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
Vvi3g186 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g187 . Blo15g00474 . Bda08g00984 Bpe07g00712 Bpe12g00129 . Bma12g00917 Cmo19g00763 Cmo11g01752 Cma02g00269 Cma20g00740 . Car20g00642 . Cpe04g00604 Cpe15g00605 . . . . . . . Cla02g00410 Cam02g0416 Cec02g0415 Cco02g0433 Clacu02g0419 Cmu02g0415 Cre02g0750 Cone12ag1243 Cone8ag1300 . . Lsi10g00506 Csa07g00117 Chy11g00244 Cme01g01240 . Blo13g00497 Bda15g01025 Bda14g00624 Bpe15g00803 Bpe05g00296 Bma03g00616 Bma08g00611 . Cmo02g00266 Cmo20g00737 Cma11g01366 Cma19g00750 . Car19g00585 Cpe16g00325 Cpe05g01363 . . . . . . . Cla02g01181 . Cec02g1269 . . . . Lsi11g01215 Csa02g01405 Chy01g00665 Cme11g00367
Vvi3g188 . . Bda06g00474 Bda08g00983 . . . . . . Cma02g00270 Cma20g00739 . Car20g00641 . . . . . . . . . . . . . . . . . . . . . Lsi10g00507 . Chy11g00243 . . . . . . . . . . Cmo02g00267 Cmo20g00736 . . . . Cpe16g00326 Cpe05g01362 . . . . . . . Cla02g01182 Cam02g1259 Cec02g1270 Cco02g1308 Clacu02g1241 Cmu02g1208 Cre02g1523 . Csa02g01406 . Cme11g00366
Vvi3g189 . Blo15g00385 . . Bpe07g00711 . . Bma12g00916 . . Cma02g00271 Cma20g00738 . Car20g00640 Sed01g0659 . . Bhi05g01686 Tan02g0658 Cmetu01g0591 . Hepe02g0409 . . Cla02g00409 Cam02g0415 Cec02g0414 Cco02g0432 Clacu02g0418 Cmu02g0414 Cre02g0749 Cone12ag1244 Cone8ag1301 . . Lsi10g00508 Csa07g00120 Chy11g00242 Cme01g01239 . . . . . Bpe05g00297 . . . Cmo02g00268 Cmo20g00735 . . . . Cpe16g00328 Cpe05g01361 . . . . . . . Cla02g01183 Cam02g1260 Cec02g1271 Cco02g1309 Clacu02g1242 Cmu02g1209 Cre02g1524 Lsi11g01216 Csa02g01407 Chy01g00663 Cme11g00365
Vvi3g190 . . . Bda08g00982 . . . . . . . Cma20g00737 . Car20g00639 . . . . . . . . . . . . . . . . . . . . . Lsi10g00509 . Chy11g00241 . . . . . . Bpe05g00298 . . . . Cmo20g00734 . . . . Cpe16g00329 . . . . . . . . Cla02g01184 Cam02g1261 Cec02g1272 Cco02g1310 Clacu02g1243 Cmu02g1210 Cre02g1525 . Csa02g01408 . Cme11g00364
Vvi3g191 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g192 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g193 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g194 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g195 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 6763367 6777188 - Bda023719.2 Bda06g00474 474
8 19840341 19845435 - Bda029655.1 Bda08g00982 982
8 19876072 19878601 - Bda029657.1 Bda08g00983 983
8 19880455 19881655 - Bda029658.1 Bda08g00984 984
14 4685272 4687669 + Bda027379.1 Bda14g00624 624
15 19217571 19224377 - Bda013007.1 Bda15g01025 1025
5 55016540 55019161 - XM_039031493.1 Bhi05g01686 1686
13 26208463 26221867 - BLOR05778 Blo13g00497 497
15 5425386 5427726 - BLOR06779 Blo15g00385 385
15 7686524 7690807 - BLOR06868 Blo15g00474 474
3 5088697 5091052 + Bma016907.1 Bma03g00616 616
8 38538594 38544981 - Bma031452 Bma08g00611 611
12 40604457 40606713 + Bma008247.1 Bma12g00916 916
12 40612620 40614365 - Bma008248.1 Bma12g00917 917
5 16261037 16262684 + Bpe025805 Bpe05g00296 296
5 16279535 16281655 - Bpe025806 Bpe05g00297 297
5 16282019 16288064 + Bpe017711.1 Bpe05g00298 298
7 13686335 13688565 + Bpe021555.1 Bpe07g00711 711
