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
Vvi5g259 . . . . . . . . Cmo08g01213 Cmo17g00328 Cma06g01533 . . . Sed02g1163 . . Bhi01g01041 Tan10g1033 Cmetu06g0197 Lac11g0857 Hepe05g1419 . Lcy11g1391 Cla06g00463 Cam06g0495 Cec06g0498 Cco06g0497 Clacu06g0481 Cmu06g0482 Cre06g1255 Cone14ag0748 Cone15ag0754 . Cone4ag0137 Lsi05g01558 . Chy11g01528 Cme06g00752 . . . . Bpe05g00827 . . . . Cmo06g01513 . Cma08g01239 Cma17g00341 . . . . . . . . . . . Cla05g00670 Cam05g0734 Cec05g0742 Cco05g0741 Clacu05g0727 Cmu05g0692 Cre05g0766 Lsi09g01450 Csa03g01487 Chy06g00724 Cme11g02031
Vvi5g260 . Blo12g00372 Bda03g00838 . Bpe04g00793 . Bma04g00736 . . . . . Car06g01348 . Sed02g1104 Cpe08g00132 . Bhi01g01131 Tan10g1125 Cmetu06g1995 . Hepe05g1343 . Lcy11g1303 . . . . . . . Cone14ag0677 Cone15ag0688 . . Lsi05g01384 . . Cme06g00832 . . . . . . . . . Cmo06g01582 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g261 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g262 Blo01g00021 . . . . . . Bma05g00983 . . . Cma14g01555 . Car14g01370 . Cpe08g00128 Cpe03g01300 . . . . . . . Cla06g00391 . . . . . Cre06g1179 Cone14ag0676 Cone15ag0687 . . Lsi05g01381 . . . . . . . Bpe05g00792 . . . . . Cmo14g01590 . . . . . . Bhi12g01998 . . . . . Lcy12g0913 . . . . . . . . . . .
Vvi5g263 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g264 Blo01g00018 . . Bda08g00342 . . . Bma05g00982 . . . . . . . . . . . . . . . . Cla06g00388 Cam06g0410 Cec06g0419 Cco06g0418 Clacu06g0398 Cmu06g0397 Cre06g1174 Cone14ag0674 Cone15ag0685 . . . . . . . . . . Bpe05g00791 . . . Sed06g1479 . . . . . . Cpe12g00351 . Bhi12g02002 Tan06g2820 Cmetu10g0038 . Hepe03g0005 . . . . . . . . . . . . .
Vvi5g265 . . . . . . Bma04g01150 . . . . . . . . . . . . . . . . . Cla06g00387 Cam06g0409 . Cco06g0417 Clacu06g0397 Cmu06g0396 Cre06g1173 . . . . . . . . . . . . . . . . Sed09g0582 . . . . . . Cpe12g00352 . Bhi12g02004 Tan06g2821 Cmetu11g1819 Lac11g1073 Hepe03g0004 . Lcy12g0920 . . . . . . . . . . .
Vvi5g266 Blo01g00017 . . . . . . Bma05g00981 . . . . . . . . . . . . . . . . Cla06g00386 . Cec06g0417 . . . . . Cone15ag0684 . . . . . . . . . . Bpe05g00790 . . . Sed11g1035 . . . . . . Cpe12g00353 . Bhi12g02006 Tan06g2823 Cmetu03g0819 Lac11g1075 Hepe03g0003 . Lcy12g0924 . . . . . . . . . . .
