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
Vvi2g392 . . . . . . . . . . . Cma15g01205 . . . . . . . . . . . . . . . . . . . . . . . . Csa05g00315 . . . . . . . . . . . . Cmo15g01271 . . . . . . . . . . . . . . . . . . . . Lsi09g00295 . . .
Vvi2g393 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo03g00368 . . . . . . . . Cmo02g01512 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g394 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo15g01485 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g395 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g396 . . Bda06g00074 . . Bpe07g00125 . . Cmo06g01134 Cmo16g01048 . . . . . . . . . . . . . . Cla10g00351 Cam10g0363 Cec10g0381 Cco10g0376 Clacu10g0367 Cmu10g1203 Cre10g0618 . . . . Lsi07g01414 . . Cme06g02700 . . . . . . . Bma12g00101 . . . Cma06g01106 Cma16g01005 Car06g00943 . Cpe08g00511 . . . . . . . . . . . . . . . . Csa03g00373 Chy06g01940 .
Vvi2g397 . . . . . . . . . . . Cma15g01411 . Car15g01273 . . . . . . . . . . . . . . . . . . . Cone6ag0752 Cone9ag0755 . . . . . . . . . . . . . . Cmo15g01487 . . . . . . Bhi12g00530 . . . . . . . . . . . . . . . . .
Vvi2g398 . Blo03g00195 Bda06g00073 . . Bpe07g00126 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g399 . Blo03g00194 Bda06g00072 . Bpe05g00629 Bpe07g00127 Bma07g01635 . Cmo06g00727 Cmo16g01049 . . . . . . . . . . . . . . Cla10g00350 Cam10g0362 Cec10g0380 Cco10g0375 Clacu10g0366 Cmu10g1202 Cre10g0617 Cone8ag0329 . Cone6ag0751 Cone9ag0754 Lsi07g01413 . . Cme06g02699 . Blo19g00309 . Bda09g00053 Bpe08g01475 . Bma05g00806 Bma12g00103 . . . . Cma16g01006 Car06g00632 . Cpe08g00804 . . . . . . . . . . . . . . . . Csa03g00372 Chy06g01941 .
Vvi2g400 . . . . . . . . . . Cma02g01482 Cma15g01199 Car02g01242 Car15g01086 . . Cpe05g00307 . . . . . . . . . . . . . . Cone8ag0330 . Cone6ag0749 Cone9ag0752 . Csa05g00322 . . Blo03g00373 . . . . Bpe11g00685 . . . Cmo02g01521 Cmo15g01264 . . . . . Cpe13g00176 Bhi12g00205 . . Lac11g2136 Hepe06g1582 . Lcy12g1700 Cla01g00299 Cam01g0311 Cec01g0302 Cco01g0318 Clacu01g0311 Cmu01g0296 Cre09g2212 Lsi09g00305 . . Cme09g01720
Vvi2g401 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 738604 741905 - Bda023243.2 Bda06g00072 72
6 742537 744305 + Bda023244.2 Bda06g00073 73
6 746604 747177 - Bda023245.1 Bda06g00074 74
9 1160839 1163806 - Bda030577.1 Bda09g00053 53
12 6564230 6566399 + XM_039019863.1 Bhi12g00205 205
12 17016926 17027597 + XM_039050929.1 Bhi12g00530 530
3 4621418 4624581 - BLOR11375 Blo03g00194 194
3 4625074 4627035 + BLOR11376 Blo03g00195 195
3 8359902 8361685 - BLOR11549 Blo03g00368 368
3 8580464 8582050 + BLOR11554 Blo03g00373 373
19 19826076 19829070 + BLOR09652 Blo19g00309 309
5 45406935 45410044 - Bma021909.1 Bma05g00806 806
7 51951886 51954851 + Bma026932.1 Bma07g01635 1635
12 1672463 1673962 + Bma006973.1 Bma12g00101 101
12 1677757 1681052 + Bma006975.2 Bma12g00103 103
5 20186820 20189911 - Bpe018045.2 Bpe05g00629 629
7 892790 894384 + Bpe020937.1 Bpe07g00125 125
7 895620 897547 - Bpe020938.1 Bpe07g00126 126
7 897998 901388 + Bpe020939.1 Bpe07g00127 127
8 15487487 15490515 + Bpe023587.1 Bpe08g01475 1475
11 5274598 5276190 - Bpe004041.1 Bpe11g00685 685
1 3442506 3444140 - CaPI482276_01g003110.1 Cam01g0311 311
10 5862182 5867275 - CaPI482276_10g003620.1 Cam10g0362 362
10 5881571 5883418 - CaPI482276_10g003630.1 Cam10g0363 363
2 8404265 8405794 - Carg02506-RA Car02g01242 1242
6 3698760 3703528 + Carg21650-RA Car06g00632 632
6 7284177 7284713 + Carg23878-RA Car06g00943 943
15 8530961 8532460 + Carg16656-RA Car15g01086 1086
15 9945714 9951649 + Carg20769-RA Car15g01273 1273
1 3078883 3080532 - CcPI632755_01g003180.1 Cco01g0318 318
10 4373661 4380106 - CcPI632755_10g003750.1 Cco10g0375 375
10 4392225 4394069 - CcPI632755_10g003760.1 Cco10g0376 376