7 13703790 13705677 - Bpe021556.1 Bpe07g00712 712
12 923008 924741 + Bpe024873 Bpe12g00129 129
15 18230296 18232769 - Bpe001729.1 Bpe15g00803 803
2 4891452 4893979 + CaPI482276_02g004150.1 Cam02g0415 415
2 4896996 4900283 - CaPI482276_02g004160.1 Cam02g0416 416
2 24827992 24840495 + CaPI482276_02g012590.1 Cam02g1259 1259
2 24840980 24843487 - CaPI482276_02g012600.1 Cam02g1260 1260
2 24856752 24860590 + CaPI482276_02g012610.1 Cam02g1261 1261
19 7264932 7268329 + Carg25760-RA Car19g00585 585
20 3601007 3606531 - Carg16159-RA Car20g00639 639
20 3607749 3611680 + Carg16160-RA Car20g00640 640
20 3611140 3613893 - Carg16161-RA Car20g00641 641
20 3616045 3620310 - Carg16162-RA Car20g00642 642
2 3898661 3901189 + CcPI632755_02g004320.1 Cco02g0432 432
2 3904189 3907472 - CcPI632755_02g004330.1 Cco02g0433 433
2 24825880 24838408 + CcPI632755_02g013080.1 Cco02g1308 1308
2 24838804 24841310 - CcPI632755_02g013090.1 Cco02g1309 1309
2 24851292 24858424 + CcPI632755_02g013100.1 Cco02g1310 1310
2 3925039 3927563 + CePI673135_02g004140.1 Cec02g0414 414
2 3930559 3933845 - CePI673135_02g004150.1 Cec02g0415 415
2 29348677 29352324 + CePI673135_02g012690.1 Cec02g1269 1269
2 29358558 29362672 + CePI673135_02g012700.1 Cec02g1270 1270
2 29363159 29365662 - CePI673135_02g012710.1 Cec02g1271 1271
2 29375696 29379455 + CePI673135_02g012720.1 Cec02g1272 1272
1 4768530 4769710 + Chy1G006630.1 Chy01g00663 663
1 4773126 4776280 - Chy1G006650.1 Chy01g00665 665
11 2273285 2277040 - Chy11G188210.1 Chy11g00241 241
11 2278927 2282211 + Chy11G188220.1 Chy11g00242 242
11 2282607 2285787 - Chy11G188230.1 Chy11g00243 243
11 2291313 2293789 - Chy11G188240.1 Chy11g00244 244
2 3767004 3769533 + ClG42_02g0041800.10 Clacu02g0418 418
2 3772477 3775742 - ClG42_02g0041900.10 Clacu02g0419 419
2 24995670 25008074 + ClG42_02g0124100.10 Clacu02g1241 1241
2 25008555 25011062 - ClG42_02g0124200.10 Clacu02g1242 1242
2 25021229 25025069 + ClG42_02g0124300.10 Clacu02g1243 1243
2 4004959 4007775 + ClCG02G003930.2 Cla02g00409 409
2 4009353 4014768 - ClCG02G003940.2 Cla02g00410 410
2 25301031 25303772 + ClCG02G012050.1 Cla02g01181 1181
2 25309164 25313278 + ClCG02G012060.2 Cla02g01182 1182
2 25313578 25316324 - ClCG02G012070.2 Cla02g01183 1183
2 25326193 25330467 + ClCG02G012080.2 Cla02g01184 1184
2 1227050 1231220 + CmaCh02G002690.1 Cma02g00269 269
2 1233109 1236151 + CmaCh02G002700.1 Cma02g00270 270
2 1236918 1239840 - CmaCh02G002710.1 Cma02g00271 271
11 9047629 9052310 - CmaCh11G013660.1 Cma11g01366 1366
19 7473265 7477876 + CmaCh19G007500.1 Cma19g00750 750
20 3450444 3459859 - CmaCh20G007370.1 Cma20g00737 737
20 3460175 3466320 + CmaCh20G007380.1 Cma20g00738 738
20 3463463 3466735 - CmaCh20G007390.1 Cma20g00739 739
20 3468634 3472570 - CmaCh20G007400.1 Cma20g00740 740
1 15759007 15761928 + MELO3C013335.2.1 Cme01g01239 1239
1 15763954 15768089 - MELO3C013336.2.1 Cme01g01240 1240
11 3709270 3713859 - MELO3C020832.2.1 Cme11g00364 364
11 3715328 3720301 + MELO3C020831.2.1 Cme11g00365 365
11 3718481 3722930 - MELO3C020830.2.1 Cme11g00366 366
11 3727600 3731542 - MELO3C020829.2.1 Cme11g00367 367
