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
Vvi17g56 . . . . . . . . . . . . . . Sed08g0454 . . Bhi02g00646 Tan09g1740 Cmetu06g1175 . Hepe09g0021 . . Cla06g01769 Cam06g1961 Cec06g2012 Cco06g2018 Clacu06g1919 Cmu06g1860 Cre06g2673 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g57 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g58 . Blo16g00285 . . . Bpe13g00190 Bma06g00278 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone19ag0227 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy02g02687 .
Vvi17g59 . . . . . Bpe13g00191 Bma06g00277 . . . Cma10g00038 Cma11g00015 Car10g00028 . Sed01g3768 . . Bhi02g00651 Tan09g2409 Cmetu09g1954 . Hepe09g0026 . . Cla06g01766 . . . Clacu06g1915 Cmu06g1856 Cre06g2669 . . Cone13ag0245 . . Csa01g00769 . . . . . . . . . . . . Cmo11g00014 . . . . . . . . . . . . . . . . . . . . . Csa01g00029 . Cme02g02092
Vvi17g60 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g61 . Blo16g00284 . Bda15g00685 . . Bma06g00276 . Cmo13g00856 Cmo18g00090 . Cma11g00016 . Car11g00014 Sed12g2536 . Cpe04g01632 Bhi02g00652 Tan09g2408 Cmetu02g1647 . Hepe09g0027 . . Cla06g01763 Cam06g1957 Cec06g2007 Cco06g2013 Clacu06g1914 Cmu06g1854 Cre06g2668 . . . . Lsi02g00290 Csa01g00985 . Cme12g01567 . Blo15g00197 . . Bpe07g00901 . Bma03g01232 Bma08g00270 . Cmo10g00034 Cmo11g00015 Cma13g00825 Cma18g00300 . . Cpe09g00947 Cpe18g00923 Bhi08g01532 . . . . . . Cla03g00374 Cam03g0394 Cec03g0380 Cco03g0395 Clacu03g0393 Cmu03g0998 Cre03g0690 Lsi06g01664 Csa01g00030 Chy02g02685 Cme02g02091
Vvi17g62 . . . Bda15g00684 Bpe12g00468 . . . Cmo13g00855 Cmo18g00234 . Cma11g00017 Car10g00030 Car11g00015 Sed12g2535 Cpe20g00293 . Bhi02g00653 Tan09g2407 . . Hepe09g0028 . . . . . . . . . . Cone16ag0001 Cone13ag0243 Cone19ag0226 . . Chy12g01148 Cme12g01568 . . . Bda14g01343 . Bpe15g00236 . Bma08g00269 Sed08g2418 Cmo10g00036 Cmo11g00016 Cma13g00824 . Car13g00668 . . Cpe18g00922 Bhi08g01529 Tan05g3000 Cmetu12g1505 Lac10g0605 Hepe07g2090 . . Cla03g00373 Cam03g0393 Cec03g0379 Cco03g0394 Clacu03g0392 Cmu03g0997 Cre03g0689 Lsi06g01663 Csa01g00031 Chy02g02684 Cme02g02090
Vvi17g63 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g64 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g65 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
14 15486013 15487645 + Bda011034.1 Bda14g01343 1343
15 10259683 10260758 - Bda012535.1 Bda15g00684 684
15 10268926 10270544 - Bda012536.1 Bda15g00685 685
2 12479965 12486437 + XM_039023470.1 Bhi02g00646 646
2 12539088 12540950 + XM_039022402.1 Bhi02g00651 651
2 12541435 12544735 + XM_039022401.1 Bhi02g00652 652
2 12549222 12550947 + XM_039023916.1 Bhi02g00653 653
8 43824263 43826541 - XM_039039287.1 Bhi08g01529 1529
8 43917780 43919620 - XM_039039219.1 Bhi08g01532 1532
15 2034951 2042102 + BLOR06591 Blo15g00197 197
16 6784960 6790924 - BLOR07532 Blo16g00284 284
16 6813530 6815439 + BLOR07533 Blo16g00285 285
3 20098605 20099738 + Bma017683.1 Bma03g01232 1232
6 3830378 3831790 - Bma022911.1 Bma06g00276 276
6 3836824 3838101 - Bma031278 Bma06g00277 277
6 3841738 3843428 + Bma022912.1 Bma06g00278 278
