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
Vvi18g340 . Blo12g00691 . Bda03g00512 Bpe02g00085 Bpe04g00468 . Bma01g02633 . . Cma01g01411 . . . . . . . . . . . . . . . . . . . . Cone4ag1365 Cone7ag1566 . . Lsi04g02356 Csa04g01838 . . . . Bda11g00752 Bda13g01409 . . . . Sed12g1436 Cmo01g01461 . . . . . . Cpe02g00532 Bhi09g02629 Tan01g3975 Cmetu07g0508 . Hepe01g2251 Mch11g0798 . Cla11g01508 Cam11g1567 Cec11g1596 Cco11g1594 Clacu11g1723 Cmu11g1543 Cre11g1958 . . Chy07g00694 Cme07g00907
Vvi18g341 . Blo12g00692 . Bda03g00511 Bpe02g00086 Bpe04g00467 . Bma01g02632 Cmo05g00502 . . . . . Sed04g0056 . Cpe07g00117 Bhi04g00715 Tan02g2354 Cmetu03g0634 . Hepe10g0527 . . Cla08g01085 Cam08g1537 Cec08g1111 Cco08g1238 Clacu08g1240 . Cre08g1021 Cone4ag1364 Cone7ag1567 . . . . . Cme03g01497 . . Bda11g00753 . Bpe02g01610 . . Bma02g00148 . . . Cma12g00138 Cma05g00479 Car05g00427 . Cpe11g00419 . . . . . . . . . . . . . . . Lsi08g00942 . Chy03g01008 .
Vvi18g342 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g343 . . . . Bpe02g00087 . . Bma01g02631 Cmo05g00503 . . . . . . . . . . . . . . . Cla08g01086 Cam08g1538 Cec08g1112 Cco08g1239 Clacu08g1241 . Cre08g1022 . . . . . . . Cme03g01498 . . . . . . . . . . . . Cma05g00480 Car05g00428 . Cpe11g00420 . . . . . . . . . . . . . . . Lsi08g00943 . Chy03g01009 .
Vvi18g344 . . . . . . . . . Cmo12g00109 . . . . . . Cpe07g00115 Bhi04g00720 . . . . . . Cla08g01082 Cam08g1533 Cec08g1109 Cco08g1236 Clacu08g1238 . Cre08g1019 . . . . . . . Cme03g01492 . . . Bda01g01398 . . . . . . . Cma12g00135 . . . . . . . . . . . . . . . . . . . Lsi08g00938 . . .
Vvi18g345 . . . . Bpe02g00088 . . Bma01g02630 . . . . . . Sed04g0058 . . Bhi04g00721 Tan02g2350 Cmetu03g2083 . . . . Cla08g01081 Cam08g1532 Cec08g1108 Cco08g1235 Clacu08g1237 . Cre08g1018 . . . . . . . Cme03g01491 . . Bda11g00754 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi08g00937 . . .
Vvi18g346 . . . . . . . . . . . . . . Sed11g2301 . . Bhi04g02508 Tan11g0077 . . Hepe02g3445 . . Cla08g01072 Cam08g1522 Cec08g1100 Cco08g1226 Clacu08g1229 . Cre08g1009 Cone4ag1363 . . Cone20ag0480 . Csa03g04575 . Cme03g01483 . . . . . . Bma01g00856 . . . . . . . . . . . . . . . . . Cla11g00770 Cam11g0805 Cec11g0786 Cco11g0792 Clacu11g1053 Cmu11g0914 Cre11g1250 Lsi08g00395 . Chy03g00061 .
