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
Vvi18g1040 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0834 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1041 Blo01g01583 . Bda01g00506 . Bpe02g00365 . . . Cmo05g00289 Cmo12g00380 Cma01g01945 . Car01g01519 Car12g00406 . . Cpe07g00385 Bhi04g00162 . . . . . . Cla08g01445 Cam08g1926 Cec08g1501 Cco08g1638 Clacu08g1616 . Cre08g1403 Cone4ag1948 . Cone17ag1378 Cone20ag0105 . . . Cme03g01907 . Blo18g00789 Bda08g01236 Bda01g01521 Bpe02g01717 Bpe05g00126 Bma01g00739 Bma05g00152 . Cmo01g02006 . Cma12g00429 Cma05g00283 . . Cpe11g00234 Cpe02g00094 . . . . . . . Cla11g00377 Cam11g0424 Cec11g0420 Cco11g0413 Clacu11g0546 Cmu11g0403 Cre11g0890 Lsi08g01348 Csa02g02104 Chy03g01411 .
Vvi18g1042 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla11g00372 Cam11g0417 Cec11g0413 Cco11g0406 Clacu11g0540 Cmu11g0397 Cre11g0884 . . . .
Vvi18g1043 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1044 . Blo12g00897 . . . Bpe04g00230 Bma04g00226 . . . Cma01g01947 . Car01g01521 . . . . . . . . . . . . . . . . . . . . Cone17ag1380 Cone20ag0103 Lsi04g01717 . . . . . . . . . . . . . . . . . . . Cpe02g00092 . . . . . . . Cla05g01899 Cam05g2035 Cec05g2043 Cco05g2099 Clacu05g2027 Cmu05g1907 Cre05g2029 . . . .
Vvi18g1045 Blo01g01584 Blo12g00896 Bda01g00505 Bda03g00276 . Bpe04g00231 . Bma01g02349 . . Cma01g01948 Cma09g00123 Car01g01522 . . Cpe06g00083 . . . . . . . . . . . . . . . Cone4ag1950 Cone7ag1862 Cone17ag1381 Cone20ag0101 Lsi04g01718 . . . . . . . . . . . . Cmo01g02008 Cmo09g00121 . . . Car09g00109 . Cpe02g00091 . . . . . . . Cla05g01897 Cam05g2033 Cec05g2042 Cco05g2098 Clacu05g2025 Cmu05g1905 Cre05g2028 . . . .
Vvi18g1046 . . . . . . . . Cmo05g00291 Cmo12g00378 . . . Car12g00404 . . Cpe07g00383 Bhi04g00228 . . . . . . Cla08g01443 Cam08g1924 Cec08g1499 Cco08g1635 Clacu08g1614 . Cre08g1400 . . Cone17ag1382 . . . . Cme03g01903 . Blo18g00788 . . . . Bma01g00738 . . . . Cma12g00427 Cma05g00285 Car05g00235 . Cpe11g00236 . . . . . . . . . . . . . . . Lsi08g01346 Csa02g02109 Chy03g01407 .
Vvi18g1047 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone17ag1384 Cone20ag0097 . . . . . Blo18g00787 . Bda01g01522 Bpe02g01719 . Bma01g00737 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1048 . . . . . . . . Cmo05g00292 Cmo12g00376 . . . Car12g00402 . . Cpe07g00381 Bhi04g00231 . . . Hepe10g0128 . . Cla08g01442 Cam08g1923 Cec08g1498 Cco08g1634 Clacu08g1613 . Cre08g1399 . . Cone17ag1385 Cone20ag0096 . . . Cme03g01901 Blo17g00754 Blo18g00786 Bda08g01233 Bda01g01523 Bpe02g01720 Bpe05g00128 Bma01g00736 Bma05g00154 . . . Cma12g00426 Cma05g00286 Car05g00236 . Cpe11g00237 . . . . . . . . . . . . . . . Lsi08g01344 Csa02g02111 Chy03g01405 .
