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
Vvi19g544 Blo03g00550 . Bda07g00371 . . . . . . . Cma01g01118 . Car01g00991 . . . Cpe02g00783 Bhi09g01665 . . . . Mch11g1203 . . . . . . . . . Cone9ag0063 . . Lsi02g01892 Csa07g01109 . . . . . . Bpe11g00556 . . Bma14g00330 . Cmo01g01166 . . . . . . . . . . . . . . Cla09g01021 Cam09g1077 Cec09g1077 Cco09g1098 . . Cre09g1043 . . . .
Vvi19g545 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g546 . . Bda07g00372 . Bpe09g00163 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0052 Cone9ag0062 . . . . . . . Blo10g00842 . . Bpe11g00557 . . Bma14g00329 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g547 . . . . . . Bma10g00564 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo07g00894 . Bda05g00711 . . Bpe03g00783 . . . . . . . . . Cpe14g00742 . . . . . . . . . . . . . . . . . . .
Vvi19g548 Blo03g00548 . Bda07g00373 . . . . . . . . Cma09g00963 . Car09g00878 . Cpe06g00778 . Bhi09g01679 . . . Hepe01g1258 . . . . . . . . . Cone6ag0051 . . . Lsi02g01891 Csa07g01110 . . . . . . Bpe11g00558 . . Bma14g00328 . . Cmo09g00963 . . . . . . . . . . . . . Cla09g01024 Cam09g1078 Cec09g1078 Cco09g1099 . . Cre09g1044 . . . Cme01g01014
Vvi19g549 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g550 . . . . Bpe09g00162 . Bma10g00565 Bma13g01070 . . . Cma09g00964 Car01g00990 Car09g00879 . Cpe06g00779 Cpe02g00784 Bhi09g01681 . . . Hepe01g1257 . . . . . . . . . . . . Cone15ag1177 Lsi02g01890 Csa07g01111 . . Blo07g00893 Blo10g00843 Bda05g00710 . . . . . . Cmo01g01165 Cmo09g00966 . . . . . . . . . . . . . Cla09g01025 Cam09g1080 Cec09g1079 Cco09g1100 . . Cre09g1045 . . . Cme01g01013
Vvi19g551 . . . . . . Bma10g00566 . Cmo16g00936 . . . . . . . . . . . . . . . Cla10g00491 Cam10g0482 Cec10g0500 Cco10g0486 Clacu10g0502 Cmu10g1329 Cre10g0732 . . . . . Csa03g00495 . Cme06g02859 Blo07g00892 . Bda05g00709 . . Bpe03g00781 . . Sed08g1364 . . . Cma16g00900 . Car16g00876 Cpe14g00724 . Bhi11g00594 Tan01g1726 Cmetu06g2572 . Hepe06g0003 . . . . . . . . . Lsi05g00580 . Chy06g01831 .
Vvi19g552 . . . . . . . . . Cmo06g00897 . . . . . . . . . . . . . . Cla10g00490 Cam10g0480 Cec10g0499 Cco10g0485 Clacu10g0499 Cmu10g1326 Cre10g0731 . . . . . Csa03g00494 . Cme06g02858 . . . . . . . . Sed14g0140 . . . . . . . . Bhi11g00593 Tan01g1728 Cmetu06g2813 . . . . . . . . . . . Lsi05g00579 . . .
Vvi19g553 . . . . . . Bma10g00567 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone15ag1178 . Csa03g00493 . Cme06g02856 . . Bda05g00708 . . Bpe03g00780 . . . . . . . . . Cpe14g00723 . . . . . . . . . . . . . . . Lsi05g00578 . Chy06g01833 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 55340812 55341417 + Bda021845.1 Bda05g00708 708
5 55345489 55348350 - Bda021846.1 Bda05g00709 709
5 55351709 55355304 - Bda021847.1 Bda05g00710 710
5 55367648 55370618 - Bda021849.1 Bda05g00711 711
7 4705641 4719174 - Bda025457.1 Bda07g00371 371
7 4728861 4733673 + Bda025459.1 Bda07g00372 372
7 4734197 4744599 + Bda025460.1 Bda07g00373 373
9 44875342 44929313 - XM_039042905.1 Bhi09g01665 1665
9 44972236 45005651 + XM_039041822.1 Bhi09g01679 1679
9 45035358 45043908 + XM_039042498.1 Bhi09g01681 1681
11 13578814 13583890 + XM_039049492.1 Bhi11g00593 593
