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
Vvi18g1340 Blo01g01741 Blo12g00775 . Bda03g00403 Bpe02g00202 Bpe04g00367 . Bma01g02519 . . . . Car01g00860 . . Cpe06g00910 . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g00863 . . . . . Sed07g2827 . . . . . . . . Bhi09g01539 Tan01g3074 Cmetu01g0774 . . Mch11g1488 . Cla09g00950 Cam09g1001 Cec09g1004 Cco09g1014 . . Cre09g0965 . . . .
Vvi18g1341 Blo01g01740 Blo12g00776 . . . . . Bma01g02518 Cmo04g02573 Cmo15g00588 . Cma09g01193 . . . . Cpe13g00695 Bhi04g02163 . . . . . . Cla08g00315 Cam08g0751 Cec08g0301 . Clacu08g0464 . . . . . . . . . Cme03g00294 Blo17g00135 Blo18g00147 . Bda13g01419 . Bpe14g00438 Bma01g01432 Bma02g00155 . . Cmo09g01215 . . Car04g02366 Car15g00540 Cpe01g02128 . . . . . . . . . . . . . . . Lsi08g00257 . . .
Vvi18g1342 Blo01g01739 . . Bda03g00402 Bpe02g00203 Bpe04g00366 Bma04g00383 . Cmo04g02572 Cmo15g00589 . . . . Sed11g1371 . Cpe13g00694 Bhi04g01756 Tan11g1116 Cmetu03g0534 . Hepe02g2808 . Lcy10g1365 . . . . . . . Cone4ag1473 Cone7ag1467 . . . . . . . . Bda11g00864 . . . . . . . . . . Car04g02365 Car15g00541 Cpe01g02127 . . . . . . . . . . . . . . . Lsi08g00569 . Chy03g00492 .
Vvi18g1343 Blo01g01738 . . . . . . Bma01g02517 . . . Cma09g01247 Car01g00780 . . . . Bhi04g02165 . . . . . . Cla08g00325 Cam08g0756 Cec08g0290 . Clacu08g0468 . . Cone4ag1474 . . . . . . Cme03g00895 . . Bda11g00865 . . . . . . . Cmo09g01213 . . . Car09g01082 . . . . . . . . . . . . . . . . Lsi08g00253 . Chy03g00280 .
Vvi18g1344 . Blo12g00777 . Bda03g00401 . . Bma04g00382 . . . . Cma09g01197 . . . . . . . . . . . . Cla08g00327 Cam08g0757 Cec08g0287 . Clacu08g0471 . . . . . . . . . Cme03g00903 . . . . . . . . . . Cmo09g01212 . . . Car09g01081 . . . . . . . . . . . . . . . . Lsi08g00252 . . .
Vvi18g1345 . Blo12g00778 Bda01g00866 . . Bpe04g00365 . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1479 . . . . . . . Blo17g00137 . . Bda13g01421 Bpe02g01104 Bpe14g00436 Bma01g01433 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1346 . . . . Bpe02g00205 . . Bma01g02515 . Cmo15g00590 . . . . . . Cpe13g00693 Bhi04g01757 . . . . . Lcy10g1364 . . . . . . . . . . . . . . Cme03g00296 . . . . . . . . . . . . . Car04g02364 Car15g00542 Cpe01g02126 . . . . . . . . . . . . . . . Lsi08g00568 . Chy03g00493 .
Vvi18g1347 . . Bda01g00865 . . . . . . . . . . . . . Cpe13g00692 Bhi04g02533 . . . . . . . . . . . . . . . . . . . . . . Blo18g00148 . . Bpe02g01103 . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi08g00567 . . .
Vvi18g1348 . . . . . . . . . Cmo15g00591 . . . . . . . Bhi04g01759 Tan11g1119 . . . . . . . . . . . . . . . . . . . Cme03g00297 . . . . . . . . . . . . . . Car15g00543 . . . . . . . . . . . . . . . . . . Chy03g00494 .
