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
Vvi4g1122 . . . . Bpe15g00474 . . . . . . Cma07g00422 Car03g00627 . Sed11g1095 Cpe19g00864 . Bhi03g00860 Tan03g2090 Cmetu03g1857 . Hepe04g1597 . . Cla01g01986 Cam01g2080 Cec04g1739 Cco04g1805 Clacu01g2102 Cmu01g1977 Cre04g1653 Cone8ag0854 . . Cone9ag1609 Lsi01g00594 . . Cme08g00938 . . Bda11g01832 . Bpe10g00159 Bpe06g00130 . . Sed05g3597 . Cmo07g00418 . Cma20g00763 . . . . Bhi10g01869 Tan05g1161 . . Hepe08g0278 . . . . . . . . . Lsi07g01099 Csa06g03334 Chy02g00565 .
Vvi4g1123 . . . . . . . . . . . Cma07g00419 . Car07g00368 . Cpe19g00865 . Bhi03g00850 . . . . . . . . . . . . . . . Cone6ag1688 Cone9ag1610 Lsi01g00593 . . Cme08g00939 Blo05g00708 . . . . Bpe06g00131 . . . . Cmo07g00416 . . . . . . . . . . . . . . . . . . . . . Csa06g03336 Chy02g00563 .
Vvi4g1124 . . . Bda10g00188 . . . Bma15g00937 . . Cma03g00679 . . . . . Cpe10g00670 . . . . . . . Cla01g01987 Cam01g2082 Cec04g1741 Cco04g1807 Clacu01g2103 Cmu01g1979 Cre04g1655 Cone8ag0855 . . . . . . Cme08g00940 . Blo06g00297 . . Bpe10g00160 . . . . Cmo03g00704 . . . . . . . . . . . . . . . . . . . . . . Csa06g03337 Chy02g00562 .
Vvi4g1125 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1126 . . . Bda10g00189 . . . . . . Cma03g00678 . Car03g00626 . Sed05g0671 . . Bhi03g00848 Tan03g2092 Cmetu04g1543 . Hepe04g1601 . . . . . . . . . . . Cone6ag1689 Cone9ag1611 Lsi01g00592 . . Cme08g00941 . Blo06g00294 . . Bpe10g00161 . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa06g03339 Chy02g00561 .
Vvi4g1127 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1128 . . . . . . . . . . . . . . . . Cpe10g00671 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo03g00703 . . Cma20g00760 . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1129 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag1690 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1130 . . . . . . . . . . Cma03g00677 . Car03g00625 . Sed10g1012 . . Bhi03g00847 Tan03g2093 Cmetu04g2856 . Hepe04g1602 . . Cla01g01988 Cam01g2086 Cec04g1743 Cco04g1808 . Cmu01g1980 Cre04g1657 . . . . . . . Cme08g00942 . . . . . Bpe06g00334 . . . . . . . . . . . Bhi10g02362 . . . . . . Cla02g00101 Cam02g0107 Cec02g0108 Cco02g0100 Clacu02g0104 Cmu02g0098 Cre02g0439 . Csa06g03340 . Cme11g00109
Vvi4g1131 Blo04g00881 Blo16g00083 . . Bpe15g00475 Bpe13g00411 . Bma15g00911 . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag0818 . . . . . . . . Bda11g01831 . . . Bma03g00957 . . . . Cma16g01241 . . . . . . . . . . . . . . . . . . . Lsi07g01097 . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
10 6551750 6561677 - Bda006694.2 Bda10g00188 188
10 6580434 6582622 - Bda006695.1 Bda10g00189 189
11 53561581 53566229 - Bda008768.2 Bda11g01831 1831
11 53567266 53567933 - Bda008769.1 Bda11g01832 1832
3 15497492 15501737 - XM_039025526.1 Bhi03g00847 847
3 15560827 15571038 + XM_039024885.1 Bhi03g00848 848
3 15616181 15622128 + XM_039027868.1 Bhi03g00850 850
3 15628113 15630407 - XM_039024969.1 Bhi03g00860 860
10 46621274 46623585 - XM_039046775.1 Bhi10g01869 1869
10 62070519 62078567 - XM_039045168.1 Bhi10g02362 2362
4 10026084 10039987 - BLOR13793 Blo04g00881 881
