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
Vvi4g232 . . . . Bpe02g01203 . Bma04g00356 . . . Cma01g01590 . . . . . . Bhi04g01128 . . . Hepe10g0333 . Lcy13g1373 . . . . . . . . . Cone17ag1097 . . . . Cme03g01716 Blo17g00052 . . Bda13g01309 . . . . . Cmo01g01638 . Cma09g00544 . . . . Cpe02g00388 . . . . . . . Cla08g01247 Cam08g1705 Cec08g1285 Cco08g1406 Clacu08g1402 . Cre08g1187 Lsi08g01110 Csa02g02300 . Cme04g00311
Vvi4g233 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g234 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g235 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g236 . . . . . . . . . . . . . . Sed03g1514 . . Bhi04g01126 Tan02g2592 Cmetu03g2104 . Hepe10g0332 . Lcy13g1371 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi08g01112 . . .
Vvi4g237 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g238 . . . . . . Bma04g00357 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma09g00543 . . . . . . . . . . . . . . . . . . . . . . Cme04g00314
Vvi4g239 . . . . . . . . . . Cma01g01588 . . . . . . Bhi04g01117 . . . Hepe10g0331 . Lcy13g1370 . . . . . . . . . . Cone20ag0620 . . . Cme03g01714 . . . . . . . Bma02g00085 . Cmo01g01636 . Cma09g00542 . . . . Cpe02g00390 . . . . . . . Cla08g01250 Cam08g1708 Cec08g1288 Cco08g1409 Clacu08g1405 . Cre08g1189 Lsi08g01113 Csa02g02303 . Cme04g00316
Vvi4g240 . . . . . . . . . Cmo12g00227 . . . . Sed08g1434 . . Bhi04g01115 Tan02g2596 Cmetu01g1445 . Hepe10g0330 . Lcy13g1369 . . . . . . . . . . Cone20ag0621 . . . Cme03g01712 . . Bda01g00957 . . . Bma01g01350 . . . . . Cma12g00273 . . . . . . . . . . . Cla08g01251 Cam08g1709 Cec08g1289 Cco08g1410 Clacu08g1406 . Cre08g1190 . Csa02g02304 . .
Vvi4g241 . . . . . . . . . . Cma01g01587 . . Car12g00258 Sed03g1518 Cpe07g00236 . Bhi04g01114 Tan02g2598 . . . . Lcy13g1366 . . . . . . . . . . Cone20ag0622 . . . Cme03g01710 . . . . . . . . . Cmo01g01635 . Cma09g00541 . . . . Cpe02g00391 . . . . . . . Cla08g01252 . . . . . Cre08g1191 Lsi08g01114 Csa02g02305 . Cme04g00317
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 43116448 43119879 - Bda003114.1 Bda01g00957 957
13 35322646 35328853 + Bda000118.2 Bda13g01309 1309
4 27211392 27213733 + XM_039028374.1 Bhi04g01114 1114
4 27216581 27221862 + XM_039028068.1 Bhi04g01115 1115
4 27273434 27282342 + XM_039030199.1 Bhi04g01117 1117
4 27356383 27358178 + XM_039029940.1 Bhi04g01126 1126
4 27369528 27372898 + XM_039029939.1 Bhi04g01128 1128
17 359643 361255 + BLOR15873 Blo17g00052 52
1 20177825 20180445 + Bma001681.1 Bma01g01350 1350
2 705440 711095 + Bma030853 Bma02g00085 85
4 2872199 2872961 - Bma031094 Bma04g00356 356
4 2876574 2888630 + Bma018815.1 Bma04g00357 357
2 15744908 15746245 - Bpe009063.1 Bpe02g01203 1203
8 23354668 23357783 - CaPI482276_08g017050.1 Cam08g1705 1705
8 23382714 23390504 - CaPI482276_08g017080.1 Cam08g1708 1708
8 23391860 23395977 - CaPI482276_08g017090.1 Cam08g1709 1709
12 1735695 1738586 - Carg03865-RA Car12g00258 258
8 25988418 25991573 - CcPI632755_08g014060.1 Cco08g1406 1406
8 26018933 26019788 + CcPI632755_08g014090.1 Cco08g1409 1409
8 26028688 26032847 - CcPI632755_08g014100.1 Cco08g1410 1410
8 24836401 24839569 - CePI673135_08g012850.1 Cec08g1285 1285
8 24864303 24872079 - CePI673135_08g012880.1 Cec08g1288 1288
8 24873449 24877609 - CePI673135_08g012890.1 Cec08g1289 1289
8 24106339 24109502 - ClG42_08g0140200.10 Clacu08g1402 1402
8 24133792 24141997 - ClG42_08g0140500.10 Clacu08g1405 1405
8 24143359 24147469 - ClG42_08g0140600.10 Clacu08g1406 1406
8 25402204 25413808 - ClCG08G012490.2 Cla08g01247 1247
8 25430125 25438024 - ClCG08G012520.1 Cla08g01250 1250
8 25439140 25443683 - ClCG08G012530.1 Cla08g01251 1251
