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
Vvi1g21 . . . . . Bpe10g00903 . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0899 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g22 . . . . . Bpe10g00902 Bma14g01667 Bma15g00129 Cmo04g01793 Cmo18g01121 . Cma18g01099 . Car18g01014 Sed01g3463 Cpe09g00227 Cpe01g01511 Bhi07g01477 Tan04g0980 Cmetu09g1194 . . . . Cla05g02387 . . Cco05g2632 Clacu05g2560 Cmu05g2417 Cre05g2534 Cone13ag0900 Cone19ag0898 . . Lsi04g00357 Csa05g02520 Chy10g01064 Cme10g00350 . Blo11g00795 . . . . . . . . . Cma04g01708 . Car04g01742 . . . . . . . . . . . . . . . . . . . . .
Vvi1g23 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g24 Blo01g00458 . Bda01g02122 . . . . . . . . Cma18g01101 . Car18g01015 Sed06g1783 Cpe09g00225 . Bhi07g01479 Tan04g0982 Cmetu10g0201 . . . . Cla05g02388 . . Cco05g2634 Clacu05g2561 Cmu05g2418 Cre05g2536 . . . Cone9ag0533 Lsi04g00358 Csa05g02519 Chy10g01063 Cme10g00352 . . . . . Bpe02g02311 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g25 Blo01g00457 . . . . . . . . Cmo18g01122 . Cma18g01102 . Car18g01016 . Cpe09g00224 . . . . . . . . . . . . . . . Cone13ag0901 Cone19ag0899 . . . . . . . . . . . . Bma01g00127 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g26 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone9ag0038 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g27 Blo01g00456 . Bda01g02123 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0519 Cone9ag0534 . . . . . . . . . Bpe02g02312 Bma01g00126 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g28 Blo01g00455 Blo16g01083 Bda01g02124 Bda11g01173 Bpe13g01371 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0523 Cone9ag0536 . . . . . . . Bda11g01173 . Bpe02g02313 Bma01g00125 . . . . . . . . . Cpe07g00090 . . . . . . . . . . . . . . . . . .
Vvi1g29 . . Bda01g02125 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma01g00124 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g30 . . . . . Bpe10g00901 . Bma15g00130 Cmo04g01790 . . . . . Sed06g1781 . Cpe01g01509 Bhi07g01483 Tan04g0990 Cmetu10g1518 Lac13g0381 Hepe10g1800 . . Cla05g02389 . . Cco05g2636 Clacu05g2563 Cmu05g2420 Cre05g2537 Cone13ag0903 Cone19ag0900 . . Lsi04g00360 Csa05g02517 Chy10g01061 Cme10g00354 Blo06g00929 . . . . . . . . . . Cma04g01705 . Car04g01740 . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 57248819 57260175 - Bda004453.1 Bda01g02122 2122
1 57261078 57262730 - Bda004454.1 Bda01g02123 2123
1 57263586 57264810 - Bda004455.1 Bda01g02124 2124
1 57266698 57268328 - Bda004456.1 Bda01g02125 2125
11 12092347 12093184 - Bda007671.1 Bda11g01173 1173
7 43274748 43278362 - XM_039037181.1 Bhi07g01477 1477
7 43287860 43292634 - XM_039035616.1 Bhi07g01479 1479
