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
Vvi18g1160 . . . . Bpe02g00337 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma12g00389 . . . Cpe11g00272 . . . . . . . . . . . . . . . . . . .
Vvi18g1161 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1162 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1163 . . . . . . . . . . . . . . . . . Bhi04g00111 . . . . . . . . . . . . . . Cone7ag1905 . . . . . . Blo17g00738 Blo18g00770 Bda08g01208 Bda01g01542 Bpe02g01739 Bpe05g00151 . Bma05g00182 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1164 . . . Bda03g00294 . Bpe04g00254 Bma04g00254 . . . . . . Car12g00369 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1165 Blo01g01610 . Bda01g00472 . Bpe02g00336 . . Bma01g02383 . . . Cma09g00091 . . . Cpe06g00054 . . . . . . . . . . . . . . . . . . . Lsi04g01764 Csa03g04296 Chy04g00401 . . . . . . . . . . . Cmo09g00090 . . . Car09g00079 . . Bhi09g02070 . . . Hepe01g1601 Mch11g0100 . . . . . . . . . . . .
Vvi18g1166 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1167 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe05g00152 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1168 . Blo12g00877 . Bda03g00295 . . Bma04g00255 . . . Cma01g01985 . Car01g01556 . . . . . . . . . . . . . . . . . . . Cone7ag1906 Cone17ag1422 Cone20ag0060 Lsi04g01766 Csa03g04297 Chy04g00400 . . . Bda08g01199 Bda01g01544 Bpe02g01740 Bpe05g00153 . Bma05g00183 Sed13g1555 Cmo01g02043 . . . . . . Cpe02g00060 Bhi09g02069 Tan01g5044 Cmetu04g1063 . . Mch11g0099 . . . . . . . . . . . Cme04g00449
Vvi18g1169 . . . . . . . . . . Cma01g01986 . Car01g01557 . . . . . . . . . . . . . . . . . . . . . . Lsi04g01768 Csa03g04299 Chy04g00399 . Blo17g00729 . Bda08g01193 . . . . Bma05g00184 Sed01g3759 Cmo01g02044 . . . . . . Cpe02g00059 Bhi09g02067 Tan01g5046 Cmetu04g0271 . Hepe01g1598 Mch11g0098 . . . . . . . . . . . Cme04g00447
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 31796977 31799785 + Bda002473.1 Bda01g00472 472
1 51334203 51336109 + Bda003807.1 Bda01g01542 1542
1 51339071 51342229 - Bda003809.1 Bda01g01544 1544
3 2610458 2611916 + Bda033481 Bda03g00294 294
3 2614677 2618366 - Bda016253.1 Bda03g00295 295
8 48038839 48040108 - Bda030145.1 Bda08g01193 1193
8 48720726 48722552 - Bda030160.1 Bda08g01199 1199
8 49561213 49563217 - Bda030188.1 Bda08g01208 1208
4 2993239 2997483 + XM_039028135.1 Bhi04g00111 111
9 58970747 58973728 - XM_039044117.1 Bhi09g02067 2067
9 59071697 59077038 + XM_039042001.1 Bhi09g02069 2069
9 59096732 59102803 + XM_039040470.1 Bhi09g02070 2070
1 55990548 56001759 - BLOR01610 Blo01g01610 1610
12 26973872 26977568 + BLOR04896 Blo12g00877 877
17 22228439 22232313 + BLOR08275 Blo17g00729 729
17 22673484 22688378 - BLOR08284 Blo17g00738 738
18 21749367 21751281 - BLOR09258 Blo18g00770 770
1 81441380 81444096 - Bma003254.1 Bma01g02383 2383
4 2155932 2157161 + Bma018706.1 Bma04g00254 254
4 2160032 2163599 - Bma018707.1 Bma04g00255 255
5 5119900 5131225 + Bma020908.2 Bma05g00182 182
5 5137688 5140783 - Bma020909.1 Bma05g00183 183
5 5157125 5158540 + Bma020910.1 Bma05g00184 184
