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
Vvi5g149 . . . . . Bpe14g01113 . . . . Cma06g01540 Cma14g01608 . Car14g01427 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo14g01644 . . . . . . . . . . . . . Cla05g00673 . . Cco05g0746 . . . . . Chy06g00728 .
Vvi5g150 . . . . . . . . . . . . . Car14g01428 . . . . . . . . . . . . . . . . . . . Cone7ag0131 Cone4ag0136 . . . . . . . . . Bpe13g00673 . Bma06g01491 . . Cmo14g01646 . . . . . . . . . . . . . . . . . . . . . . Chy06g00727 .
Vvi5g151 . . Bda03g01133 . Bpe04g01076 . . . . . . . . . . . . . . . . . . . Cla06g00408 Cam06g0430 Cec06g0437 Cco06g0436 Clacu06g0416 Cmu06g0416 Cre06g1196 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g152 . . . . . Bpe14g01116 . . . . Cma06g01525 Cma14g01609 . . . . Cpe03g01351 . . . . . . . . . . . . . . . . . . . . . . Blo02g00495 Blo07g00167 Bda11g00518 . . Bpe13g00672 Bma02g00911 Bma06g01492 . . Cmo14g01647 . . . . . . . . . . . . . Cla05g00671 Cam05g0735 Cec05g0743 Cco05g0742 Clacu05g0728 Cmu05g0693 Cre05g0767 . Csa03g01488 Chy06g00725 .
Vvi5g153 Blo01g00064 . . Bda08g00298 . . . . Cmo08g01213 Cmo17g00328 Cma06g01518 . . Car14g01429 . Cpe08g00172 Cpe03g01352 . . . . . . . Cla06g00463 Cam06g0495 Cec06g0498 Cco06g0497 Clacu06g0481 Cmu06g0482 Cre06g1255 Cone14ag0748 Cone15ag0754 . Cone4ag0137 . Csa06g01790 Chy11g01528 . . . . . Bpe05g00827 . . . Sed02g0010 . Cmo14g01648 Cma08g01239 Cma17g00341 . . . . Bhi12g02036 Tan06g2699 Cmetu02g1549 . Hepe03g0084 . Lcy12g0754 Cla05g00670 Cam05g0734 Cec05g0742 Cco05g0741 Clacu05g0727 Cmu05g0692 Cre05g0766 Lsi09g01450 Csa03g01487 Chy06g00724 Cme11g02031
Vvi5g154 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone15ag0756 Cone7ag0133 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g155 . . . . . . Bma04g01148 . Cmo08g01212 . . . . . . . . . . . . . . . Cla06g00465 Cam06g0497 Cec06g0500 Cco06g0499 Clacu06g0483 Cmu06g0484 Cre06g1257 . . . . . Csa06g01792 Chy11g01526 . . . . . . . . . Sed09g0252 . . Cma08g01238 . . . . Cpe17g00035 Bhi12g02038 Tan06g2695 Cmetu11g2595 . Hepe03g0089 . Lcy12g0749 . . . . . . . Lsi09g01448 . . Cme11g02029
Vvi5g156 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda13g00197 . . Bma02g00908 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g157 . . . . . Bpe14g01119 . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0750 . . . . . . . Blo02g00497 . . Bda13g00196 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g158 . . . . . Bpe14g01120 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda13g00195 . . Bma02g00907 . . . . . . . . . . . . . . . . . Cla05g00668 Cam05g0732 Cec05g0740 Cco05g0739 Clacu05g0725 Cmu05g0690 Cre05g0764 . Csa03g01485 Chy06g00722 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 11932993 11937468 - Bda017183.1 Bda03g01133 1133
8 3125938 3129826 - Bda024733.1 Bda08g00298 298
11 5490748 5495914 + Bda005253.1 Bda11g00518 518
13 2427074 2428236 - Bda001063.1 Bda13g00195 195
13 2433821 2435090 - Bda001064.1 Bda13g00196 196
13 2442464 2443633 - Bda001065.1 Bda13g00197 197
12 63545398 63547272 + XM_039019915.1 Bhi12g02036 2036
12 63567651 63568620 + XM_039019549.1 Bhi12g02038 2038
1 789868 791749 + BLOR00064 Blo01g00064 64
2 7703862 7709053 + BLOR10225 Blo02g00495 495
2 7731702 7732873 + BLOR10227 Blo02g00497 497
7 2145473 2150634 + BLOR18099 Blo07g00167 167