Vvi18g347 . Blo12g00693 . . . Bpe04g00465 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo09g00642 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g348 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g349 . Blo12g00694 . . Bpe02g00090 . . Bma01g02627 . . . . . . Sed03g0662 . . Bhi04g02504 Tan11g0081 Cmetu03g1659 . Hepe02g3443 . Lcy10g2334 . . . . . . . . Cone7ag1570 . . . . . . . . Bda11g00757 . . . . . . . . . . . . . . . . . . . . . Cla11g00768 Cam11g0802 Cec11g0784 Cco11g0790 Clacu11g1056 Cmu11g0916 Cre11g1248 . . Chy03g00063 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 49895756 49898161 + Bda032950 Bda01g01398 1398
3 4326566 4327622 + Bda016480.1 Bda03g00511 511
3 4329291 4331873 - Bda016481.1 Bda03g00512 512
11 7532732 7535656 + Bda005498.1 Bda11g00752 752
11 7536973 7538030 - Bda033060 Bda11g00753 753
11 7546006 7547819 - Bda005499.1 Bda11g00754 754
11 7580736 7585780 - Bda005504.1 Bda11g00757 757
13 36811282 36813087 + Bda000236.1 Bda13g01409 1409
4 17171077 17173497 + XM_039030606.1 Bhi04g00715 715
4 17240361 17250859 + XM_039028502.1 Bhi04g00720 720
4 17270891 17273289 - XM_039030528.1 Bhi04g00721 721
4 67723561 67730277 + XM_039030597.1 Bhi04g02504 2504
4 67789684 67795011 + XM_039030013.1 Bhi04g02508 2508
9 70848254 70851803 - XM_039042005.1 Bhi09g02629 2629
12 25140161 25142559 + BLOR04710 Blo12g00691 691
12 25144241 25145317 - BLOR04711 Blo12g00692 692
12 25164122 25174586 + BLOR04712 Blo12g00693 693
12 25179809 25190721 - BLOR04713 Blo12g00694 694
1 8069629 8071692 + Bma001077.1 Bma01g00856 856
1 83844362 83849381 + Bma003512.2 Bma01g02627 2627
1 83860153 83862240 + Bma003515.1 Bma01g02630 2630
1 83862902 83865173 + Bma003516.1 Bma01g02631 2631
1 83870667 83871735 + Bma003517.1 Bma01g02632 2632
1 83873129 83875988 - Bma003518.1 Bma01g02633 2633
2 1309261 1311065 + Bma014604.1 Bma02g00148 148
2 649929 652743 + Bpe007936.1 Bpe02g00085 85
2 654121 655180 - Bpe007937.1 Bpe02g00086 86
2 660964 663187 - Bpe007938.1 Bpe02g00087 87
2 663871 665931 - Bpe007939.1 Bpe02g00088 88
2 677193 682056 - Bpe007941.1 Bpe02g00090 90
2 18987704 18988784 - Bpe009457.1 Bpe02g01610 1610
4 2958508 2959098 - Bpe015152.1 Bpe04g00465 465
4 2965614 2966678 + Bpe025625 Bpe04g00467 467
4 2968314 2970901 - Bpe015154.3 Bpe04g00468 468
8 21424077 21427882 - CaPI482276_08g015220.1 Cam08g1522 1522
8 21580229 21582316 + CaPI482276_08g015320.1 Cam08g1532 1532
8 21583997 21587982 - CaPI482276_08g015330.1 Cam08g1533 1533
8 21600274 21602694 - CaPI482276_08g015370.1 Cam08g1537 1537
8 21622177 21625094 - CaPI482276_08g015380.1 Cam08g1538 1538
11 10181443 10186224 + CaPI482276_11g008020.1 Cam11g0802 802
11 10206026 10210297 + CaPI482276_11g008050.1 Cam11g0805 805
11 28449128 28449585 - CaPI482276_11g015670.1 Cam11g1567 1567
5 2446501 2447585 - Carg09231-RA Car05g00427 427
5 2457567 2460071 - Carg09230-RA Car05g00428 428
8 23976270 23980111 - CcPI632755_08g012260.1 Cco08g1226 1226
8 24141843 24143926 + CcPI632755_08g012350.1 Cco08g1235 1235
8 24145558 24149573 - CcPI632755_08g012360.1 Cco08g1236 1236
