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
Vvi5g59 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g60 . . . . . . . . . . . Cma14g01588 . Car14g01398 Sed02g1135 . Cpe03g01325 Bhi01g01093 Tan10g1080 Cmetu06g1917 . Hepe05g1373 . Lcy11g1335 . . . . . . . . . . Cone4ag0104 Lsi05g01418 . . Cme06g00792 . Blo07g00142 . . . Bpe13g00699 . . . . Cmo14g01618 . . . . . . . . . . . . . Cla05g00709 Cam05g0776 Cec05g0784 Cco05g0777 Clacu05g0766 Cmu05g0732 Cre05g0806 . Csa03g01521 Chy06g00757 .
Vvi5g61 . . . . . . . . Cmo08g01245 Cmo17g00360 . . . . . . . . . . . . . . Cla06g00426 Cam06g0448 Cec06g0455 Cco06g0454 Clacu06g0435 Cmu06g0436 Cre06g1213 . . Cone7ag0099 Cone4ag0105 . Csa06g01869 Chy11g01574 . . Blo07g00143 Bda11g00499 . . Bpe13g00698 . Bma06g01465 Sed09g0311 . . . Cma17g00370 . Car17g00345 Cpe12g00325 . Bhi12g01936 Tan06g2768 Cmetu11g2114 . . . Lcy12g0853 . . . . . . . Lsi09g01494 . . Cme11g02083
Vvi5g62 Blo01g00031 . Bda03g01183 Bda08g00332 Bpe04g01116 . . Bma05g00994 Cmo08g01244 Cmo17g00359 . . . . . . . . . . . . . . Cla06g00427 . . . . . . Cone14ag0716 Cone15ag0728 . . . Csa06g01870 Chy11g01573 . . . . . . . . . . . . Cma08g01276 Cma17g00369 Car08g01146 Car17g00344 Cpe12g00324 Cpe17g00068 Bhi12g01932 . . . . . Lcy12g0852 . . . . . . . Lsi09g01493 . . Cme11g02082
Vvi5g63 Blo01g00030 . . Bda08g00333 . . . Bma05g00993 . . Cma06g01564 Cma14g01590 Car06g01329 Car14g01399 Sed02g1136 Cpe08g00149 Cpe03g01327 Bhi01g01090 Tan10g1077 Cmetu06g1585 . Hepe05g1374 . Lcy11g1336 . . . . . . . Cone14ag0717 Cone15ag0729 . . Lsi05g01420 . . Cme06g00790 . Blo07g00144 Bda11g00500 . Bpe05g00798 Bpe13g00697 . Bma06g01466 . Cmo06g01560 Cmo14g01619 . . . . . . . . . . . . . Cla05g00707 Cam05g0774 Cec05g0782 Cco05g0775 Clacu05g0764 Cmu05g0730 Cre05g0804 . Csa03g01519 Chy06g00756 .
Vvi5g64 Blo01g00029 . . Bda08g00334 . Bpe14g01099 . Bma05g00992 Cmo08g01243 Cmo17g00358 . . . . . . . . . . . . . . Cla06g00428 Cam06g0450 Cec06g0457 Cco06g0456 Clacu06g0437 Cmu06g0438 Cre06g1215 Cone14ag0718 Cone15ag0730 . . . Csa06g01871 Chy11g01572 . . . Bda11g00501 Bda13g00217 Bpe05g00797 Bpe13g00696 Bma02g00929 Bma06g01467 Sed04g3099 . . Cma08g01275 Cma17g00368 Car08g01145 Car17g00343 Cpe12g00323 Cpe17g00067 Bhi12g01930 Tan06g2763 Cmetu07g1185 . . . Lcy12g0851 . . . . . . . Lsi09g01492 . . Cme11g02081
Vvi5g65 . . Bda03g01182 . Bpe04g01115 . Bma04g01126 . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0721 . . . . Csa06g01740 Chy11g01566 . . . . . . . . . Sed04g3104 . . . Cma17g00367 . Car17g00340 . . Bhi12g01926 Tan06g2753 Cmetu11g0714 . . . Lcy12g0804 . . . . . . . Lsi09g01487 . . Cme11g02078
Vvi5g66 . Blo12g00079 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g67 . . . . . Bpe14g01100 . . . . . . . . . . . . . . . . . . Cla06g00429 Cam06g0452 Cec06g0459 Cco06g0458 Clacu06g0439 Cmu06g0440 Cre06g1217 . . . . . . . . . . . Bda13g00216 . . Bma02g00928 . . . . . . . . Cpe12g00319 . Bhi12g01927 . . . . . . . . . . . . . . . . .