8 3662315 3663921 - Bma027288.1 Bma08g00269 269
8 3672580 3673995 - Bma027289.1 Bma08g00270 270
7 15024113 15030091 - Bpe021742.1 Bpe07g00901 901
12 10446441 10447841 + Bpe005728.1 Bpe12g00468 468
13 9845521 9846097 - Bpe006310.1 Bpe13g00190 190
13 9849382 9850673 + Bpe006311.1 Bpe13g00191 191
15 13536126 13537681 - Bpe001172.1 Bpe15g00236 236
3 5030003 5037413 - CaPI482276_03g003930.1 Cam03g0393 393
3 5049088 5050489 - CaPI482276_03g003940.1 Cam03g0394 394
6 30442249 30447938 - CaPI482276_06g019570.1 Cam06g1957 1957
6 30459545 30466016 - CaPI482276_06g019610.1 Cam06g1961 1961
10 130751 132272 + Carg10260-RA Car10g00028 28
10 137130 138585 + Carg10262-RA Car10g00030 30
11 64737 65843 + Carg24554-RA Car11g00014 14
11 66905 68395 + Carg24553-RA Car11g00015 15
13 8157622 8159231 - Carg07618-RA Car13g00668 668
3 4259159 4266174 - CcPI632755_03g003940.1 Cco03g0394 394
3 4276663 4278053 - CcPI632755_03g003950.1 Cco03g0395 395
6 30188563 30189869 - CcPI632755_06g020130.1 Cco06g2013 2013
6 30206559 30210115 - CcPI632755_06g020180.1 Cco06g2018 2018
3 4207913 4215104 - CePI673135_03g003790.1 Cec03g0379 379
3 4225913 4227321 - CePI673135_03g003800.1 Cec03g0380 380
6 33268183 33269484 - CePI673135_06g020070.1 Cec06g2007 2007
6 33287619 33295577 - CePI673135_06g020120.1 Cec06g2012 2012
2 29768317 29771334 - Chy2G049510.1 Chy02g02684 2684
2 29774384 29779499 - Chy2G049520.1 Chy02g02685 2685
2 29785121 29787612 + Chy2G049540.1 Chy02g02687 2687
12 16425314 16427122 + Chy12G217480.1 Chy12g01148 1148
3 4351076 4353154 - ClG42_03g0039200.10 Clacu03g0392 392
3 4364649 4366053 - ClG42_03g0039300.10 Clacu03g0393 393
6 29483010 29484302 - ClG42_06g0191400.10 Clacu06g1914 1914
6 29493006 29498688 - ClG42_06g0191500.10 Clacu06g1915 1915
6 29510228 29511688 - ClG42_06g0191900.10 Clacu06g1919 1919
3 4309383 4315514 - ClCG03G003960.2 Cla03g00373 373
3 4324017 4325553 - ClCG03G003970.1 Cla03g00374 374
6 31142687 31154586 - ClCG06G018140.1 Cla06g01763 1763
6 31156663 31158500 - ClCG06G018150.1 Cla06g01766 1766
6 31170166 31171120 - ClCG06G018180.1 Cla06g01769 1769
10 136516 151213 + CmaCh10G000380.1 Cma10g00038 38
11 65941 68019 + CmaCh11G000150.1 Cma11g00015 15
11 69886 71224 + CmaCh11G000160.1 Cma11g00016 16
11 71969 73649 + CmaCh11G000170.1 Cma11g00017 17
13 6907227 6909004 - CmaCh13G008240.1 Cma13g00824 824
13 6912096 6914203 - CmaCh13G008250.1 Cma13g00825 825
18 1606591 1609190 + CmaCh18G003000.1 Cma18g00300 300
2 26760731 26762656 - MELO3C026184.2.1 Cme02g02090 2090
2 26767146 26768816 - MELO3C026183.2.1 Cme02g02091 2091
2 26770398 26772169 - MELO3C026182.2.1 Cme02g02092 2092
12 23064158 23066068 + MELO3C002381.2.1 Cme12g01567 1567
12 23073732 23075677 + MELO3C002380.2.1 Cme12g01568 1568
2 25090516 25092398 - PI0011155.1 Cmetu02g1647 1647
6 3309517 3311519 - PI0028306.1 Cmetu06g1175 1175
9 971753 974991 + PI0006917.1 Cmetu09g1954 1954
12 3314447 3316251 - PI0025952.1 Cmetu12g1505 1505
10 175238 178761 + CmoCh10G000340.1 Cmo10g00034 34
10 180299 182106 + CmoCh10G000360.1 Cmo10g00036 36
11 60592 62641 + CmoCh11G000140.1 Cmo11g00014 14
11 64141 65351 + CmoCh11G000150.1 Cmo11g00015 15
