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
Vvi18g1000 . . . . . . . . Cmo05g00269 . . . . . . . . Bhi04g00203 . . . Hepe10g0610 . . Cla08g01461 Cam08g1947 Cec08g1522 Cco08g1660 Clacu08g1637 . Cre08g1423 . . Cone17ag1361 Cone20ag0120 . . . Cme03g01926 . Blo18g00800 . . Bpe02g01707 . . . . . . . Cma05g00266 Car05g00221 . Cpe11g00219 . . . . . . . . . . . . . . . Lsi08g01369 Csa02g02084 Chy03g01430 .
Vvi18g1001 . . . . . . . . Cmo05g00271 . . . . . . . . Bhi04g00204 . . . . . . Cla08g01460 Cam08g1946 . Cco08g1659 Clacu08g1636 . Cre08g1422 . . Cone17ag1362 Cone20ag0119 . . . Cme03g01925 . Blo18g00799 Bda08g01258 Bda01g01512 Bpe02g01708 . Bma01g00746 . . . . . Cma05g00268 Car05g00222 . Cpe11g00221 . . . . . . . . . . . . . . . Lsi08g01368 Csa02g02085 Chy03g01429 .
Vvi18g1002 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1936 Cone7ag1848 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1003 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1937 Cone7ag1849 . . . . . . Blo17g00777 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1004 . . . Bda03g00271 . Bpe04g00226 Bma04g00221 . . . . Cma09g00132 . . . Cpe06g00092 . . . . . . . . . . . . . . . . . Cone17ag1363 Cone20ag0118 Lsi04g01703 Csa03g04243 Chy04g00472 . . . . . . . . . . Cmo01g01996 Cmo09g00129 . . . Car09g00118 . . . . . . . . . Cla05g01909 Cam05g2046 Cec05g2055 Cco05g2110 Clacu05g2039 Cmu05g1918 Cre05g2040 . . . Cme04g00518
Vvi18g1005 Blo01g01577 . Bda01g00515 . Bpe02g00372 . . Bma01g02340 . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1938 Cone7ag1850 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1006 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1007 . Blo12g00899 . Bda03g00272 . . Bma04g00222 . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1939 Cone7ag1851 . . . . . . . . . Bda01g01513 Bpe02g01709 . Bma01g00745 Bma05g00135 . . . . . . . . . . . . . . . . Cla11g00386 Cam11g0432 Cec11g0426 Cco11g0420 Clacu11g0554 Cmu11g0411 Cre11g0897 . . . .
Vvi18g1008 . . . . . . . . . Cmo12g00393 . . . Car12g00419 . . Cpe07g00397 Bhi04g00206 . . . . . . Cla08g01459 Cam08g1945 Cec08g1519 Cco08g1658 Clacu08g1635 . Cre08g1421 . . . Cone20ag0117 . . . Cme03g01923 . . . . . Bpe05g00109 . . . . . Cma12g00443 . . . . . . . . . . . . . . . . . . . Lsi08g01365 Csa02g02087 Chy03g01427 .