8 24155278 24165521 - CcPI632755_08g012380.1 Cco08g1238 1238
8 24183360 24187874 - CcPI632755_08g012390.1 Cco08g1239 1239
11 9007751 9012929 + CcPI632755_11g007900.1 Cco11g0790 790
11 9033724 9038403 + CcPI632755_11g007920.1 Cco11g0792 792
11 28816406 28817058 - CcPI632755_11g015940.1 Cco11g1594 1594
8 22827086 22830949 - CePI673135_08g011000.1 Cec08g1100 1100
8 22990668 22992763 + CePI673135_08g011080.1 Cec08g1108 1108
8 22994482 22999659 - CePI673135_08g011090.1 Cec08g1109 1109
8 23010732 23013134 - CePI673135_08g011110.1 Cec08g1111 1111
8 23032518 23035436 - CePI673135_08g011120.1 Cec08g1112 1112
11 9225914 9232034 + CePI673135_11g007840.1 Cec11g0784 784
11 9252329 9256498 + CePI673135_11g007860.1 Cec11g0786 786
11 30272478 30272922 - CePI673135_11g015960.1 Cec11g1596 1596
3 617777 621606 - Chy3G050410.1 Chy03g00061 61
3 639236 643952 - Chy3G050430.1 Chy03g00063 63
3 13626353 13628923 - Chy3G059880.1 Chy03g01008 1008
3 13648245 13652876 - Chy3G059890.1 Chy03g01009 1009
7 6725827 6728615 + Chy7G135240.1 Chy07g00694 694
8 22184320 22195921 - ClG42_08g0122900.10 Clacu08g1229 1229
8 22349024 22351112 + ClG42_08g0123700.10 Clacu08g1237 1237
8 22352774 22356672 - ClG42_08g0123800.10 Clacu08g1238 1238
8 22369021 22371439 - ClG42_08g0124000.10 Clacu08g1240 1240
8 22390236 22393088 - ClG42_08g0124100.10 Clacu08g1241 1241
11 13091079 13095763 - ClG42_11g0105300.10 Clacu11g1053 1053
11 13115164 13119947 - ClG42_11g0105600.10 Clacu11g1056 1056
11 28475378 28475821 - ClG42_11g0172300.10 Clacu11g1723 1723
8 23407805 23412886 - ClCG08G010730.1 Cla08g01072 1072
8 23574088 23576539 + ClCG08G010830.1 Cla08g01081 1081
8 23577532 23582812 - ClCG08G010840.2 Cla08g01082 1082
8 23590580 23600005 - ClCG08G010880.2 Cla08g01085 1085
8 23617792 23622519 - ClCG08G010890.2 Cla08g01086 1086
11 11050539 11057057 + ClCG11G008030.2 Cla11g00768 768
11 11078086 11083974 + ClCG11G008050.2 Cla11g00770 770
11 28741829 28745537 - ClCG11G015450.2 Cla11g01508 1508
1 9966020 9970659 + CmaCh01G014110.1 Cma01g01411 1411
5 2253405 2254605 - CmaCh05G004790.1 Cma05g00479 479
5 2263818 2266659 - CmaCh05G004800.1 Cma05g00480 480
12 582077 586281 - CmaCh12G001350.1 Cma12g00135 135
12 594664 595818 - CmaCh12G001380.1 Cma12g00138 138
3 24038498 24045878 - MELO3C011388.2.1 Cme03g01483 1483
3 24174035 24176336 + MELO3C011379.2.1 Cme03g01491 1491
3 24178427 24187153 - MELO3C011378.2.1 Cme03g01492 1492
3 24198642 24200788 - MELO3C011375.2.1 Cme03g01497 1497
3 24218301 24220693 - MELO3C011374.2.1 Cme03g01498 1498
7 9464671 9468102 + MELO3C010431.2.1 Cme07g00907 907
3 5188209 5190526 + PI0014456.1 Cmetu03g0634 634
3 25882806 25887295 + PI0010681.1 Cmetu03g1659 1659
3 5201563 5203900 - PI0012130.2 Cmetu03g2083 2083
7 19265316 19268900 - PI0006129.1 Cmetu07g0508 508
1 11376793 11380293 + CmoCh01G014610.1 Cmo01g01461 1461
5 2412391 2413734 - CmoCh05G005020.1 Cmo05g00502 502
5 2423661 2426178 - CmoCh05G005030.1 Cmo05g00503 503
9 3211492 3212324 - CmoCh09G006420.1 Cmo09g00642 642
12 626966 632457 - CmoCh12G001090.1 Cmo12g00109 109
11 12420174 12424858 - CmPI595203_11g009140.1 Cmu11g0914 914
