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
Vvi2g142 . . Bda06g00150 . . Bpe07g00068 . . . . . . . . . Cpe14g00458 . . . . . . . . Cla07g01097 Cam07g1401 . Cco07g1239 . Cmu07g1140 . . . . . . . . . . . . . . . . Bma12g00611 . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00665 Chy07g01147 .
Vvi2g143 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g144 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g145 Blo02g01152 Blo03g00251 Bda06g00151 Bda08g00463 Bpe05g00696 Bpe07g00067 . . . . Cma02g00928 . Car02g00677 . . Cpe14g00457 . . . . . . . . Cla07g01096 Cam07g1402 Cec07g1259 Cco07g1236 Clacu07g1160 Cmu07g1139 Cre07g1520 . . Cone6ag0856 Cone9ag0858 . . . . . . . . . . Bma05g00878 Bma12g00612 . Cmo02g00937 . . . . . . . . . . . . . . . . . . . . . . Csa04g00666 Chy07g01146 .
Vvi2g146 . . Bda06g00152 Bda08g00462 Bpe05g00697 Bpe07g00066 . . . . . . . . . Cpe14g00456 . . . . . . . . Cla07g01094 . Cec07g1258 Cco07g1235 . . Cre07g1519 . . Cone6ag0857 Cone9ag0859 . . . Cme07g01570 . . . . . . Bma05g00879 Bma12g00613 . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00667 Chy07g01144 .
Vvi2g147 . . . . . . . . . Cmo16g00593 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme07g01568 . . . . . . Bma05g00880 . . . . . Cma16g00541 . . . . . . . . . . . . . . . . . . . . . .
Vvi2g148 . Blo03g00254 Bda06g00153 . Bpe05g00698 Bpe07g00257 . . . . . . Car02g00675 . . . . . . . . . . . . . . . . . . Cone8ag0240 . . . . . . . . . . . . . Bma05g00882 . . Cmo02g00935 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g149 Blo02g01154 Blo03g00256 . . Bpe05g00700 Bpe07g00063 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0859 Cone9ag0861 . . . . . . . . . . Bma05g00884 Bma12g00263 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g150 Blo02g01157 . . . Bpe05g00701 . . . . Cmo16g00592 . . . . . Cpe14g00455 . . . . . . . . Cla07g01093 Cam07g1405 Cec07g1256 Cco07g1233 Clacu07g1158 Cmu07g1137 Cre07g1517 . . . Cone9ag0862 . . . . . . . . . . Bma05g00885 . . . . . Cma16g00540 . . . . . . . . . . . . . . . . . . . . Chy07g01142 .
Vvi2g151 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda07g01932 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 2211573 2216463 + Bda023352.1 Bda06g00150 150
6 2218264 2222152 + Bda023353.1 Bda06g00151 151
6 2223738 2228350 + Bda023354.1 Bda06g00152 152
6 2249597 2250906 + Bda023355.1 Bda06g00153 153
7 36827367 36828632 - Bda033998 Bda07g01932 1932
8 4819488 4823854 - Bda033806 Bda08g00462 462
8 4825635 4827421 - Bda024914.1 Bda08g00463 463
2 43148301 43167190 + BLOR10882 Blo02g01152 1152
2 43170024 43172145 - BLOR10884 Blo02g01154 1154
2 43191993 43193900 + BLOR10887 Blo02g01157 1157
3 5367150 5385080 + BLOR11432 Blo03g00251 251
3 5437209 5442921 + BLOR11435 Blo03g00254 254
3 5445453 5447409 - BLOR11437 Blo03g00256 256
5 46494159 46497551 + Bma022001.1 Bma05g00878 878
5 46509099 46513454 + Bma031213 Bma05g00879 879
5 46589807 46593148 + Bma031214 Bma05g00880 880
5 46605307 46606728 + Bma031216 Bma05g00882 882
5 46609627 46611719 - Bma022003.5 Bma05g00884 884
5 46612118 46616318 + Bma031218 Bma05g00885 885
12 3473160 3489788 + Bma007157.2 Bma12g00263 263
12 27421915 27426803 + Bma007788.3 Bma12g00611 611
12 27429194 27432773 + Bma007789.1 Bma12g00612 612
12 27434445 27438983 + Bma007790.2 Bma12g00613 613
5 20583964 20587701 + Bpe018109.1 Bpe05g00696 696
5 20589179 20593491 + Bpe018110.1 Bpe05g00697 697
5 20595755 20597178 + Bpe018111.1 Bpe05g00698 698
5 20599967 20602050 - Bpe018113.1 Bpe05g00700 700
5 20604374 20606536 + Bpe018114.1 Bpe05g00701 701
7 493606 495697 + Bpe020875.1 Bpe07g00063 63
