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
Vvi19g614 . . . . Bpe09g00134 . . Bma13g01108 Cmo16g00983 . . . . . . . . . . . . . . . Cla10g00432 Cam10g0430 Cec10g0453 Cco10g0442 Clacu10g0438 Cmu10g1269 Cre10g0686 . . Cone14ag1207 . . Csa03g00440 . Cme06g02786 . Blo10g00862 . Bda12g00952 . . . . Sed08g2939 . . . Cma16g00944 . Car16g00908 Cpe14g00768 . Bhi11g00497 Tan01g1808 Cmetu06g1047 . Hepe06g1230 . . . . . . . . . Lsi05g00522 . Chy06g01877 .
Vvi19g615 . . . . Bpe09g00133 . . Bma13g01109 . . . . . . . . . . . . . . . . Cla10g00431 Cam10g0429 . Cco10g0441 Clacu10g0437 . Cre10g0685 . . . . . Csa03g00439 . Cme06g02785 . . . Bda12g00953 . . . . Sed03g1366 . . . . . . . . Bhi11g00496 Tan01g1809 Cmetu06g0341 . . . . . . . . . . . Lsi05g00521 . Chy06g01878 .
Vvi19g616 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g617 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0026 Cone9ag0025 . . . . . . . . . . . . Bma07g01269 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme01g00946
Vvi19g618 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g619 . . . . Bpe09g00132 . . Bma13g01110 Cmo16g00984 . . . . . . . . . . . . . . . Cla10g00430 Cam10g0428 Cec10g0450 Cco10g0440 Clacu10g0435 Cmu10g1266 Cre10g0683 . . Cone14ag1209 Cone15ag1226 . Csa03g00438 . Cme06g02784 . . . Bda12g00954 . . . . Sed08g2938 . . . Cma16g00946 . Car16g00909 Cpe14g00769 . Bhi11g00494 Tan01g1811 . . . . . . . . . . . . Lsi05g00520 . Chy06g01879 .
Vvi19g620 . . . . . . . . . . . . . . . . . Bhi09g01735 . . . . . . . . . . . . . . . . . . Csa07g00960 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g621 . . . . . . . . . . . . . . Sed04g3674 . . Bhi09g01736 Tan01g3167 Cmetu01g0479 . . Mch11g1246 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g622 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g623 . . Bda07g00396 . . . . . . . Cma01g01088 . Car01g00964 . . . . . . . . . . . . . . . . . . Cone6ag0023 Cone9ag0023 . . . . . . . . . . Bpe11g00574 . . Bma14g00305 . Cmo01g01134 . . . . . . . . . . . . . . Cla09g02052 Cam09g2140 Cec09g2207 . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 4932750 4942824 + Bda025485.1 Bda07g00396 396
12 40595240 40596238 - Bda009499.1 Bda12g00952 952
12 40599243 40602142 - Bda009500.1 Bda12g00953 953
12 40604724 40605797 - Bda009501.1 Bda12g00954 954
9 47217395 47224250 - XM_039041707.1 Bhi09g01735 1735
9 47217395 47224250 - XM_039041706.1 Bhi09g01736 1736
11 11776194 11779447 + XM_039049836.1 Bhi11g00494 494
11 11801904 11804040 + XM_039047406.1 Bhi11g00496 496
11 11818755 11821850 + XM_039048147.1 Bhi11g00497 497
10 27163983 27165512 - BLOR02652 Blo10g00862 862
7 48215839 48218335 + Bma026536.1 Bma07g01269 1269
13 44033288 44034817 - Bma010234.1 Bma13g01108 1108
13 44038767 44041790 - Bma010235.1 Bma13g01109 1109
13 44062643 44064786 - Bma010237.1 Bma13g01110 1110
14 3824824 3834847 - Bma010728.1 Bma14g00305 305
9 898331 899687 + Bpe023807.1 Bpe09g00132 132
9 902261 905193 + Bpe023808.1 Bpe09g00133 133
9 908298 909845 + Bpe023809.1 Bpe09g00134 134
11 4396614 4406711 + Bpe003940.1 Bpe11g00574 574
9 35976406 35985534 + CaPI482276_09g021400.1 Cam09g2140 2140
10 6630625 6632848 + CaPI482276_10g004280.1 Cam10g0428 428
10 6642380 6645447 + CaPI482276_10g004290.1 Cam10g0429 429
10 6656386 6658023 + CaPI482276_10g004300.1 Cam10g0430 430
1 9210322 9214598 - Carg22399-RA Car01g00964 964
16 7434890 7436524 - Carg22346-RA Car16g00908 908
16 7457349 7460154 - Carg22345-RA Car16g00909 909
10 5182573 5184794 + CcPI632755_10g004400.1 Cco10g0440 440
10 5189737 5191615 + CcPI632755_10g004410.1 Cco10g0441 441
10 5210510 5212147 + CcPI632755_10g004420.1 Cco10g0442 442
