00944 . . . . . . . Car15g01019 . . . . . . . . . . Cla01g00539 Cam01g0562 Cec01g0553 Cco01g0577 Clacu01g0559 Cmu01g0531 Cre09g1979 Cone1ag1149 Cone5ag0858 . . . Csa05g00573 Chy09g00932 . . . Bda06g00677 Bda15g00734 . Bpe12g00420 Bma08g00339 . . . Cmo15g01157 . . . . . Cpe13g00046 Bhi12g00545 . . . . . Lcy12g1230 . . . . . . . . . . Cme09g01459
Vvi16g649 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g650 Blo06g01116 . . . . . . . . . . Cma15g01099 . . . . . . . . . . . . . . . . . . . . . Cone14ag0096 Cone15ag0102 . Csa05g00572 Chy09g00933 . . . . . . Bpe12g00421 Bma08g00338 . . . . . . . . . Cpe13g00047 . . . . . . . . . . . . . . Lsi09g00581 . . Cme09g01460
Vvi16g651 . . Bda05g00063 . Bpe03g00292 . . . Cmo16g00136 Cmo18g01264 . . . . Sed01g3910 . Cpe14g00111 Bhi01g01334 Tan01g0265 Cmetu09g1530 . Hepe07g0168 Mch10g0165 . Cla01g00286 Cam01g0298 Cec01g0291 Cco01g0304 Clacu01g0297 Cmu01g0284 Cre09g2225 . . . . Lsi05g01239 Csa05g00308 Chy09g01198 . Blo07g00416 . . . . . . . . . . Cma16g00131 Cma18g01241 . Car18g01146 Cpe09g00096 . Bhi12g00219 . . . . . . Cla05g00869 Cam05g0957 Cec05g0962 Cco05g0962 Clacu05g0943 Cmu05g0901 Cre05g0985 . Csa03g01700 Chy06g00936 .
Vvi16g652 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g653 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 3513656 3515888 - Bda020651.2 Bda05g00063 63
6 9395028 9395624 - Bda023969.1 Bda06g00676 676
6 9396443 9397471 - Bda023970.1 Bda06g00677 677
15 10828386 10829848 + Bda012590.1 Bda15g00734 734
1 26748648 26753606 + XM_039034549.1 Bhi01g01334 1334
1 26805010 26806100 + XM_039045152.1 Bhi01g01338 1338
12 7171952 7186386 - XM_039019439.1 Bhi12g00219 219
12 17487414 17497701 - XM_039018750.1 Bhi12g00545 545
6 34572663 34579091 - BLOR17699 Blo06g01116 1116
7 7830230 7833264 + BLOR18348 Blo07g00416 416
15 1651026 1651625 - BLOR06555 Blo15g00161 161
15 1652911 1654591 - BLOR06556 Blo15g00162 162
8 6079002 6079728 + Bma027381.1 Bma08g00338 338
8 6100997 6102505 + Bma027382.2 Bma08g00339 339
3 3972209 3975378 + Bpe012144.1 Bpe03g00292 292
7 15295903 15297070 + Bpe021786.1 Bpe07g00944 944
7 15297792 15298448 + Bpe021787.1 Bpe07g00945 945
12 9807498 9808714 - Bpe005676.1 Bpe12g00420 420
12 9810995 9811710 - Bpe005677.1 Bpe12g00421 421
1 3340446 3348580 + CaPI482276_01g002980.1 Cam01g0298 298
1 5973475 5980812 + CaPI482276_01g005620.1 Cam01g0562 562
5 8635952 8636551 - CaPI482276_05g009540.1 Cam05g0954 954
5 8643139 8647069 - CaPI482276_05g009570.1 Cam05g0957 957
15 7959961 7961448 + Carg23195-RA Car15g01019 1019
18 11331787 11332398 - Carg22091-RA Car18g01143 1143
18 11336415 11338714 - Carg22094-RA Car18g01146 1146
1 2976658 2984462 + CcPI632755_01g003040.1 Cco01g0304 304
1 5696934 5704561 + CcPI632755_01g005770.1 Cco01g0577 577
5 8402314 8402913 - CcPI632755_05g009590.1 Cco05g0959 959
5 8409582 8413464 - CcPI632755_05g009620.1 Cco05g0962 962
1 2943199 2951329 + CePI673135_01g002910.1 Cec01g0291 291
1 5739665 5745587 + CePI673135_01g005530.1 Cec01g0553 553
5 8384843 8385442 - CePI673135_05g009590.1 Cec05g0959 959
5 8392047 8395970 - CePI673135_05g009620.1 Cec05g0962 962
6 6865348 6867781 - Chy6G114620.1 Chy06g00934 934
6 6871677 6875860 - Chy6G114640.1 Chy06g00936 936
9 12085717 12088821 - Chy9G166480.1 Chy09g00932 932
9 12095206 12097276 - Chy9G166490.1 Chy09g00933 933
9 14148738 14157481 - Chy9G169140.1 Chy09g01198 1198
1 2950981 2951217 + ClG42_01g0029700.10 Clacu01g0297 297
1 5609295 5614294 + ClG42_01g0055900.10 Clacu01g0559 559
5 8345936 8346535 - ClG42_05g0094100.10 Clacu05g0941 941