7 43302410 43308242 - XM_039036647.1 Bhi07g01483 1483
1 5053461 5059967 + BLOR00455 Blo01g00455 455
1 5061529 5063180 + BLOR00456 Blo01g00456 456
1 5066223 5074398 + BLOR00457 Blo01g00457 457
1 5075519 5077378 + BLOR00458 Blo01g00458 458
6 32516010 32527215 + BLOR17512 Blo06g00929 929
11 12154674 12155806 + BLOR03671 Blo11g00795 795
16 39372010 39372860 - BLOR21870 Blo16g01083 1083
1 1232262 1233928 + Bma000289.1 Bma01g00124 124
1 1236056 1237257 + Bma000290.1 Bma01g00125 125
1 1238269 1239910 + Bma000291.1 Bma01g00126 126
1 1244103 1256984 + Bma000292.2 Bma01g00127 127
14 35349435 35350915 + Bma012400.2 Bma14g01667 1667
15 1405910 1407300 - Bma013107.1 Bma15g00129 129
15 1411187 1416971 - Bma013108.3 Bma15g00130 130
2 23775693 23786933 - Bpe010127.2 Bpe02g02311 2311
2 23787688 23789099 - Bpe010128.1 Bpe02g02312 2312
2 23791628 23792860 - Bpe010129.1 Bpe02g02313 2313
10 14683472 14689404 + Bpe003205.1 Bpe10g00901 901
10 14694021 14695411 + Bpe003206.1 Bpe10g00902 902
10 14696423 14710926 - Bpe003207.3 Bpe10g00903 903
13 18960934 18961754 - Bpe025292 Bpe13g01371 1371
4 9960222 9965558 + Carg14365-RA Car04g01740 1740
4 9981470 9984917 + Carg14363-RA Car04g01742 1742
18 10565825 10569941 - Carg17316-RA Car18g01014 1014
18 10576054 10578411 - Carg17315-RA Car18g01015 1015
18 10579415 10589269 - Carg17314-RA Car18g01016 1016
5 34466605 34471957 - CcPI632755_05g026320.1 Cco05g2632 2632
5 34478876 34483666 - CcPI632755_05g026340.1 Cco05g2634 2634
5 34492576 34498026 - CcPI632755_05g026360.1 Cco05g2636 2636
10 15779827 15787892 + Chy10G182550.1 Chy10g01061 1061
10 15795155 15797359 + Chy10G182570.1 Chy10g01063 1063
10 15805247 15806890 + Chy10G182580.1 Chy10g01064 1064
5 33569405 33573632 - ClG42_05g0256000.10 Clacu05g2560 2560
5 33580746 33586387 - ClG42_05g0256100.10 Clacu05g2561 2561
5 33595114 33600548 - ClG42_05g0256300.10 Clacu05g2563 2563
5 35419729 35424315 - ClCG05G023630.2 Cla05g02387 2387
5 35432356 35437337 - ClCG05G023640.1 Cla05g02388 2388
5 35438332 35451717 - ClCG05G023650.2 Cla05g02389 2389
4 8562198 8568865 + CmaCh04G017050.1 Cma04g01705 1705
4 8585126 8588679 + CmaCh04G017080.1 Cma04g01708 1708
18 9000091 9003211 - CmaCh18G010990.1 Cma18g01099 1099
18 9006750 9012575 - CmaCh18G011010.1 Cma18g01101 1101
18 9013246 9022929 - CmaCh18G011020.1 Cma18g01102 1102
10 2266935 2269528 - MELO3C012159.2.1 Cme10g00350 350
10 2277853 2280449 - MELO3C012158.2.1 Cme10g00352 352
10 2288279 2294060 - MELO3C012156.2.1 Cme10g00354 354
9 118441 120375 + PI0023593.1 Cmetu09g1194 1194
10 19731370 19733801 + PI0009256.1 Cmetu10g0201 201
10 19717419 19722995 + PI0027176.1 Cmetu10g1518 1518
4 8996915 9003756 + CmoCh04G017900.1 Cmo04g01790 1790
