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
Vvi19g554 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g555 Blo03g00547 Blo03g01456 Bda07g00374 Bda09g00405 . Bpe08g01116 . . Cmo16g00939 . . . . . . . . . . . . . . . . . . . . . . Cone6ag0050 Cone9ag0060 . . . . . . . . . . Bpe11g00559 . Bma07g01287 Bma14g00327 . . . . Cma16g00904 . Car16g00879 Cpe14g00721 . . . . . . . . . . . . . . . . . . .
Vvi19g556 Blo03g00546 Blo03g01457 Bda07g00375 Bda09g00406 . Bpe08g01115 . . . . Cma01g01117 Cma09g00966 Car01g00988 Car09g00881 Sed01g1878 Cpe06g00781 Cpe02g00786 Bhi09g01684 Tan01g3114 Cmetu01g0669 . Hepe01g1255 Mch11g1207 . . . . . . . . Cone6ag0049 Cone9ag0059 Cone14ag1166 Cone15ag1179 Lsi02g01888 Csa07g01113 . . . . . . . . . Bma14g00326 . Cmo01g01163 Cmo09g00968 . . . . . . . . . . . . . Cla09g01026 Cam09g1081 Cec09g1080 Cco09g1101 . . Cre09g1046 . . . Cme01g01006
Vvi19g557 . . . . Bpe09g00160 . . Bma13g01072 Cmo16g00940 . . . . . . . . . . . . . . . Cla10g00489 Cam10g0478 Cec10g0498 Cco10g0484 Clacu10g0497 Cmu10g1324 Cre10g0730 . . . Cone15ag1182 . . . Cme06g02850 . Blo10g00844 . Bda12g00925 . . . . . . . . Cma16g00905 . Car16g00880 Cpe14g00720 . . . . . . . . . . . . . . . Lsi05g00576 . . .
Vvi19g558 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g00492 . . . . . . . . . . Sed01g2981 . . . . . . Cpe14g00722 . Bhi11g00591 Tan01g1733 Cmetu06g0270 . . . . . . . . . . . . . Chy06g01834 .
Vvi19g559 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g560 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g561 . . . . . . . . Cmo16g00941 . . . . . . . . . . . . . . . Cla10g00487 Cam10g0473 Cec10g0494 Cco10g0481 Clacu10g0493 Cmu10g1321 Cre10g0727 . . . . . Csa03g00488 . Cme06g02847 . . . . . . . . . . . . Cma16g00906 . Car16g00881 Cpe14g00719 . Bhi11g00588 . . . . . . . . . . . . . . . Chy06g01835 .
Vvi19g562 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g563 . . . . . . Bma10g00571 Bma13g01074 Cmo16g00942 Cmo06g00896 . . . . . . . . . . . . . . Cla10g00485 . Cec10g0492 Cco10g0479 Clacu10g0491 Cmu10g1319 Cre10g0725 Cone6ag0046 Cone9ag0055 . Cone15ag1184 . Csa03g00485 . Cme06g02845 Blo07g00888 . Bda05g00704 Bda12g00929 . . . . . . . . Cma16g00907 . Car16g00882 Cpe14g00718 . Bhi11g00586 . . . . . . . . . . . . . Lsi05g00572 . Chy06g01837 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 55321713 55322684 - Bda021841.1 Bda05g00704 704
7 4745627 4748119 - Bda025461.2 Bda07g00374 374
7 4752708 4755260 + Bda033837 Bda07g00375 375
9 5077612 5079582 - Bda030984.1 Bda09g00405 405
9 5083445 5085648 + Bda030985.1 Bda09g00406 406
12 40374613 40378218 - Bda009470.1 Bda12g00925 925
12 40405955 40407313 + Bda009474.1 Bda12g00929 929
9 45176611 45179525 + XM_039041947.1 Bhi09g01684 1684
11 13350685 13352879 - XM_039050052.1 Bhi11g00586 586
11 13408541 13412479 + XM_039048298.1 Bhi11g00588 588
11 13442978 13451988 + XM_039049783.1 Bhi11g00591 591