Vvi18g1009 Blo01g01578 . Bda01g00514 . Bpe02g00371 . . Bma01g02341 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 32108533 32110800 - Bda002519.1 Bda01g00514 514
1 32123874 32126210 + Bda002521.1 Bda01g00515 515
1 50963820 50966605 - Bda003769.1 Bda01g01512 1512
1 50968677 50970229 - Bda003770.1 Bda01g01513 1513
3 2390450 2396447 - Bda016228.1 Bda03g00271 271
3 2397758 2399687 - Bda016229.1 Bda03g00272 272
8 51286119 51289015 - Bda030269.1 Bda08g01258 1258
4 4900020 4902510 + XM_039030651.1 Bhi04g00203 203
4 4902505 4906776 - XM_039030650.1 Bhi04g00204 204
4 5004927 5010737 + XM_039030265.1 Bhi04g00206 206
1 55576788 55579432 - BLOR01577 Blo01g01577 1577
1 55586351 55587667 + BLOR01578 Blo01g01578 1578
12 27179806 27198509 + BLOR04918 Blo12g00899 899
17 24823913 24825286 - BLOR08323 Blo17g00777 777
18 23390841 23393751 + BLOR09287 Blo18g00799 799
18 23394126 23395418 - BLOR09288 Blo18g00800 800
1 6871474 6873024 + Bma000960.1 Bma01g00745 745
1 6874570 6877429 + Bma000961.1 Bma01g00746 746
1 81010313 81012477 - Bma003206.1 Bma01g02340 2340
1 81016736 81018359 + Bma003207.1 Bma01g02341 2341
4 1885866 1893484 - Bma018672.1 Bma04g00221 221
4 1894730 1896960 - Bma018673.1 Bma04g00222 222
5 4158704 4160270 + Bma020842.1 Bma05g00135 135
2 2444122 2445733 - Bpe025074 Bpe02g00371 371
2 2450902 2453134 + Bpe008213.1 Bpe02g00372 372
2 19572995 19574398 + Bpe025174 Bpe02g01707 1707
2 19575021 19579714 - Bpe009540.1 Bpe02g01708 1708
2 19581890 19583438 - Bpe009541.1 Bpe02g01709 1709
4 1520395 1526408 - Bpe014941.1 Bpe04g00226 226
5 2048485 2055369 - Bpe025786 Bpe05g00109 109
5 29134256 29146683 + CaPI482276_05g020460.1 Cam05g2046 2046
8 25365422 25370602 - CaPI482276_08g019450.1 Cam08g1945 1945
8 25373543 25382611 + CaPI482276_08g019460.1 Cam08g1946 1946
8 25383104 25385487 - CaPI482276_08g019470.1 Cam08g1947 1947
11 5734054 5737177 + CaPI482276_11g004320.1 Cam11g0432 432
5 1151180 1152476 + Carg11780-RA Car05g00221 221
5 1152949 1159947 - Carg11779-RA Car05g00222 222
9 571189 579272 + Carg08702-RA Car09g00118 118
12 2671840 2675308 - Carg04027-RA Car12g00419 419
5 30074401 30081916 + CcPI632755_05g021100.1 Cco05g2110 2110
8 28045784 28050920 - CcPI632755_08g016580.1 Cco08g1658 1658
8 28053881 28063195 + CcPI632755_08g016590.1 Cco08g1659 1659
8 28063688 28066051 - CcPI632755_08g016600.1 Cco08g1660 1660
11 4344386 4347513 + CcPI632755_11g004200.1 Cco11g0420 420
5 32447404 32454846 + CePI673135_05g020550.1 Cec05g2055 2055
8 26908801 26914000 - CePI673135_08g015190.1 Cec08g1519 1519
8 26926588 26928979 - CePI673135_08g015220.1 Cec08g1522 1522
11 4464511 4467635 + CePI673135_11g004260.1 Cec11g0426 426
3 16973273 16978365 - Chy3G064070.1 Chy03g01427 1427
3 16983142 16986630 + Chy3G064090.1 Chy03g01429 1429
3 16987116 16989778 - Chy3G064100.1 Chy03g01430 1430
4 4406611 4417585 + Chy4G071900.1 Chy04g00472 472
5 29339154 29346675 + ClG42_05g0203900.10 Clacu05g2039 2039
8 26111393 26116534 - ClG42_08g0163500.10 Clacu08g1635 1635
