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
Vvi5g699 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g700 . Blo12g00161 . . Bpe04g00796 Bpe14g01250 . . . Cmo17g00165 Cma06g01328 Cma14g01810 . . . . Cpe03g01515 . . . . . . . Cla06g00662 Cam06g0711 Cec06g0715 Cco06g0725 Clacu06g0701 Cmu06g0688 Cre06g1458 Cone14ag0148 . . Cone4ag0326 Lsi05g01727 . . Cme06g00498 Blo02g00741 Blo07g00259 Bda11g00628 Bda13g00067 . Bpe13g00560 Bma02g00789 Bma06g01597 . Cmo06g01332 Cmo14g01847 . Cma17g00166 . . Cpe12g00143 . . . . . . . . Cla05g00449 Cam05g0490 Cec05g0499 Cco05g0498 Clacu05g0485 Cmu05g0462 Cre05g0525 Lsi09g01236 Csa03g01215 Chy06g00477 Cme05g00564
Vvi5g701 . Blo12g00368 Bda03g00842 . . Bpe14g01251 Bma04g00741 . . . . Cma14g01811 . . . Cpe08g00332 . . . . . . . . . . . . . . . . . . . Lsi05g01728 Csa02g01063 Chy05g00324 Cme06g00497 Blo02g00743 Blo07g00260 Bda11g00629 Bda13g00066 . Bpe13g00559 Bma02g00786 Bma06g01598 . . Cmo14g01849 . . . . . . . . . . . . . Cla05g00448 Cam05g0488 Cec05g0498 Cco05g0497 Clacu05g0483 Cmu05g0461 Cre05g0524 . Csa03g01213 Chy06g00476 .
Vvi5g702 . . . . . Bpe14g01252 . . . . Cma06g01327 Cma14g01812 Car06g01140 Car14g01625 . Cpe08g00333 Cpe03g01516 . . . . . . . . . . . . . . . . Cone7ag0322 Cone4ag0328 Lsi05g01729 . . Cme06g00496 . Blo07g00261 . Bda13g00065 . . Bma02g00785 . . Cmo06g01331 Cmo14g01850 . . . . . . . . . . . . . Cla05g00447 . . . . . . . Csa03g01212 Chy06g00475 .
Vvi5g703 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g704 . . . . . Bpe14g01253 . . . Cmo17g00164 . . . . . . . . . . . . . . Cla06g00663 Cam06g0712 Cec06g0716 Cco06g0726 Clacu06g0702 Cmu06g0689 Cre06g1459 . . . . . . Chy05g00323 . . Blo07g00262 Bda11g00630 Bda13g00064 . Bpe13g00558 Bma02g00784 Bma06g01599 . . . . Cma17g00165 . Car17g00146 Cpe12g00142 . Bhi12g01623 . . . Hepe03g0282 . Lcy13g0375 . . . . . . . . . . Cme05g00565
Vvi5g705 . . . . . Bpe14g01254 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda13g00063 . . Bma02g00783 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g706 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g707 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo07g00263 Bda11g00631 . . . . Bma06g01600 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g708 . . . . . . . . Cmo08g01059 Cmo17g00163 Cma06g01325 . . . . . . . . . . . . . . . . . . . . . . . . Lsi05g01732 . . Cme06g00494 . . . . . . . . . Cmo06g01330 . Cma08g01083 Cma17g00164 Car08g00958 Car17g00145 . . . . . . . . . Cla05g00445 . . . . . . . Csa03g01210 Chy06g00473 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 7243440 7245047 - Bda016831.1 Bda03g00842 842
11 6302815 6309649 + Bda005373.2 Bda11g00628 628
11 6322381 6323949 + Bda005375.1 Bda11g00629 629
11 6328341 6331597 - Bda005376.1 Bda11g00630 630
11 6334975 6336038 + Bda005377.2 Bda11g00631 631
13 881391 881741 + Bda000909.1 Bda13g00063 63
13 883157 886302 + Bda000910.1 Bda13g00064 64
13 887300 888585 + Bda000911.1 Bda13g00065 65
13 891856 893433 - Bda000912.1 Bda13g00066 66
13 903680 905263 - Bda000913.1 Bda13g00067 67
12 52376898 52382384 + XM_039018509.1 Bhi12g01623 1623
2 24376470 24378047 - BLOR10471 Blo02g00741 741
2 24501486 24503069 - BLOR10473 Blo02g00743 743
7 3144444 3148552 + BLOR18191 Blo07g00259 259
