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
Vvi5g839 . . . . . . . Bma05g01270 Cmo08g01010 Cmo17g00120 . . . . . . . . . . . . . . . . . . . . . Cone14ag0207 . . . . . Chy05g00265 . . . . . . . . . . . . . . Car08g00914 . . . . . . . . . . . . . . . . . . . . .
Vvi5g840 . . . Bda08g00022 . . . Bma05g01275 Cmo08g01008 . . Cma14g01867 Car06g01090 Car14g01671 Sed02g1574 . . Bhi01g00249 Tan10g0368 Cmetu06g0103 . . . . Cla06g00732 Cam06g0782 Cec06g0786 Cco06g0797 Clacu06g0780 Cmu06g0756 Cre06g1533 . . . . Lsi05g01805 Csa02g00984 . Cme06g00415 . . . . Bpe05g01130 . . . Sed02g1466 Cmo06g01277 Cmo14g01913 Cma08g01037 . Car08g00912 . . . Bhi12g01520 Tan06g2330 Cmetu06g0990 Lac12g2087 Hepe03g0336 . Lcy13g0440 Cla05g00377 Cam05g0410 Cec05g0415 . Clacu05g0406 Cmu05g0389 Cre05g0451 Lsi09g01164 Csa03g01134 Chy06g00400 .
Vvi5g841 . Blo12g00129 Bda03g01112 . Bpe04g01057 . Bma04g01040 . . . Cma06g01268 . . . . Cpe08g00379 . Bhi01g00007 . . . . . . . . . . . . . . . . . Lsi05g01807 . . Cme06g00414 . . . . . . . . . . . . . . . . . . . . . . . . Cla05g00376 . . Cco05g0415 Clacu05g0405 . . . Csa03g01133 Chy06g00399 .
Vvi5g842 . . . . . . . . Cmo08g01007 . . . . . . . Cpe03g01568 . . . . . . . . . . . . . . Cone14ag0208 Cone15ag0229 . . . . . . . . . . . . . . . . . Cma08g01036 . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g843 . . . . . . . . . . . Cma14g01871 . Car14g01673 . . Cpe03g01569 Bhi01g00003 . . . . . . . . . . . . . Cone14ag0209 Cone15ag0230 . . Lsi05g01811 . . Cme06g00411 . Blo07g00295 Bda11g00658 . . Bpe13g00533 . Bma06g01624 . . Cmo14g01917 . . . . . . . . . . . . . Cla05g00373 Cam05g0406 Cec05g0411 Cco05g0411 Clacu05g0401 Cmu05g0386 Cre05g0448 . Csa03g01129 Chy06g00396 .
Vvi5g844 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g845 . Blo12g00125 Bda03g01113 . Bpe04g01058 Bpe14g01295 Bma04g01041 . Cmo08g01006 Cmo17g00119 Cma06g01265 Cma14g01872 Car06g01087 Car14g01674 . Cpe08g00382 . Bhi01g00001 . . . . . Lcy11g1767 Cla06g00739 Cam06g0790 Cec06g0796 . Clacu06g0789 Cmu06g0763 Cre06g1543 Cone14ag0210 Cone15ag0231 . Cone4ag0383 Lsi05g01813 . Chy05g00262 Cme06g00410 . . . Bda13g00500 . . . . . Cmo06g01274 Cmo14g01918 Cma08g01035 Cma17g00116 Car08g00910 Car17g00103 Cpe12g00102 Cpe17g00243 Bhi12g01517 Tan06g2326 . . . . Lcy13g0445 Cla05g00372 Cam05g0405 Cec05g0410 Cco05g0410 Clacu05g0400 Cmu05g0385 Cre05g0447 Lsi09g01161 Csa03g01128 Chy06g00395 .
