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
Vvi3g726 . . Bda06g01178 Bda08g00682 Bpe07g00286 . . Bma12g00293 . . . . . . . . . . . . . . . . Cla10g00968 Cam10g0992 Cec10g1022 Cco10g0984 Clacu10g1012 Cmu10g1797 Cre10g1169 . . Cone3ag1038 Cone10ag1054 . . . . . . . . . . . . Sed07g1252 Cmo04g00469 Cmo16g00329 . . . . Cpe14g00258 Cpe01g00392 Bhi11g01120 Tan01g0616 Cmetu07g0418 . . Mch10g0415 . . . . . . . . Lsi03g01010 . . Cme07g02203
Vvi3g727 . Blo03g00065 Bda06g01176 . Bpe07g00287 . . Bma12g00294 . Cmo11g01426 . . . . Sed05g2635 Cpe04g00332 . Bhi05g01014 Tan02g1036 Cmetu01g1272 Lac12g0154 Hepe02g0660 . . . . . . . . . . . . Cone10ag1055 . Csa07g00674 . Cme01g00131 . . . . . . . . . . . Cma11g01694 . Car11g01149 . . . . . . . . . . . . . . . . . . . Chy01g00141 .
Vvi3g728 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g729 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g730 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g731 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g732 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g733 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g734 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g735 . Blo03g00064 Bda06g01175 . Bpe07g00288 . . Bma12g00295 Cmo19g00556 Cmo11g01427 . . . . . Cpe04g00333 . . . . . . . . Cla02g00695 Cam02g0728 Cec02g0743 Cco02g0767 Clacu02g0739 Cmu02g0734 Cre02g1047 . Cone8ag1071 Cone3ag1040 . . Csa07g00673 . Cme01g00132 . . . . . . . . . . . Cma11g01693 Cma19g00542 Car11g01150 Car19g00399 . . . . . . . . . . . . . . . . . . Chy01g00142 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 41170785 41175600 + Bda022983.1 Bda06g01175 1175
6 41176943 41177457 + Bda022984.1 Bda06g01176 1176
6 41199874 41200263 - Bda022987.1 Bda06g01178 1178
8 7262200 7262631 - Bda029138.1 Bda08g00682 682
5 36218393 36220883 + XM_039031512.1 Bhi05g01014 1014
11 32675637 32677467 - XM_039049288.1 Bhi11g01120 1120
3 2282535 2286239 + BLOR11245 Blo03g00064 64
3 2293986 2294505 + BLOR11246 Blo03g00065 65
12 4131204 4131590 + Bma007198.1 Bma12g00293 293
12 4170526 4171041 - Bma007200.1 Bma12g00294 294
12 4172559 4175923 - Bma007201.1 Bma12g00295 295
7 2068577 2069324 + Bpe021095.1 Bpe07g00286 286
7 2076204 2076718 - Bpe021096.1 Bpe07g00287 287
7 2078333 2081725 - Bpe021097.1 Bpe07g00288 288
2 8800409 8805043 - CaPI482276_02g007280.1 Cam02g0728 728
10 22061959 22062881 - CaPI482276_10g009920.1 Cam10g0992 992
11 9217506 9218094 - Carg23043-RA Car11g01149 1149
11 9219259 9222861 - Carg23044-RA Car11g01150 1150
19 5901130 5905045 + Carg16320-RA Car19g00399 399
2 8113785 8118378 - CcPI632755_02g007670.1 Cco02g0767 767
10 21267859 21268768 - CcPI632755_10g009840.1 Cco10g0984 984
2 8076644 8081279 - CePI673135_02g007430.1 Cec02g0743 743