Vvi18g1049 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 32051746 32054136 + Bda002510.1 Bda01g00505 505
1 32057229 32058203 - Bda002511.1 Bda01g00506 506
1 51110063 51111194 + Bda003780.1 Bda01g01521 1521
1 51130670 51132793 + Bda003781.1 Bda01g01522 1522
1 51135067 51138993 - Bda003782.1 Bda01g01523 1523
3 2419493 2421889 - Bda016233.1 Bda03g00276 276
8 50557061 50568849 + Bda030228.1 Bda08g01233 1233
8 50639497 50640659 - Bda030233.1 Bda08g01236 1236
4 3937081 3939674 - XM_039029595.1 Bhi04g00162 162
4 5569632 5577517 + XM_039028481.1 Bhi04g00228 228
4 5731172 5734974 - XM_039030713.1 Bhi04g00231 231
1 55642228 55651633 + BLOR01583 Blo01g01583 1583
1 55662432 55664825 - BLOR01584 Blo01g01584 1584
12 27143235 27145625 + BLOR04915 Blo12g00896 896
12 27148241 27150543 - BLOR04916 Blo12g00897 897
17 23956477 23966652 + BLOR08300 Blo17g00754 754
18 22728964 22734207 + BLOR09274 Blo18g00786 786
18 22736496 22739888 - BLOR09275 Blo18g00787 787
18 22760359 22765179 - BLOR09276 Blo18g00788 788
18 22814417 22815618 - BLOR09277 Blo18g00789 789
1 6736647 6740677 + Bma000949.1 Bma01g00736 736
1 6741667 6745053 - Bma000950.1 Bma01g00737 737
1 6758247 6768658 - Bma000952.2 Bma01g00738 738
1 6771919 6773063 - Bma000953.1 Bma01g00739 739
1 81066375 81068762 - Bma030298 Bma01g02349 2349
4 1921507 1923828 + Bma018678.1 Bma04g00226 226
5 4548087 4549208 + Bma020864.1 Bma05g00152 152
5 4560624 4565627 - Bma020866.1 Bma05g00154 154
2 2405816 2406544 - Bpe008206.1 Bpe02g00365 365
2 19653960 19655090 + Bpe009548.1 Bpe02g01717 1717
2 19667228 19670650 + Bpe009550.1 Bpe02g01719 1719
2 19671655 19675581 - Bpe009551.1 Bpe02g01720 1720
4 1554812 1557144 + Bpe014946.1 Bpe04g00230 230
4 1559730 1562123 - Bpe025586 Bpe04g00231 231
5 2779190 2780315 + Bpe017511.1 Bpe05g00126 126
5 2904653 2923307 - Bpe025791 Bpe05g00128 128
5 29029022 29031418 + CaPI482276_05g020330.1 Cam05g2033 2033
5 29035005 29038264 - CaPI482276_05g020350.1 Cam05g2035 2035
8 25172111 25181743 + CaPI482276_08g019230.1 Cam08g1923 1923
8 25183213 25189643 - CaPI482276_08g019240.1 Cam08g1924 1924
8 25194146 25197099 - CaPI482276_08g019260.1 Cam08g1926 1926
11 5587324 5591779 + CaPI482276_11g004170.1 Cam11g0417 417
11 5660017 5660589 - CaPI482276_11g004240.1 Cam11g0424 424
1 12832885 12833667 + Carg17174-RA Car01g01519 1519
1 12835838 12841107 + Carg17176-RA Car01g01521 1521
1 12842057 12844453 - Carg17177-RA Car01g01522 1522
5 1309408 1314082 + Carg09424-RA Car05g00235 235
5 1314692 1324055 - Carg09423-RA Car05g00236 236
9 538151 540538 + Carg08693-RA Car09g00109 109
12 2563400 2567434 + Carg04010-RA Car12g00402 402
12 2574653 2580377 - Carg04012-RA Car12g00404 404
12 2587799 2589216 - Carg04014-RA Car12g00406 406
5 29963740 29966136 + CcPI632755_05g020980.1 Cco05g2098 2098
5 29969770 29973034 - CcPI632755_05g020990.1 Cco05g2099 2099
8 27850420 27859517 + CcPI632755_08g016340.1 Cco08g1634 1634
8 27860982 27867396 - CcPI632755_08g016350.1 Cco08g1635 1635
