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
Vvi5g479 . . . . . Bpe14g01182 . . . . Cma06g01416 . Car06g01221 . Sed02g1246 Cpe08g00255 . Bhi01g00823 Tan10g0855 Cmetu06g2393 . Hepe05g1540 . Lcy11g1531 . . . . . . . . . . Cone4ag0236 Lsi05g01427 . . Cme06g00617 Blo02g00544 . . Bda13g00130 . . . . . Cmo06g01418 . . . . . . . . . . . . . . Cla05g00553 Cam05g0603 Cec05g0612 Cco05g0610 Clacu05g0599 Cmu05g0569 Cre05g0638 . Csa03g01341 Chy06g00587 .
Vvi5g480 . Blo12g00326 . . . . Bma04g00788 . . Cmo17g00227 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi12g01716 Tan06g2527 . Lac12g2288 Hepe03g0191 . Lcy13g0276 . . . . . . . Lsi09g01326 . . .
Vvi5g481 . . . . . . . . . . . Cma14g01697 . Car14g01528 . . . Bhi01g00821 . . . . . Lcy11g1537 . . . . . . . . . . . Lsi05g01426 . . . . . . . . . . . . . Cmo14g01742 . . . . . . . . . . . . . Cla05g00552 . . . . . . . . . .
Vvi5g482 . . . . . . Bma04g00787 . . Cmo17g00226 . . . . . . . . . . . . . . Cla06g00578 Cam06g0616 Cec06g0617 Cco06g0623 Clacu06g0603 Cmu06g0596 Cre06g1365 . . . . . . Chy05g00402 . . . . . . . . . Sed04g1901 . . . Cma17g00240 . . . Cpe17g00145 Bhi12g01715 Tan06g2526 Cmetu05g0015 Lac12g2287 Hepe03g0192 . Lcy13g0277 . . . . . . . Lsi09g01325 . . .
Vvi5g483 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g484 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g485 . Blo12g00327 . . . . . . . . . . . . . . . . . . . . . . Cla06g00580 Cam06g0618 Cec06g0620 Cco06g0626 Clacu06g0605 Cmu06g0598 Cre06g1366 . . . . . . . . . . . . . . . . . . . . . . . . . Bhi12g01714 . . Lac12g2284 Hepe03g0193 . Lcy13g0278 . . . . . . . Lsi09g01324 . . .
Vvi5g486 . . Bda03g00890 . Bpe04g00834 . Bma04g00786 . Cmo08g01122 Cmo17g00225 . . . . . . . . . . . . . . Cla06g00581 Cam06g0619 Cec06g0621 Cco06g0627 Clacu06g0606 Cmu06g0599 Cre06g1367 . . . Cone4ag0238 . . . . . . . . . . . . Sed01g3969 . . Cma08g01145 Cma17g00239 Car08g01028 Car17g00217 Cpe12g00201 . Bhi12g01713 Tan06g2525 Cmetu01g1582 Lac12g2283 Hepe03g0194 . Lcy13g0279 . . . . . . . Lsi09g01323 . . .
Vvi5g487 . . . . . . . . . . . Cma14g01701 . Car14g01537 Sed12g0915 . Cpe03g01430 Bhi01g00820 Tan10g0851 Cmetu06g1845 . Hepe05g1544 . Lcy11g1539 . . . . . . . . . . . Lsi05g01597 Csa02g01145 . Cme06g00615 . Blo07g00214 Bda11g00572 . . Bpe13g00611 . Bma06g01551 . . Cmo14g01744 . . . . . . . . . . . . . Cla05g00551 Cam05g0599 Cec05g0610 Cco05g0607 Clacu05g0597 Cmu05g0567 Cre05g0635 . Csa03g01338 Chy06g00585 .
