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
Vvi19g944 . . . . Bpe09g00281 . . . . Cmo04g00691 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda05g00797 Bda12g00789 . Bpe03g00857 . . . . . . Cma16g00460 Car04g00599 Car16g00417 Cpe14g00387 Cpe01g00581 . . . . . . . Cla07g01003 Cam07g1078 Cec07g1150 Cco07g1128 Clacu07g1053 Cmu07g1043 Cre07g1420 . . . .
Vvi19g945 . . . . . . . . . Cmo04g00689 . Cma09g00749 . . . . Cpe02g00634 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe03g00860 . . . . Cmo09g00741 . Cma16g00463 Car04g00597 Car16g00419 Cpe14g00389 Cpe01g00579 . . . . . . . Cla07g01006 Cam07g1081 Cec07g1153 Cco07g1131 . Cmu07g1046 . . . . .
Vvi19g946 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g947 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g948 . . . . Bpe09g00284 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo07g00997 Blo10g00691 . Bda12g00786 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g949 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g950 . . . . . . . . Cmo16g00503 Cmo04g00685 . . . . . . . . . . . . . . . . . . . . . . . . Cone15ag0987 . . . . . . . . . Bpe03g00862 . . . . . Cma04g00637 . Car04g00596 Car16g00420 Cpe14g00392 Cpe01g00575 . . . . . . . Cla07g01009 Cam07g1086 Cec07g1158 Cco07g1136 Clacu07g1060 Cmu07g1051 Cre07g1427 . . Chy07g01044 .
Vvi19g951 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo01g01333 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g952 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g953 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 56431360 56432868 + Bda021953.1 Bda05g00797 797
12 36784256 36788889 - Bda009286.1 Bda12g00786 786
12 36862993 36864765 - Bda009290.1 Bda12g00789 789
7 29503816 29507843 + BLOR18929 Blo07g00997 997
10 22182439 22191216 - BLOR02481 Blo10g00691 691
3 28379238 28381043 + Bpe012765.1 Bpe03g00857 857
3 28400383 28406250 + Bpe012768.1 Bpe03g00860 860
3 28409099 28410484 - Bpe012770.1 Bpe03g00862 862
9 2170871 2172640 - Bpe023952.1 Bpe09g00281 281
9 2217108 2217686 + Bpe023955.1 Bpe09g00284 284
7 25222620 25224407 + CaPI482276_07g010780.1 Cam07g1078 1078
7 25268862 25278278 + CaPI482276_07g010810.1 Cam07g1081 1081
7 25316578 25318005 - CaPI482276_07g010860.1 Cam07g1086 1086
4 3400951 3402303 + Carg13109-RA Car04g00596 596
4 3409660 3419658 - Carg13108-RA Car04g00597 597
4 3428565 3430316 - Carg13106-RA Car04g00599 599
16 2589729 2591670 + Carg11384-RA Car16g00417 417
16 2601804 2609410 + Carg11386-RA Car16g00419 419
16 2621183 2622851 - Carg11387-RA Car16g00420 420
7 24952136 24953932 + CcPI632755_07g011280.1 Cco07g1128 1128
7 24995670 25007769 + CcPI632755_07g011310.1 Cco07g1131 1131
7 25050990 25052414 - CcPI632755_07g011360.1 Cco07g1136 1136
7 26851756 26853555 + CePI673135_07g011500.1 Cec07g1150 1150
7 26894648 26906985 + CePI673135_07g011530.1 Cec07g1153 1153
7 26947970 26949394 - CePI673135_07g011580.1 Cec07g1158 1158
7 15376101 15377516 - Chy7G138740.1 Chy07g01044 1044
7 25038787 25040574 + ClG42_07g0105300.10 Clacu07g1053 1053
7 25129721 25131148 - ClG42_07g0106000.10 Clacu07g1060 1060
7 26364685 26366472 + ClCG07G010550.1 Cla07g01003 1003
7 26405281 26421009 + ClCG07G010575.1 Cla07g01006 1006
7 26461792 26463219 - ClCG07G010620.1 Cla07g01009 1009
4 3267258 3268625 + CmaCh04G006370.1 Cma04g00637 637
9 3585886 3589570 - CmaCh09G007490.1 Cma09g00749 749
16 2304169 2305953 + CmaCh16G004600.1 Cma16g00460 460
16 2316505 2324719 + CmaCh16G004630.1 Cma16g00463 463
1 10578058 10580692 - CmoCh01G013330.1 Cmo01g01333 1333
4 3397380 3407054 + CmoCh04G006850.1 Cmo04g00685 685
4 3414434 3424998 - CmoCh04G006890.1 Cmo04g00689 689
4 3434234 3435985 - CmoCh04G006910.1 Cmo04g00691 691
9 3715039 3720429 - CmoCh09G007410.1 Cmo09g00741 741
16 2420978 2422381 - CmoCh16G005030.1 Cmo16g00503 503
7 25275679 25277466 + CmPI595203_07g010430.1 Cmu07g1043 1043
7 25327163 25336580 + CmPI595203_07g010460.1 Cmu07g1046 1046
7 25374442 25375869 - CmPI595203_07g010510.1 Cmu07g1051 1051
15 7895874 7897391 - Conep15aG0100800.1 Cone15ag0987 987
1 3331191 3332543 + Cp4.1LG01g00900.1 Cpe01g00575 575
1 3340407 3351479 - Cp4.1LG01g00830.1 Cpe01g00579 579
1 3360292 3362052 - Cp4.1LG01g00800.1 Cpe01g00581 581
2 3859647 3863613 + Cp4.1LG02g02380.1 Cpe02g00634 634
14 2384527 2386299 + Cp4.1LG14g03280.1 Cpe14g00387 387
14 2397539 2403834 + Cp4.1LG14g03300.1 Cpe14g00389 389
14 2415706 2417109 - Cp4.1LG14g03210.1 Cpe14g00392 392
7 29195766 29197565 + CrPI670011_07g014200.1 Cre07g1420 1420
7 29299355 29300779 - CrPI670011_07g014270.1 Cre07g1427 1427
19 17645199 17647650 + Vvi19g944 Vvi19g944 944
19 17668877 17700404 - Vvi19g945 Vvi19g945 945
19 17731445 17757520 + Vvi19g946 Vvi19g946 946
19 17767657 17774586 - Vvi19g947 Vvi19g947 947
19 17849971 17876784 - Vvi19g948 Vvi19g948 948
19 18056452 18061495 + Vvi19g949 Vvi19g949 949
19 18129429 18130854 - Vvi19g950 Vvi19g950 950
19 18194904 18198944 + Vvi19g951 Vvi19g951 951
19 18220088 18220624 - Vvi19g952 Vvi19g952 952
19 18235215 18236248 - Vvi19g953 Vvi19g953 953
       

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