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
Vvi18g1330 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1331 . . . . . . . . Cmo04g02578 Cmo15g00582 . . . . Sed05g0790 . Cpe13g00699 Bhi04g01747 Tan11g1101 Cmetu03g1735 . Hepe02g2813 . Lcy10g1370 Cla08g00747 Cam08g1174 Cec08g0764 Cco08g0871 Clacu08g0880 . Cre08g0682 . . . Cone20ag0664 . . . Cme03g01052 . . . . . . . . . . . . . Car04g02371 Car15g00536 Cpe01g02132 . . . . . . . . . . . . . . . Lsi08g00573 . Chy03g00489 .
Vvi18g1332 . . . . . . . . . . . . Car01g00858 . . . . . . . . . . . . . . . . . . . . . Cone20ag0360 . . . Cme03g00894 . . . . . . . . . Cmo01g01052 . . . . Car09g01083 . . . . . . . . . . . . . . . . . . Chy03g00281 .
Vvi18g1333 . Blo12g00773 . Bda03g00406 . Bpe04g00370 Bma04g00386 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone17ag0769 Cone20ag0359 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme01g00777
Vvi18g1334 . . . . . . . . Cmo04g02580 Cmo15g00580 . . . . . . Cpe13g00701 Bhi04g01737 . . . . . . Cla08g00742 Cam08g1169 Cec08g0759 Cco08g0867 Clacu08g0876 . Cre08g0677 . . Cone17ag0768 Cone20ag0358 . . . . . . . Bda13g01416 . . Bma01g01429 . . . . . . Car04g02373 Car15g00534 Cpe01g02134 . . . . . . . . . . . . . . . Lsi08g00578 . Chy03g00484 .
Vvi18g1335 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1336 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1337 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1338 Blo01g01743 . . Bda03g00405 Bpe02g00200 Bpe04g00369 Bma04g00385 Bma01g02521 Cmo04g02575 Cmo15g00584 . . Car01g00859 . Sed11g1374 Cpe06g00911 Cpe13g00697 Bhi04g01750 Tan11g1107 Cmetu03g2287 . Hepe02g2811 . Lcy10g1368 Cla08g00749 Cam08g1176 Cec08g0766 Cco08g0874 Clacu08g0882 . Cre08g0684 . . Cone7ag0250 Cone4ag0244 . . . Cme03g01050 . . Bda11g00861 . . . . . . . . . . Car04g02368 Car15g00538 Cpe01g02130 . Bhi09g01541 Tan01g3072 Cmetu01g0853 . . Mch11g1490 . Cla09g00951 Cam09g1002 Cec09g1005 Cco09g1016 . . Cre09g0966 Lsi08g00572 . Chy03g00490 Cme01g00784
Vvi18g1339 Blo01g01742 Blo12g00774 . Bda03g00404 Bpe02g00201 Bpe04g00368 Bma04g00384 Bma01g02520 Cmo04g02574 Cmo15g00586 . . . . . . Cpe13g00696 Bhi04g01752 . . . Hepe02g2810 . Lcy10g1367 Cla08g00750 Cam08g1177 Cec08g0767 Cco08g0875 Clacu08g0883 . Cre08g0685 Cone4ag1470 Cone7ag1470 . . . . . Cme03g01049 . . Bda11g00862 Bda01g01473 . . Bma01g00781 . . . . . . Car04g02367 Car15g00539 Cpe01g02129 . . . . . . . . . . . . . . . Lsi08g00571 . Chy03g00491 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 50645139 50647921 + Bda003724.1 Bda01g01473 1473
3 3369058 3371815 + Bda016368.1 Bda03g00404 404
3 3372608 3376878 - Bda016369.1 Bda03g00405 405
3 3377835 3379730 - Bda016370.1 Bda03g00406 406
11 8488119 8501235 + Bda005613.1 Bda11g00861 861
11 8503193 8504723 - Bda005614.1 Bda11g00862 862
13 36862151 36867710 + Bda000243.1 Bda13g01416 1416
4 42377372 42396545 + XM_039028591.1 Bhi04g01737 1737
4 42446570 42479759 - XM_039030611.1 Bhi04g01747 1747
4 42593855 42595637 + XM_039028362.1 Bhi04g01750 1750
4 42620932 42625242 - XM_039028148.1 Bhi04g01752 1752
9 41447310 41450150 + XM_039040712.1 Bhi09g01541 1541
1 57110414 57112810 + BLOR01742 Blo01g01742 1742
1 57114552 57138333 - BLOR01743 Blo01g01743 1743
12 26144529 26150983 + BLOR04792 Blo12g00773 773
