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
Vvi1g991 . Blo16g01081 . Bda11g01171 Bpe13g01369 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone9ag0519 . . . . . . . Bda11g01171 . . . . . . . . . . . . Cpe07g00099 . . . . . . . . . . . . . . . . . .
Vvi1g992 . . . . . . Bma14g01669 . Cmo04g01649 . . . Car04g01626 . . . Cpe01g01398 Bhi07g01448 . . . . . . . . . . . . . . . . . . Csa05g02531 Chy10g01075 Cme10g01398 . Blo11g00797 Bda07g01492 . Bpe11g01659 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g993 . . . . . Bpe10g00909 . . . Cmo18g01111 . Cma18g01086 . Car18g01007 . Cpe09g00236 . . . . . . . . Cla05g02379 Cam05g2550 Cec05g2582 Cco05g2622 Clacu05g2550 Cmu05g2409 Cre05g2526 . . . . Lsi04g00348 . . . . Blo11g00799 Bda07g01494 . Bpe11g01661 . . . . . . . . . . . Cpe07g00098 . . . . . . . . . . . . . . . . . .
Vvi1g994 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g995 Blo01g00463 . Bda01g02117 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe02g02305 Bma01g00133 . . . . . . . . . Cpe07g00096 . . . . . . . . . . . . . . . . . .
Vvi1g996 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g997 . . Bda01g02115 . . . . Bma15g00124 Cmo04g01648 Cmo18g01105 . Cma18g01083 Car04g01625 Car18g01004 . Cpe09g00240 . . . . . . . . Cla05g02377 Cam05g2547 Cec05g2578 Cco05g2618 Clacu05g2546 Cmu05g2405 Cre05g2522 . . . . Lsi04g00344 Csa05g02534 Chy10g01077 Cme10g00335 Blo06g00934 . . . . Bpe02g02303 Bma01g00135 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g998 . Blo16g01074 . Bda11g01165 Bpe13g01363 . . . Cmo04g01646 . . . Car04g01624 . Sed06g1810 . Cpe01g01396 Bhi07g01447 Tan04g0956 Cmetu10g0683 Lac13g0409 Hepe10g1821 . . Cla05g02376 Cam05g2545 Cec05g2577 Cco05g2616 Clacu05g2544 Cmu05g2403 Cre05g2520 . . . . Lsi04g00342 Csa05g02535 Chy10g01078 Cme10g00333 . . . Bda11g01165 . . . Bma06g00746 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g999 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1000 . . . . . . . . Cmo04g01645 . . . Car04g01622 . Sed07g2016 . Cpe01g01394 Bhi07g01446 Tan04g0955 Cmetu04g0673 . . . . Cla05g02374 Cam05g2544 Cec05g2576 Cco05g2615 Clacu05g2543 Cmu05g2402 Cre05g2519 . . . . Lsi04g00341 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 57200060 57201988 - Bda004446.1 Bda01g02115 2115
1 57215403 57218162 + Bda004448.1 Bda01g02117 2117
7 27694569 27696715 - Bda028332.1 Bda07g01492 1492
7 27701926 27703697 - Bda028334.1 Bda07g01494 1494
11 11971126 11973097 + Bda007657.1 Bda11g01165 1165
11 12086396 12089159 - Bda007669.1 Bda11g01171 1171
7 42634344 42638685 - XM_039036464.1 Bhi07g01446 1446
7 42641998 42645810 + XM_039036467.1 Bhi07g01447 1447
7 42675450 42681403 - XM_039036836.1 Bhi07g01448 1448