2 47999239 48000412 - Bma030913 Bma02g00907 907
2 48161840 48163010 - Bma015687.1 Bma02g00908 908
2 48168220 48172682 - Bma015690.1 Bma02g00911 911
4 29330313 29330958 + Bma031130 Bma04g01148 1148
6 51444250 51446111 - Bma024603.1 Bma06g01491 1491
6 51448252 51453421 + Bma024604.1 Bma06g01492 1492
4 8241063 8245524 - Bpe015748.1 Bpe04g01076 1076
5 21532637 21538853 + Bpe018240.1 Bpe05g00827 827
13 13460889 13466916 - Bpe010373.1 Bpe13g00672 672
13 13468549 13470318 + Bpe010374.2 Bpe13g00673 673
14 8312439 8313747 - Bpe014488.1 Bpe14g01113 1113
14 8334244 8338657 + Bpe014491.1 Bpe14g01116 1116
14 8345007 8346278 + Bpe014494.1 Bpe14g01119 1119
14 8349808 8350194 - Bpe014495.1 Bpe14g01120 1120
5 6371751 6375381 - CaPI482276_05g007320.1 Cam05g0732 732
5 6389342 6391137 - CaPI482276_05g007340.1 Cam05g0734 734
5 6394247 6400953 - CaPI482276_05g007350.1 Cam05g0735 735
6 6419345 6430700 - CaPI482276_06g004300.1 Cam06g0430 430
6 7060431 7062143 + CaPI482276_06g004950.1 Cam06g0495 495
6 7072843 7073488 + CaPI482276_06g004970.1 Cam06g0497 497
14 11956320 11958996 - Carg19649-RA Car14g01427 1427
14 11959557 11961740 - Carg19650-RA Car14g01428 1428
14 11971932 11976049 + Carg19651-RA Car14g01429 1429
5 6067861 6071931 - CcPI632755_05g007390.1 Cco05g0739 739
5 6085978 6087773 - CcPI632755_05g007410.1 Cco05g0741 741
5 6090860 6097601 - CcPI632755_05g007420.1 Cco05g0742 742
5 6117046 6119578 + CcPI632755_05g007460.1 Cco05g0746 746
6 4792647 4804311 - CcPI632755_06g004360.1 Cco06g0436 436
6 5453474 5455186 + CcPI632755_06g004970.1 Cco06g0497 497
6 5466078 5466723 + CcPI632755_06g004990.1 Cco06g0499 499
5 6093684 6097618 - CePI673135_05g007400.1 Cec05g0740 740
5 6111351 6113137 - CePI673135_05g007420.1 Cec05g0742 742
5 6116236 6122968 - CePI673135_05g007430.1 Cec05g0743 743
6 4932261 4943624 - CePI673135_06g004370.1 Cec06g0437 437
6 5588404 5590116 + CePI673135_06g004980.1 Cec06g0498 498
6 5601379 5602045 + CePI673135_06g005000.1 Cec06g0500 500
6 4916322 4919735 - Chy6G112500.1 Chy06g00722 722
6 4926168 4930318 - Chy6G112520.1 Chy06g00724 724
6 4931646 4938184 - Chy6G112530.1 Chy06g00725 725
6 4952032 4953813 + Chy6G112550.1 Chy06g00727 727
6 4955719 4959759 + Chy6G112560.1 Chy06g00728 728
11 21872355 21873013 - Chy11G201060.1 Chy11g01526 1526
11 21877871 21879689 - Chy11G201080.1 Chy11g01528 1528
5 6092742 6096422 - ClG42_05g0072500.10 Clacu05g0725 725
5 6110359 6112154 - ClG42_05g0072700.10 Clacu05g0727 727
5 6115201 6121898 - ClG42_05g0072800.10 Clacu05g0728 728
6 4956869 4968202 - ClG42_06g0041600.10 Clacu06g0416 416
6 5595222 5596934 + ClG42_06g0048100.10 Clacu06g0481 481
6 5608140 5608783 + ClG42_06g0048300.10 Clacu06g0483 483
5 6200140 6204217 - ClCG05G006240.2 Cla05g00668 668
5 6218084 6219879 - ClCG05G006250.1 Cla05g00670 670
5 6222726 6229868 - ClCG05G006260.2 Cla05g00671 671
5 6246081 6253472 + ClCG05G006275.1 Cla05g00673 673
6 4985504 4998146 - ClCG06G004370.1 Cla06g00408 408
6 5642876 5644588 + ClCG06G004960.2 Cla06g00463 463
6 5655731 5656518 + ClCG06G004980.1 Cla06g00465 465
6 9594721 9596580 - CmaCh06G015180.1 Cma06g01518 1518
6 9610049 9614356 - CmaCh06G015250.1 Cma06g01525 1525
6 9660334 9665322 + CmaCh06G015400.1 Cma06g01540 1540
8 7590093 7590961 - CmaCh08G012380.1 Cma08g01238 1238
8 7592616 7594593 - CmaCh08G012390.1 Cma08g01239 1239
14 12084155 12085878 - CmaCh14G016080.1 Cma14g01608 1608