11 66311 67779 + CmoCh11G000160.1 Cmo11g00016 16
13 7841375 7843293 - CmoCh13G008550.1 Cmo13g00855 855
13 7847191 7848790 - CmoCh13G008560.1 Cmo13g00856 856
18 598992 603706 - CmoCh18G000900.1 Cmo18g00090 90
18 1527600 1530120 - CmoCh18G002340.1 Cmo18g00234 234
3 4565131 4567208 - CmPI595203_03g009970.1 Cmu03g0997 997
3 4578776 4580186 - CmPI595203_03g009980.1 Cmu03g0998 998
6 29393036 29394368 - CmPI595203_06g018540.1 Cmu06g1854 1854
6 29402095 29409194 - CmPI595203_06g018560.1 Cmu06g1856 1856
6 29420734 29422194 - CmPI595203_06g018600.1 Cmu06g1860 1860
13 1617855 1619208 - Conep13aG0025300.1 Cone13ag0243 243
13 1642103 1643813 + Conep13aG0025500.1 Cone13ag0245 245
16 31282 32530 + Conep16aG0000100.1 Cone16ag0001 1
19 1448956 1450301 - Conep19aG0023200.1 Cone19ag0226 226
19 1463482 1464309 + Conep19aG0023400.1 Cone19ag0227 227
4 12629845 12633668 - Cp4.1LG04g16370.1 Cpe04g01632 1632
9 8490911 8493506 + Cp4.1LG09g09470.1 Cpe09g00947 947
18 8191155 8192783 - Cp4.1LG18g09250.1 Cpe18g00922 922
18 8194804 8200993 - Cp4.1LG18g09230.1 Cpe18g00923 923
20 1640104 1646797 + Cp4.1LG20g02920.1 Cpe20g00293 293
3 5774713 5781915 - CrPI670011_03g006890.1 Cre03g0689 689
3 5792778 5794177 - CrPI670011_03g006900.1 Cre03g0690 690
6 34224477 34230064 - CrPI670011_06g026680.1 Cre06g2668 2668
6 34231049 34233881 - CrPI670011_06g026690.1 Cre06g2669 2669
6 34246208 34252675 - CrPI670011_06g026730.1 Cre06g2673 2673
1 180793 182032 + CsaV3_1G000290.1 Csa01g00029 29
1 184264 186169 + CsaV3_1G000300.1 Csa01g00030 30
1 190592 192566 + CsaV3_1G000310.1 Csa01g00031 31
1 4880415 4885229 - CsaV3_1G007690.1 Csa01g00769 769
1 6127468 6129304 - CsaV3_1G009850.1 Csa01g00985 985
7 65196619 65198878 + Hsped.07g20900.1 Hepe07g2090 2090
9 177158 192661 + Hsped.09g00210.1 Hepe09g0021 21
9 209627 218418 + Hsped.09g00260.1 Hepe09g0026 26
9 218776 219770 + Hsped.09g00270.1 Hepe09g0027 27
9 223144 224793 + Hsped.09g00280.1 Hepe09g0028 28
10 4641993 4644288 - Lag0024650.1 Lac10g0605 605
2 2480434 2486088 - Lsi02G002900.1 Lsi02g00290 290
6 26895089 26896872 - Lsi06G016630.1 Lsi06g01663 1663
6 26902233 26907852 - Lsi06G016640.1 Lsi06g01664 1664
1 66823486 66827202 + Sed0019052.1 Sed01g3768 3768
8 2829493 2832440 + Sed0013792.1 Sed08g0454 454
8 37254697 37257111 + Sed0011822.2 Sed08g2418 2418
12 34682155 34683512 - Sed0023171.1 Sed12g2535 2535
12 34688637 34689764 - Sed0019580.1 Sed12g2536 2536
5 81938795 81941574 - Tan0008229.1 Tan05g3000 3000
9 68991787 68994589 - Tan0015313.1 Tan09g1740 1740
9 73724293 73726599 - Tan0008720.1 Tan09g2407 2407
9 73730574 73731956 - Tan0015094.1 Tan09g2408 2408
9 73733799 73736208 - Tan0006294.1 Tan09g2409 2409
17 484105 501880 + Vvi17g56 Vvi17g56 56
17 502630 504861 - Vvi17g57 Vvi17g57 57
17 507530 508662 - Vvi17g58 Vvi17g58 58
17 512335 514836 + Vvi17g59 Vvi17g59 59
17 514980 521034 - Vvi17g60 Vvi17g60 60
17 546419 548495 + Vvi17g61 Vvi17g61 61
17 551029 552902 + Vvi17g62 Vvi17g62 62
17 558937 562728 - Vvi17g63 Vvi17g63 63
17 563631 567370 - Vvi17g64 Vvi17g64 64
17 568126 580106 + Vvi17g65 Vvi17g65 65
       

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