Vvi18g1349 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 41369489 41374017 + Bda002996.2 Bda01g00865 865
1 41378043 41379333 + Bda002997.1 Bda01g00866 866
3 3357306 3357560 + Bda016365.1 Bda03g00401 401
3 3358791 3362199 - Bda016366.1 Bda03g00402 402
3 3364121 3366655 - Bda016367.1 Bda03g00403 403
11 8508786 8511577 + Bda005615.1 Bda11g00863 863
11 8513372 8515691 + Bda005616.1 Bda11g00864 864
11 8516932 8518213 + Bda005617.1 Bda11g00865 865
13 36904134 36904748 + Bda000246.3 Bda13g01419 1419
13 36908920 36910227 - Bda000248.1 Bda13g01421 1421
4 42813884 42816986 + XM_039028788.1 Bhi04g01756 1756
4 42818468 42820112 - XM_039028787.1 Bhi04g01757 1757
4 42826306 42834462 - XM_039029121.1 Bhi04g01759 1759
4 59142980 59152042 + XM_039028746.1 Bhi04g02163 2163
4 59210358 59214951 + XM_039030843.1 Bhi04g02165 2165
4 68216819 68228679 - XM_039028700.1 Bhi04g02533 2533
9 41368433 41388948 - XM_039042359.1 Bhi09g01539 1539
1 57093845 57096219 - BLOR01738 Blo01g01738 1738
1 57097480 57098182 - BLOR01739 Blo01g01739 1739
1 57099828 57100379 - BLOR01740 Blo01g01740 1740
1 57104505 57109226 - BLOR01741 Blo01g01741 1741
12 26164914 26169126 + BLOR04794 Blo12g00775 775
12 26171348 26171719 + BLOR04795 Blo12g00776 776
12 26174858 26175112 - BLOR04796 Blo12g00777 777
12 26177442 26178930 - BLOR04797 Blo12g00778 778
17 1258366 1259031 + BLOR15956 Blo17g00135 135
17 1282181 1283472 - BLOR15958 Blo17g00137 137
18 1351498 1352166 + BLOR08635 Blo18g00147 147
18 1355141 1361493 - BLOR08636 Blo18g00148 148
1 24353923 24354678 + Bma001804.2 Bma01g01432 1432
1 24364086 24365383 - Bma001805.1 Bma01g01433 1433
1 82814345 82815442 + Bma003395.1 Bma01g02515 2515
1 82820724 82823163 - Bma003397.1 Bma01g02517 2517
1 82824421 82826782 - Bma003398.1 Bma01g02518 2518
1 82828670 82831668 - Bma003399.1 Bma01g02519 2519
2 1376219 1376833 + Bma014610.1 Bma02g00155 155
4 3079947 3080201 + Bma018843.2 Bma04g00382 382
4 3081450 3095159 - Bma018844.1 Bma04g00383 383
2 1411502 1414331 + Bpe008052.1 Bpe02g00202 202
2 1416199 1418533 + Bpe008053.1 Bpe02g00203 203
2 1435335 1436432 - Bpe008055.1 Bpe02g00205 205
2 14638943 14644350 + Bpe008961.2 Bpe02g01103 1103
2 14647783 14649074 + Bpe008962.2 Bpe02g01104 1104
4 2297277 2298668 + Bpe015056.1 Bpe04g00365 365
4 2301344 2302854 - Bpe015057.1 Bpe04g00366 366
4 2306547 2309073 - Bpe025614 Bpe04g00367 367
14 4015317 4016627 + Bpe007087.1 Bpe14g00436 436
14 4020333 4020947 - Bpe007089.2 Bpe14g00438 438
8 7461375 7464181 + CaPI482276_08g007510.1 Cam08g0751 751
8 7643073 7647596 + CaPI482276_08g007560.1 Cam08g0756 756
8 7793460 7793723 + CaPI482276_08g007570.1 Cam08g0757 757
9 10395570 10400359 - CaPI482276_09g010010.1 Cam09g1001 1001
1 4830404 4833554 - Carg28066-RA Car01g00780 780
1 7377878 7391159 + Carg27778-RA Car01g00860 860
4 18989015 18990175 + Carg15799-RA Car04g02364 2364
4 18990772 18992866 - Carg15800-RA Car04g02365 2365
4 18994619 18995832 - Carg15801-RA Car04g02366 2366
9 10108354 10108617 + Carg27055-RA Car09g01081 1081
9 10127893 10132934 - Carg27056-RA Car09g01082 1082
15 2954432 2957388 + Carg01616-RA Car15g00540 540
15 2958714 2961484 + Carg01615-RA Car15g00541 541
15 2962291 2963436 - Carg01614-RA Car15g00542 542
15 2965011 2977249 - Carg01613-RA Car15g00543 543
9 9684507 9689219 - CcPI632755_09g010140.1 Cco09g1014 1014
8 5968153 5968416 - CePI673135_08g002870.1 Cec08g0287 287
8 6246007 6250525 - CePI673135_08g002900.1 Cec08g0290 290
8 6544553 6545221 - CePI673135_08g003010.1 Cec08g0301 301
9 9715612 9716879 - CePI673135_09g010040.1 Cec09g1004 1004
3 2978617 2982637 - Chy3G052600.1 Chy03g00280 280
