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
Vvi2g332 . . . Bda08g00363 . . . . . . Cma02g01017 Cma15g01389 Car02g00762 Car15g01252 . . Cpe05g00704 . . . . . . . . . . . . . . . . Cone6ag0771 . . . . . . . . . . . Bma05g00816 Bma12g00167 . . Cmo15g01454 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g333 Blo02g01106 . . Bda08g00522 Bpe05g00640 . . . . Cmo16g00640 . . . . . Cpe14g00502 . . . . . . . . Cla07g00766 Cam07g0822 Cec07g0880 Cco07g0857 Clacu07g0801 Cmu07g0806 Cre07g1161 . . . Cone9ag0776 . . . Cme07g01625 . . . . . . Bma05g00815 . . . . . Cma16g00590 . . . . . . . . . . . . . . . . . . . Csa04g00600 Chy07g01212 .
Vvi2g334 . . . . Bpe05g00417 . . . . . Cma02g01462 . Car02g01227 . . . Cpe05g00327 . . . . . . . . . . . . . . . . . . . Csa05g00291 Chy09g01215 . . Blo19g00320 . . . . . . . Cmo02g01497 . . . . . . . . . . . . . . Cla01g00273 Cam01g0282 Cec01g0274 Cco01g0289 Clacu01g0281 Cmu01g0269 Cre09g2239 Lsi09g00270 . . Cme09g01752
Vvi2g335 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi12g00240 . . . . . Lcy12g1661 . . . . . . . . . . .
Vvi2g336 . . . . . . . Bma14g00071 . . Cma02g01464 . Car02g01229 . . . Cpe05g00325 . . . . . . . . . . . . . . . . . Cone9ag0773 . Csa05g00293 Chy09g01213 . Blo03g00336 . . . . . . . . Cmo02g01499 . . . . . . . Bhi12g00238 . . Lac11g2107 Hepe06g1557 . Lcy12g1663 Cla01g00275 Cam01g0285 Cec01g0278 Cco01g0291 Clacu01g0284 Cmu01g0271 Cre09g2237 Lsi09g00272 . . Cme09g01750
Vvi2g337 . Blo03g00210 Bda06g00086 . . Bpe07g00113 . . . . . . . . . . Cpe05g00324 . . . . . . . . . . . . . . . . . Cone9ag0772 . Csa05g00294 Chy09g01212 . . . . . . . . Bma12g00086 . . . . . . . . . Bhi12g00237 . . . . . . . . . . . . . Lsi09g00273 . . Cme09g01749
Vvi2g338 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g339 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g340 . . . . . . . Bma14g00617 . . Cma02g01465 Cma15g01219 . Car15g01099 . . Cpe05g00323 . . . . . . . . . . . . . . Cone8ag0314 Cone12ag0314 . . . Csa05g00295 Chy09g01211 . Blo03g00335 . . . . Bpe11g00652 . . . Cmo02g01502 Cmo15g01284 . . . . . Cpe13g00161 Bhi12g00235 . . Lac11g2109 . . Lcy12g1665 Cla01g00276 Cam01g0286 Cec01g0279 Cco01g0292 Clacu01g0285 Cmu01g0272 Cre09g2235 . . . Cme09g01748
Vvi2g341 . . Bda06g00084 . . Bpe07g00114 . . . Cmo16g01091 Cma02g01466 Cma15g01218 Car02g01230 Car15g01098 . Cpe14g00501 Cpe05g00322 . . . . . . . Cla07g00765 . . . . . . Cone8ag0315 . . Cone9ag0768 . Csa05g00296 Chy09g01210 Cme07g01624 . . . . . . . . . Cmo02g01503 Cmo15g01283 . Cma16g00589 . . . Cpe13g00162 Bhi12g00234 . . . . . . Cla01g00277 . . . . . . Lsi09g00275 Csa04g00601 Chy07g01211 Cme09g01747
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 836131 839875 + Bda023257.1 Bda06g00084 84
6 841375 843194 - Bda023259.1 Bda06g00086 86
8 3718709 3731298 - Bda024804.2 Bda08g00363 363
8 5246720 5249011 + Bda024977.1 Bda08g00522 522
12 7490495 7495239 + XM_039050542.1 Bhi12g00234 234
12 7495851 7499709 - XM_039019945.1 Bhi12g00235 235
12 7502913 7523659 - XM_039019223.1 Bhi12g00237 237
12 7542439 7545245 - XM_039018843.1 Bhi12g00238 238
12 7597760 7607250 + XM_039050784.1 Bhi12g00240 240
2 42052326 42058355 - BLOR10836 Blo02g01106 1106
3 4858742 4862013 - BLOR11391 Blo03g00210 210
3 7124844 7127710 + BLOR11516 Blo03g00335 335
3 7137070 7140099 - BLOR11517 Blo03g00336 336
19 20753187 20762592 - BLOR09663 Blo19g00320 320