Vvi5g488 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 7771245 7772583 + Bda016885.1 Bda03g00890 890
11 5898803 5900533 + Bda005311.1 Bda11g00572 572
13 1694281 1696568 + Bda000989.1 Bda13g00130 130
1 15320906 15323995 - XM_039041445.1 Bhi01g00820 820
1 15384245 15389434 + XM_039022127.1 Bhi01g00821 821
1 15544281 15547091 + XM_039024258.1 Bhi01g00823 823
12 55415054 55423665 + XM_039018454.1 Bhi12g01713 1713
12 55415056 55423665 + XM_039018455.1 Bhi12g01714 1714
12 55415703 55423665 + XM_039018457.1 Bhi12g01715 1715
12 55423913 55426988 + XM_039018458.1 Bhi12g01716 1716
2 9361029 9363232 + BLOR10274 Blo02g00544 544
7 2714740 2716470 + BLOR18146 Blo07g00214 214
12 18812417 18817342 - BLOR04345 Blo12g00326 326
12 18826225 18829029 - BLOR04346 Blo12g00327 327
4 8783909 8786497 + Bma019310.1 Bma04g00786 786
4 8916414 8918983 + Bma019312.1 Bma04g00787 787
4 8933389 8934812 + Bma019313.1 Bma04g00788 788
6 51840576 51842306 + Bma024668.1 Bma06g01551 1551
4 5482779 5487593 + Bpe015494.1 Bpe04g00834 834
13 13128945 13130675 - Bpe010309.1 Bpe13g00611 611
14 8839825 8842142 - Bpe014555.1 Bpe14g01182 1182
5 5257937 5259661 - CaPI482276_05g005990.1 Cam05g0599 599
5 5275239 5277708 + CaPI482276_05g006030.1 Cam05g0603 603
6 8389221 8393314 + CaPI482276_06g006160.1 Cam06g0616 616
6 8407320 8414771 + CaPI482276_06g006180.1 Cam06g0618 618
6 8417433 8430361 - CaPI482276_06g006190.1 Cam06g0619 619
6 8854498 8855917 + Carg17414-RA Car06g01221 1221
8 7014287 7017609 - Carg15907-RA Car08g01028 1028
14 12556838 12563129 - Carg23804-RA Car14g01528 1528
14 12685666 12688489 - Carg23527-RA Car14g01537 1537
17 1316647 1329852 + Carg05421-RA Car17g00217 217
5 4932495 4934219 - CcPI632755_05g006070.1 Cco05g0607 607
5 4956975 4959508 + CcPI632755_05g006100.1 Cco05g0610 610
6 6850907 6854880 + CcPI632755_06g006230.1 Cco06g0623 623
6 6894321 6903139 - CcPI632755_06g006260.1 Cco06g0626 626
6 6927766 6928599 - CcPI632755_06g006270.1 Cco06g0627 627
5 4960530 4962254 - CePI673135_05g006100.1 Cec05g0610 610
5 4978392 4980868 + CePI673135_05g006120.1 Cec05g0612 612
6 6925483 6929444 + CePI673135_06g006170.1 Cec06g0617 617
6 6961800 6969569 + CePI673135_06g006200.1 Cec06g0620 620
6 6972197 6984928 - CePI673135_06g006210.1 Cec06g0621 621
5 4303411 4308191 + Chy5G094480.1 Chy05g00402 402
6 3985127 3986851 - Chy6G111130.1 Chy06g00585 585
6 3995793 3998345 + Chy6G111150.1 Chy06g00587 587
5 4973143 4974867 - ClG42_05g0059700.10 Clacu05g0597 597
5 4990755 4993234 + ClG42_05g0059900.10 Clacu05g0599 599
6 6936698 6940723 + ClG42_06g0060300.10 Clacu06g0603 603
6 6968989 6975904 + ClG42_06g0060500.10 Clacu06g0605 605
6 6978507 6991374 - ClG42_06g0060600.10 Clacu06g0606 606
5 5024101 5025825 - ClCG05G005200.2 Cla05g00551 551
5 5030842 5034088 + ClCG05G005210.1 Cla05g00552 552
5 5041798 5044673 + ClCG05G005220.1 Cla05g00553 553
6 7038827 7043005 + ClCG06G006140.2 Cla06g00578 578
6 7072481 7079400 + ClCG06G006160.1 Cla06g00580 580
6 7081883 7094862 - ClCG06G006180.1 Cla06g00581 581
6 9119732 9122843 + CmaCh06G014160.1 Cma06g01416 1416
8 7059926 7064583 - CmaCh08G011450.1 Cma08g01145 1145
14 12600490 12604509 - CmaCh14G016970.1 Cma14g01697 1697
14 12612912 12615729 - CmaCh14G017010.1 Cma14g01701 1701
17 1218191 1221879 + CmaCh17G002390.1 Cma17g00239 239
17 1222505 1226844 + CmaCh17G002400.1 Cma17g00240 240
6 3937542 3940791 - MELO3C006536.2.1 Cme06g00615 615
6 3948143 3951179 + MELO3C006538.2.1 Cme06g00617 617
1 7698439 7704364 - PI0028568.1 Cmetu01g1582 1582
5 21073893 21079678 - PI0017891.1 Cmetu05g0015 15
6 4178107 4181286 - PI0015778.1 Cmetu06g1845 1845
6 4193966 4197028 + PI0023376.1 Cmetu06g2393 2393