Vvi5g68 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 13918499 13922127 + Bda017257.2 Bda03g01182 1182
3 13994706 13999310 + Bda017258.1 Bda03g01183 1183
8 3407379 3412932 - Bda024770.1 Bda08g00332 332
8 3416139 3419344 - Bda024771.1 Bda08g00333 333
8 3423600 3428689 - Bda033801 Bda08g00334 334
11 5314935 5316105 + Bda033038 Bda11g00499 499
11 5316805 5320800 - Bda005235.1 Bda11g00500 500
11 5322356 5329695 - Bda005236.1 Bda11g00501 501
13 2762498 2762797 + Bda001092.1 Bda13g00216 216
13 2769280 2774045 + Bda001093.1 Bda13g00217 217
1 20690762 20696990 + XM_039027715.1 Bhi01g01090 1090
1 20700152 20702949 - XM_039033027.1 Bhi01g01093 1093
12 61320906 61325901 + XM_039050723.1 Bhi12g01926 1926
12 61418728 61420945 + XM_039020313.1 Bhi12g01927 1927
12 61588948 61595300 + XM_039050583.1 Bhi12g01930 1930
12 61603333 61609020 + XM_039018432.1 Bhi12g01932 1932
12 61609760 61612051 - XM_039051017.1 Bhi12g01936 1936
1 388292 392717 + BLOR00029 Blo01g00029 29
1 401409 405778 + BLOR00030 Blo01g00030 30
1 414282 416975 + BLOR00031 Blo01g00031 31
7 1901559 1903673 + BLOR18074 Blo07g00142 142
7 1905119 1906302 + BLOR18075 Blo07g00143 143
7 1906954 1919183 - BLOR18076 Blo07g00144 144
12 5419271 5421832 + BLOR04098 Blo12g00079 79
2 48970453 48970752 + Bma015715.1 Bma02g00928 928
2 49015260 49019978 + Bma015717.2 Bma02g00929 929
4 27498073 27500146 - Bma019832.2 Bma04g01126 1126
5 48407560 48412417 + Bma022143.1 Bma05g00992 992
5 48415383 48420014 + Bma022144.1 Bma05g00993 993
5 48438779 48444173 + Bma022147.2 Bma05g00994 994
6 51312474 51313666 + Bma024579.1 Bma06g01465 1465
6 51314368 51318348 - Bma024580.1 Bma06g01466 1466
6 51319833 51324006 - Bma024581.1 Bma06g01467 1467
4 9050351 9052240 + Bpe015792.2 Bpe04g01115 1115
4 9134316 9139461 + Bpe015793.1 Bpe04g01116 1116
5 21315067 21319504 + Bpe018210.1 Bpe05g00797 797
5 21322307 21327142 + Bpe018211.1 Bpe05g00798 798
13 13593783 13597913 + Bpe010397.1 Bpe13g00696 696
13 13599291 13603279 + Bpe010398.1 Bpe13g00697 697
13 13603982 13605147 - Bpe010399.1 Bpe13g00698 698
13 13605771 13607967 - Bpe010400.1 Bpe13g00699 699
14 8192448 8197178 - Bpe014473.2 Bpe14g01099 1099
14 8205527 8205832 - Bpe025530 Bpe14g01100 1100
5 6748343 6753598 + CaPI482276_05g007740.1 Cam05g0774 774
5 6757638 6761177 - CaPI482276_05g007760.1 Cam05g0776 776
6 6625005 6626961 + CaPI482276_06g004480.1 Cam06g0448 448
6 6641274 6647358 - CaPI482276_06g004500.1 Cam06g0450 450