11 13585575 13587931 - XM_039047311.1 Bhi11g00594 594
3 21450859 21461096 - BLOR11729 Blo03g00548 548
3 21535419 21556717 + BLOR11731 Blo03g00550 550
7 27683916 27687040 - BLOR18824 Blo07g00892 892
7 27743872 27747593 - BLOR18825 Blo07g00893 893
7 27751928 27763715 - BLOR18826 Blo07g00894 894
10 26884707 26887560 + BLOR02632 Blo10g00842 842
10 26889489 26900133 + BLOR02633 Blo10g00843 843
10 7052269 7066493 + Bma004269.1 Bma10g00564 564
10 7068483 7072420 + Bma004270.1 Bma10g00565 565
10 7073860 7076797 + Bma004271.1 Bma10g00566 566
10 7078982 7079563 - Bma004272.1 Bma10g00567 567
13 43568865 43572937 + Bma010194.1 Bma13g01070 1070
14 4075110 4085116 - Bma010749.1 Bma14g00328 328
14 4085610 4098429 - Bma010750.1 Bma14g00329 329
14 4110064 4123569 + Bma010751.3 Bma14g00330 330
3 27773991 27774572 + Bpe012691.1 Bpe03g00780 780
3 27776583 27779408 - Bpe012692.1 Bpe03g00781 781
3 27797564 27801347 - Bpe012695.1 Bpe03g00783 783
9 1082920 1087522 - Bpe026207 Bpe09g00162 162
9 1092712 1094651 - Bpe023835.1 Bpe09g00163 163
11 4265464 4276810 - Bpe003923.1 Bpe11g00556 556
11 4280979 4285407 + Bpe003924.1 Bpe11g00557 557
11 4285953 4296472 + Bpe003925.3 Bpe11g00558 558
9 11150608 11169588 - CaPI482276_09g010770.1 Cam09g1077 1077
9 11182791 11206346 + CaPI482276_09g010780.1 Cam09g1078 1078
9 11223093 11225148 + CaPI482276_09g010800.1 Cam09g1080 1080
10 7228311 7228664 + CaPI482276_10g004800.1 Cam10g0480 480
10 7245120 7249951 - CaPI482276_10g004820.1 Cam10g0482 482
1 9383086 9390391 - Carg22372-RA Car01g00990 990
1 9392170 9409624 + Carg22371-RA Car01g00991 991
9 5378737 5395308 + Carg12832-RA Car09g00878 878
9 5397087 5403237 + Carg12833-RA Car09g00879 879
16 6661412 6664169 + Carg27293-RA Car16g00876 876
9 10506069 10512968 - CcPI632755_09g010980.1 Cco09g1098 1098
9 10514563 10538155 + CcPI632755_09g010990.1 Cco09g1099 1099
9 10542070 10555496 + CcPI632755_09g011000.1 Cco09g1100 1100
10 5784967 5785374 + CcPI632755_10g004850.1 Cco10g0485 485
10 5785674 5805487 - CcPI632755_10g004860.1 Cco10g0486 486
9 10520439 10538770 - CePI673135_09g010770.1 Cec09g1077 1077
9 10545492 10568231 + CePI673135_09g010780.1 Cec09g1078 1078
9 10572748 10586089 + CePI673135_09g010790.1 Cec09g1079 1079
10 5998158 5998568 + CePI673135_10g004990.1 Cec10g0499 499
10 5998911 6011730 - CePI673135_10g005000.1 Cec10g0500 500
6 22078134 22080023 + Chy6G123590.1 Chy06g01831 1831
6 22084791 22094773 - Chy6G123610.1 Chy06g01833 1833
10 6060871 6061224 + ClG42_10g0049900.10 Clacu10g0499 499
10 6077855 6082695 - ClG42_10g0050200.10 Clacu10g0502 502
9 10752436 10776981 - ClCG09G010950.2 Cla09g01021 1021
9 10783277 10806496 + ClCG09G010970.2 Cla09g01024 1024
9 10810948 10828185 + ClCG09G010980.2 Cla09g01025 1025
10 6446390 6447666 + ClCG10G005240.2 Cla10g00490 490
10 6447918 6471355 - ClCG10G005250.2 Cla10g00491 491
1 8194586 8230140 + CmaCh01G011180.1 Cma01g01118 1118
9 4869909 4883127 + CmaCh09G009630.1 Cma09g00963 963
9 4884643 4892089 + CmaCh09G009640.1 Cma09g00964 964
16 6615552 6618014 + CmaCh16G009000.1 Cma16g00900 900
1 12323134 12331326 - MELO3C013140.2.1 Cme01g01013 1013
1 12334762 12384378 - MELO3C013141.2.1 Cme01g01014 1014
6 36003343 36004156 + MELO3C014190.2.1 Cme06g02856 2856