2 2194518 2197330 + Bpe008177.1 Bpe02g00336 336
2 2197541 2199276 - Bpe008178.1 Bpe02g00337 337
2 19796947 19800325 + Bpe009570.1 Bpe02g01739 1739
2 19801897 19805013 - Bpe009571.1 Bpe02g01740 1740
4 1696325 1697768 + Bpe014967.1 Bpe04g00254 254
5 4360817 4362728 + Bpe017538.1 Bpe05g00151 151
5 4372289 4373078 - Bpe017539.1 Bpe05g00152 152
5 4380409 4382835 - Bpe017540.1 Bpe05g00153 153
1 12994787 12999248 - Carg17211-RA Car01g01556 1556
1 13001709 13003868 + Carg17212-RA Car01g01557 1557
9 398345 401449 + Carg08662-RA Car09g00079 79
12 2357661 2360213 + Carg03976-RA Car12g00369 369
4 3533198 3535934 - Chy4G071170.1 Chy04g00399 399
4 3555101 3559317 + Chy4G071180.1 Chy04g00400 400
4 3564610 3569623 + Chy4G071190.1 Chy04g00401 401
1 12768388 12773070 - CmaCh01G019850.1 Cma01g01985 1985
1 12775567 12777637 + CmaCh01G019860.1 Cma01g01986 1986
9 398986 402326 + CmaCh09G000910.1 Cma09g00091 91
12 2010444 2012883 + CmaCh12G003890.1 Cma12g00389 389
4 3546623 3549664 - MELO3C003735.2.1 Cme04g00447 447
4 3571633 3576714 + MELO3C003736.2.1 Cme04g00449 449
4 29806761 29809852 + PI0011918.1 Cmetu04g0271 271
4 29786340 29790768 - PI0008659.1 Cmetu04g1063 1063
1 14309021 14313597 - CmoCh01G020430.1 Cmo01g02043 2043
1 14317207 14319394 + CmoCh01G020440.1 Cmo01g02044 2044
9 416229 419837 + CmoCh09G000900.1 Cmo09g00090 90
7 12210370 12211819 + Conep07aG0196200.1 Cone7ag1905 1905
7 12214154 12218731 - Conep07aG0196300.1 Cone7ag1906 1906
17 9741583 9745483 - Conep17aG0146000.1 Cone17ag1422 1422
20 288760 290999 + Conep20aG0006200.1 Cone20ag0060 60
2 305614 307911 - Cp4.1LG02g08130.1 Cpe02g00059 59
2 309296 313832 + Cp4.1LG02g08190.1 Cpe02g00060 60
6 275921 279755 + Cp4.1LG06g00390.1 Cpe06g00054 54
11 1463381 1465303 - Cp4.1LG11g02690.1 Cpe11g00272 272
3 37610482 37616661 - CsaV3_3G046020.1 Csa03g04296 4296
3 37620313 37625573 - CsaV3_3G046030.1 Csa03g04297 4297
3 37636221 37639388 + CsaV3_3G046050.1 Csa03g04299 4299
1 81270372 81272759 - Hsped.01g15980.1 Hepe01g1598 1598
1 81294671 81295285 + Hsped.01g16010.1 Hepe01g1601 1601
4 24883208 24887993 - Lsi04G017640.1 Lsi04g01764 1764
4 24898911 24903998 - Lsi04G017660.1 Lsi04g01766 1766
4 24917137 24921450 + Lsi04G017680.1 Lsi04g01768 1768
11 637420 640172 - MC11g0087 Mch11g0098 98
11 648260 655490 + MC11g0088 Mch11g0099 99
11 658316 663793 + MC11g0089 Mch11g0100 100
1 66687275 66691941 + Sed0018975.2 Sed01g3759 3759
13 20761146 20764546 + Sed0024981.1 Sed13g1555 1555
1 115999466 116006249 - Tan0021668.1 Tan01g5044 5044
1 116044690 116048143 + Tan0008166.1 Tan01g5046 5046
18 12863065 12871523 + Vvi18g1160 Vvi18g1160 1160
18 12879998 12882177 - Vvi18g1161 Vvi18g1161 1161
18 12887373 12890186 - Vvi18g1162 Vvi18g1162 1162
18 12893669 12898468 + Vvi18g1163 Vvi18g1163 1163
18 12900788 12904974 + Vvi18g1164 Vvi18g1164 1164
18 12908877 12912473 - Vvi18g1165 Vvi18g1165 1165
18 12914011 12933737 - Vvi18g1166 Vvi18g1166 1166
18 12936463 12938187 - Vvi18g1167 Vvi18g1167 1167
18 12941201 12948404 - Vvi18g1168 Vvi18g1168 1168
18 12954357 12956416 + Vvi18g1169 Vvi18g1169 1169
       

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