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
Vvi1g261 Blo01g00485 Blo16g01053 Bda01g02095 . . . . . . . . . . . . . Cpe01g01762 . . . . . . . . . . . . . . Cone13ag0856 Cone19ag0856 . . . . . . . . . . . Bpe02g02285 Bma01g00154 . . . . Cma04g02007 . . . . . Bhi12g01376 . . . . . . . . . . . . . . Csa05g01509 . Cme09g00814
Vvi1g262 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g263 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g264 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g265 Blo01g00486 . Bda01g02093 . . . . . . . . . . . . . Cpe01g01765 . . . . . . . . . . . . . . Cone13ag0854 . Cone6ag0469 Cone9ag0482 . . . . . . . . . Bpe02g02283 Bma01g00156 . . . . Cma04g02011 . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g266 . . Bda01g02092 . . Bpe10g00947 Bma14g01697 Bma15g00077 . Cmo18g01060 . Cma18g01042 . Car18g00968 Sed06g1865 Cpe09g00275 Cpe01g01766 Bhi07g01368 Tan04g0897 Cmetu10g0653 Lac13g0460 Hepe01g1220 . . Cla05g02328 Cam05g2502 Cec05g2525 Cco05g2568 Clacu05g2496 Cmu05g2358 Cre05g2474 Cone13ag0853 Cone19ag0854 Cone6ag0468 Cone9ag0480 Lsi04g00288 Csa05g02582 Chy10g01117 Cme10g00289 Blo06g00971 Blo11g00830 Bda07g01526 . Bpe11g01690 Bpe02g02282 Bma01g00157 . . . Cmo15g01051 Cma04g02012 Cma15g00991 . . . . . . . . . . . . . . . . . . . . Chy09g00618 .
Vvi1g267 . . . . . . Bma14g01698 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0467 Cone9ag0479 . . . . . Blo11g00831 . . Bpe11g01691 . . . . . . . . . . . . Bhi12g01373 . . . . . Lcy10g0912 . . . . . . . . . . .
Vvi1g268 Blo01g00488 . Bda01g02091 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0466 Cone9ag0478 . . . . . . . . . . Bma01g00158 . . . Cmo15g01036 . Cma15g00990 . Car15g00931 . . Bhi12g01372 . . . . . Lcy10g0916 . . . . . . . . . . .
Vvi1g269 . . . Bda11g01137 Bpe13g01331 . . . . . . . . . . . Cpe01g01767 . . . . . . . . . . . . . . . . Cone6ag0465 Cone9ag0477 . . . . . . . Bda11g01137 . . . Bma06g00769 . Cmo04g02100 . Cma04g02013 . Car04g01957 . . . . . . . . . . . . . . . . . . . Chy09g00609 .
Vvi1g270 Blo01g00489 Blo16g01054 Bda01g02090 . Bpe13g01332 . Bma14g01699 . . Cmo18g01059 . Cma18g01041 . Car18g00967 Sed06g1866 Cpe09g00276 . Bhi07g01367 Tan04g0896 Cmetu10g0277 Lac13g0461 Hepe01g1219 . . Cla05g02327 Cam05g2500 Cec05g2524 Cco05g2566 Clacu05g2494 Cmu05g2357 Cre05g2473 Cone13ag0852 Cone19ag0853 Cone6ag0464 Cone9ag0476 Lsi04g00286 Csa05g02583 Chy10g01118 Cme10g00288 . Blo11g00832 Bda07g01528 . . Bpe02g02281 . Bma06g00768 . . . . . . Car15g00854 Cpe13g00409 . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 57054572 57056116 - Bda004418.1 Bda01g02090 2090
1 57060868 57061729 - Bda004419.2 Bda01g02091 2091
1 57063080 57064111 - Bda004420.1 Bda01g02092 2092
1 57071314 57075482 - Bda004421.1 Bda01g02093 2093
1 57081341 57084261 + Bda004423.1 Bda01g02095 2095
7 28386869 28387981 + Bda028379.1 Bda07g01526 1526
7 28404371 28406160 + Bda028381.1 Bda07g01528 1528
11 11545511 11546505 - Bda007622.1 Bda11g01137 1137
7 41194092 41196218 - XM_039035972.1 Bhi07g01367 1367
7 41285107 41286957 - XM_039037278.1 Bhi07g01368 1368
12 42902859 42905149 - XM_039050701.1 Bhi12g01372 1372
12 42955110 42987362 + XM_039018606.1 Bhi12g01373 1373
12 43599787 43605389 - XM_039019455.1 Bhi12g01376 1376