7 501488 506123 - Bpe020878.1 Bpe07g00066 66
7 507464 511265 - Bpe020879.1 Bpe07g00067 67
7 512669 517821 - Bpe020880.1 Bpe07g00068 68
7 1856659 1858958 + Bpe021069.1 Bpe07g00257 257
7 28535515 28542385 + CaPI482276_07g014010.1 Cam07g1401 1401
7 28550530 28554988 + CaPI482276_07g014020.1 Cam07g1402 1402
7 28571600 28573614 + CaPI482276_07g014050.1 Cam07g1405 1405
2 5042119 5044483 - Carg08548-RA Car02g00675 675
2 5054038 5058250 + Carg08546-RA Car02g00677 677
7 26220086 26222131 - CcPI632755_07g012330.1 Cco07g1233 1233
7 26229918 26236142 - CcPI632755_07g012350.1 Cco07g1235 1235
7 26238840 26243311 - CcPI632755_07g012360.1 Cco07g1236 1236
7 26256541 26262386 - CcPI632755_07g012390.1 Cco07g1239 1239
7 28076216 28078223 - CePI673135_07g012560.1 Cec07g1256 1256
7 28086076 28092194 - CePI673135_07g012580.1 Cec07g1258 1258
7 28094946 28099375 - CePI673135_07g012590.1 Cec07g1259 1259
7 16342375 16347415 - Chy7G139720.1 Chy07g01142 1142
7 16354073 16359598 - Chy7G139740.1 Chy07g01144 1144
7 16361517 16365511 - Chy7G139760.1 Chy07g01146 1146
7 16365603 16378281 - Chy7G139770.1 Chy07g01147 1147
7 26244958 26246969 - ClG42_07g0115800.10 Clacu07g1158 1158
7 26254732 26267992 - ClG42_07g0116000.10 Clacu07g1160 1160
7 27629710 27631721 - ClCG07G011520.2 Cla07g01093 1093
7 27634422 27646429 - ClCG07G011540.2 Cla07g01094 1094
7 27648478 27653495 - ClCG07G011550.2 Cla07g01096 1096
7 27661214 27668473 - ClCG07G011560.2 Cla07g01097 1097
2 5523267 5527316 + CmaCh02G009280.1 Cma02g00928 928
16 2759104 2769507 - CmaCh16G005400.1 Cma16g00540 540
16 2769550 2783030 - CmaCh16G005410.1 Cma16g00541 541
7 21516858 21521108 + MELO3C016300.2.1 Cme07g01568 1568
7 21522889 21529052 + MELO3C016301.2.1 Cme07g01570 1570
2 5736911 5738625 - CmoCh02G009350.1 Cmo02g00935 935
2 5743472 5748456 + CmoCh02G009370.1 Cmo02g00937 937
16 2858975 2869570 - CmoCh16G005920.1 Cmo16g00592 592
16 2870211 2884508 - CmoCh16G005930.1 Cmo16g00593 593
7 26487807 26489818 - CmPI595203_07g011370.1 Cmu07g1137 1137
7 26493283 26510807 - CmPI595203_07g011390.1 Cmu07g1139 1139
7 26519214 26525842 - CmPI595203_07g011400.1 Cmu07g1140 1140
6 4371206 4375392 + Conep06aG0088300.1 Cone6ag0856 856
6 4375968 4381242 + Conep06aG0088400.1 Cone6ag0857 857
6 4385775 4386846 - Conep06aG0088600.1 Cone6ag0859 859
8 1371464 1373760 - Conep08aG0024900.1 Cone8ag0240 240
9 4189143 4192922 + Conep09aG0087900.1 Cone9ag0858 858
9 4193511 4198874 + Conep09aG0088000.1 Cone9ag0859 859
9 4202309 4205100 - Conep09aG0088200.1 Cone9ag0861 861
9 4205878 4207811 - Conep09aG0088300.1 Cone9ag0862 862
14 2860042 2863064 - Cp4.1LG14g02600.1 Cpe14g00455 455
14 2864059 2875197 - Cp4.1LG14g02670.1 Cpe14g00456 456
14 2875980 2881476 - Cp4.1LG14g02610.1 Cpe14g00457 457
14 2882514 2889861 - Cp4.1LG14g02650.1 Cpe14g00458 458
7 30450717 30452749 - CrPI670011_07g015170.1 Cre07g1517 1517
7 30455819 30466522 - CrPI670011_07g015190.1 Cre07g1519 1519
7 30469241 30473688 - CrPI670011_07g015200.1 Cre07g1520 1520
4 4466494 4473509 + CsaV3_4G006650.1 Csa04g00665 665
4 4479124 4483827 + CsaV3_4G006660.1 Csa04g00666 666
4 4484581 4492271 + CsaV3_4G006670.1 Csa04g00667 667
2 1464113 1471910 - Vvi2g142 Vvi2g142 142
2 1473461 1474469 + Vvi2g143 Vvi2g143 143
2 1482107 1488349 + Vvi2g144 Vvi2g144 144
2 1500920 1506241 + Vvi2g145 Vvi2g145 145
2 1509183 1518615 - Vvi2g146 Vvi2g146 146
2 1521768 1530974 - Vvi2g147 Vvi2g147 147
2 1532066 1535757 + Vvi2g148 Vvi2g148 148
2 1560082 1563272 - Vvi2g149 Vvi2g149 149
2 1570282 1576084 + Vvi2g150 Vvi2g150 150
2 1576332 1578897 - Vvi2g151 Vvi2g151 151
       

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