7 3157480 3159084 + BLOR18192 Blo07g00260 260
7 3163090 3163938 - BLOR18193 Blo07g00261 261
7 3167194 3170738 - BLOR18194 Blo07g00262 262
7 3173026 3174851 + BLOR18195 Blo07g00263 263
12 10706585 10709586 + BLOR04180 Blo12g00161 161
12 20050241 20051842 + BLOR04387 Blo12g00368 368
2 41662365 41662892 + Bma015510.1 Bma02g00783 783
2 41664247 41667042 + Bma015511.1 Bma02g00784 784
2 41669605 41670934 + Bma015512.1 Bma02g00785 785
2 41680992 41682572 - Bma015513.1 Bma02g00786 786
2 42073813 42075399 + Bma015518.1 Bma02g00789 789
4 7785440 7787050 - Bma019251.1 Bma04g00741 741
6 52179781 52181379 + Bma024713.1 Bma06g01597 1597
6 52185446 52187014 + Bma024714.1 Bma06g01598 1598
6 52191898 52194697 - Bma024715.1 Bma06g01599 1599
6 52196365 52197768 + Bma024716.1 Bma06g01600 1600
4 5217528 5219135 - Bpe025665 Bpe04g00796 796
13 12798137 12801621 + Bpe010261.1 Bpe13g00558 558
13 12805630 12807198 - Bpe010262.1 Bpe13g00559 559
13 12810216 12811808 - Bpe010263.1 Bpe13g00560 560
14 9442454 9444040 + Bpe014610.1 Bpe14g01250 1250
14 9465693 9467270 + Bpe014611.1 Bpe14g01251 1251
14 9470349 9471685 - Bpe014612.1 Bpe14g01252 1252
14 9473216 9476057 - Bpe014613.1 Bpe14g01253 1253
14 9477471 9477954 - Bpe014614.1 Bpe14g01254 1254
5 4307355 4308932 - CaPI482276_05g004880.1 Cam05g0488 488
5 4323056 4325360 - CaPI482276_05g004900.1 Cam05g0490 490
6 9628168 9629781 + CaPI482276_06g007110.1 Cam06g0711 711
6 9632799 9637100 - CaPI482276_06g007120.1 Cam06g0712 712
6 8465238 8466672 + Carg06217-RA Car06g01140 1140
8 6394980 6396345 - Carg10964-RA Car08g00958 958
14 13063957 13065293 - Carg16562-RA Car14g01625 1625
17 899845 901206 - Carg10086-RA Car17g00145 145
17 911746 917316 + Carg10085-RA Car17g00146 146
5 3970309 3971886 - CcPI632755_05g004970.1 Cco05g0497 497
5 3986016 3988380 - CcPI632755_05g004980.1 Cco05g0498 498
6 8259503 8261116 + CcPI632755_06g007250.1 Cco06g0725 725
6 8264342 8268655 - CcPI632755_06g007260.1 Cco06g0726 726
5 3960688 3965258 - CePI673135_05g004980.1 Cec05g0498 498
5 3979998 3982292 - CePI673135_05g004990.1 Cec05g0499 499
6 8292162 8293775 + CePI673135_06g007150.1 Cec06g0715 715
6 8297093 8300993 - CePI673135_06g007160.1 Cec06g0716 716
5 3243394 3247549 + Chy5G093690.1 Chy05g00323 323
5 3253657 3255267 - Chy5G093700.1 Chy05g00324 324
6 3159076 3160027 - Chy6G110010.1 Chy06g00473 473
6 3173791 3174992 + Chy6G110030.1 Chy06g00475 475
6 3178352 3179911 - Chy6G110040.1 Chy06g00476 476
6 3190573 3192530 - Chy6G110050.1 Chy06g00477 477
5 4012247 4013824 - ClG42_05g0048300.10 Clacu05g0483 483
5 4028377 4030705 - ClG42_05g0048500.10 Clacu05g0485 485
6 8185682 8187295 + ClG42_06g0070100.10 Clacu06g0701 701
6 8190508 8194406 - ClG42_06g0070200.10 Clacu06g0702 702
5 3973032 3974282 - ClCG05G004315.1 Cla05g00445 445
5 3987535 3988823 + ClCG05G004340.1 Cla05g00447 447
5 3994632 3996209 - ClCG05G004345.1 Cla05g00448 448
5 4011771 4016441 - ClCG05G004350.2 Cla05g00449 449
6 8381823 8383436 + ClCG06G006970.1 Cla06g00662 662
6 8385577 8391163 - ClCG06G006980.1 Cla06g00663 663
6 8732032 8733012 - CmaCh06G013250.1 Cma06g01325 1325
6 8740309 8741618 + CmaCh06G013270.1 Cma06g01327 1327
6 8742265 8744488 - CmaCh06G013280.1 Cma06g01328 1328
8 6754231 6755908 - CmaCh08G010830.1 Cma08g01083 1083
14 12979490 12986054 + CmaCh14G018100.1 Cma14g01810 1810