6 6666387 6666902 - CaPI482276_06g004520.1 Cam06g0452 452
6 9492019 9497705 + Carg23733-RA Car06g01329 1329
8 7710310 7716473 + Carg18887-RA Car08g01145 1145
8 7718281 7722853 + Carg18888-RA Car08g01146 1146
14 11798268 11802356 + Carg19619-RA Car14g01398 1398
14 11804661 11810485 - Carg19620-RA Car14g01399 1399
17 2128883 2132774 + Carg05546-RA Car17g00340 340
17 2146131 2152107 + Carg05549-RA Car17g00343 343
17 2156736 2162011 + Carg05550-RA Car17g00344 344
17 2162391 2164816 - Carg05551-RA Car17g00345 345
5 6464507 6469759 + CcPI632755_05g007750.1 Cco05g0775 775
5 6473703 6477220 - CcPI632755_05g007770.1 Cco05g0777 777
6 5010730 5012703 + CcPI632755_06g004540.1 Cco06g0454 454
6 5027142 5033191 - CcPI632755_06g004560.1 Cco06g0456 456
6 5053690 5054205 - CcPI632755_06g004580.1 Cco06g0458 458
5 6481878 6487131 + CePI673135_05g007820.1 Cec05g0782 782
5 6491144 6494638 - CePI673135_05g007840.1 Cec05g0784 784
6 5143693 5145690 + CePI673135_06g004550.1 Cec06g0455 455
6 5160299 5169415 - CePI673135_06g004570.1 Cec06g0457 457
6 5190259 5190825 - CePI673135_06g004590.1 Cec06g0459 459
6 5211189 5219961 + Chy6G112840.1 Chy06g00756 756
6 5220415 5222539 - Chy6G112850.1 Chy06g00757 757
11 22184029 22188431 + Chy11G201460.1 Chy11g01566 1566
11 22279645 22284106 + Chy11G201520.1 Chy11g01572 1572
11 22290741 22294527 + Chy11G201530.1 Chy11g01573 1573
11 22296703 22299259 - Chy11G201540.1 Chy11g01574 1574
5 6460879 6466131 + ClG42_05g0076400.10 Clacu05g0764 764
5 6470043 6473542 - ClG42_05g0076600.10 Clacu05g0766 766
6 5160009 5161973 + ClG42_06g0043500.10 Clacu06g0435 435
6 5176337 5182409 - ClG42_06g0043700.10 Clacu06g0437 437
6 5201817 5202332 - ClG42_06g0043900.10 Clacu06g0439 439
5 6599070 6605017 + ClCG05G006570.1 Cla05g00707 707
5 6607335 6613444 - ClCG05G006580.2 Cla05g00709 709
6 5194441 5196711 + ClCG06G004560.1 Cla06g00426 426
6 5198086 5203070 - ClCG06G004570.1 Cla06g00427 427
6 5210788 5215721 - ClCG06G004580.2 Cla06g00428 428
6 5232125 5251108 - ClCG06G004590.1 Cla06g00429 429
6 9793752 9799807 + CmaCh06G015640.1 Cma06g01564 1564
8 7748697 7754376 + CmaCh08G012750.1 Cma08g01275 1275
8 7757374 7761520 + CmaCh08G012760.1 Cma08g01276 1276
14 11920033 11923287 + CmaCh14G015880.1 Cma14g01588 1588
14 11927099 11932745 - CmaCh14G015900.1 Cma14g01590 1590
17 2039521 2043480 + CmaCh17G003670.1 Cma17g00367 367
17 2050794 2057310 + CmaCh17G003680.1 Cma17g00368 368