4 9019060 9022587 + CmoCh04G017930.1 Cmo04g01793 1793
18 11575300 11579438 - CmoCh18G011210.1 Cmo18g01121 1121
18 11582886 11599330 - CmoCh18G011220.1 Cmo18g01122 1122
5 33307178 33313897 - CmPI595203_05g024170.1 Cmu05g2417 2417
5 33318517 33324156 - CmPI595203_05g024180.1 Cmu05g2418 2418
5 33332902 33338336 - CmPI595203_05g024200.1 Cmu05g2420 2420
6 2591809 2593843 - Conep06aG0053100.1 Cone6ag0519 519
6 2602241 2603302 - Conep06aG0053500.1 Cone6ag0523 523
9 160918 162320 - Conep09aG0003800.1 Cone9ag0038 38
9 2547813 2549647 - Conep09aG0054300.1 Cone9ag0533 533
9 2552386 2554369 - Conep09aG0054400.1 Cone9ag0534 534
9 2563109 2564913 - Conep09aG0054600.1 Cone9ag0536 536
13 7946615 7949603 + Conep13aG0092700.1 Cone13ag0899 899
13 7949758 7951611 - Conep13aG0092800.1 Cone13ag0900 900
13 7955235 7961815 - Conep13aG0092900.1 Cone13ag0901 901
13 7968958 7973064 - Conep13aG0093100.1 Cone13ag0903 903
19 7005887 7007734 - Conep19aG0092300.1 Cone19ag0898 898
19 7013667 7020032 - Conep19aG0092400.1 Cone19ag0899 899
19 7020545 7023728 - Conep19aG0092500.1 Cone19ag0900 900
1 8997533 9003277 + Cp4.1LG01g12100.1 Cpe01g01509 1509
1 9019436 9022239 + Cp4.1LG01g12080.1 Cpe01g01511 1511
7 436648 439777 - Cp4.1LG07g00840.1 Cpe07g00090 90
9 1284728 1294294 + Cp4.1LG09g02300.1 Cpe09g00224 224
9 1294978 1297412 + Cp4.1LG09g02280.1 Cpe09g00225 225
9 1303048 1309092 + Cp4.1LG09g02270.1 Cpe09g00227 227
5 36657101 36661032 - CrPI670011_05g025340.1 Cre05g2534 2534
5 36662567 36674311 - CrPI670011_05g025360.1 Cre05g2536 2536
5 36675650 36688712 - CrPI670011_05g025370.1 Cre05g2537 2537
5 26725050 26730675 + CsaV3_5G033360.1 Csa05g02517 2517
5 26738302 26744983 + CsaV3_5G033380.1 Csa05g02519 2519
5 26748134 26751256 + CsaV3_5G033390.1 Csa05g02520 2520
10 54742658 54747864 + Hsped.10g18000.1 Hepe10g1800 1800
13 2685778 2690912 + Lag0040177.1 Lac13g0381 381
4 3571581 3573756 - Lsi04G003570.1 Lsi04g00357 357
4 3585339 3587536 - Lsi04G003580.1 Lsi04g00358 358
4 3596747 3602422 - Lsi04G003600.1 Lsi04g00360 360
1 63748376 63751940 + Sed0008471.1 Sed01g3463 3463
6 42477864 42485283 + Sed0024899.3 Sed06g1781 1781
6 42496588 42499664 + Sed0001803.1 Sed06g1783 1783
4 8876993 8882042 - Tan0000292.5 Tan04g0980 980
4 8883892 8892221 - Tan0011903.2 Tan04g0982 982
4 8927565 8929779 - Tan0000634.1 Tan04g0990 990
1 305942 311685 + Vvi1g21 Vvi1g21 21
1 312338 317465 - Vvi1g22 Vvi1g22 22
1 334517 337539 - Vvi1g23 Vvi1g23 23
1 339374 341595 - Vvi1g24 Vvi1g24 24
1 342582 373752 - Vvi1g25 Vvi1g25 25
1 376806 378298 + Vvi1g26 Vvi1g26 26
1 381266 382921 - Vvi1g27 Vvi1g27 27
1 390749 395260 - Vvi1g28 Vvi1g28 28
1 397350 400531 + Vvi1g29 Vvi1g29 29
1 400559 418459 - Vvi1g30 Vvi1g30 30
       

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