Vvi5g846 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g847 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g848 . . . . . . . . . . . Cma14g01873 . Car14g01675 Sed12g0408 . Cpe03g01571 Bhi01g00061 Tan10g0557 Cmetu06g2760 . . . Lcy11g1746 . . . . . . . . . . Cone4ag0384 Lsi05g01814 Csa02g00942 . Cme06g00409 . Blo07g00296 Bda11g00659 . . . . Bma06g01625 . . Cmo14g01919 . . . . . . . . . . . . . Cla05g00371 Cam05g0404 Cec05g0409 Cco05g0409 Clacu05g0399 Cmu05g0384 Cre05g0446 . Csa03g01127 Chy06g00394 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 11504080 11504850 - Bda017160.1 Bda03g01112 1112
3 11543447 11544570 - Bda017162.1 Bda03g01113 1113
8 198089 198526 - Bda024413.1 Bda08g00022 22
11 6508645 6510752 + Bda005404.1 Bda11g00658 658
11 6511165 6516641 + Bda005405.2 Bda11g00659 659
13 5884157 5885505 - Bda032855 Bda13g00500 500
1 16751 22177 + XM_039039085.1 Bhi01g00001 1
1 24633 34182 - XM_039048906.1 Bhi01g00003 3
1 155762 172273 + XM_039021636.1 Bhi01g00007 7
1 1237221 1242868 - XM_039021387.1 Bhi01g00061 61
1 4775560 4780345 + XM_039023307.1 Bhi01g00249 249
12 49105909 49109857 - XM_039050540.1 Bhi12g01517 1517
12 49444525 49444962 + XM_039019083.1 Bhi12g01520 1520
7 3420719 3422359 + BLOR18227 Blo07g00295 295
7 3423424 3432667 + BLOR18228 Blo07g00296 296
12 8720829 8738300 + BLOR04144 Blo12g00125 125
12 8822134 8825741 + BLOR04148 Blo12g00129 129
4 18808291 18812796 - Bma019667.1 Bma04g01040 1040
4 18879376 18880500 - Bma019668.1 Bma04g01041 1041
5 52072442 52074136 + Bma022461.1 Bma05g01270 1270
5 52082569 52083003 - Bma022466.1 Bma05g01275 1275
6 52367799 52378218 + Bma024739.1 Bma06g01624 1624
6 52378698 52381152 + Bma024740.1 Bma06g01625 1625
4 7851566 7855180 - Bpe015726.1 Bpe04g01057 1057
4 7873781 7874906 - Bpe015727.1 Bpe04g01058 1058
5 23605179 23605613 - Bpe018548.1 Bpe05g01130 1130
13 12613546 12615229 - Bpe025225 Bpe13g00533 533
14 9892444 9894285 - Bpe014651.1 Bpe14g01295 1295
5 3704880 3712611 - CaPI482276_05g004040.1 Cam05g0404 404
5 3733631 3738301 + CaPI482276_05g004050.1 Cam05g0405 405
5 3741340 3745789 - CaPI482276_05g004060.1 Cam05g0406 406
5 3768859 3779032 + CaPI482276_05g004100.1 Cam05g0410 410
6 10569828 10570265 - CaPI482276_06g007820.1 Cam06g0782 782
6 10686862 10694995 - CaPI482276_06g007900.1 Cam06g0790 790
6 8171712 8175910 + Carg06272-RA Car06g01087 1087
6 8189567 8197297 + Carg06269-RA Car06g01090 1090
8 6115148 6119577 + Carg11014-RA Car08g00910 910
8 6139373 6139804 - Carg11012-RA Car08g00912 912
8 6145582 6150270 - Carg11010-RA Car08g00914 914
14 13309637 13310071 - Carg16516-RA Car14g01671 1671
14 13323458 13327258 + Carg16514-RA Car14g01673 1673
14 13329725 13334248 - Carg16513-RA Car14g01674 1674
14 13340679 13345409 + Carg16512-RA Car14g01675 1675
17 607458 611297 + Carg10129-RA Car17g00103 103
5 3364065 3368611 - CcPI632755_05g004090.1 Cco05g0409 409
5 3388023 3393050 + CcPI632755_05g004100.1 Cco05g0410 410
5 3397414 3400733 - CcPI632755_05g004110.1 Cco05g0411 411
5 3423082 3430405 + CcPI632755_05g004150.1 Cco05g0415 415
6 9312439 9312876 - CcPI632755_06g007970.1 Cco06g0797 797
5 3356073 3360486 - CePI673135_05g004090.1 Cec05g0409 409
5 3382931 3387580 + CePI673135_05g004100.1 Cec05g0410 410