17 2061563 2066944 + CmaCh17G003690.1 Cma17g00369 369
17 2067067 2069353 - CmaCh17G003700.1 Cma17g00370 370
6 5236998 5242817 + MELO3C006717.2.1 Cme06g00790 790
6 5248695 5249758 - MELO3C031619.2.1 Cme06g00792 792
11 28457595 28462276 + MELO3C021271.2.1 Cme11g02078 2078
11 28478972 28484571 + MELO3C021268.2.1 Cme11g02081 2081
11 28488715 28494245 + MELO3C021267.2.1 Cme11g02082 2082
11 28494888 28496990 - MELO3C021266.2.1 Cme11g02083 2083
6 5450876 5456049 + PI0026962.1 Cmetu06g1585 1585
6 5459424 5462125 - PI0007662.1 Cmetu06g1917 1917
7 12899350 12903887 - PI0010065.2 Cmetu07g1185 1185
11 3768898 3773342 - PI0016333.1 Cmetu11g0714 714
11 3716377 3718510 + PI0006303.1 Cmetu11g2114 2114
6 10988616 10994777 + CmoCh06G015600.1 Cmo06g01560 1560
8 7862576 7869417 + CmoCh08G012430.1 Cmo08g01243 1243
8 7873002 7878695 + CmoCh08G012440.1 Cmo08g01244 1244
8 7879377 7880273 - CmoCh08G012450.1 Cmo08g01245 1245
14 12855319 12858860 + CmoCh14G016180.1 Cmo14g01618 1618
14 12864015 12869343 - CmoCh14G016190.1 Cmo14g01619 1619
17 2194119 2200211 + CmoCh17G003580.1 Cmo17g00358 358
17 2204776 2209598 + CmoCh17G003590.1 Cmo17g00359 359
17 2210461 2213353 - CmoCh17G003600.1 Cmo17g00360 360
5 6316831 6322083 + CmPI595203_05g007300.1 Cmu05g0730 730
5 6326080 6329567 - CmPI595203_05g007320.1 Cmu05g0732 732
6 4963100 4965064 + CmPI595203_06g004360.1 Cmu06g0436 436
6 4979409 4985478 - CmPI595203_06g004380.1 Cmu06g0438 438
6 5004860 5005375 - CmPI595203_06g004400.1 Cmu06g0440 440
4 498331 499607 + Conep04aG0010800.1 Cone4ag0104 104
4 501906 503552 + Conep04aG0010900.1 Cone4ag0105 105
7 433306 434541 + Conep07aG0010000.1 Cone7ag0099 99
14 3916480 3922248 - Conep14aG0073200.1 Cone14ag0716 716
14 3926212 3932032 - Conep14aG0073300.1 Cone14ag0717 717
14 3932902 3946567 - Conep14aG0073400.1 Cone14ag0718 718
14 3980682 3983975 - Conep14aG0073700.1 Cone14ag0721 721
15 4150184 4156540 - Conep15aG0074300.1 Cone15ag0728 728
15 4161999 4167730 - Conep15aG0074400.1 Cone15ag0729 729
15 4169218 4175490 - Conep15aG0074500.1 Cone15ag0730 730
3 10777213 10782033 + Cp4.1LG03g11960.1 Cpe03g01325 1325
3 10783802 10791086 - Cp4.1LG03g11870.1 Cpe03g01327 1327
8 975528 981686 - Cp4.1LG08g05280.1 Cpe08g00149 149
12 2118726 2121004 + Cp4.1LG12g03150.1 Cpe12g00319 319
12 2131617 2136921 + Cp4.1LG12g03190.1 Cpe12g00323 323
12 2140956 2147125 + Cp4.1LG12g03200.1 Cpe12g00324 324
12 2146617 2149254 - Cp4.1LG12g03280.1 Cpe12g00325 325