5 24410799 24413734 + BLOR15670 Blo05g00708 708
6 16327254 16329471 + BLOR16877 Blo06g00294 294
6 16435765 16440051 + BLOR16880 Blo06g00297 297
16 2219208 2230406 + BLOR07331 Blo16g00083 83
3 10172429 10176238 - Bma017296.1 Bma03g00957 957
15 31845693 31849309 + Bma014124.1 Bma15g00911 911
15 34187213 34191364 - Bma014177.1 Bma15g00937 937
6 2250709 2251804 + Bpe019581.1 Bpe06g00130 130
6 2253376 2256278 - Bpe019582.1 Bpe06g00131 131
6 14737733 14739764 + Bpe019832.1 Bpe06g00334 334
10 3831886 3832997 + Bpe002470.1 Bpe10g00159 159
10 3955269 3959016 - Bpe002471.1 Bpe10g00160 160
10 3972121 3974327 - Bpe002472.1 Bpe10g00161 161
13 11809069 11814123 - Bpe006536.1 Bpe13g00411 411
15 16079990 16085687 + Bpe001408.1 Bpe15g00474 474
15 16087782 16091638 + Bpe001409.5 Bpe15g00475 475
1 33856751 33858784 + CaPI482276_01g020800.1 Cam01g2080 2080
1 33873886 33878485 - CaPI482276_01g020820.1 Cam01g2082 2082
1 33890388 33904884 + CaPI482276_01g020860.1 Cam01g2086 2086
2 2236540 2238635 - CaPI482276_02g001070.1 Cam02g0107 107
3 5708297 5710253 - Carg00585-RA Car03g00625 625
3 5709680 5718574 + Carg00586-RA Car03g00626 626
3 5720392 5722041 - Carg00587-RA Car03g00627 627
7 1841893 1844776 + Carg07948-RA Car07g00368 368
2 1144179 1146277 - CcPI632755_02g001000.1 Cco02g0100 100
4 32936641 32938168 + CcPI632755_04g018050.1 Cco04g1805 1805
4 32948773 32958756 - CcPI632755_04g018070.1 Cco04g1807 1807
4 32961566 32975346 + CcPI632755_04g018080.1 Cco04g1808 1808
2 1149419 1151504 - CePI673135_02g001080.1 Cec02g0108 108
4 36427812 36429446 + CePI673135_04g017390.1 Cec04g1739 1739
4 36440240 36448643 - CePI673135_04g017410.1 Cec04g1741 1741
4 36456528 36465770 + CePI673135_04g017430.1 Cec04g1743 1743
2 3370165 3374203 + Chy2G028280.1 Chy02g00561 561
2 3389536 3390286 + Chy2G028290.1 Chy02g00562 562
2 3393606 3398177 + Chy2G028300.1 Chy02g00563 563
2 3402686 3403985 - Chy2G028320.1 Chy02g00565 565
1 32719573 32721158 + ClG42_01g0210200.10 Clacu01g2102 2102
1 32726301 32730897 - ClG42_01g0210300.10 Clacu01g2103 2103
2 1129486 1131596 - ClG42_02g0010400.10 Clacu02g0104 104
1 34501575 34513572 + ClCG01G020370.1 Cla01g01986 1986
1 34518541 34532404 - ClCG01G020380.1 Cla01g01987 1987
1 34534926 34549049 + ClCG01G020390.1 Cla01g01988 1988
2 1146532 1149042 - ClCG02G000960.1 Cla02g00101 101
3 5608658 5619570 - CmaCh03G006770.1 Cma03g00677 677
3 5619504 5623435 + CmaCh03G006780.1 Cma03g00678 678
3 5623861 5627489 + CmaCh03G006790.1 Cma03g00679 679
7 1807965 1810391 + CmaCh07G004190.1 Cma07g00419 419
7 1812385 1814188 - CmaCh07G004220.1 Cma07g00422 422
16 9376688 9388144 + CmaCh16G012410.1 Cma16g01241 1241
20 3584342 3587351 + CmaCh20G007600.1 Cma20g00760 760
20 3600503 3602189 - CmaCh20G007630.1 Cma20g00763 763
8 6173985 6176332 + MELO3C007913.2.1 Cme08g00938 938
8 6182715 6185617 - MELO3C007914.2.1 Cme08g00939 939
8 6187415 6191205 - MELO3C007915.2.1 Cme08g00940 940
8 6191968 6196574 - MELO3C007916.2.1 Cme08g00941 941
8 6198288 6200424 + MELO3C007917.2.1 Cme08g00942 942
11 988825 991215 + MELO3C023292.2.1 Cme11g00109 109
3 2430874 2433141 + PI0021535.1 Cmetu03g1857 1857
4 3648735 3652778 + PI0026613.1 Cmetu04g1543 1543