3 21369433 21371462 - BLOR11727 Blo03g00546 546
3 21447841 21449698 + BLOR11728 Blo03g00547 547
3 41177742 41179872 - BLOR12637 Blo03g01456 1456
3 41194603 41196813 + BLOR12638 Blo03g01457 1457
7 27656946 27658394 - BLOR18820 Blo07g00888 888
10 26900812 26904095 - BLOR02634 Blo10g00844 844
7 48512230 48514157 + Bma026559.1 Bma07g01287 1287
10 7095982 7097315 + Bma004276.1 Bma10g00571 571
13 43577421 43580968 - Bma030622 Bma13g01072 1072
13 43596152 43601120 + Bma010196.1 Bma13g01074 1074
14 4063250 4065446 - Bma010747.1 Bma14g00326 326
14 4071800 4073112 + Bma010748.1 Bma14g00327 327
8 13153687 13155902 - Bpe023241.1 Bpe08g01115 1115
8 13158547 13160520 + Bpe023242.1 Bpe08g01116 1116
9 1074358 1077858 + Bpe023833.1 Bpe09g00160 160
11 4297285 4298270 - Bpe003926.1 Bpe11g00559 559
9 11242579 11245093 + CaPI482276_09g010810.1 Cam09g1081 1081
10 7184320 7187626 + CaPI482276_10g004730.1 Cam10g0473 473
10 7212356 7214890 + CaPI482276_10g004780.1 Cam10g0478 478
1 9371052 9373853 - Carg22374-RA Car01g00988 988
9 5413993 5416376 + Carg12835-RA Car09g00881 881
16 6674059 6683651 + Carg27290-RA Car16g00879 879
16 6687019 6690477 - Carg27289-RA Car16g00880 880
16 6699733 6701729 - Carg27288-RA Car16g00881 881
16 6732729 6734317 + Carg27287-RA Car16g00882 882
9 10574698 10576783 + CcPI632755_09g011010.1 Cco09g1101 1101
10 5732569 5734390 - CcPI632755_10g004790.1 Cco10g0479 479
10 5747324 5750763 + CcPI632755_10g004810.1 Cco10g0481 481
10 5775157 5775711 + CcPI632755_10g004840.1 Cco10g0484 484
9 10605363 10607694 + CePI673135_09g010800.1 Cec09g1080 1080
10 5941252 5943091 - CePI673135_10g004920.1 Cec10g0492 492
10 5956073 5959484 + CePI673135_10g004940.1 Cec10g0494 494
10 5982746 5983276 + CePI673135_10g004980.1 Cec10g0498 498
6 22098212 22100942 - Chy6G123620.1 Chy06g01834 1834
6 22105485 22115642 - Chy6G123630.1 Chy06g01835 1835
6 22128374 22129862 + Chy6G123650.1 Chy06g01837 1837
10 6005065 6006885 - ClG42_10g0049100.10 Clacu10g0491 491
10 6024622 6027936 + ClG42_10g0049300.10 Clacu10g0493 493
10 6044903 6048002 + ClG42_10g0049700.10 Clacu10g0497 497
9 10851747 10854512 + ClCG09G011000.2 Cla09g01026 1026
10 6387130 6389000 - ClCG10G005180.1 Cla10g00485 485
10 6407741 6411077 + ClCG10G005200.2 Cla10g00487 487
10 6422360 6438554 + ClCG10G005220.2 Cla10g00489 489
1 8174311 8193527 - CmaCh01G011170.1 Cma01g01117 1117
9 4899923 4902580 + CmaCh09G009660.1 Cma09g00966 966
16 6632618 6641442 + CmaCh16G009040.1 Cma16g00904 904
16 6646511 6650106 - CmaCh16G009050.1 Cma16g00905 905
16 6652872 6654957 - CmaCh16G009060.1 Cma16g00906 906
16 6717508 6719071 + CmaCh16G009070.1 Cma16g00907 907
1 12223955 12227154 - MELO3C013136.2.1 Cme01g01006 1006
6 35931713 35933480 - MELO3C014182.2.1 Cme06g02845 2845
6 35957097 35959414 + MELO3C014184.2.1 Cme06g02847 2847
6 35963141 35974709 + MELO3C014186.2.1 Cme06g02850 2850
1 11309215 11312261 + PI0026310.1 Cmetu01g0669 669
6 26419346 26424325 - PI0016137.2 Cmetu06g0270 270