1 5101653 5104641 + PI0013537.1 Cmetu01g0591 591
2 1281411 1285521 + CmoCh02G002660.1 Cmo02g00266 266
2 1287151 1290809 + CmoCh02G002670.1 Cmo02g00267 267
2 1291084 1294060 - CmoCh02G002680.1 Cmo02g00268 268
11 12348584 12353957 + CmoCh11G017520.1 Cmo11g01752 1752
19 7736007 7740348 + CmoCh19G007630.1 Cmo19g00763 763
20 3662142 3669044 - CmoCh20G007340.1 Cmo20g00734 734
20 3670238 3673131 + CmoCh20G007350.1 Cmo20g00735 735
20 3673262 3676664 - CmoCh20G007360.1 Cmo20g00736 736
20 3678588 3681878 - CmoCh20G007370.1 Cmo20g00737 737
2 3762929 3765458 + CmPI595203_02g004140.1 Cmu02g0414 414
2 3768399 3771664 - CmPI595203_02g004150.1 Cmu02g0415 415
2 24863102 24875513 + CmPI595203_02g012080.1 Cmu02g1208 1208
2 24875997 24878504 - CmPI595203_02g012090.1 Cmu02g1209 1209
2 24888671 24892511 + CmPI595203_02g012100.1 Cmu02g1210 1210
8 10628497 10630766 + Conep08aG0133800.1 Cone8ag1300 1300
8 10630899 10632735 - Conep08aG0133900.1 Cone8ag1301 1301
12 9613531 9615882 + Conep12aG0128300.1 Cone12ag1243 1243
12 9615434 9617547 - Conep12aG0128400.1 Cone12ag1244 1244
4 6319570 6321458 + Cp4.1LG04g04910.1 Cpe04g00604 604
5 9577302 9582429 + Cp4.1LG05g13600.1 Cpe05g01361 1361
5 9579431 9584489 - Cp4.1LG05g13660.1 Cpe05g01362 1362
5 9586872 9590430 - Cp4.1LG05g13710.1 Cpe05g01363 1363
15 6773776 6775865 + Cp4.1LG15g06080.1 Cpe15g00605 605
16 5096653 5100850 + Cp4.1LG16g03220.1 Cpe16g00325 325
16 5102200 5105865 + Cp4.1LG16g03170.1 Cpe16g00326 326
16 5106519 5109246 - Cp4.1LG16g03240.1 Cpe16g00328 328
16 5110327 5115965 + Cp4.1LG16g03360.1 Cpe16g00329 329
2 4334617 4337495 + CrPI670011_02g007490.1 Cre02g0749 749
2 4340037 4343326 - CrPI670011_02g007500.1 Cre02g0750 750
2 27503923 27514959 + CrPI670011_02g015230.1 Cre02g1523 1523
2 27515976 27518770 - CrPI670011_02g015240.1 Cre02g1524 1524
2 27530419 27534272 + CrPI670011_02g015250.1 Cre02g1525 1525
2 13428092 13432415 + CsaV3_2G016210.1 Csa02g01405 1405
2 13436249 13440821 + CsaV3_2G016220.1 Csa02g01406 1406
2 13440327 13443846 - CsaV3_2G016230.1 Csa02g01407 1407
2 13445341 13449702 + CsaV3_2G016240.1 Csa02g01408 1408
7 1051293 1051973 + CsaV3_7G001170.1 Csa07g00117 117
7 1057614 1059019 - CsaV3_7G001200.1 Csa07g00120 120
2 3907352 3911559 + Hsped.02g04090.1 Hepe02g0409 409
10 7237062 7243302 + Lsi10G005060.1 Lsi10g00506 506
10 7246929 7250240 + Lsi10G005070.1 Lsi10g00507 507
10 7248434 7254153 - Lsi10G005080.1 Lsi10g00508 508
10 7256855 7261030 + Lsi10G005090.1 Lsi10g00509 509
11 20727281 20731989 + Lsi11G012150.1 Lsi11g01215 1215
11 20733810 20736545 - Lsi11G012160.1 Lsi11g01216 1216
1 4845136 4852259 + Sed0025180.1 Sed01g0659 659
2 6070082 6072625 + Tan0012862.1 Tan02g0658 658
3 1871441 1872348 + Vvi3g186 Vvi3g186 186
3 1872347 1877380 + Vvi3g187 Vvi3g187 187
3 1886319 1890421 + Vvi3g188 Vvi3g188 188
3 1891647 1896304 - Vvi3g189 Vvi3g189 189
3 1897678 1903139 + Vvi3g190 Vvi3g190 190
3 1904171 1912587 + Vvi3g191 Vvi3g191 191
3 1913088 1913969 - Vvi3g192 Vvi3g192 192
3 1914434 1914955 + Vvi3g193 Vvi3g193 193
3 1914964 1915753 + Vvi3g194 Vvi3g194 194
3 1915763 1917733 + Vvi3g195 Vvi3g195 195
       

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