11 12444331 12449116 - CmPI595203_11g009160.1 Cmu11g0916 916
11 27727740 27728183 - CmPI595203_11g015430.1 Cmu11g1543 1543
4 11088249 11090092 + Conep04aG0141100.1 Cone4ag1363 1363
4 11096816 11098071 + Conep04aG0141300.1 Cone4ag1364 1364
4 11099088 11102859 - Conep04aG0141400.1 Cone4ag1365 1365
7 10749008 10752411 + Conep07aG0161200.1 Cone7ag1566 1566
7 10753507 10754792 - Conep07aG0161300.1 Cone7ag1567 1567
7 10762903 10767430 - Conep07aG0161700.1 Cone7ag1570 1570
20 2568276 2571404 + Conep20aG0049500.1 Cone20ag0480 480
2 3155187 3160210 - Cp4.1LG02g03320.1 Cpe02g00532 532
7 635797 641267 - Cp4.1LG07g01210.1 Cpe07g00115 115
7 647142 648947 - Cp4.1LG07g01160.1 Cpe07g00117 117
11 2358273 2360492 - Cp4.1LG11g04180.1 Cpe11g00419 419
11 2370712 2373596 - Cp4.1LG11g04210.1 Cpe11g00420 420
8 23189625 23193503 - CrPI670011_08g010090.1 Cre08g1009 1009
8 23347706 23349790 + CrPI670011_08g010180.1 Cre08g1018 1018
8 23351496 23356381 - CrPI670011_08g010190.1 Cre08g1019 1019
8 23359843 23370092 - CrPI670011_08g010210.1 Cre08g1021 1021
8 23389783 23392696 - CrPI670011_08g010220.1 Cre08g1022 1022
11 10845012 10849776 + CrPI670011_11g012480.1 Cre11g1248 1248
11 10870287 10875020 + CrPI670011_11g012500.1 Cre11g1250 1250
11 31374491 31374935 - CrPI670011_11g019580.1 Cre11g1958 1958
3 39806582 39817079 + CsaV3_3G048810.1 Csa03g04575 4575
4 18015303 18019322 + CsaV3_4G028640.1 Csa04g01838 1838
1 87160329 87163759 - Hsped.01g22510.1 Hepe01g2251 2251
2 83791264 83797593 + Hsped.02g34430.1 Hepe02g3443 3443
2 83814221 83818989 + Hsped.02g34450.1 Hepe02g3445 3445
10 6095217 6096687 - Hsped.10g05270.1 Hepe10g0527 527
10 46934370 46941834 + Maker00039160 Lcy10g2334 2334
4 30756174 30759860 - Lsi04G023560.1 Lsi04g02356 2356
8 10972139 10975663 + Lsi08G003950.1 Lsi08g00395 395
8 17848223 17851194 + Lsi08G009370.1 Lsi08g00937 937
8 17851552 17856108 - Lsi08G009380.1 Lsi08g00938 938
8 17877016 17880008 - Lsi08G009420.1 Lsi08g00942 942
8 17904841 17907751 - Lsi08G009430.1 Lsi08g00943 943
11 5379801 5386130 - MC11g0673 Mch11g0798 798
3 4016070 4031082 + Sed0003415.1 Sed03g0662 662
4 295544 298089 + Sed0012248.1 Sed04g0056 56
4 305041 308026 - Sed0027281.1 Sed04g0058 58
11 36090263 36092615 + Sed0016927.3 Sed11g2301 2301
12 11984589 11989064 - Sed0023569.1 Sed12g1436 1436
1 104581157 104585858 - Tan0013426.1 Tan01g3975 3975
2 92180770 92183403 + Tan0009786.1 Tan02g2350 2350
2 92199075 92206380 - Tan0017846.1 Tan02g2354 2354
11 915203 919373 - Tan0013162.5 Tan11g0077 77
11 940337 945676 - Tan0017040.1 Tan11g0081 81
18 3822866 3829701 + Vvi18g340 Vvi18g340 340
18 3830999 3832521 - Vvi18g341 Vvi18g341 341
18 3832556 3832826 + Vvi18g342 Vvi18g342 342
18 3842547 3845101 - Vvi18g343 Vvi18g343 343
18 3845615 3852022 + Vvi18g344 Vvi18g344 344
18 3852040 3861196 - Vvi18g345 Vvi18g345 345
18 3861741 3869760 - Vvi18g346 Vvi18g346 346
18 3875299 3878509 + Vvi18g347 Vvi18g347 347
18 3879306 3882855 + Vvi18g348 Vvi18g348 348
18 3887489 3898689 - Vvi18g349 Vvi18g349 349
       

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