17 398142 403891 + Cp4.1LG17g00300.1 Cpe17g00067 67
17 406723 410830 + Cp4.1LG17g00310.1 Cpe17g00068 68
5 7106237 7111488 + CrPI670011_05g008040.1 Cre05g0804 804
5 7115507 7118991 - CrPI670011_05g008060.1 Cre05g0806 806
6 6018322 6020288 + CrPI670011_06g012130.1 Cre06g1213 1213
6 6034838 6040922 - CrPI670011_06g012150.1 Cre06g1215 1215
6 6060936 6061499 - CrPI670011_06g012170.1 Cre06g1217 1217
3 11284430 11290401 + CsaV3_3G015190.1 Csa03g01519 1519
3 11292633 11295973 - CsaV3_3G015210.1 Csa03g01521 1521
6 15300634 15305471 - CsaV3_6G022350.1 Csa06g01740 1740
6 16860816 16865509 + CsaV3_6G028590.1 Csa06g01869 1869
6 16863776 16869162 - CsaV3_6G028600.1 Csa06g01870 1870
6 16874910 16881017 - CsaV3_6G028610.1 Csa06g01871 1871
5 62495464 62500236 + Hsped.05g13730.1 Hepe05g1373 1373
5 62514273 62519643 - Hsped.05g13740.1 Hepe05g1374 1374
11 37015131 37017457 + Maker00031260 Lcy11g1335 1335
11 37022952 37028430 - Maker00032163 Lcy11g1336 1336
12 10485161 10488683 + Maker00024812 Lcy12g0804 804
12 11759777 11764643 + Maker00025057 Lcy12g0851 851
12 11767451 11773189 + Maker00024778 Lcy12g0852 852
12 11775270 11777199 - Maker00024734 Lcy12g0853 853
5 22144237 22147702 + Lsi05G014180.1 Lsi05g01418 1418
5 22155641 22161365 - Lsi05G014200.1 Lsi05g01420 1420
9 22924191 22929646 + Lsi09G014870.1 Lsi09g01487 1487
9 22966325 22973865 + Lsi09G014920.1 Lsi09g01492 1492
9 22981246 22986890 + Lsi09G014930.1 Lsi09g01493 1493
9 22989382 22992090 - Lsi09G014940.1 Lsi09g01494 1494
2 48559192 48563144 + Sed0016883.1 Sed02g1135 1135
2 48568134 48574356 - Sed0024815.1 Sed02g1136 1136
4 41928577 41935031 - Sed0019440.3 Sed04g3099 3099
4 41954974 41958922 - Sed0008389.3 Sed04g3104 3104
9 2776032 2779057 - Sed0009015.1 Sed09g0311 311
6 79806068 79810801 + Tan0003015.2 Tan06g2753 2753
6 79875081 79880902 + Tan0012490.1 Tan06g2763 2763
6 79893531 79895900 - Tan0008425.1 Tan06g2768 2768
10 10020219 10025998 + Tan0012167.1 Tan10g1077 1077
10 10080749 10083390 - Tan0016113.1 Tan10g1080 1080
5 681455 682628 - Vvi5g59 Vvi5g59 59
5 686535 688008 + Vvi5g60 Vvi5g60 60
5 690220 694301 + Vvi5g61 Vvi5g61 61
5 694777 701765 - Vvi5g62 Vvi5g62 62
5 710743 719210 - Vvi5g63 Vvi5g63 63
5 720563 727760 - Vvi5g64 Vvi5g64 64
5 745679 748011 - Vvi5g65 Vvi5g65 65
5 749323 751897 + Vvi5g66 Vvi5g66 66
5 753417 753947 - Vvi5g67 Vvi5g67 67
5 768915 769818 + Vvi5g68 Vvi5g68 68
       

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