10 22937084 22937996 - CePI673135_10g010220.1 Cec10g1022 1022
1 963792 964817 - Chy1G001410.1 Chy01g00141 141
1 965737 967348 - Chy1G001420.1 Chy01g00142 142
2 7807272 7811898 - ClG42_02g0073900.10 Clacu02g0739 739
10 21727227 21728146 - ClG42_10g0101200.10 Clacu10g1012 1012
2 8172424 8177482 - ClCG02G007110.1 Cla02g00695 695
10 22725665 22727418 - ClCG10G010090.2 Cla10g00968 968
11 11177026 11180703 + CmaCh11G016930.1 Cma11g01693 1693
11 11181777 11182522 + CmaCh11G016940.1 Cma11g01694 1694
19 6234736 6236640 + CmaCh19G005420.1 Cma19g00542 542
1 948876 950586 - MELO3C018528.2.1 Cme01g00131 131
1 951607 955779 - MELO3C018529.2.1 Cme01g00132 132
7 26280093 26281972 + MELO3C018019.2.1 Cme07g02203 2203
1 1105527 1107422 - PI0023348.1 Cmetu01g1272 1272
7 318950 320621 - PI0026788.1 Cmetu07g0418 418
4 2336398 2338168 - CmoCh04G004690.1 Cmo04g00469 469
11 10047861 10048707 - CmoCh11G014260.1 Cmo11g01426 1426
11 10049721 10053375 - CmoCh11G014270.1 Cmo11g01427 1427
16 1499033 1500458 - CmoCh16G003290.1 Cmo16g00329 329
19 6400264 6404335 + CmoCh19G005560.1 Cmo19g00556 556
2 7715367 7719990 - CmPI595203_02g007340.1 Cmu02g0734 734
10 22337488 22338407 - CmPI595203_10g017970.1 Cmu10g1797 1797
3 29205593 29206414 + Conep03aG0153900.1 Cone3ag1038 1038
3 29212260 29215372 - Conep03aG0154100.1 Cone3ag1040 1040
8 9710444 9711946 + Conep08aG0110000.1 Cone8ag1071 1071
10 7331601 7332479 + Conep10aG0108100.1 Cone10ag1054 1054
10 7344763 7346114 - Conep10aG0108200.1 Cone10ag1055 1055
1 2271022 2272106 - Cp4.1LG01g02770.1 Cpe01g00392 392
4 4075090 4075934 - Cp4.1LG04g07370.1 Cpe04g00332 332
4 4076562 4080749 - Cp4.1LG04g07410.1 Cpe04g00333 333
14 1483296 1485056 - Cp4.1LG14g04510.1 Cpe14g00258 258
2 8353547 8358171 - CrPI670011_02g010470.1 Cre02g1047 1047
10 23990465 23991375 - CrPI670011_10g011690.1 Cre10g1169 1169
7 4805859 4807449 + CsaV3_7G007720.1 Csa07g00673 673
7 4808561 4810245 + CsaV3_7G007730.1 Csa07g00674 674
2 7072612 7074892 - Hsped.02g06600.1 Hepe02g0660 660
12 1707613 1709613 + Lag0014526.1 Lac12g0154 154
3 19426223 19427621 - Lsi03G010100.1 Lsi03g01010 1010
10 2731094 2731892 - MC10g0342 Mch10g0415 415
5 37933193 37935082 - Sed0007395.1 Sed05g2635 2635
7 9339662 9341098 - Sed0020406.2 Sed07g1252 1252
1 5701664 5703815 - Tan0019942.1 Tan01g0616 616
2 15614369 15617208 - Tan0016091.1 Tan02g1036 1036
3 7704337 7705956 + Vvi3g726 Vvi3g726 726
3 7710714 7711709 - Vvi3g727 Vvi3g727 727
3 7716201 7726782 - Vvi3g728 Vvi3g728 728
3 7739420 7741910 - Vvi3g729 Vvi3g729 729
3 7741935 7749302 - Vvi3g730 Vvi3g730 730
3 7759652 7762665 + Vvi3g731 Vvi3g731 731
3 7771296 7774507 - Vvi3g732 Vvi3g732 732
3 7813666 7818295 - Vvi3g733 Vvi3g733 733
3 7826668 7826884 - Vvi3g734 Vvi3g734 734
3 7831769 7853146 - Vvi3g735 Vvi3g735 735
       

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