6 10321581 10324286 + CmoCh06G014180.1 Cmo06g01418 1418
8 7151886 7155326 - CmoCh08G011220.1 Cmo08g01122 1122
14 13568320 13574654 - CmoCh14G017420.1 Cmo14g01742 1742
14 13583561 13586514 - CmoCh14G017440.1 Cmo14g01744 1744
17 1328935 1332158 + CmoCh17G002250.1 Cmo17g00225 225
17 1332798 1337080 + CmoCh17G002260.1 Cmo17g00226 226
17 1337408 1340231 + CmoCh17G002270.1 Cmo17g00227 227
5 4816819 4818543 - CmPI595203_05g005670.1 Cmu05g0567 567
5 4834430 4836909 + CmPI595203_05g005690.1 Cmu05g0569 569
6 6742938 6746962 + CmPI595203_06g005960.1 Cmu06g0596 596
6 6775251 6782164 + CmPI595203_06g005980.1 Cmu06g0598 598
6 6784761 6797621 - CmPI595203_06g005990.1 Cmu06g0599 599
4 1069729 1073955 - Conep04aG0024500.1 Cone4ag0236 236
4 1074827 1077125 - Conep04aG0024700.1 Cone4ag0238 238
3 11495538 11498381 - Cp4.1LG03g10670.1 Cpe03g01430 1430
8 1672752 1676118 - Cp4.1LG08g04220.1 Cpe08g00255 255
12 1281573 1297606 + Cp4.1LG12g02030.1 Cpe12g00201 201
17 927736 931812 + Cp4.1LG17g01490.1 Cpe17g00145 145
5 5607172 5608896 - CrPI670011_05g006350.1 Cre05g0635 635
5 5623627 5626145 + CrPI670011_05g006380.1 Cre05g0638 638
6 7833463 7834522 + CrPI670011_06g013650.1 Cre06g1365 1365
6 7839191 7846986 + CrPI670011_06g013660.1 Cre06g1366 1366
6 7849692 7865130 - CrPI670011_06g013670.1 Cre06g1367 1367
2 11187049 11192930 + CsaV3_2G013610.1 Csa02g01145 1145
3 10118261 10119976 - CsaV3_3G013380.1 Csa03g01338 1338
3 10126521 10130109 + CsaV3_3G013410.1 Csa03g01341 1341
3 2455145 2461583 + Hsped.03g01910.1 Hepe03g0191 191
3 2482179 2488983 + Hsped.03g01920.1 Hepe03g0192 192
3 2490058 2499759 - Hsped.03g01930.1 Hepe03g0193 193
3 2500881 2507551 - Hsped.03g01940.1 Hepe03g0194 194
5 65030458 65033359 - Hsped.05g15400.1 Hepe05g1540 1540
5 65063270 65066555 + Hsped.05g15440.1 Hepe05g1544 1544
12 39962890 39964970 - Lag0016655.1 Lac12g2283 2283
12 39965007 39965549 - Lag0016656.1 Lac12g2284 2284
12 40014218 40020379 + Lag0016659.1 Lac12g2287 2287
12 40030291 40032594 - Lag0016660.1 Lac12g2288 2288
11 39213084 39216262 - Maker00031904 Lcy11g1531 1531
11 39250447 39252148 - Maker00031864 Lcy11g1537 1537
11 39263235 39267590 + Maker00032096 Lcy11g1539 1539
13 2952592 2961635 + Maker00024062 Lcy13g0276 276
13 2975101 2979769 - Maker00023814 Lcy13g0277 277
13 2998477 3021205 - Maker00023825 Lcy13g0278 278
13 3032075 3041225 + Maker00023498 Lcy13g0279 279
5 22172567 22173337 + Lsi05G014260.1 Lsi05g01426 1426
5 22184118 22186978 + Lsi05G014270.1 Lsi05g01427 1427
5 23711795 23714625 + Lsi05G015970.1 Lsi05g01597 1597
9 21084246 21092425 + Lsi09G013230.1 Lsi09g01323 1323
9 21093135 21097263 + Lsi09G013240.1 Lsi09g01324 1324
9 21104611 21112034 - Lsi09G013250.1 Lsi09g01325 1325
9 21121169 21125001 - Lsi09G013260.1 Lsi09g01326 1326
1 68825927 68832078 + Sed0000044.1 Sed01g3969 3969
2 49239444 49242336 + Sed0025383.1 Sed02g1246 1246
4 33742613 33752331 + Sed0003906.4 Sed04g1901 1901
12 5737452 5740479 + Sed0020943.1 Sed12g0915 915
6 77873252 77885734 + Tan0015204.1 Tan06g2525 2525
6 77887454 77899809 - Tan0008526.1 Tan06g2526 2526
6 77903523 77904304 - Tan0017716.1 Tan06g2527 2527
10 7064577 7066837 - Tan0012939.1 Tan10g0851 851
10 7115063 7118573 + Tan0017080.1 Tan10g0855 855
5 4962404 4965738 - Vvi5g479 Vvi5g479 479
5 5040288 5043717 + Vvi5g480 Vvi5g480 480
5 5047103 5051884 - Vvi5g481 Vvi5g481 481
5 5055643 5059039 + Vvi5g482 Vvi5g482 482
5 5060180 5063457 + Vvi5g483 Vvi5g483 483
5 5063541 5068415 - Vvi5g484 Vvi5g484 484
5 5082856 5085083 - Vvi5g485 Vvi5g485 485
5 5085635 5088671 - Vvi5g486 Vvi5g486 486
5 5092691 5096187 + Vvi5g487 Vvi5g487 487
5 5098464 5099793 - Vvi5g488 Vvi5g488 488
       

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