3 6819330 6825422 + Chy3G054720.1 Chy03g00492 492
3 6826908 6828059 - Chy3G054730.1 Chy03g00493 493
3 6833266 6844410 - Chy3G054740.1 Chy03g00494 494
8 7347637 7357424 + ClG42_08g0046400.10 Clacu08g0464 464
8 7526495 7531019 + ClG42_08g0046800.10 Clacu08g0468 468
8 7677115 7677378 + ClG42_08g0047100.10 Clacu08g0471 471
8 7400253 7411774 + ClCG08G003050.1 Cla08g00315 315
8 7581863 7586943 + ClCG08G003130.1 Cla08g00325 325
8 7734419 7736322 + ClCG08G003150.2 Cla08g00327 327
9 9955526 9971950 - ClCG09G010190.2 Cla09g00950 950
9 7670772 7679367 + CmaCh09G011930.1 Cma09g01193 1193
9 7725739 7726002 - CmaCh09G011970.1 Cma09g01197 1197
9 8355019 8361558 - CmaCh09G012470.1 Cma09g01247 1247
3 3783167 3786268 + MELO3C008326.2.1 Cme03g00294 294
3 3795027 3796855 - MELO3C008328.2.1 Cme03g00296 296
3 3804756 3813278 - MELO3C008329.2.1 Cme03g00297 297
3 17052593 17056860 + MELO3C024972.2.1 Cme03g00895 895
3 17234659 17235191 + MELO3C024975.2.1 Cme03g00903 903
1 16302408 16315801 + PI0010502.1 Cmetu01g0774 774
3 8605784 8608850 + PI0018217.1 Cmetu03g0534 534
4 18826031 18828196 - CmoCh04G025720.1 Cmo04g02572 2572
4 18829104 18830833 - CmoCh04G025730.1 Cmo04g02573 2573
9 9339342 9339605 + CmoCh09G012120.1 Cmo09g01212 1212
9 9362476 9367622 - CmoCh09G012130.1 Cmo09g01213 1213
9 9387808 9397096 - CmoCh09G012150.1 Cmo09g01215 1215
15 2837303 2838182 + CmoCh15G005880.1 Cmo15g00588 588
15 2838210 2842645 + CmoCh15G005890.1 Cmo15g00589 589
15 2844691 2845629 - CmoCh15G005900.1 Cmo15g00590 590
15 2847649 2860396 - CmoCh15G005910.1 Cmo15g00591 591
4 11590200 11591460 + Conep04aG0152500.1 Cone4ag1473 1473
4 11592676 11595398 + Conep04aG0152600.1 Cone4ag1474 1474
4 11599858 11601257 - Conep04aG0153100.1 Cone4ag1479 1479
7 10331088 10332145 - Conep07aG0150900.1 Cone7ag1467 1467
1 17944071 17944451 + Cp4.1LG01g21230.1 Cpe01g02126 2126
1 17945464 17947870 - Cp4.1LG01g21260.1 Cpe01g02127 2127
1 17949368 17951892 - Cp4.1LG01g21300.1 Cpe01g02128 2128
6 6288915 6298165 - Cp4.1LG06g07490.1 Cpe06g00910 910
13 6459993 6472625 + Cp4.1LG13g03890.1 Cpe13g00692 692
13 6474340 6475485 + Cp4.1LG13g03910.1 Cpe13g00693 693
13 6478460 6480214 - Cp4.1LG13g03820.1 Cpe13g00694 694
13 6481426 6484239 - Cp4.1LG13g03840.1 Cpe13g00695 695
9 9893081 9900634 - CrPI670011_09g009650.1 Cre09g0965 965
2 77136116 77138441 - Hsped.02g28080.1 Hepe02g2808 2808
10 36832151 36833317 + Maker00008597 Lcy10g1364 1364
10 36834460 36836591 - Maker00008527 Lcy10g1365 1365
8 5680461 5680724 - Lsi08G002520.1 Lsi08g00252 252
8 5723596 5728036 - Lsi08G002530.1 Lsi08g00253 253
8 5861165 5871794 - Lsi08G002570.1 Lsi08g00257 257
8 13908697 13919646 + Lsi08G005670.1 Lsi08g00567 567
8 13928215 13929375 + Lsi08G005680.1 Lsi08g00568 568
8 13931047 13933730 - Lsi08G005690.1 Lsi08g00569 569
11 11771392 11781631 - MC11g1206 Mch11g1488 1488
7 43106713 43114762 + Sed0008098.1 Sed07g2827 2827
11 29725975 29729501 - Sed0015682.1 Sed11g1371 1371
1 78687635 78701928 + Tan0014631.1 Tan01g3074 3074
11 8822776 8825913 + Tan0007290.2 Tan11g1116 1116
11 8833335 8847314 - Tan0011403.2 Tan11g1119 1119
18 19128787 19136915 + Vvi18g1340 Vvi18g1340 1340
18 19143645 19150562 + Vvi18g1341 Vvi18g1341 1341
18 19152606 19156541 + Vvi18g1342 Vvi18g1342 1342
18 19179443 19182979 + Vvi18g1343 Vvi18g1343 1343
18 19184318 19184948 - Vvi18g1344 Vvi18g1344 1344
18 19199495 19202915 - Vvi18g1345 Vvi18g1345 1345
18 19223277 19225297 - Vvi18g1346 Vvi18g1346 1346
18 19242563 19274978 - Vvi18g1347 Vvi18g1347 1347
18 19280779 19290355 - Vvi18g1348 Vvi18g1348 1348
18 19321735 19326281 - Vvi18g1349 Vvi18g1349 1349
       

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