6 36021648 36025948 + MELO3C014192.2.1 Cme06g02858 2858
6 36021975 36025792 - MELO3C014193.2.1 Cme06g02859 2859
6 26401784 26403612 + PI0028362.1 Cmetu06g2572 2572
6 26403963 26406321 - PI0016604.1 Cmetu06g2813 2813
1 9514265 9522309 - CmoCh01G011650.1 Cmo01g01165 1165
1 9524191 9542468 + CmoCh01G011660.1 Cmo01g01166 1166
6 5352062 5353790 + CmoCh06G008970.1 Cmo06g00897 897
9 5078539 5091617 + CmoCh09G009630.1 Cmo09g00963 963
9 5094136 5100000 + CmoCh09G009660.1 Cmo09g00966 966
16 5903863 5906411 + CmoCh16G009360.1 Cmo16g00936 936
10 6184637 6184990 + CmPI595203_10g013260.1 Cmu10g1326 1326
10 6201624 6206466 - CmPI595203_10g013290.1 Cmu10g1329 1329
6 289924 295475 - Conep06aG0005100.1 Cone6ag0051 51
6 295695 297252 - Conep06aG0005200.1 Cone6ag0052 52
9 290263 297196 - Conep09aG0006200.1 Cone9ag0062 62
9 298234 304827 + Conep09aG0006300.1 Cone9ag0063 63
15 9486215 9490820 - Conep15aG0120600.1 Cone15ag1177 1177
15 9500478 9501245 - Conep15aG0120700.1 Cone15ag1178 1178
2 4991498 5009865 - Cp4.1LG02g00900.1 Cpe02g00783 783
2 5011342 5018632 + Cp4.1LG02g00950.1 Cpe02g00784 784
6 4927183 4940304 + Cp4.1LG06g08750.1 Cpe06g00778 778
6 4941956 4948936 + Cp4.1LG06g08780.1 Cpe06g00779 779
14 5058297 5058779 + Cp4.1LG14g07210.1 Cpe14g00723 723
14 5061751 5064765 - Cp4.1LG14g07270.1 Cpe14g00724 724
14 5593059 5597229 - Cp4.1LG14g07450.1 Cpe14g00742 742
9 10691138 10715900 - CrPI670011_09g010430.1 Cre09g1043 1043
9 10723878 10747468 + CrPI670011_09g010440.1 Cre09g1044 1044
9 10751519 10764961 + CrPI670011_09g010450.1 Cre09g1045 1045
10 7077434 7077913 + CrPI670011_10g007310.1 Cre10g0731 731
10 7078256 7095673 - CrPI670011_10g007320.1 Cre10g0732 732
3 4118689 4120234 + CsaV3_3G004930.1 Csa03g00493 493
3 4126617 4131678 + CsaV3_3G004940.1 Csa03g00494 494
3 4129081 4131467 - CsaV3_3G004950.1 Csa03g00495 495
7 10713565 10741649 - CsaV3_7G021980.1 Csa07g01109 1109
7 10744617 10783314 + CsaV3_7G021990.1 Csa07g01110 1110
7 10807216 10814041 + CsaV3_7G022000.1 Csa07g01111 1111
1 77819418 77826209 - Hsped.01g12570.1 Hepe01g1257 1257
1 77829609 77851848 - Hsped.01g12580.1 Hepe01g1258 1258
6 164806 166869 - Hsped.06g00030.1 Hepe06g0003 3
2 24769138 24775830 - Lsi02G018900.1 Lsi02g01890 1890
2 24781184 24796178 - Lsi02G018910.1 Lsi02g01891 1891
2 24797870 24823751 + Lsi02G018920.1 Lsi02g01892 1892
5 7169169 7169717 + Lsi05G005780.1 Lsi05g00578 578
5 7178457 7181313 + Lsi05G005790.1 Lsi05g00579 579
5 7180075 7183918 - Lsi05G005800.1 Lsi05g00580 580
11 8475488 8490203 - MC11g0994 Mch11g1203 1203
8 28231706 28238790 - Sed0015579.1 Sed08g1364 1364
14 1537189 1539572 + Sed0007270.1 Sed14g0140 140
1 18447885 18450286 + Tan0010873.3 Tan01g1726 1726
1 18451642 18455734 - Tan0012075.2 Tan01g1728 1728
19 6901740 6924736 - Vvi19g544 Vvi19g544 544
19 6924770 6926335 - Vvi19g545 Vvi19g545 545
19 6956977 6958495 + Vvi19g546 Vvi19g546 546
19 6960132 6964793 + Vvi19g547 Vvi19g547 547
19 6966539 7003205 + Vvi19g548 Vvi19g548 548
19 7005368 7014427 + Vvi19g549 Vvi19g549 549
19 7014971 7045143 + Vvi19g550 Vvi19g550 550
19 7053770 7059043 + Vvi19g551 Vvi19g551 551
19 7059266 7061190 - Vvi19g552 Vvi19g552 552
19 7070074 7070686 - Vvi19g553 Vvi19g553 553
       

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