14 12987095 12990427 + CmaCh14G018110.1 Cma14g01811 1811
14 12991373 12992997 - CmaCh14G018120.1 Cma14g01812 1812
17 841438 842894 - CmaCh17G001640.1 Cma17g00164 164
17 851311 858298 + CmaCh17G001650.1 Cma17g00165 165
17 859051 860640 - CmaCh17G001660.1 Cma17g00166 166
5 5659701 5661314 + MELO3C022994.2.1 Cme05g00564 564
5 5666014 5670839 - MELO3C022995.2.1 Cme05g00565 565
6 3105851 3107484 - MELO3C006425.2.1 Cme06g00494 494
6 3118936 3120509 + MELO3C006426.2.1 Cme06g00496 496
6 3123150 3127341 - MELO3C006427.2.1 Cme06g00497 497
6 3137502 3140086 - MELO3C006428.2.1 Cme06g00498 498
6 9908122 9911952 - CmoCh06G013300.1 Cmo06g01330 1330
6 9913945 9920280 + CmoCh06G013310.1 Cmo06g01331 1331
6 9921850 9923421 - CmoCh06G013320.1 Cmo06g01332 1332
8 6834339 6836086 - CmoCh08G010590.1 Cmo08g01059 1059
14 13968135 13969998 + CmoCh14G018470.1 Cmo14g01847 1847
14 13972822 13974384 + CmoCh14G018490.1 Cmo14g01849 1849
14 13975738 13977250 - CmoCh14G018500.1 Cmo14g01850 1850
17 943790 945206 - CmoCh17G001630.1 Cmo17g00163 163
17 955191 962950 + CmoCh17G001640.1 Cmo17g00164 164
17 963739 965328 - CmoCh17G001650.1 Cmo17g00165 165
5 3848366 3852997 - CmPI595203_05g004610.1 Cmu05g0461 461
5 3864557 3866885 - CmPI595203_05g004620.1 Cmu05g0462 462
6 7997819 7999432 + CmPI595203_06g006880.1 Cmu06g0688 688
6 8002642 8006540 - CmPI595203_06g006890.1 Cmu06g0689 689
4 1480205 1481809 + Conep04aG0033800.1 Cone4ag0326 326
4 1498130 1499714 - Conep04aG0034000.1 Cone4ag0328 328
7 1402285 1403864 - Conep07aG0033000.1 Cone7ag0322 322
14 726930 728522 + Conep14aG0015200.1 Cone14ag0148 148
3 11869612 11876277 + Cp4.1LG03g10070.1 Cpe03g01515 1515
3 11877354 11878807 - Cp4.1LG03g09920.1 Cpe03g01516 1516
8 2075312 2076883 + Cp4.1LG08g03560.1 Cpe08g00332 332
8 2077895 2079363 - Cp4.1LG08g03440.1 Cpe08g00333 333
12 910538 916115 + Cp4.1LG12g01420.1 Cpe12g00142 142
12 916974 918563 - Cp4.1LG12g01500.1 Cpe12g00143 143
5 4646408 4650925 - CrPI670011_05g005240.1 Cre05g0524 524
5 4662610 4664940 - CrPI670011_05g005250.1 Cre05g0525 525
6 9103398 9105011 + CrPI670011_06g014580.1 Cre06g1458 1458
6 9108031 9112345 - CrPI670011_06g014590.1 Cre06g1459 1459
2 10325177 10328938 - CsaV3_2G012790.1 Csa02g01063 1063
3 9342320 9343930 - CsaV3_3G012100.1 Csa03g01210 1210
3 9357402 9358596 + CsaV3_3G012120.1 Csa03g01212 1212
3 9360966 9365368 - CsaV3_3G012130.1 Csa03g01213 1213
3 9373442 9376131 - CsaV3_3G012150.1 Csa03g01215 1215
3 3726867 3732923 - Hsped.03g02820.1 Hepe03g0282 282
13 4267691 4273031 - Maker00023199 Lcy13g0375 375
5 24715306 24718738 + Lsi05G017270.1 Lsi05g01727 1727
5 24728682 24733115 + Lsi05G017280.1 Lsi05g01728 1728
5 24743827 24745420 - Lsi05G017290.1 Lsi05g01729 1729
5 24759401 24760752 + Lsi05G017320.1 Lsi05g01732 1732
9 19877147 19878757 - Lsi09G012360.1 Lsi09g01236 1236
5 7922303 7924729 + Vvi5g699 Vvi5g699 699
5 7925221 7933404 + Vvi5g700 Vvi5g700 700
5 7949426 7953006 + Vvi5g701 Vvi5g701 701
5 7967257 7969061 - Vvi5g702 Vvi5g702 702
5 7973214 7973394 + Vvi5g703 Vvi5g703 703
5 7973467 7984266 - Vvi5g704 Vvi5g704 704
5 7989419 7993613 - Vvi5g705 Vvi5g705 705
5 7997775 7998800 - Vvi5g706 Vvi5g706 706
5 8009900 8031782 + Vvi5g707 Vvi5g707 707
5 8035770 8037251 + Vvi5g708 Vvi5g708 708
       

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