1 5114912 5117551 - BLOR00463 Blo01g00463 463
6 32556549 32558450 - BLOR17517 Blo06g00934 934
11 12256959 12269459 + BLOR03673 Blo11g00797 797
11 12325121 12330737 - BLOR03675 Blo11g00799 799
16 39297959 39299633 + BLOR21861 Blo16g01074 1074
16 39364982 39368205 - BLOR21868 Blo16g01081 1081
1 1296842 1300396 - Bma000298.1 Bma01g00133 133
1 1315134 1317062 + Bma000300.1 Bma01g00135 135
6 38662344 38666975 - Bma031295 Bma06g00746 746
14 35387756 35394263 - Bma012403.1 Bma14g01669 1669
15 1376887 1378677 + Bma013102.1 Bma15g00124 124
2 23728972 23730900 - Bpe010120.1 Bpe02g02303 2303
2 23741337 23744114 + Bpe025214 Bpe02g02305 2305
10 14733706 14735408 - Bpe003212.1 Bpe10g00909 909
11 12769811 12776220 - Bpe004972.1 Bpe11g01659 1659
11 12782792 12784605 - Bpe004974.1 Bpe11g01661 1661
13 18871136 18877045 + Bpe025291 Bpe13g01363 1363
13 18949327 18952113 - Bpe011030.1 Bpe13g01369 1369
5 33256684 33262751 - CaPI482276_05g025440.1 Cam05g2544 2544
5 33264664 33266218 + CaPI482276_05g025450.1 Cam05g2545 2545
5 33271513 33272882 - CaPI482276_05g025470.1 Cam05g2547 2547
5 33292861 33297428 - CaPI482276_05g025500.1 Cam05g2550 2550
4 9369166 9375464 - Carg01777-RA Car04g01622 1622
4 9376831 9378865 + Carg01776-RA Car04g01624 1624
4 9380463 9382400 - Carg01775-RA Car04g01625 1625
4 9385682 9393554 - Carg01774-RA Car04g01626 1626
18 10485211 10487142 - Carg17326-RA Car18g01004 1004
18 10508754 10509956 - Carg17323-RA Car18g01007 1007
5 34363090 34364498 - CcPI632755_05g026150.1 Cco05g2615 2615
5 34368723 34370263 + CcPI632755_05g026160.1 Cco05g2616 2616
5 34375549 34376948 - CcPI632755_05g026180.1 Cco05g2618 2618
5 34399759 34402082 - CcPI632755_05g026220.1 Cco05g2622 2622
5 36697461 36702472 - CePI673135_05g025760.1 Cec05g2576 2576
5 36705160 36706709 + CePI673135_05g025770.1 Cec05g2577 2577
5 36709802 36713402 - CePI673135_05g025780.1 Cec05g2578 2578
5 36733372 36737984 - CePI673135_05g025820.1 Cec05g2582 2582
10 15863118 15868793 + Chy10G182690.1 Chy10g01075 1075
10 15876016 15877953 + Chy10G182710.1 Chy10g01077 1077
10 15881260 15882752 - Chy10G182720.1 Chy10g01078 1078
5 33467520 33472398 - ClG42_05g0254300.10 Clacu05g2543 2543
5 33472547 33476631 + ClG42_05g0254400.10 Clacu05g2544 2544
5 33481828 33483335 - ClG42_05g0254600.10 Clacu05g2546 2546
5 33503271 33505456 - ClG42_05g0255000.10 Clacu05g2550 2550
5 35304103 35311649 - ClCG05G023480.1 Cla05g02374 2374
5 35312378 35313928 + ClCG05G023500.1 Cla05g02376 2376
5 35314094 35322229 - ClCG05G023510.2 Cla05g02377 2377
5 35348689 35353238 - ClCG05G023540.2 Cla05g02379 2379
18 8932562 8934493 - CmaCh18G010830.1 Cma18g01083 1083
18 8945146 8947215 - CmaCh18G010860.1 Cma18g01086 1086
10 2194117 2196104 + MELO3C012172.2.1 Cme10g00333 333