Vvi5g267 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g268 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 7175936 7179403 + Bda016823.1 Bda03g00838 838
8 3493359 3496020 + Bda024781.1 Bda08g00342 342
1 19209496 19211456 - XM_039018905.1 Bhi01g01041 1041
1 21932224 21936827 - XM_039025819.1 Bhi01g01131 1131
12 62725796 62733998 - XM_039050699.1 Bhi12g01998 1998
12 62794991 62798310 + XM_039019589.1 Bhi12g02002 2002
12 62800741 62804760 - XM_039019942.1 Bhi12g02004 2004
12 62807753 62817235 - XM_039018553.1 Bhi12g02006 2006
1 250641 294163 + BLOR00017 Blo01g00017 17
1 294713 297839 - BLOR00018 Blo01g00018 18
1 318551 322266 + BLOR00021 Blo01g00021 21
12 20102911 20106410 - BLOR04391 Blo12g00372 372
4 7718617 7722086 + Bma019244.1 Bma04g00736 736
4 29502229 29505542 + Bma019880.1 Bma04g01150 1150
5 48298498 48320521 + Bma022130.2 Bma05g00981 981
5 48320894 48322486 - Bma022131.1 Bma05g00982 982
5 48338294 48341503 + Bma022133.1 Bma05g00983 983
4 5177433 5180827 + Bpe015454.1 Bpe04g00793 793
5 21247704 21254984 + Bpe018202.1 Bpe05g00790 790
5 21255728 21258429 - Bpe018203.1 Bpe05g00791 791
5 21266905 21270099 + Bpe018205.1 Bpe05g00792 792
5 21532637 21538853 + Bpe018240.1 Bpe05g00827 827
5 6389342 6391137 - CaPI482276_05g007340.1 Cam05g0734 734
6 6187615 6203398 + CaPI482276_06g004090.1 Cam06g0409 409
6 6204612 6207759 - CaPI482276_06g004100.1 Cam06g0410 410
6 7060431 7062143 + CaPI482276_06g004950.1 Cam06g0495 495
6 9659173 9662868 - Carg25657-RA Car06g01348 1348
14 11579298 11582654 - Carg19591-RA Car14g01370 1370
5 6085978 6087773 - CcPI632755_05g007410.1 Cco05g0741 741
6 4537802 4553444 + CcPI632755_06g004170.1 Cco06g0417 417
6 4555182 4557838 - CcPI632755_06g004180.1 Cco06g0418 418
6 5453474 5455186 + CcPI632755_06g004970.1 Cco06g0497 497
5 6111351 6113137 - CePI673135_05g007420.1 Cec05g0742 742
6 4683399 4699052 + CePI673135_06g004170.1 Cec06g0417 417
6 4702025 4703424 - CePI673135_06g004190.1 Cec06g0419 419
6 5588404 5590116 + CePI673135_06g004980.1 Cec06g0498 498
6 4926168 4930318 - Chy6G112520.1 Chy06g00724 724
11 21877871 21879689 - Chy11G201080.1 Chy11g01528 1528
5 6110359 6112154 - ClG42_05g0072700.10 Clacu05g0727 727
6 4725513 4741336 + ClG42_06g0039700.10 Clacu06g0397 397
6 4743046 4745696 - ClG42_06g0039800.10 Clacu06g0398 398
6 5595222 5596934 + ClG42_06g0048100.10 Clacu06g0481 481
5 6218084 6219879 - ClCG05G006250.1 Cla05g00670 670
6 4744245 4757676 + ClCG06G004150.2 Cla06g00386 386
6 4759389 4763004 + ClCG06G004160.2 Cla06g00387 387
6 4764253 4766821 - ClCG06G004170.2 Cla06g00388 388
6 4802415 4812126 + ClCG06G004200.2 Cla06g00391 391
6 5642876 5644588 + ClCG06G004960.2 Cla06g00463 463
6 9645268 9648291 - CmaCh06G015330.1 Cma06g01533 1533
8 7592616 7594593 - CmaCh08G012390.1 Cma08g01239 1239
14 11700857 11704156 - CmaCh14G015550.1 Cma14g01555 1555
17 1855462 1857484 - CmaCh17G003410.1 Cma17g00341 341
6 4959491 4961365 - MELO3C006683.2.1 Cme06g00752 752
6 5681166 5685699 - MELO3C006752.2.1 Cme06g00832 832
11 28124390 28126396 - MELO3C021311.2.1 Cme11g02031 2031
3 1837992 1844709 - PI0019716.1 Cmetu03g0819 819
6 5167875 5170088 - PI0028651.1 Cmetu06g0197 197
6 5772533 5777139 - PI0009309.1 Cmetu06g1995 1995
10 17439258 17444437 + PI0025282.1 Cmetu10g0038 38
11 3356901 3359950 - PI0000043.1 Cmetu11g1819 1819
6 10795720 10797520 - CmoCh06G015130.1 Cmo06g01513 1513
6 11110765 11114618 - CmoCh06G015820.1 Cmo06g01582 1582
8 7701057 7702855 - CmoCh08G012130.1 Cmo08g01213 1213