1 5329380 5332345 - BLOR00485 Blo01g00485 485
1 5338974 5342886 + BLOR00486 Blo01g00486 486
1 5373297 5374020 + BLOR00488 Blo01g00488 488
1 5393225 5394785 + BLOR00489 Blo01g00489 489
6 32997555 32998667 + BLOR17554 Blo06g00971 971
11 14148534 14149646 + BLOR03706 Blo11g00830 830
11 14214829 14220375 + BLOR03707 Blo11g00831 831
11 14222147 14223845 + BLOR03708 Blo11g00832 832
16 39048920 39055546 - BLOR21840 Blo16g01053 1053
16 39063120 39064593 + BLOR21841 Blo16g01054 1054
1 1445481 1448479 - Bma000321.1 Bma01g00154 154
1 1456898 1468717 + Bma030172 Bma01g00156 156
1 1471963 1472994 + Bma000323.1 Bma01g00157 157
1 1487925 1488452 + Bma000324.3 Bma01g00158 158
6 39463142 39464593 - Bma023765.1 Bma06g00768 768
6 39469829 39470830 + Bma023766.1 Bma06g00769 769
14 36122169 36123281 + Bma012445.1 Bma14g01697 1697
14 36125380 36130006 + Bma012446.1 Bma14g01698 1698
14 36135175 36136820 + Bma012447.1 Bma14g01699 1699
15 893677 894792 - Bma013051.1 Bma15g00077 77
2 23606081 23607633 - Bpe010098.1 Bpe02g02281 2281
2 23612580 23613611 - Bpe010099.1 Bpe02g02282 2282
2 23620588 23624856 - Bpe010100.1 Bpe02g02283 2283
2 23630490 23633506 + Bpe010102.1 Bpe02g02285 2285
10 15006814 15007929 + Bpe003252.1 Bpe10g00947 947
11 13188925 13190037 + Bpe005004.1 Bpe11g01690 1690
11 13192096 13197010 + Bpe005005.1 Bpe11g01691 1691
13 18557497 18558464 - Bpe025287 Bpe13g01331 1331
13 18565463 18566904 + Bpe010994.1 Bpe13g01332 1332
5 32823814 32825267 - CaPI482276_05g025000.1 Cam05g2500 2500
5 32833227 32834273 - CaPI482276_05g025020.1 Cam05g2502 2502
4 13407527 13409450 - Carg28275-RA Car04g01957 1957
15 4960227 4961573 - Carg26881-RA Car15g00854 854
15 6390790 6391632 - Carg27850-RA Car15g00931 931
18 10226071 10227428 - Carg21563-RA Car18g00967 967
18 10229397 10230428 - Carg21562-RA Car18g00968 968
5 33919454 33920904 - CcPI632755_05g025660.1 Cco05g2566 2566
5 33928450 33929496 - CcPI632755_05g025680.1 Cco05g2568 2568
5 36250793 36252244 - CePI673135_05g025240.1 Cec05g2524 2524
5 36260130 36261176 - CePI673135_05g025250.1 Cec05g2525 2525
9 7432797 7433739 - Chy9G163250.1 Chy09g00609 609
9 7677062 7678015 + Chy9G163340.1 Chy09g00618 618
10 16208218 16209252 + Chy10G183110.1 Chy10g01117 1117
10 16213952 16215394 + Chy10G183120.1 Chy10g01118 1118
5 33037201 33038653 - ClG42_05g0249400.10 Clacu05g2494 2494
5 33046443 33047489 - ClG42_05g0249600.10 Clacu05g2496 2496
5 34851069 34853015 - ClCG05G022990.1 Cla05g02327 2327
5 34860451 34861497 - ClCG05G023000.1 Cla05g02328 2328
4 12511061 12514956 - CmaCh04G020070.1 Cma04g02007 2007
4 12566862 12580353 + CmaCh04G020110.1 Cma04g02011 2011
4 12585554 12586537 + CmaCh04G020120.1 Cma04g02012 2012
4 12697785 12699404 + CmaCh04G020130.1 Cma04g02013 2013
15 5758377 5759389 - CmaCh15G009900.1 Cma15g00990 990
15 5901090 5918567 + CmaCh15G009910.1 Cma15g00991 991
18 8663506 8665131 - CmaCh18G010410.1 Cma18g01041 1041
18 8666735 8667745 - CmaCh18G010420.1 Cma18g01042 1042
9 10485043 10491251 + MELO3C033871.2.1 Cme09g00814 814
10 1872211 1874137 - MELO3C012218.2.1 Cme10g00288 288
10 1878784 1879958 - MELO3C012217.2.1 Cme10g00289 289
10 20208522 20210457 + PI0003422.1 Cmetu10g0277 277
10 20200213 20201655 + PI0012697.1 Cmetu10g0653 653