5 3390640 3395115 - CePI673135_05g004110.1 Cec05g0411 411
5 3418169 3429645 + CePI673135_05g004150.1 Cec05g0415 415
6 9382063 9382506 - CePI673135_06g007860.1 Cec06g0786 786
6 9552578 9560636 - CePI673135_06g007960.1 Cec06g0796 796
5 2297202 2300372 - Chy5G093080.1 Chy05g00262 262
5 2361701 2390702 - Chy5G093110.1 Chy05g00265 265
6 2656680 2657227 - Chy6G109220.1 Chy06g00394 394
6 2675533 2680018 + Chy6G109230.1 Chy06g00395 395
6 2683120 2686962 - Chy6G109240.1 Chy06g00396 396
6 2701618 2707659 + Chy6G109270.1 Chy06g00399 399
6 2707918 2711022 + Chy6G109280.1 Chy06g00400 400
5 3421747 3426417 - ClG42_05g0039900.10 Clacu05g0399 399
5 3446645 3451261 + ClG42_05g0040000.10 Clacu05g0400 400
5 3455539 3458830 - ClG42_05g0040100.10 Clacu05g0401 401
5 3481504 3487821 + ClG42_05g0040500.10 Clacu05g0405 405
5 3488221 3493211 + ClG42_05g0040600.10 Clacu05g0406 406
6 9215957 9216394 - ClG42_06g0078000.10 Clacu06g0780 780
6 9323202 9331627 - ClG42_06g0078900.10 Clacu06g0789 789
5 3373741 3379041 - ClCG05G003580.2 Cla05g00371 371
5 3399550 3404164 + ClCG05G003590.2 Cla05g00372 372
5 3407462 3411793 - ClCG05G003600.2 Cla05g00373 373
5 3435834 3443256 + ClCG05G003620.1 Cla05g00376 376
5 3443595 3451777 + ClCG05G003630.1 Cla05g00377 377
6 9462015 9462452 - ClCG06G007584.1 Cla06g00732 732
6 9598542 9601854 - ClCG06G007620.1 Cla06g00739 739
6 8417871 8422489 + CmaCh06G012650.1 Cma06g01265 1265
6 8434863 8442960 + CmaCh06G012680.1 Cma06g01268 1268
8 6481057 6485649 + CmaCh08G010350.1 Cma08g01035 1035
8 6491688 6495756 + CmaCh08G010360.1 Cma08g01036 1036
8 6503578 6504012 - CmaCh08G010370.1 Cma08g01037 1037
14 13241842 13242213 - CmaCh14G018670.1 Cma14g01867 1867
14 13258596 13263263 + CmaCh14G018710.1 Cma14g01871 1871
14 13264747 13269813 - CmaCh14G018720.1 Cma14g01872 1872
14 13276276 13280847 + CmaCh14G018730.1 Cma14g01873 1873
17 574066 577886 + CmaCh17G001160.1 Cma17g00116 116
6 2604920 2609890 - MELO3C006337.2.1 Cme06g00409 409
6 2629054 2634424 + MELO3C006338.2.1 Cme06g00410 410
6 2636085 2640419 - MELO3C031602.2.1 Cme06g00411 411
6 2657365 2660522 + MELO3C006341.2.1 Cme06g00414 414
6 2661578 2664801 + MELO3C006342.2.1 Cme06g00415 415
6 1823022 1827106 - PI0025815.1 Cmetu06g0103 103
6 2866212 2869300 + PI0022465.1 Cmetu06g0990 990
6 2806311 2812108 - PI0007867.1 Cmetu06g2760 2760
6 9615807 9620035 + CmoCh06G012740.1 Cmo06g01274 1274
6 9634622 9644063 + CmoCh06G012770.1 Cmo06g01277 1277
8 6539045 6542888 + CmoCh08G010060.1 Cmo08g01006 1006
8 6551945 6555540 + CmoCh08G010070.1 Cmo08g01007 1007
8 6564576 6565010 - CmoCh08G010080.1 Cmo08g01008 1008
8 6571076 6576046 - CmoCh08G010100.1 Cmo08g01010 1010
14 14230057 14230491 - CmoCh14G019130.1 Cmo14g01913 1913
14 14243947 14248852 + CmoCh14G019170.1 Cmo14g01917 1917
14 14249841 14254506 - CmoCh14G019180.1 Cmo14g01918 1918
14 14261156 14265774 + CmoCh14G019190.1 Cmo14g01919 1919
17 645851 651864 + CmoCh17G001190.1 Cmo17g00119 119
17 661522 665650 + CmoCh17G001200.1 Cmo17g00120 120
5 3259715 3264385 - CmPI595203_05g003840.1 Cmu05g0384 384
5 3284639 3289253 + CmPI595203_05g003850.1 Cmu05g0385 385
5 3293519 3296814 - CmPI595203_05g003860.1 Cmu05g0386 386
5 3319534 3331221 + CmPI595203_05g003890.1 Cmu05g0389 389
6 9033413 9033850 - CmPI595203_06g007560.1 Cmu06g0756 756