14 12623954 12626952 - CmoCh14G015900.1 Cmo14g01590 1590
17 1985349 1987158 - CmoCh17G003280.1 Cmo17g00328 328
5 5953726 5955521 - CmPI595203_05g006920.1 Cmu05g0692 692
6 4520774 4536624 + CmPI595203_06g003960.1 Cmu06g0396 396
6 4538334 4540984 - CmPI595203_06g003970.1 Cmu06g0397 397
6 5397785 5399497 + CmPI595203_06g004820.1 Cmu06g0482 482
4 626754 628558 + Conep04aG0014200.1 Cone4ag0137 137
14 3466210 3468623 - Conep14aG0068900.1 Cone14ag0674 674
14 3489720 3494147 + Conep14aG0069100.1 Cone14ag0676 676
14 3499354 3501721 + Conep14aG0069200.1 Cone14ag0677 677
14 4183617 4185549 + Conep14aG0076500.1 Cone14ag0748 748
15 3674328 3679288 + Conep15aG0069800.1 Cone15ag0684 684
15 3679364 3681311 - Conep15aG0069900.1 Cone15ag0685 685
15 3700415 3704152 + Conep15aG0070100.1 Cone15ag0687 687
15 3704573 3707005 + Conep15aG0070200.1 Cone15ag0688 688
15 4429604 4431428 + Conep15aG0076900.1 Cone15ag0754 754
3 10556643 10560168 - Cp4.1LG03g12070.1 Cpe03g01300 1300
8 840252 843666 - Cp4.1LG08g05460.1 Cpe08g00128 128
8 862572 866322 + Cp4.1LG08g05500.1 Cpe08g00132 132
12 2393010 2395959 + Cp4.1LG12g03520.1 Cpe12g00351 351
12 2396553 2399744 - Cp4.1LG12g03540.1 Cpe12g00352 352
12 2401042 2415388 - Cp4.1LG12g03550.1 Cpe12g00353 353
5 6754181 6755976 - CrPI670011_05g007660.1 Cre05g0766 766
6 5573611 5589700 + CrPI670011_06g011730.1 Cre06g1173 1173
6 5591463 5594119 - CrPI670011_06g011740.1 Cre06g1174 1174
6 5631596 5641289 + CrPI670011_06g011790.1 Cre06g1179 1179
6 6464256 6465968 + CrPI670011_06g012550.1 Cre06g1255 1255
3 11030190 11032329 - CsaV3_3G014870.1 Csa03g01487 1487
3 40953 62978 + Hsped.03g00030.1 Hepe03g0003 3
3 68664 71826 + Hsped.03g00040.1 Hepe03g0004 4
3 72941 74041 - Hsped.03g00050.1 Hepe03g0005 5
5 61848298 61852794 + Hsped.05g13430.1 Hepe05g1343 1343
5 63144801 63146609 + Hsped.05g14190.1 Hepe05g1419 1419
11 9235100 9236913 - Lag0031495.1 Lac11g0857 857
11 12538863 12543120 - Lag0031711.1 Lac11g1073 1073
11 12562137 12574301 - Lag0031713.1 Lac11g1075 1075
11 36518890 36523504 + Maker00032128 Lcy11g1303 1303
11 37701898 37703598 + Maker00032119 Lcy11g1391 1391
12 13498007 13504639 - Maker00024998 Lcy12g0913 913
12 13756344 13760840 - Maker00024800 Lcy12g0920 920
12 13806621 13813031 - Maker00024809 Lcy12g0924 924
5 21702250 21704360 - Lsi05G013810.1 Lsi05g01381 1381
5 21728938 21750489 + Lsi05G013850.1 Lsi05g01384 1384
5 23346044 23348212 - Lsi05G015580.1 Lsi05g01558 1558
9 22477690 22479819 - Lsi09G014500.1 Lsi09g01450 1450
2 48351629 48356789 + Sed0028101.2 Sed02g1104 1104
2 48755114 48757363 + Sed0007418.1 Sed02g1163 1163
6 39509595 39514238 + Sed0027668.4 Sed06g1479 1479
9 6670615 6680317 - Sed0027195.2 Sed09g0582 582
11 25583006 25590301 - Sed0009494.1 Sed11g1035 1035
6 80345860 80347738 + Tan0005618.1 Tan06g2820 2820
6 80348804 80351407 - Tan0019427.1 Tan06g2821 2821
6 80420802 80487550 - Tan0006599.1 Tan06g2823 2823
10 9186330 9188120 - Tan0017977.1 Tan10g1033 1033
10 10870767 10875819 - Tan0003883.1 Tan10g1125 1125
5 2656160 2658162 + Vvi5g259 Vvi5g259 259
5 2661986 2665997 - Vvi5g260 Vvi5g260 260
5 2667667 2671970 + Vvi5g261 Vvi5g261 261
5 2672327 2676586 - Vvi5g262 Vvi5g262 262
5 2683949 2685430 - Vvi5g263 Vvi5g263 263
5 2694320 2697616 + Vvi5g264 Vvi5g264 264
5 2697637 2700935 - Vvi5g265 Vvi5g265 265
5 2701608 2715812 - Vvi5g266 Vvi5g266 266
5 2719816 2732762 + Vvi5g267 Vvi5g267 267
5 2734307 2737282 + Vvi5g268 Vvi5g268 268
       

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