1 3046923 3048584 - CePI673135_01g003020.1 Cec01g0302 302
10 4566996 4572077 - CePI673135_10g003800.1 Cec10g0380 380
10 4584171 4586022 - CePI673135_10g003810.1 Cec10g0381 381
6 23311455 23312992 + Chy6G124680.1 Chy06g01940 1940
6 23324266 23329326 + Chy6G124690.1 Chy06g01941 1941
1 3057901 3059535 - ClG42_01g0031100.10 Clacu01g0311 311
10 4644543 4649658 - ClG42_10g0036600.10 Clacu10g0366 366
10 4661715 4663556 - ClG42_10g0036700.10 Clacu10g0367 367
1 3136005 3137639 - ClCG01G003100.1 Cla01g00299 299
10 4660235 4660791 - ClCG10G003730.1 Cla10g00350 350
10 4673017 4674858 - ClCG10G003740.2 Cla10g00351 351
2 8484877 8488237 - CmaCh02G014820.1 Cma02g01482 1482
6 7469583 7472658 + CmaCh06G011060.1 Cma06g01106 1106
15 7601304 7602836 + CmaCh15G011990.1 Cma15g01199 1199
15 7628276 7629088 + CmaCh15G012050.1 Cma15g01205 1205
15 8900528 8907457 + CmaCh15G014110.1 Cma15g01411 1411
16 7742864 7745147 + CmaCh16G010050.1 Cma16g01005 1005
16 7748416 7753696 + CmaCh16G010060.1 Cma16g01006 1006
6 34190410 34196167 - MELO3C014054.2.1 Cme06g02699 2699
6 34222095 34224401 - MELO3C014055.2.1 Cme06g02700 2700
9 21840559 21842268 + MELO3C005632.2.1 Cme09g01720 1720
2 8825626 8827818 - CmoCh02G015120.1 Cmo02g01512 1512
2 8857277 8858869 - CmoCh02G015210.1 Cmo02g01521 1521
6 3726271 3730922 + CmoCh06G007270.1 Cmo06g00727 727
6 8713628 8716430 + CmoCh06G011340.1 Cmo06g01134 1134
15 8670196 8671695 + CmoCh15G012640.1 Cmo15g01264 1264
15 8700802 8701876 + CmoCh15G012710.1 Cmo15g01271 1271
15 10071738 10073895 + CmoCh15G014850.1 Cmo15g01485 1485
15 10080984 10088849 + CmoCh15G014870.1 Cmo15g01487 1487
16 7332909 7335180 + CmoCh16G010480.1 Cmo16g01048 1048
16 7338772 7343946 + CmoCh16G010490.1 Cmo16g01049 1049
1 3013897 3015534 - CmPI595203_01g002960.1 Cmu01g0296 296
10 4785424 4790541 - CmPI595203_10g012020.1 Cmu10g1202 1202
10 4802605 4804446 - CmPI595203_10g012030.1 Cmu10g1203 1203
6 3800156 3801926 + Conep06aG0077200.1 Cone6ag0749 749
6 3808904 3811375 - Conep06aG0077400.1 Cone6ag0751 751
6 3817061 3819377 + Conep06aG0077500.1 Cone6ag0752 752
8 1891318 1894610 + Conep08aG0034400.1 Cone8ag0329 329
8 1897600 1899141 - Conep08aG0034500.1 Cone8ag0330 330
9 3599118 3601529 + Conep09aG0076900.1 Cone9ag0752 752
9 3605448 3608406 - Conep09aG0077100.1 Cone9ag0754 754
9 3610605 3612383 + Conep09aG0077200.1 Cone9ag0755 755
5 1719551 1721440 + Cp4.1LG05g03880.1 Cpe05g00307 307
8 3302818 3306415 - Cp4.1LG08g01530.1 Cpe08g00511 511
8 6412955 6417492 - Cp4.1LG08g08110.1 Cpe08g00804 804
13 1382965 1384464 - Cp4.1LG13g01730.1 Cpe13g00176 176
9 41297212 41298861 + CrPI670011_09g022120.1 Cre09g2212 2212
10 5713437 5718519 - CrPI670011_10g006170.1 Cre10g0617 617
10 5730922 5732762 - CrPI670011_10g006180.1 Cre10g0618 618
3 3144421 3150579 - CsaV3_3G003720.1 Csa03g00372 372
3 3156341 3158654 - CsaV3_3G003730.1 Csa03g00373 373
5 1964512 1965320 - CsaV3_5G003150.1 Csa05g00315 315
5 2008197 2009994 - CsaV3_5G003220.1 Csa05g00322 322
6 66575254 66577338 - Hsped.06g15820.1 Hepe06g1582 1582
11 37396122 37397702 - Lag0032774.1 Lac11g2136 2136
12 37491609 37493189 - Maker00003029 Lcy12g1700 1700
7 20636925 20644619 - Lsi07G014130.1 Lsi07g01413 1413
7 20657229 20659923 - Lsi07G014140.1 Lsi07g01414 1414
9 3048392 3052274 - Lsi09G002950.1 Lsi09g00295 295
9 3118896 3120569 - Lsi09G003050.1 Lsi09g00305 305
2 3822829 3825957 + Vvi2g392 Vvi2g392 392
2 3829798 3832542 + Vvi2g393 Vvi2g393 393
2 3833680 3835488 - Vvi2g394 Vvi2g394 394
2 3838089 3841971 - Vvi2g395 Vvi2g395 395
2 3852687 3856475 + Vvi2g396 Vvi2g396 396
2 3857080 3867232 - Vvi2g397 Vvi2g397 397
2 3870912 3876274 - Vvi2g398 Vvi2g398 398
2 3880217 3885160 + Vvi2g399 Vvi2g399 399
2 3894150 3895743 - Vvi2g400 Vvi2g400 400
2 3898373 3904052 - Vvi2g401 Vvi2g401 401
       

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