1 9500763 9504386 - CmoCh01G011630.1 Cmo01g01163 1163
6 5311584 5313807 - CmoCh06G008960.1 Cmo06g00896 896
9 5110949 5115497 + CmoCh09G009680.1 Cmo09g00968 968
16 5917835 5927194 + CmoCh16G009390.1 Cmo16g00939 939
16 5930491 5934030 - CmoCh16G009400.1 Cmo16g00940 940
16 5956181 5958105 - CmoCh16G009410.1 Cmo16g00941 941
16 5993139 5994730 + CmoCh16G009420.1 Cmo16g00942 942
10 6128552 6130371 - CmPI595203_10g013190.1 Cmu10g1319 1319
10 6148165 6151473 + CmPI595203_10g013210.1 Cmu10g1321 1321
10 6167936 6171799 + CmPI595203_10g013240.1 Cmu10g1324 1324
6 274666 275837 - Conep06aG0004600.1 Cone6ag0046 46
6 280862 283633 - Conep06aG0004900.1 Cone6ag0049 49
6 284609 286644 + Conep06aG0005000.1 Cone6ag0050 50
9 271613 273249 - Conep09aG0005500.1 Cone9ag0055 55
9 281607 284525 - Conep09aG0005900.1 Cone9ag0059 59
9 285296 287419 + Conep09aG0006000.1 Cone9ag0060 60
14 9595960 9598980 - Conep14aG0119000.1 Cone14ag1166 1166
15 9509378 9512063 + Conep15aG0120800.1 Cone15ag1179 1179
15 9515931 9519385 - Conep15aG0121100.1 Cone15ag1182 1182
15 9530413 9532327 + Conep15aG0121300.1 Cone15ag1184 1184
2 5028083 5031160 + Cp4.1LG02g00930.1 Cpe02g00786 786
6 4958985 4962306 + Cp4.1LG06g08740.1 Cpe06g00781 781
14 5022419 5024188 - Cp4.1LG14g07200.1 Cpe14g00718 718
14 5032805 5033539 + Cp4.1LG14g07190.1 Cpe14g00719 719
14 5035439 5039035 + Cp4.1LG14g07180.1 Cpe14g00720 720
14 5042435 5051585 - Cp4.1LG14g07260.1 Cpe14g00721 721
14 5053516 5057296 + Cp4.1LG14g07220.1 Cpe14g00722 722
9 10784446 10786974 + CrPI670011_09g010460.1 Cre09g1046 1046
10 7026559 7028398 - CrPI670011_10g007250.1 Cre10g0725 725
10 7040936 7044312 + CrPI670011_10g007270.1 Cre10g0727 727
10 7069463 7069993 + CrPI670011_10g007300.1 Cre10g0730 730
3 4085211 4087148 - CsaV3_3G004850.1 Csa03g00485 485
3 4099561 4101664 + CsaV3_3G004880.1 Csa03g00488 488
3 4112254 4116591 + CsaV3_3G004920.1 Csa03g00492 492
7 10855041 10858579 + CsaV3_7G022020.1 Csa07g01113 1113
1 77797379 77800393 - Hsped.01g12550.1 Hepe01g1255 1255
2 24744781 24748260 - Lsi02G018880.1 Lsi02g01888 1888
5 7117268 7119350 - Lsi05G005720.1 Lsi05g00572 572
5 7150902 7157940 + Lsi05G005760.1 Lsi05g00576 576
11 8559313 8562464 + MC11g0998 Mch11g1207 1207
1 13915440 13920092 - Sed0003516.1 Sed01g1878 1878
1 27283208 27285994 + Sed0025734.2 Sed01g2981 2981
1 18516295 18520272 + Tan0017463.2 Tan01g1733 1733
1 83910254 83913485 + Tan0007835.1 Tan01g3114 3114
19 7076143 7087746 - Vvi19g554 Vvi19g554 554
19 7088026 7094310 - Vvi19g555 Vvi19g555 555
19 7105462 7108433 + Vvi19g556 Vvi19g556 556
19 7112181 7119503 + Vvi19g557 Vvi19g557 557
19 7121823 7124124 - Vvi19g558 Vvi19g558 558
19 7124167 7133937 - Vvi19g559 Vvi19g559 559
19 7134472 7135460 + Vvi19g560 Vvi19g560 560
19 7136386 7138873 - Vvi19g561 Vvi19g561 561
19 7139584 7146224 + Vvi19g562 Vvi19g562 562
19 7150538 7152429 + Vvi19g563 Vvi19g563 563
       

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