12 26152098 26154845 - BLOR04793 Blo12g00774 774
1 7161262 7163763 - Bma030203 Bma01g00781 781
1 24253914 24258404 + Bma001798.1 Bma01g01429 1429
1 82835675 82838039 + Bma003400.1 Bma01g02520 2520
1 82839108 82840127 - Bma003401.1 Bma01g02521 2521
4 3098987 3101760 + Bma018845.1 Bma04g00384 384
4 3102804 3104025 - Bma018846.1 Bma04g00385 385
4 3104708 3107210 - Bma018847.1 Bma04g00386 386
2 1403114 1404224 + Bpe008050.1 Bpe02g00200 200
2 1405361 1407650 - Bpe008051.1 Bpe02g00201 201
4 2311724 2314482 + Bpe015058.1 Bpe04g00368 368
4 2316683 2318134 - Bpe015059.1 Bpe04g00369 369
4 2318624 2321130 - Bpe025615 Bpe04g00370 370
8 18043088 18049663 + CaPI482276_08g011690.1 Cam08g1169 1169
8 18069576 18077836 - CaPI482276_08g011740.1 Cam08g1174 1174
8 18106796 18119692 + CaPI482276_08g011760.1 Cam08g1176 1176
8 18124371 18127594 - CaPI482276_08g011770.1 Cam08g1177 1177
9 10411771 10422607 + CaPI482276_09g010020.1 Cam09g1002 1002
1 7275028 7277737 - Carg27776-RA Car01g00858 858
1 7343382 7347604 + Carg27777-RA Car01g00859 859
4 19002419 19006269 + Carg15802-RA Car04g02367 2367
4 19006698 19008539 - Carg15803-RA Car04g02368 2368
4 19023545 19028710 + Carg15806-RA Car04g02371 2371
4 19040626 19047109 - Carg15808-RA Car04g02373 2373
9 10136033 10146388 - Carg27057-RA Car09g01083 1083
15 2904525 2911204 + Carg01623-RA Car15g00534 534
15 2919035 2926057 - Carg01621-RA Car15g00536 536
15 2943213 2945212 + Carg01619-RA Car15g00538 538
15 2945878 2949293 - Carg01618-RA Car15g00539 539
8 20528643 20535232 + CcPI632755_08g008670.1 Cco08g0867 867
8 20555207 20563164 - CcPI632755_08g008710.1 Cco08g0871 871
8 20605752 20607330 + CcPI632755_08g008740.1 Cco08g0874 874
8 20611279 20615308 - CcPI632755_08g008750.1 Cco08g0875 875
9 9709208 9711460 + CcPI632755_09g010160.1 Cco09g1016 1016
8 19319595 19326159 + CePI673135_08g007590.1 Cec08g0759 759
8 19346605 19354672 - CePI673135_08g007640.1 Cec08g0764 764
8 19384486 19396792 + CePI673135_08g007660.1 Cec08g0766 766
8 19401479 19404664 - CePI673135_08g007670.1 Cec08g0767 767
9 9725259 9727536 + CePI673135_09g010050.1 Cec09g1005 1005
3 2989833 3001106 - Chy3G052610.1 Chy03g00281 281
3 6722511 6728427 + Chy3G054640.1 Chy03g00484 484
3 6756595 6764439 - Chy3G054690.1 Chy03g00489 489
3 6782852 6794297 + Chy3G054700.1 Chy03g00490 490
3 6797045 6800757 - Chy3G054710.1 Chy03g00491 491
8 18831939 18838501 + ClG42_08g0087600.10 Clacu08g0876 876
8 18858415 18866690 - ClG42_08g0088000.10 Clacu08g0880 880
8 18895412 18908288 + ClG42_08g0088200.10 Clacu08g0882 882
8 18912922 18916144 - ClG42_08g0088300.10 Clacu08g0883 883
8 19720332 19737125 + ClCG08G007300.2 Cla08g00742 742
8 19756856 19763726 - ClCG08G007350.1 Cla08g00747 747
8 19793846 19806955 + ClCG08G007370.2 Cla08g00749 749
8 19811127 19814976 - ClCG08G007390.1 Cla08g00750 750
9 9976444 9982936 + ClCG09G010200.2 Cla09g00951 951
1 8003590 8016025 + MELO3C024061.2.1 Cme01g00777 777
1 8121482 8124027 - MELO3C024071.2.1 Cme01g00784 784
3 17017175 17025921 + MELO3C024971.2.1 Cme03g00894 894
3 19742186 19747174 + MELO3C019980.2.1 Cme03g01049 1049
3 19759500 19761361 - MELO3C019979.2.1 Cme03g01050 1050
3 19804624 19808580 + MELO3C019978.2.1 Cme03g01052 1052
1 16253849 16256360 - PI0007150.1 Cmetu01g0853 853
3 8533927 8542085 - PI0007832.1 Cmetu03g1735 1735
3 8575912 8577863 + PI0001303.1 Cmetu03g2287 2287