8 25445258 25451661 - ClCG08G012540.2 Cla08g01252 1252
1 10950028 10952719 + CmaCh01G015870.1 Cma01g01587 1587
1 10954404 10959800 + CmaCh01G015880.1 Cma01g01588 1588
1 10983078 10984711 + CmaCh01G015900.1 Cma01g01590 1590
9 2421162 2425049 + CmaCh09G005410.1 Cma09g00541 541
9 2426196 2430526 + CmaCh09G005420.1 Cma09g00542 542
9 2431918 2445512 - CmaCh09G005430.1 Cma09g00543 543
9 2452419 2453741 + CmaCh09G005440.1 Cma09g00544 544
12 1417007 1426780 - CmaCh12G002730.1 Cma12g00273 273
3 25726925 25729202 + MELO3C011173.2.1 Cme03g01710 1710
3 25735038 25735501 + MELO3C000704.2.1 Cme03g01712 1712
3 25743444 25745801 + MELO3C011170.2.1 Cme03g01714 1714
3 25759234 25762184 + MELO3C011168.2.1 Cme03g01716 1716
4 2422114 2423979 - MELO3C003598.2.1 Cme04g00311 311
4 2451864 2465954 + MELO3C003601.2.1 Cme04g00314 314
4 2475256 2478123 - MELO3C030364.2.1 Cme04g00316 316
4 2482557 2485586 - MELO3C003603.2.1 Cme04g00317 317
1 18760491 18763924 - PI0026301.1 Cmetu01g1445 1445
3 3685069 3695484 - PI0002307.1 Cmetu03g2104 2104
1 12408928 12411732 + CmoCh01G016350.1 Cmo01g01635 1635
1 12413390 12416497 + CmoCh01G016360.1 Cmo01g01636 1636
1 12436187 12437773 + CmoCh01G016380.1 Cmo01g01638 1638
12 1499070 1512924 - CmoCh12G002270.1 Cmo12g00227 227
17 8153446 8154238 - Conep17aG0112500.1 Cone17ag1097 1097
20 3712821 3713868 - Conep20aG0063800.1 Cone20ag0620 620
20 3714335 3717674 - Conep20aG0063900.1 Cone20ag0621 621
20 3718320 3720891 - Conep20aG0064000.1 Cone20ag0622 622
2 2143857 2145426 - Cp4.1LG02g04780.1 Cpe02g00388 388
2 2162755 2168755 - Cp4.1LG02g04750.1 Cpe02g00390 390
2 2170403 2173724 - Cp4.1LG02g04760.1 Cpe02g00391 391
7 1543678 1546285 - Cp4.1LG07g02160.1 Cpe07g00236 236
8 25146717 25149815 - CrPI670011_08g011870.1 Cre08g1187 1187
8 25174718 25182527 - CrPI670011_08g011890.1 Cre08g1189 1189
8 25183891 25188000 - CrPI670011_08g011900.1 Cre08g1190 1190
8 25190192 25191528 - CrPI670011_08g011910.1 Cre08g1191 1191
2 20533589 20535997 - CsaV3_2G031190.1 Csa02g02300 2300
2 20556695 20559496 - CsaV3_2G031220.1 Csa02g02303 2303
2 20560976 20565902 - CsaV3_2G031230.1 Csa02g02304 2304
2 20567804 20570355 - CsaV3_2G031240.1 Csa02g02305 2305
10 3556274 3560756 + Hsped.10g03300.1 Hepe10g0330 330
10 3562388 3566781 + Hsped.10g03310.1 Hepe10g0331 331
10 3572118 3574256 + Hsped.10g03320.1 Hepe10g0332 332
10 3586592 3590304 + Hsped.10g03330.1 Hepe10g0333 333
13 31743894 31746233 + Maker00025644 Lcy13g1366 1366
13 31783673 31789653 + Maker00025704 Lcy13g1369 1369
13 31793504 31796464 + Maker00025666 Lcy13g1370 1370
13 31815173 31818311 + Maker00025499 Lcy13g1371 1371
13 31837999 31841102 + Maker00025619 Lcy13g1373 1373
8 19746142 19749611 - Lsi08G011100.1 Lsi08g01110 1110
8 19763414 19764789 - Lsi08G011120.1 Lsi08g01112 1112
8 19768629 19772277 - Lsi08G011130.1 Lsi08g01113 1113
8 19773926 19783414 - Lsi08G011140.1 Lsi08g01114 1114
3 9659200 9665339 - Sed0000657.5 Sed03g1514 1514
3 9681751 9684505 - Sed0024396.1 Sed03g1518 1518
8 28901102 28905833 - Sed0012147.5 Sed08g1434 1434
2 94592125 94594231 - Tan0018843.1 Tan02g2592 2592
2 94612824 94618137 - Tan0012675.1 Tan02g2596 2596
2 94619615 94622227 - Tan0005589.2 Tan02g2598 2598
4 2294134 2295171 - Vvi4g232 Vvi4g232 232
4 2303749 2304814 + Vvi4g233 Vvi4g233 233
4 2304859 2312434 - Vvi4g234 Vvi4g234 234
4 2315531 2324965 - Vvi4g235 Vvi4g235 235
4 2331223 2332505 - Vvi4g236 Vvi4g236 236
4 2332531 2334116 - Vvi4g237 Vvi4g237 237
4 2344161 2361062 + Vvi4g238 Vvi4g238 238
4 2362222 2365439 + Vvi4g239 Vvi4g239 239
4 2365569 2368924 - Vvi4g240 Vvi4g240 240
4 2369933 2373379 - Vvi4g241 Vvi4g241 241
       

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