4 13168839 13170051 - CmoCh04G021000.1 Cmo04g02100 2100
15 6423988 6425032 - CmoCh15G010360.1 Cmo15g01036 1036
15 6789326 6790300 + CmoCh15G010510.1 Cmo15g01051 1051
18 11226784 11228321 - CmoCh18G010590.1 Cmo18g01059 1059
18 11230116 11231120 - CmoCh18G010600.1 Cmo18g01060 1060
5 32775414 32776866 - CmPI595203_05g023570.1 Cmu05g2357 2357
5 32784659 32785705 - CmPI595203_05g023580.1 Cmu05g2358 2358
6 2290524 2292234 - Conep06aG0047400.1 Cone6ag0464 464
6 2295739 2296823 + Conep06aG0047500.1 Cone6ag0465 465
6 2299116 2300313 - Conep06aG0047600.1 Cone6ag0466 466
6 2301071 2303491 - Conep06aG0047700.1 Cone6ag0467 467
6 2305115 2307040 - Conep06aG0047800.1 Cone6ag0468 468
6 2312667 2317355 - Conep06aG0047900.1 Cone6ag0469 469
9 2270650 2272349 - Conep09aG0048600.1 Cone9ag0476 476
9 2278423 2279452 + Conep09aG0048700.1 Cone9ag0477 477
9 2286367 2287504 - Conep09aG0048800.1 Cone9ag0478 478
9 2287817 2290208 - Conep09aG0048900.1 Cone9ag0479 479
9 2293951 2295406 - Conep09aG0049000.1 Cone9ag0480 480
9 2300771 2305328 - Conep09aG0049200.1 Cone9ag0482 482
13 7621202 7622966 - Conep13aG0087800.1 Cone13ag0852 852
13 7632578 7633852 - Conep13aG0087900.1 Cone13ag0853 853
13 7638713 7643113 - Conep13aG0088000.1 Cone13ag0854 854
13 7645752 7649058 + Conep13aG0088200.1 Cone13ag0856 856
19 6697499 6699462 - Conep19aG0087700.1 Cone19ag0853 853
19 6703569 6704804 - Conep19aG0087800.1 Cone19ag0854 854
19 6713578 6717396 + Conep19aG0088000.1 Cone19ag0856 856
1 13279746 13283715 - Cp4.1LG01g17640.1 Cpe01g01762 1762
1 13349174 13365202 + Cp4.1LG01g17630.1 Cpe01g01765 1765
1 13371389 13372369 + Cp4.1LG01g17620.1 Cpe01g01766 1766
1 13481581 13483282 + Cp4.1LG01g17580.1 Cpe01g01767 1767
9 1629908 1630924 + Cp4.1LG09g02730.1 Cpe09g00275 275
9 1632809 1634299 + Cp4.1LG09g02740.1 Cpe09g00276 276
13 4437223 4439784 + Cp4.1LG13g06810.1 Cpe13g00409 409
5 36111059 36112510 - CrPI670011_05g024730.1 Cre05g2473 2473
5 36120339 36121385 - CrPI670011_05g024740.1 Cre05g2474 2474
5 17523065 17534103 + CsaV3_5G023280.1 Csa05g01509 1509
5 27134879 27137672 + CsaV3_5G034010.1 Csa05g02582 2582
5 27140404 27142435 + CsaV3_5G034020.1 Csa05g02583 2583
1 77366530 77368415 - Hsped.01g12190.1 Hepe01g1219 1219
1 77380913 77382241 - Hsped.01g12200.1 Hepe01g1220 1220
13 3330246 3331310 + Lag0040256.1 Lac13g0460 460
13 3340474 3341945 + Lag0040257.1 Lac13g0461 461
10 28915008 28926284 + Maker00020862 Lcy10g0912 912
10 28957062 28958559 + Maker00020786 Lcy10g0916 916
4 2865253 2867244 - Lsi04G002860.1 Lsi04g00286 286
4 2883210 2884262 - Lsi04G002880.1 Lsi04g00288 288
6 43035548 43036883 + Sed0026901.1 Sed06g1865 1865
6 43048076 43050571 + Sed0010552.1 Sed06g1866 1866
4 7666739 7668774 - Tan0009811.1 Tan04g0896 896
4 7685937 7687660 - Tan0020251.1 Tan04g0897 897
1 2692099 2698939 - Vvi1g261 Vvi1g261 261
1 2699661 2703084 - Vvi1g262 Vvi1g262 262
1 2714898 2717647 + Vvi1g263 Vvi1g263 263
1 2717669 2719510 - Vvi1g264 Vvi1g264 264
1 2726714 2743674 + Vvi1g265 Vvi1g265 265
1 2751619 2752908 + Vvi1g266 Vvi1g266 266
1 2754309 2765820 + Vvi1g267 Vvi1g267 267
1 2766596 2767442 + Vvi1g268 Vvi1g268 268
1 2770672 2771827 - Vvi1g269 Vvi1g269 269
1 2781374 2783587 + Vvi1g270 Vvi1g270 270
       

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