8 27872136 27875070 - CcPI632755_08g016380.1 Cco08g1638 1638
11 4194429 4198447 + CcPI632755_11g004060.1 Cco11g0406 406
11 4270059 4270634 - CcPI632755_11g004130.1 Cco11g0413 413
5 32338008 32340404 + CePI673135_05g020420.1 Cec05g2042 2042
5 32344018 32347278 - CePI673135_05g020430.1 Cec05g2043 2043
8 26709158 26720737 + CePI673135_08g014980.1 Cec08g1498 1498
8 26722206 26728693 - CePI673135_08g014990.1 Cec08g1499 1499
8 26733185 26736136 - CePI673135_08g015010.1 Cec08g1501 1501
11 4317639 4321586 + CePI673135_11g004130.1 Cec11g0413 413
11 4393937 4394497 - CePI673135_11g004200.1 Cec11g0420 420
3 16799778 16803019 + Chy3G063850.1 Chy03g01405 1405
3 16810914 16815775 - Chy3G063870.1 Chy03g01407 1407
3 16842241 16843362 + Chy3G063910.1 Chy03g01411 1411
5 29228835 29231231 + ClG42_05g0202500.10 Clacu05g2025 2025
5 29234850 29238086 - ClG42_05g0202700.10 Clacu05g2027 2027
8 25918745 25928240 + ClG42_08g0161300.10 Clacu08g1613 1613
8 25929034 25936045 - ClG42_08g0161400.10 Clacu08g1614 1614
8 25940514 25943467 - ClG42_08g0161600.10 Clacu08g1616 1616
11 5074041 5077997 + ClG42_11g0054000.10 Clacu11g0540 540
11 5147407 5147982 - ClG42_11g0054600.10 Clacu11g0546 546
5 30825421 30827817 + ClCG05G018570.1 Cla05g01897 1897
5 30830319 30835030 - ClCG05G018590.2 Cla05g01899 1899
8 27286060 27295555 + ClCG08G014480.2 Cla08g01442 1442
8 27296725 27303672 - ClCG08G014510.2 Cla08g01443 1443
8 27322483 27332135 + ClCG08G014540.2 Cla08g01445 1445
11 4175359 4182311 + ClCG11G003960.2 Cla11g00372 372
11 4256371 4256946 - ClCG11G004010.1 Cla11g00377 377
1 12606514 12607547 + CmaCh01G019450.1 Cma01g01945 1945
1 12609595 12614071 + CmaCh01G019470.1 Cma01g01947 1947
1 12614276 12618250 - CmaCh01G019480.1 Cma01g01948 1948
5 1210628 1211983 + CmaCh05G002830.1 Cma05g00283 283
5 1216591 1221662 + CmaCh05G002850.1 Cma05g00285 285
5 1222353 1232003 - CmaCh05G002860.1 Cma05g00286 286
9 533869 536259 + CmaCh09G001230.1 Cma09g00123 123
12 2206254 2216411 + CmaCh12G004260.1 Cma12g00426 426
12 2217066 2223229 - CmaCh12G004270.1 Cma12g00427 427
12 2230092 2232433 - CmaCh12G004290.1 Cma12g00429 429
3 27147047 27151383 + MELO3C010990.2.1 Cme03g01901 1901
3 27157282 27162663 - MELO3C010988.2.1 Cme03g01903 1903
3 27183411 27185517 + MELO3C010985.2.1 Cme03g01907 1907
1 14141132 14142277 + CmoCh01G020060.1 Cmo01g02006 2006
1 14150600 14152996 - CmoCh01G020080.1 Cmo01g02008 2008
5 1251990 1253492 + CmoCh05G002890.1 Cmo05g00289 289
5 1257711 1262469 + CmoCh05G002910.1 Cmo05g00291 291
5 1263148 1272958 - CmoCh05G002920.1 Cmo05g00292 292
9 559499 561886 + CmoCh09G001210.1 Cmo09g00121 121
12 2327558 2331566 + CmoCh12G003760.1 Cmo12g00376 376
12 2338893 2344894 - CmoCh12G003780.1 Cmo12g00378 378
12 2352746 2354388 - CmoCh12G003800.1 Cmo12g00380 380
5 28954661 28957057 + CmPI595203_05g019050.1 Cmu05g1905 1905
5 28960677 28963918 - CmPI595203_05g019070.1 Cmu05g1907 1907
11 4385010 4388969 + CmPI595203_11g003970.1 Cmu11g0397 397