5 45460686 45462981 - Bma021919.1 Bma05g00815 815
5 45465422 45468409 + Bma021920.1 Bma05g00816 816
12 1558771 1560647 + Bma030491 Bma12g00086 86
12 2295864 2297192 - Bma007049.1 Bma12g00167 167
14 875393 877978 + Bma010475.1 Bma14g00071 71
14 6671438 6674240 - Bma011057.1 Bma14g00617 617
5 18554382 18574703 - Bpe017835.1 Bpe05g00417 417
5 20225130 20227430 - Bpe018056.1 Bpe05g00640 640
7 817808 819580 + Bpe020926.1 Bpe07g00113 113
7 821107 824697 - Bpe020927.3 Bpe07g00114 114
11 5016758 5019708 + Bpe004008.1 Bpe11g00652 652
1 3139909 3147417 - CaPI482276_01g002820.1 Cam01g0282 282
1 3198608 3205734 + CaPI482276_01g002850.1 Cam01g0285 285
1 3207020 3209803 + CaPI482276_01g002860.1 Cam01g0286 286
7 20616135 20621674 - CaPI482276_07g008220.1 Cam07g0822 822
2 5566247 5567737 + Carg08460-RA Car02g00762 762
2 8306662 8311153 - Carg02521-RA Car02g01227 1227
2 8315583 8324673 + Carg02519-RA Car02g01229 1229
2 8324649 8328757 - Carg02518-RA Car02g01230 1230
15 8653942 8658108 + Carg16644-RA Car15g01098 1098
15 8658060 8661450 - Carg16643-RA Car15g01099 1099
15 9766582 9768060 + Carg20790-RA Car15g01252 1252
1 2778041 2785540 - CcPI632755_01g002890.1 Cco01g0289 289
1 2840711 2842720 + CcPI632755_01g002910.1 Cco01g0291 291
1 2843848 2854050 + CcPI632755_01g002920.1 Cco01g0292 292
7 19885272 19890571 - CcPI632755_07g008570.1 Cco07g0857 857
1 2750086 2757481 - CePI673135_01g002740.1 Cec01g0274 274
1 2812028 2817899 + CePI673135_01g002780.1 Cec01g0278 278
1 2819459 2822242 + CePI673135_01g002790.1 Cec01g0279 279
7 21753857 21762394 - CePI673135_07g008800.1 Cec07g0880 880
7 16928563 16932589 + Chy7G140410.1 Chy07g01211 1211
7 16934657 16936985 - Chy7G140420.1 Chy07g01212 1212
9 14237132 14241195 + Chy9G169260.1 Chy09g01210 1210
9 14242249 14245382 - Chy9G169270.1 Chy09g01211 1211
9 14246759 14259386 - Chy9G169280.1 Chy09g01212 1212
9 14259472 14261455 - Chy9G169290.1 Chy09g01213 1213
9 14271972 14277355 + Chy9G169310.1 Chy09g01215 1215
1 2755620 2763083 - ClG42_01g0028100.10 Clacu01g0281 281
1 2827294 2832707 + ClG42_01g0028400.10 Clacu01g0284 284
1 2834036 2836817 + ClG42_01g0028500.10 Clacu01g0285 285
7 20331222 20337694 - ClG42_07g0080100.10 Clacu07g0801 801
1 2823528 2831925 - ClCG01G002820.2 Cla01g00273 273
1 2893647 2902117 + ClCG01G002840.2 Cla01g00275 275
1 2903398 2906357 + ClCG01G002860.1 Cla01g00276 276
1 2907211 2911668 - ClCG01G002870.1 Cla01g00277 277
7 21437950 21443446 + ClCG07G008030.2 Cla07g00765 765
7 21445627 21448681 - ClCG07G008040.1 Cla07g00766 766
2 6040691 6042175 + CmaCh02G010170.1 Cma02g01017 1017
2 8390166 8394571 - CmaCh02G014620.1 Cma02g01462 1462
2 8398833 8404680 + CmaCh02G014640.1 Cma02g01464 1464
2 8405321 8408455 + CmaCh02G014650.1 Cma02g01465 1465
2 8408336 8412318 - CmaCh02G014660.1 Cma02g01466 1466
15 7708693 7712999 + CmaCh15G012180.1 Cma15g01218 1218
15 7713149 7716392 - CmaCh15G012190.1 Cma15g01219 1219
15 8705850 8707334 + CmaCh15G013890.1 Cma15g01389 1389
16 3049601 3054878 + CmaCh16G005890.1 Cma16g00589 589
16 3054792 3058033 - CmaCh16G005900.1 Cma16g00590 590
7 22018419 22023071 + MELO3C016348.2.1 Cme07g01624 1624
7 22024841 22027473 - MELO3C016349.2.1 Cme07g01625 1625
9 21987251 21991965 + MELO3C005660.2.1 Cme09g01747 1747
9 21992503 21995901 - MELO3C005661.2.1 Cme09g01748 1748
9 21996815 22002512 - MELO3C005662.2.1 Cme09g01749 1749
9 22002747 22005182 - MELO3C005663.2.1 Cme09g01750 1750