9 39005627 39014856 + CePI673135_09g022070.1 Cec09g2207 2207
10 5368081 5370307 + CePI673135_10g004500.1 Cec10g0450 450
10 5397401 5399038 + CePI673135_10g004530.1 Cec10g0453 453
6 22636667 22638304 - Chy6G124050.1 Chy06g01877 1877
6 22653541 22654694 - Chy6G124060.1 Chy06g01878 1878
6 22654914 22658327 - Chy6G124070.1 Chy06g01879 1879
10 5424425 5426643 + ClG42_10g0043500.10 Clacu10g0435 435
10 5439902 5443403 + ClG42_10g0043700.10 Clacu10g0437 437
10 5453557 5455194 + ClG42_10g0043800.10 Clacu10g0438 438
9 38125623 38134839 + ClCG09G021080.1 Cla09g02052 2052
10 5769107 5771346 + ClCG10G004560.2 Cla10g00430 430
10 5792488 5794663 + ClCG10G004590.1 Cla10g00431 431
10 5807527 5809164 + ClCG10G004610.1 Cla10g00432 432
1 8008478 8020042 - CmaCh01G010880.1 Cma01g01088 1088
16 7274694 7276331 - CmaCh16G009440.1 Cma16g00944 944
16 7293534 7297275 - CmaCh16G009460.1 Cma16g00946 946
1 10961290 10964348 + MELO3C024909.2.1 Cme01g00946 946
6 35083072 35086088 + MELO3C014131.2.1 Cme06g02784 2784
6 35088058 35090045 + MELO3C014132.2.1 Cme06g02785 2785
6 35108031 35111294 + MELO3C014133.2.1 Cme06g02786 2786
1 12998218 12999629 - PI0005634.1 Cmetu01g0479 479
6 26933047 26934745 - PI0001018.1 Cmetu06g0341 341
6 26919650 26921287 - PI0004921.1 Cmetu06g1047 1047
1 9338401 9349989 - CmoCh01G011340.1 Cmo01g01134 1134
16 6731154 6732788 - CmoCh16G009830.1 Cmo16g00983 983
16 6754909 6758182 - CmoCh16G009840.1 Cmo16g00984 984
10 5561298 5563516 + CmPI595203_10g012660.1 Cmu10g1266 1266
10 5590385 5592022 + CmPI595203_10g012690.1 Cmu10g1269 1269
6 152638 157793 + Conep06aG0002300.1 Cone6ag0023 23
6 169433 171609 - Conep06aG0002600.1 Cone6ag0026 26
9 112991 119186 + Conep09aG0002300.1 Cone9ag0023 23
9 125158 127955 - Conep09aG0002500.1 Cone9ag0025 25
14 9818414 9819601 - Conep14aG0123900.1 Cone14ag1207 1207
14 9847765 9850867 - Conep14aG0124100.1 Cone14ag1209 1209
15 9732489 9734656 - Conep15aG0125500.1 Cone15ag1226 1226
14 6042419 6044056 - Cp4.1LG14g07710.1 Cpe14g00768 768
14 6061422 6063878 - Cp4.1LG14g07670.1 Cpe14g00769 769
10 6484727 6486941 + CrPI670011_10g006830.1 Cre10g0683 683
10 6498619 6502160 + CrPI670011_10g006850.1 Cre10g0685 685
10 6513436 6515073 + CrPI670011_10g006860.1 Cre10g0686 686
3 3708765 3712674 + CsaV3_3G004380.1 Csa03g00438 438
3 3712855 3714049 + CsaV3_3G004390.1 Csa03g00439 439
3 3721517 3724624 + CsaV3_3G004400.1 Csa03g00440 440
7 8466266 8469502 + CsaV3_7G018510.1 Csa07g00960 960
6 62029764 62031740 - Hsped.06g12300.1 Hepe06g1230 1230
5 6514040 6519507 + Lsi05G005200.1 Lsi05g00520 520
5 6525408 6527612 + Lsi05G005210.1 Lsi05g00521 521
5 6546210 6549403 + Lsi05G005220.1 Lsi05g00522 522
11 8843623 8851236 - MC11g1031 Mch11g1246 1246
3 8699038 8700522 + Sed0001315.1 Sed03g1366 1366
4 45724415 45725821 + Sed0002917.1 Sed04g3674 3674
8 40141298 40144709 + Sed0025163.6 Sed08g2938 2938
8 40146524 40150204 + Sed0007021.1 Sed08g2939 2939
1 19362918 19364552 - Tan0004155.1 Tan01g1808 1808
1 19393427 19395368 - Tan0008891.1 Tan01g1809 1809
1 19400133 19403919 - Tan0008973.2 Tan01g1811 1811
1 85287059 85289131 - Tan0016364.1 Tan01g3167 3167
19 7772105 7775176 - Vvi19g614 Vvi19g614 614
19 7779514 7780996 - Vvi19g615 Vvi19g615 615
19 7784052 7785596 - Vvi19g616 Vvi19g616 616
19 7803503 7814106 + Vvi19g617 Vvi19g617 617
19 7814148 7814340 + Vvi19g618 Vvi19g618 618
19 7815547 7820515 - Vvi19g619 Vvi19g619 619
19 7834636 7836831 + Vvi19g620 Vvi19g620 620
19 7842955 7844371 + Vvi19g621 Vvi19g621 621
19 7850484 7850859 + Vvi19g622 Vvi19g622 622
19 7850869 7866048 - Vvi19g623 Vvi19g623 623
       

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