10 2198787 2202599 - MELO3C012171.2.1 Cme10g00335 335
10 16508619 16521668 - MELO3C022620.2.1 Cme10g01398 1398
4 16180739 16183488 + PI0019770.1 Cmetu04g0673 673
10 19824582 19826538 - PI0022025.1 Cmetu10g0683 683
4 8395312 8398989 - CmoCh04G016450.1 Cmo04g01645 1645
4 8400007 8401351 + CmoCh04G016460.1 Cmo04g01646 1646
4 8403802 8405739 - CmoCh04G016480.1 Cmo04g01648 1648
4 8405987 8409924 - CmoCh04G016490.1 Cmo04g01649 1649
18 11490516 11492447 - CmoCh18G011050.1 Cmo18g01105 1105
18 11514256 11518025 - CmoCh18G011110.1 Cmo18g01111 1111
5 33205454 33210331 - CmPI595203_05g024020.1 Cmu05g2402 2402
5 33210513 33214565 + CmPI595203_05g024030.1 Cmu05g2403 2403
5 33219718 33221230 - CmPI595203_05g024050.1 Cmu05g2405 2405
5 33243413 33245705 - CmPI595203_05g024090.1 Cmu05g2409 2409
9 2483612 2487053 + Conep09aG0052900.1 Cone9ag0519 519
1 8393917 8400612 - Cp4.1LG01g13140.1 Cpe01g01394 1394
1 8401869 8403156 + Cp4.1LG01g13260.1 Cpe01g01396 1396
1 8411569 8419711 - Cp4.1LG01g13170.1 Cpe01g01398 1398
7 490815 495645 - Cp4.1LG07g01030.1 Cpe07g00096 96
7 501865 506338 + Cp4.1LG07g01010.1 Cpe07g00098 98
7 507789 519716 - Cp4.1LG07g01070.1 Cpe07g00099 99
9 1363916 1365015 + Cp4.1LG09g02330.1 Cpe09g00236 236
9 1389560 1391491 + Cp4.1LG09g02470.1 Cpe09g00240 240
5 36553565 36558593 - CrPI670011_05g025190.1 Cre05g2519 2519
5 36558742 36562757 + CrPI670011_05g025200.1 Cre05g2520 2520
5 36568041 36569442 - CrPI670011_05g025220.1 Cre05g2522 2522
5 36591894 36594208 - CrPI670011_05g025260.1 Cre05g2526 2526
5 26802138 26806537 + CsaV3_5G033500.1 Csa05g02531 2531
5 26813914 26815851 + CsaV3_5G033530.1 Csa05g02534 2534
5 26818718 26820816 - CsaV3_5G033540.1 Csa05g02535 2535
10 54978292 54980133 - Hsped.10g18210.1 Hepe10g1821 1821
13 2885284 2886933 - Lag0040205.1 Lac13g0409 409
4 3414952 3420430 - Lsi04G003410.1 Lsi04g00341 341
4 3422632 3424259 + Lsi04G003420.1 Lsi04g00342 342
4 3427395 3429332 - Lsi04G003440.1 Lsi04g00344 344
4 3456603 3461910 - Lsi04G003480.1 Lsi04g00348 348
6 42604136 42607034 - Sed0022309.1 Sed06g1810 1810
7 35096567 35103467 - Sed0026487.4 Sed07g2016 2016
4 8420975 8425269 - Tan0012015.2 Tan04g0955 955
4 8427077 8429257 + Tan0004449.1 Tan04g0956 956
1 15386734 15409114 - Vvi1g991 Vvi1g991 991
1 15443312 15464415 + Vvi1g992 Vvi1g992 992
1 15492098 15497110 - Vvi1g993 Vvi1g993 993
1 15497305 15497946 - Vvi1g994 Vvi1g994 994
1 15551006 15556266 + Vvi1g995 Vvi1g995 995
1 15586830 15619187 - Vvi1g996 Vvi1g996 996
1 15654691 15658282 + Vvi1g997 Vvi1g997 997
1 15664462 15666483 - Vvi1g998 Vvi1g998 998
1 15680855 15684455 + Vvi1g999 Vvi1g999 999
1 15701473 15704472 + Vvi1g1000 Vvi1g1000 1000
       

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