14 12087658 12093686 + CmaCh14G016090.1 Cma14g01609 1609
17 1855462 1857484 - CmaCh17G003410.1 Cma17g00341 341
11 28117866 28119227 - MELO3C021313.2.1 Cme11g02029 2029
11 28124390 28126396 - MELO3C021311.2.1 Cme11g02031 2031
2 662983 665355 + PI0027180.1 Cmetu02g1549 1549
11 4081004 4082007 + PI0015622.1 Cmetu11g2595 2595
8 7698377 7699227 - CmoCh08G012120.1 Cmo08g01212 1212
8 7701057 7702855 - CmoCh08G012130.1 Cmo08g01213 1213
14 13019985 13023980 - CmoCh14G016440.1 Cmo14g01644 1644
14 13024898 13026512 - CmoCh14G016460.1 Cmo14g01646 1646
14 13028524 13034477 + CmoCh14G016470.1 Cmo14g01647 1647
14 13035160 13041555 + CmoCh14G016480.1 Cmo14g01648 1648
17 1985349 1987158 - CmoCh17G003280.1 Cmo17g00328 328
5 5936025 5939709 - CmPI595203_05g006900.1 Cmu05g0690 690
5 5953726 5955521 - CmPI595203_05g006920.1 Cmu05g0692 692
5 5958568 5965265 - CmPI595203_05g006930.1 Cmu05g0693 693
6 4752144 4763483 - CmPI595203_06g004160.1 Cmu06g0416 416
6 5397785 5399497 + CmPI595203_06g004820.1 Cmu06g0482 482
6 5410705 5411348 + CmPI595203_06g004840.1 Cmu06g0484 484
4 617739 619158 - Conep04aG0014100.1 Cone4ag0136 136
4 626754 628558 + Conep04aG0014200.1 Cone4ag0137 137
7 549866 551210 - Conep07aG0013200.1 Cone7ag0131 131
7 560866 562118 - Conep07aG0013400.1 Cone7ag0133 133
14 4183617 4185549 + Conep14aG0076500.1 Cone14ag0748 748
14 4202564 4204407 + Conep14aG0076700.1 Cone14ag0750 750
15 4429604 4431428 + Conep15aG0076900.1 Cone15ag0754 754
15 4437878 4439113 - Conep15aG0077100.1 Cone15ag0756 756
3 10948182 10954073 + Cp4.1LG03g11660.1 Cpe03g01351 1351
3 10957574 10961377 + Cp4.1LG03g11680.1 Cpe03g01352 1352
8 1203692 1208140 + Cp4.1LG08g04980.1 Cpe08g00172 172
17 237345 238491 - Cp4.1LG17g00570.1 Cpe17g00035 35
5 6735962 6739836 - CrPI670011_05g007640.1 Cre05g0764 764
5 6754181 6755976 - CrPI670011_05g007660.1 Cre05g0766 766
5 6759040 6765682 - CrPI670011_05g007670.1 Cre05g0767 767
6 5808828 5820229 - CrPI670011_06g011960.1 Cre06g1196 1196
6 6464256 6465968 + CrPI670011_06g012550.1 Cre06g1255 1255
6 6477057 6477713 + CrPI670011_06g012570.1 Cre06g1257 1257
3 11018413 11021967 - CsaV3_3G014850.1 Csa03g01485 1485
3 11030190 11032329 - CsaV3_3G014870.1 Csa03g01487 1487
3 11033150 11040301 - CsaV3_3G014880.1 Csa03g01488 1488
6 15830169 15833747 + CsaV3_6G023840.1 Csa06g01790 1790
6 15838439 15840003 + CsaV3_6G023860.1 Csa06g01792 1792
3 992779 994558 - Hsped.03g00840.1 Hepe03g0084 84
3 1092333 1092977 + Hsped.03g00890.1 Hepe03g0089 89
12 9556113 9557109 - Maker00024880 Lcy12g0749 749
12 9647648 9649697 - Maker00024787 Lcy12g0754 754
9 22466094 22466985 - Lsi09G014480.1 Lsi09g01448 1448
9 22477690 22479819 - Lsi09G014500.1 Lsi09g01450 1450
2 1906781 1908638 + Sed0004558.1 Sed02g0010 10
9 2024780 2025502 - Sed0015120.1 Sed09g0252 252
6 79392219 79393062 - Tan0002345.1 Tan06g2695 2695
6 79431027 79433182 - Tan0008433.1 Tan06g2699 2699
5 1477610 1481214 - Vvi5g149 Vvi5g149 149
5 1481461 1483909 - Vvi5g150 Vvi5g150 150
5 1507785 1515522 + Vvi5g151 Vvi5g151 151
5 1516564 1526361 + Vvi5g152 Vvi5g152 152
5 1527456 1537313 + Vvi5g153 Vvi5g153 153
5 1538529 1539312 - Vvi5g154 Vvi5g154 154
5 1539366 1543319 + Vvi5g155 Vvi5g155 155
5 1549525 1551949 + Vvi5g156 Vvi5g156 156
5 1552747 1558300 + Vvi5g157 Vvi5g157 157
5 1558828 1560136 + Vvi5g158 Vvi5g158 158
       

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