9 22014667 22020617 + MELO3C005665.2.1 Cme09g01752 1752
2 8752694 8757356 - CmoCh02G014970.1 Cmo02g01497 1497
2 8761414 8767112 + CmoCh02G014990.1 Cmo02g01499 1499
2 8767695 8770525 + CmoCh02G015020.1 Cmo02g01502 1502
2 8770598 8774661 - CmoCh02G015030.1 Cmo02g01503 1503
15 8787987 8792175 + CmoCh15G012830.1 Cmo15g01283 1283
15 8792262 8795559 - CmoCh15G012840.1 Cmo15g01284 1284
15 9863011 9864489 + CmoCh15G014540.1 Cmo15g01454 1454
16 3156791 3160796 - CmoCh16G006400.1 Cmo16g00640 640
16 7707301 7710686 - CmoCh16G010910.1 Cmo16g01091 1091
1 2708457 2715932 - CmPI595203_01g002690.1 Cmu01g0269 269
1 2780406 2788877 + CmPI595203_01g002710.1 Cmu01g0271 271
1 2790206 2792988 + CmPI595203_01g002720.1 Cmu01g0272 272
7 20545274 20551729 - CmPI595203_07g008060.1 Cmu07g0806 806
6 3934770 3936515 + Conep06aG0079400.1 Cone6ag0771 771
8 1817251 1820189 + Conep08aG0032900.1 Cone8ag0314 314
8 1820271 1824122 - Conep08aG0033000.1 Cone8ag0315 315
9 3680827 3685069 + Conep09aG0078500.1 Cone9ag0768 768
9 3693965 3694615 - Conep09aG0078900.1 Cone9ag0772 772
9 3698762 3701308 - Conep09aG0079000.1 Cone9ag0773 773
9 3714542 3716478 - Conep09aG0079300.1 Cone9ag0776 776
12 1722709 1725533 + Conep12aG0032900.1 Cone12ag0314 314
5 1800943 1804944 + Cp4.1LG05g03560.1 Cpe05g00322 322
5 1804208 1810278 - Cp4.1LG05g03390.1 Cpe05g00323 323
5 1810926 1813913 - Cp4.1LG05g03450.1 Cpe05g00324 324
5 1814105 1816747 - Cp4.1LG05g03430.1 Cpe05g00325 325
5 1821319 1825901 + Cp4.1LG05g03530.1 Cpe05g00327 327
5 4321846 4323336 - Cp4.1LG05g07000.1 Cpe05g00704 704
13 1212735 1217374 + Cp4.1LG13g01590.1 Cpe13g00161 161
13 1215502 1220699 - Cp4.1LG13g01660.1 Cpe13g00162 162
14 3173175 3180411 + Cp4.1LG14g02190.1 Cpe14g00501 501
14 3178225 3182803 - Cp4.1LG14g02050.1 Cpe14g00502 502
7 23884971 23888470 - CrPI670011_07g011610.1 Cre07g1161 1161
9 41520935 41523719 - CrPI670011_09g022350.1 Cre09g2235 2235
9 41532277 41534269 - CrPI670011_09g022370.1 Cre09g2237 2237
9 41571191 41578586 + CrPI670011_09g022390.1 Cre09g2239 2239
4 3958161 3961178 + CsaV3_4G006000.1 Csa04g00600 600
4 3962571 3967211 - CsaV3_4G006010.1 Csa04g00601 601
5 1823864 1829914 - CsaV3_5G002910.1 Csa05g00291 291
5 1839970 1841916 + CsaV3_5G002930.1 Csa05g00293 293
5 1844415 1854863 + CsaV3_5G002940.1 Csa05g00294 294
5 1856096 1859659 + CsaV3_5G002950.1 Csa05g00295 295
5 1859980 1864879 - CsaV3_5G002960.1 Csa05g00296 296
6 66280576 66283166 + Hsped.06g15570.1 Hepe06g1557 1557
11 36993121 36995346 + Lag0032745.1 Lac11g2107 2107
11 37024201 37029305 + Lag0032747.1 Lac11g2109 2109
12 36995496 37005428 - Maker00029352 Lcy12g1661 1661
12 37040879 37044091 + Maker00029210 Lcy12g1663 1663
12 37063950 37068287 + Maker00029463 Lcy12g1665 1665
9 2813136 2836753 - Lsi09G002700.1 Lsi09g00270 270
9 2852650 2855307 + Lsi09G002720.1 Lsi09g00272 272
9 2862906 2873926 + Lsi09G002730.1 Lsi09g00273 273
9 2875086 2879594 - Lsi09G002750.1 Lsi09g00275 275
2 3144643 3153646 - Vvi2g332 Vvi2g332 332
2 3156562 3161990 + Vvi2g333 Vvi2g333 333
2 3162109 3184219 - Vvi2g334 Vvi2g334 334
2 3184221 3186776 - Vvi2g335 Vvi2g335 335
2 3194240 3196516 + Vvi2g336 Vvi2g336 336
2 3200565 3204790 + Vvi2g337 Vvi2g337 337
2 3205256 3205706 - Vvi2g338 Vvi2g338 338
2 3205705 3208737 - Vvi2g339 Vvi2g339 339
2 3210383 3214980 + Vvi2g340 Vvi2g340 340
2 3216346 3221693 - Vvi2g341 Vvi2g341 341
       

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