11 4458319 4458894 - CmPI595203_11g004030.1 Cmu11g0403 403
4 13737676 13739298 + Conep04aG0201000.1 Cone4ag1948 1948
4 13745947 13748842 - Conep04aG0201200.1 Cone4ag1950 1950
7 12035720 12038363 - Conep07aG0191700.1 Cone7ag1862 1862
8 8352982 8355311 + Conep08aG0086000.1 Cone8ag0834 834
17 9569772 9571058 + Conep17aG0141200.1 Cone17ag1378 1378
17 9575901 9577845 + Conep17aG0141500.1 Cone17ag1380 1380
17 9578475 9580829 - Conep17aG0141600.1 Cone17ag1381 1381
17 9583594 9587297 + Conep17aG0141700.1 Cone17ag1382 1382
17 9591820 9595242 + Conep17aG0142000.1 Cone17ag1384 1384
17 9596768 9599486 - Conep17aG0142100.1 Cone17ag1385 1385
20 437221 440020 + Conep20aG0010000.1 Cone20ag0096 96
20 440664 444092 - Conep20aG0010100.1 Cone20ag0097 97
20 455098 455578 + Conep20aG0010600.1 Cone20ag0101 101
20 457175 459726 - Conep20aG0010800.1 Cone20ag0103 103
20 463874 465273 - Conep20aG0011100.1 Cone20ag0105 105
2 464375 467165 + Cp4.1LG02g07840.1 Cpe02g00091 91
2 468584 473620 - Cp4.1LG02g07750.1 Cpe02g00092 92
2 475486 476908 - Cp4.1LG02g07680.1 Cpe02g00094 94
6 412245 414632 + Cp4.1LG06g00840.1 Cpe06g00083 83
7 2459194 2463228 + Cp4.1LG07g03800.1 Cpe07g00381 381
7 2470322 2476813 - Cp4.1LG07g03890.1 Cpe07g00383 383
7 2483126 2484571 - Cp4.1LG07g03880.1 Cpe07g00385 385
11 1265779 1267564 + Cp4.1LG11g02190.1 Cpe11g00234 234
11 1271716 1276505 + Cp4.1LG11g02210.1 Cpe11g00236 236
11 1277155 1287041 - Cp4.1LG11g02290.1 Cpe11g00237 237
5 32275066 32277462 + CrPI670011_05g020280.1 Cre05g2028 2028
5 32281156 32284442 - CrPI670011_05g020290.1 Cre05g2029 2029
8 26980090 26991294 + CrPI670011_08g013990.1 Cre08g1399 1399
8 26992771 26999265 - CrPI670011_08g014000.1 Cre08g1400 1400
8 27003741 27006694 - CrPI670011_08g014030.1 Cre08g1403 1403
11 6006837 6010773 + CrPI670011_11g008840.1 Cre11g0884 884
11 6083189 6083764 - CrPI670011_11g008900.1 Cre11g0890 890
2 19152113 19154409 - CsaV3_2G029230.1 Csa02g02104 2104
2 19175594 19181063 + CsaV3_2G029280.1 Csa02g02109 2109
2 19188357 19192139 - CsaV3_2G029300.1 Csa02g02111 2111
10 1312078 1316145 - Hsped.10g01280.1 Hepe10g0128 128
4 24511548 24515535 + Lsi04G017170.1 Lsi04g01717 1717
4 24518854 24521250 - Lsi04G017180.1 Lsi04g01718 1718
8 21732820 21737246 + Lsi08G013440.1 Lsi08g01344 1344
8 21749524 21756033 - Lsi08G013460.1 Lsi08g01346 1346
8 21779307 21780414 + Lsi08G013480.1 Lsi08g01348 1348
18 11539927 11541211 + Vvi18g1040 Vvi18g1040 1040
18 11546245 11548336 + Vvi18g1041 Vvi18g1041 1041
18 11552101 11558455 - Vvi18g1042 Vvi18g1042 1042
18 11561349 11567821 - Vvi18g1043 Vvi18g1043 1043
18 11577343 11581941 + Vvi18g1044 Vvi18g1044 1044
18 11581988 11587461 - Vvi18g1045 Vvi18g1045 1045
18 11600519 11607671 + Vvi18g1046 Vvi18g1046 1046
18 11608622 11613651 + Vvi18g1047 Vvi18g1047 1047
18 11613660 11620349 - Vvi18g1048 Vvi18g1048 1048
18 11630814 11630958 + Vvi18g1049 Vvi18g1049 1049
       

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