5 8353114 8357033 - ClG42_05g0094300.10 Clacu05g0943 943
1 3023573 3038039 + ClCG01G002960.2 Cla01g00286 286
1 5880948 5892289 + ClCG01G005500.1 Cla01g00539 539
5 8600324 8600923 - ClCG05G007945.1 Cla05g00867 867
5 8607502 8611662 - ClCG05G007960.2 Cla05g00869 869
15 6993319 6994032 - CmaCh15G010990.1 Cma15g01099 1099
16 589236 592312 + CmaCh16G001310.1 Cma16g00131 131
18 9715840 9716451 - CmaCh18G012390.1 Cma18g01239 1239
18 9720370 9723248 - CmaCh18G012410.1 Cma18g01241 1241
6 7023684 7024289 - MELO3C006895.2.1 Cme06g00984 984
9 19811676 19816378 - MELO3C005380.2.1 Cme09g01459 1459
9 19817394 19820549 - MELO3C005381.2.1 Cme09g01460 1460
6 7057379 7058484 - PI0024281.1 Cmetu06g0672 672
9 2235005 2240816 + PI0011683.1 Cmetu09g1530 1530
15 8084427 8085152 - CmoCh15G011570.1 Cmo15g01157 1157
16 633961 637591 + CmoCh16G001360.1 Cmo16g00136 136
16 640766 641652 + CmoCh16G001380.1 Cmo16g00138 138
18 12334128 12334739 - CmoCh18G012620.1 Cmo18g01262 1262
18 12338898 12341199 - CmoCh18G012640.1 Cmo18g01264 1264
1 2912986 2921095 + CmPI595203_01g002840.1 Cmu01g0284 284
1 5565930 5570938 + CmPI595203_01g005310.1 Cmu01g0531 531
5 8192830 8193429 - CmPI595203_05g008990.1 Cmu05g0899 899
5 8200008 8203927 - CmPI595203_05g009010.1 Cmu05g0901 901
1 55689230 55691741 - Conep01aG0119800.1 Cone1ag1149 1149
5 3666021 3668567 - Conep05aG0088400.1 Cone5ag0858 858
14 468926 469744 + Conep14aG0009900.1 Cone14ag0096 96
14 471543 472505 + Conep14aG0010000.1 Cone14ag0097 97
15 505270 505956 + Conep15aG0010400.1 Cone15ag0102 102
15 506928 507923 + Conep15aG0010500.1 Cone15ag0103 103
9 544636 548309 + Cp4.1LG09g00820.1 Cpe09g00096 96
9 551271 551882 + Cp4.1LG09g00840.1 Cpe09g00098 98
13 341736 346265 - Cp4.1LG13g00470.1 Cpe13g00046 46
13 347015 353527 - Cp4.1LG13g00450.1 Cpe13g00047 47
14 602249 615690 + Cp4.1LG14g06090.1 Cpe14g00111 111
14 617917 620980 + Cp4.1LG14g06070.1 Cpe14g00114 114
5 9076520 9077119 - CrPI670011_05g009830.1 Cre05g0983 983
5 9083845 9087568 - CrPI670011_05g009850.1 Cre05g0985 985
9 38768468 38770319 - CrPI670011_09g019790.1 Cre09g1979 1979
9 41393594 41401716 - CrPI670011_09g022250.1 Cre09g2225 2225
3 12760867 12762343 - CsaV3_3G016980.1 Csa03g01698 1698
3 12767575 12772204 - CsaV3_3G017000.1 Csa03g01700 1700
5 1939207 1947159 + CsaV3_5G003080.1 Csa05g00308 308
5 3767050 3770125 + CsaV3_5G005720.1 Csa05g00572 572
5 3771381 3776833 + CsaV3_5G005730.1 Csa05g00573 573
7 1511193 1514901 + Hsped.07g01680.1 Hepe07g0168 168
7 1519194 1521133 + Hsped.07g01700.1 Hepe07g0170 170
12 25417201 25422497 - Maker00019020 Lcy12g1230 1230
5 20227806 20232820 + Lsi05G012390.1 Lsi05g01239 1239
5 20238810 20240572 + Lsi05G012420.1 Lsi05g01242 1242
9 6257462 6261219 + Lsi09G005810.1 Lsi09g00581 581
10 992945 998397 + MC10g0137 Mch10g0165 165
10 1001807 1002418 + MC10g0138 Mch10g0167 167
1 68303260 68313259 + Sed0002800.1 Sed01g3910 3910
13 1001245 1002278 + Sed0019375.1 Sed13g0158 158
1 2244328 2247947 + Tan0002919.1 Tan01g0265 265
1 2258052 2258867 + Tan0011233.1 Tan01g0267 267
16 16682416 16684337 - Vvi16g644 Vvi16g644 644
16 16685529 16695150 - Vvi16g645 Vvi16g645 645
16 16695694 16699914 - Vvi16g646 Vvi16g646 646
16 16717904 16718516 - Vvi16g647 Vvi16g647 647
16 16727562 16729262 - Vvi16g648 Vvi16g648 648
16 16729262 16732006 - Vvi16g649 Vvi16g649 649
16 16732498 16737019 - Vvi16g650 Vvi16g650 650
16 16737595 16755347 - Vvi16g651 Vvi16g651 651
16 16783411 16788434 + Vvi16g652 Vvi16g652 652
16 16807566 16809744 + Vvi16g653 Vvi16g653 653
       

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