6 9141077 9149212 - CmPI595203_06g007630.1 Cmu06g0763 763
4 1736681 1740668 - Conep04aG0039600.1 Cone4ag0383 383
4 1744252 1747215 + Conep04aG0039700.1 Cone4ag0384 384
14 950468 955293 + Conep14aG0021100.1 Cone14ag0207 207
14 966259 969778 - Conep14aG0021200.1 Cone14ag0208 208
14 972706 975490 + Conep14aG0021300.1 Cone14ag0209 209
14 975609 978785 - Conep14aG0021400.1 Cone14ag0210 210
15 1073223 1075766 - Conep15aG0023300.1 Cone15ag0229 229
15 1076678 1078190 + Conep15aG0023400.1 Cone15ag0230 230
15 1079114 1082213 - Conep15aG0023500.1 Cone15ag0231 231
3 12135078 12140485 - Cp4.1LG03g18140.1 Cpe03g01568 1568
3 12143802 12150775 + Cp4.1LG03g18350.1 Cpe03g01569 1569
3 12160875 12165845 + Cp4.1LG03g18330.1 Cpe03g01571 1571
8 2356700 2365102 - Cp4.1LG08g02960.1 Cpe08g00379 379
8 2377087 2383037 - Cp4.1LG08g02980.1 Cpe08g00382 382
12 619595 623825 + Cp4.1LG12g00970.1 Cpe12g00102 102
17 1588320 1592293 - Cp4.1LG17g03220.1 Cpe17g00243 243
5 4043687 4048213 - CrPI670011_05g004460.1 Cre05g0446 446
5 4069326 4073984 + CrPI670011_05g004470.1 Cre05g0447 447
5 4077080 4081568 - CrPI670011_05g004480.1 Cre05g0448 448
5 4104867 4116293 + CrPI670011_05g004510.1 Cre05g0451 451
6 10214208 10214645 - CrPI670011_06g015330.1 Cre06g1533 1533
6 10356445 10359676 - CrPI670011_06g015430.1 Cre06g1543 1543
2 8886082 8894234 - CsaV3_2G011580.1 Csa02g00942 942
2 9402255 9402622 + CsaV3_2G012000.1 Csa02g00984 984
3 8873742 8879813 - CsaV3_3G011270.1 Csa03g01127 1127
3 8895882 8901195 + CsaV3_3G011280.1 Csa03g01128 1128
3 8902467 8907559 - CsaV3_3G011290.1 Csa03g01129 1129
3 8921525 8927561 + CsaV3_3G011330.1 Csa03g01133 1133
3 8927970 8930910 + CsaV3_3G011340.1 Csa03g01134 1134
3 4723266 4723880 - Hsped.03g03360.1 Hepe03g0336 336
12 37982681 37983115 + Lag0016459.1 Lac12g2087 2087
11 41280650 41285712 + Maker00031584 Lcy11g1746 1746
11 41472894 41483896 + Maker00031808 Lcy11g1767 1767
13 5138346 5138780 - Maker00023455 Lcy13g0440 440
13 5232370 5236340 - Maker00023598 Lcy13g0445 445
5 25325143 25327011 - Lsi05G018050.1 Lsi05g01805 1805
5 25330401 25336542 - Lsi05G018070.1 Lsi05g01807 1807
5 25355670 25359094 + Lsi05G018110.1 Lsi05g01811 1811
5 25363141 25367601 - Lsi05G018130.1 Lsi05g01813 1813
5 25393825 25398514 + Lsi05G018140.1 Lsi05g01814 1814
9 18677108 18681142 + Lsi09G011610.1 Lsi09g01161 1161
9 18810310 18811372 + Lsi09G011640.1 Lsi09g01164 1164
2 50671950 50672378 - Sed0021677.1 Sed02g1466 1466
2 51356720 51361453 + Sed0028009.1 Sed02g1574 1574
12 2445716 2451170 - Sed0005341.2 Sed12g0408 408
6 74603497 74606352 + Tan0005660.2 Tan06g2326 2326
6 74733367 74734050 - Tan0004735.1 Tan06g2330 2330
10 2996646 3001695 - Tan0001023.1 Tan10g0368 368
10 4493611 4497968 - Tan0012912.1 Tan10g0557 557
5 11135152 11141461 + Vvi5g839 Vvi5g839 839
5 11227880 11228306 + Vvi5g840 Vvi5g840 840
5 11240548 11267908 - Vvi5g841 Vvi5g841 841
5 11311928 11315630 - Vvi5g842 Vvi5g842 842
5 11354244 11374240 + Vvi5g843 Vvi5g843 843
5 11374925 11376714 + Vvi5g844 Vvi5g844 844
5 11376714 11380856 - Vvi5g845 Vvi5g845 845
5 11463634 11464220 + Vvi5g846 Vvi5g846 846
5 11466232 11468334 - Vvi5g847 Vvi5g847 847
5 11492333 11500753 + Vvi5g848 Vvi5g848 848
       

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