1 8334382 8337499 - CmoCh01G010520.1 Cmo01g01052 1052
4 18837561 18841867 + CmoCh04G025740.1 Cmo04g02574 2574
4 18842777 18844881 - CmoCh04G025750.1 Cmo04g02575 2575
4 18860081 18866783 + CmoCh04G025780.1 Cmo04g02578 2578
4 18877131 18886260 - CmoCh04G025800.1 Cmo04g02580 2580
15 2783779 2791573 + CmoCh15G005800.1 Cmo15g00580 580
15 2799503 2806872 - CmoCh15G005820.1 Cmo15g00582 582
15 2823941 2826498 + CmoCh15G005840.1 Cmo15g00584 584
15 2827857 2831346 - CmoCh15G005860.1 Cmo15g00586 586
4 1097486 1099048 + Conep04aG0025300.1 Cone4ag0244 244
4 11580676 11583923 - Conep04aG0152200.1 Cone4ag1470 1470
7 1049529 1051187 + Conep07aG0025500.1 Cone7ag0250 250
7 10341152 10343397 + Conep07aG0151200.1 Cone7ag1470 1470
17 5819099 5824646 + Conep17aG0078600.1 Cone17ag0768 768
17 5825263 5827905 + Conep17aG0078700.1 Cone17ag0769 769
20 1607833 1613319 + Conep20aG0037200.1 Cone20ag0358 358
20 1614811 1616770 + Conep20aG0037300.1 Cone20ag0359 359
20 1616945 1619068 - Conep20aG0037400.1 Cone20ag0360 360
20 4053556 4056000 + Conep20aG0068500.1 Cone20ag0664 664
1 17956695 17960239 + Cp4.1LG01g21200.1 Cpe01g02129 2129
1 17961919 17964015 - Cp4.1LG01g21270.1 Cpe01g02130 2130
1 17979988 17986394 + Cp4.1LG01g21220.1 Cpe01g02132 2132
1 17996928 18003614 - Cp4.1LG01g21290.1 Cpe01g02134 2134
6 6307041 6309711 + Cp4.1LG06g07440.1 Cpe06g00911 911
13 6488963 6492717 + Cp4.1LG13g03900.1 Cpe13g00696 696
13 6493318 6495360 - Cp4.1LG13g03830.1 Cpe13g00697 697
13 6511488 6518346 + Cp4.1LG13g03920.1 Cpe13g00699 699
13 6525488 6532210 - Cp4.1LG13g03870.1 Cpe13g00701 701
8 19740696 19747315 + CrPI670011_08g006770.1 Cre08g0677 677
8 19767491 19775457 - CrPI670011_08g006820.1 Cre08g0682 682
8 19802170 19815224 + CrPI670011_08g006840.1 Cre08g0684 684
8 19819946 19823598 - CrPI670011_08g006850.1 Cre08g0685 685
9 9906954 9920886 + CrPI670011_09g009660.1 Cre09g0966 966
2 77158524 77162471 + Hsped.02g28100.1 Hepe02g2810 2810
2 77164757 77166907 - Hsped.02g28110.1 Hepe02g2811 2811
2 77213621 77223136 + Hsped.02g28130.1 Hepe02g2813 2813
10 36864939 36868368 + Maker00008633 Lcy10g1367 1367
10 36869493 36871443 - Maker00008590 Lcy10g1368 1368
10 36914320 36920267 + Maker00008432 Lcy10g1370 1370
8 13962832 13966554 + Lsi08G005710.1 Lsi08g00571 571
8 13969465 13981797 - Lsi08G005720.1 Lsi08g00572 572
8 14006186 14014315 + Lsi08G005730.1 Lsi08g00573 573
8 14044178 14067777 - Lsi08G005780.1 Lsi08g00578 578
11 11847873 11850076 - MC11g1208 Mch11g1490 1490
5 6206303 6215338 + Sed0006846.4 Sed05g0790 790
11 29747756 29750556 - Sed0001431.1 Sed11g1374 1374
1 78526982 78530563 - Tan0020105.1 Tan01g3072 3072
11 8723671 8736679 - Tan0017761.1 Tan11g1101 1101
11 8785312 8787336 + Tan0008069.1 Tan11g1107 1107
18 18980573 18985327 - Vvi18g1330 Vvi18g1330 1330
18 18987561 19001786 - Vvi18g1331 Vvi18g1331 1331
18 19023717 19026944 + Vvi18g1332 Vvi18g1332 1332
18 19026977 19032485 - Vvi18g1333 Vvi18g1333 1333
18 19034332 19051176 - Vvi18g1334 Vvi18g1334 1334
18 19067282 19068738 - Vvi18g1335 Vvi18g1335 1335
18 19069468 19069755 - Vvi18g1336 Vvi18g1336 1336
18 19072732 19073722 - Vvi18g1337 Vvi18g1337 1337
18 19080414 19085513 + Vvi18g1338 Vvi18g1338 1338
18 19092793 19099983 - Vvi18g1339 Vvi18g1339 1339
       

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