4 3643577 3646183 - PI0005913.1 Cmetu04g2856 2856
3 6110681 6112759 - CmoCh03G007030.1 Cmo03g00703 703
3 6112323 6121326 + CmoCh03G007040.1 Cmo03g00704 704
7 1894613 1896961 + CmoCh07G004160.1 Cmo07g00416 416
7 1899508 1900718 - CmoCh07G004180.1 Cmo07g00418 418
1 33057100 33058685 + CmPI595203_01g019770.1 Cmu01g1977 1977
1 33069375 33077540 - CmPI595203_01g019790.1 Cmu01g1979 1979
1 33080213 33083489 + CmPI595203_01g019800.1 Cmu01g1980 1980
2 1117120 1119233 - CmPI595203_02g000980.1 Cmu02g0098 98
6 12787342 12790697 - Conep06aG0175300.1 Cone6ag1688 1688
6 12792450 12793529 - Conep06aG0175400.1 Cone6ag1689 1689
6 12793923 12795285 + Conep06aG0175500.1 Cone6ag1690 1690
8 8476467 8477246 + Conep08aG0088000.1 Cone8ag0854 854
8 8479971 8483972 - Conep08aG0088100.1 Cone8ag0855 855
9 11505533 11507468 + Conep09aG0165900.1 Cone9ag1609 1609
9 11508176 11511612 - Conep09aG0166000.1 Cone9ag1610 1610
9 11511901 11514595 - Conep09aG0166100.1 Cone9ag1611 1611
12 7449757 7453295 + Conep12aG0084300.1 Cone12ag0818 818
10 3859423 3864785 - Cp4.1LG10g00210.1 Cpe10g00670 670
10 3866268 3867882 + Cp4.1LG10g00310.1 Cpe10g00671 671
19 6375834 6381271 + Cp4.1LG19g08770.1 Cpe19g00864 864
19 6382407 6385737 - Cp4.1LG19g08650.1 Cpe19g00865 865
2 1630947 1633312 - CrPI670011_02g004390.1 Cre02g0439 439
4 34906134 34907763 + CrPI670011_04g016530.1 Cre04g1653 1653
4 34918543 34921624 - CrPI670011_04g016550.1 Cre04g1655 1655
4 34929619 34944230 + CrPI670011_04g016570.1 Cre04g1657 1657
6 27860378 27862442 + CsaV3_6G047200.1 Csa06g03334 3334
6 27867683 27871323 - CsaV3_6G047220.1 Csa06g03336 3336
6 27872309 27875348 - CsaV3_6G047230.1 Csa06g03337 3337
6 27888472 27894600 - CsaV3_6G047250.1 Csa06g03339 3339
6 27896728 27899537 + CsaV3_6G047260.1 Csa06g03340 3340
4 71470404 71471783 + Hsped.04g15970.1 Hepe04g1597 1597
4 71486269 71489963 - Hsped.04g16010.1 Hepe04g1601 1601
4 71495145 71497483 + Hsped.04g16020.1 Hepe04g1602 1602
8 2518500 2520322 + Hsped.08g02780.1 Hepe08g0278 278
1 4718451 4727915 + Lsi01G005920.1 Lsi01g00592 592
1 4728666 4731790 + Lsi01G005930.1 Lsi01g00593 593
1 4740368 4742954 - Lsi01G005940.1 Lsi01g00594 594
7 16356654 16362192 - Lsi07G010970.1 Lsi07g01097 1097
7 16390594 16391757 - Lsi07G010990.1 Lsi07g01099 1099
5 5016381 5027257 - Sed0017987.1 Sed05g0671 671
5 44399214 44402040 + Sed0003388.1 Sed05g3597 3597
10 8789704 8799876 + Sed0010125.1 Sed10g1012 1012
11 26641908 26644050 + Sed0011421.1 Sed11g1095 1095
3 75794274 75796072 + Tan0018590.1 Tan03g2090 2090
3 75804986 75814610 - Tan0010493.1 Tan03g2092 2092
3 75816253 75821548 + Tan0016139.1 Tan03g2093 2093
5 10679264 10681698 - Tan0007240.1 Tan05g1161 1161
4 20090879 20092677 + Vvi4g1122 Vvi4g1122 1122
4 20094624 20105285 - Vvi4g1123 Vvi4g1123 1123
4 20106571 20111180 - Vvi4g1124 Vvi4g1124 1124
4 20111408 20111450 - Vvi4g1125 Vvi4g1125 1125
4 20111684 20116188 - Vvi4g1126 Vvi4g1126 1126
4 20116691 20121210 + Vvi4g1127 Vvi4g1127 1127
4 20121867 20123157 + Vvi4g1128 Vvi4g1128 1128
4 20125964 20126809 + Vvi4g1129 Vvi4g1129 1129
4 20127271 20128591 - Vvi4g1130 Vvi4g1130 1130
4 20135091 20144011 + Vvi4g1131 Vvi4g1131 1131
       

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