8 26119457 26128606 + ClG42_08g0163600.10 Clacu08g1636 1636
8 26129099 26131491 - ClG42_08g0163700.10 Clacu08g1637 1637
11 5221210 5224331 + ClG42_11g0055400.10 Clacu11g0554 554
5 30937443 30945189 + ClCG05G018690.2 Cla05g01909 1909
8 27486591 27492280 - ClCG08G014710.2 Cla08g01459 1459
8 27494937 27513401 + ClCG08G014720.2 Cla08g01460 1460
8 27504654 27507047 - ClCG08G014730.1 Cla08g01461 1461
11 4333548 4338151 + ClCG11G004100.1 Cla11g00386 386
5 1127948 1129725 + CmaCh05G002660.1 Cma05g00266 266
5 1133555 1137013 - CmaCh05G002680.1 Cma05g00268 268
9 569938 577816 + CmaCh09G001320.1 Cma09g00132 132
12 2315444 2319612 - CmaCh12G004430.1 Cma12g00443 443
3 27313854 27320729 - MELO3C010971.2.1 Cme03g01923 1923
3 27325480 27329802 + MELO3C010970.2.1 Cme03g01925 1925
3 27330197 27331975 - MELO3C010969.2.1 Cme03g01926 1926
4 4269734 4279243 + MELO3C003793.2.1 Cme04g00518 518
1 14097423 14102054 - CmoCh01G019960.1 Cmo01g01996 1996
5 1166035 1167606 + CmoCh05G002690.1 Cmo05g00269 269
5 1171827 1174830 - CmoCh05G002710.1 Cmo05g00271 271
9 593893 600324 + CmoCh09G001290.1 Cmo09g00129 129
12 2437679 2441348 - CmoCh12G003930.1 Cmo12g00393 393
5 29064931 29072443 + CmPI595203_05g019180.1 Cmu05g1918 1918
11 4532079 4535200 + CmPI595203_11g004110.1 Cmu11g0411 411
4 13678624 13681203 - Conep04aG0199800.1 Cone4ag1936 1936
4 13681554 13682984 - Conep04aG0199900.1 Cone4ag1937 1937
4 13683402 13687232 - Conep04aG0200000.1 Cone4ag1938 1938
4 13687752 13689566 - Conep04aG0200100.1 Cone4ag1939 1939
7 11979132 11981302 - Conep07aG0190300.1 Cone7ag1848 1848
7 11981829 11983061 - Conep07aG0190400.1 Cone7ag1849 1849
7 11983330 11985739 - Conep07aG0190500.1 Cone7ag1850 1850
7 11987792 11989493 - Conep07aG0190600.1 Cone7ag1851 1851
17 9514482 9515601 + Conep17aG0139500.1 Cone17ag1361 1361
17 9515782 9518827 - Conep17aG0139600.1 Cone17ag1362 1362
17 9519041 9522276 + Conep17aG0139700.1 Cone17ag1363 1363
20 520589 523629 - Conep20aG0012300.1 Cone20ag0117 117
20 524054 526567 - Conep20aG0012400.1 Cone20ag0118 118
20 527030 530060 + Conep20aG0012500.1 Cone20ag0119 119
20 530019 531261 - Conep20aG0012600.1 Cone20ag0120 120
6 448897 457274 + Cp4.1LG06g00810.1 Cpe06g00092 92
7 2567901 2573566 - Cp4.1LG07g04010.1 Cpe07g00397 397
11 1182593 1183886 + Cp4.1LG11g02200.1 Cpe11g00219 219
11 1187994 1191505 - Cp4.1LG11g02320.1 Cpe11g00221 221
5 32391779 32399295 + CrPI670011_05g020400.1 Cre05g2040 2040
8 27176151 27181357 - CrPI670011_08g014210.1 Cre08g1421 1421
8 27184034 27193162 + CrPI670011_08g014220.1 Cre08g1422 1422
8 27193654 27196050 - CrPI670011_08g014230.1 Cre08g1423 1423
11 6157965 6161085 + CrPI670011_11g008970.1 Cre11g0897 897
2 18998305 19000569 + CsaV3_2G029030.1 Csa02g02084 2084
2 19000585 19004466 - CsaV3_2G029040.1 Csa02g02085 2085
2 19009566 19017150 + CsaV3_2G029060.1 Csa02g02087 2087
3 37159917 37169846 - CsaV3_3G045490.1 Csa03g04243 4243
10 7515786 7518421 - Hsped.10g06100.1 Hepe10g0610 610
4 24404378 24414031 - Lsi04G017030.1 Lsi04g01703 1703
8 21952240 21964975 - Lsi08G013650.1 Lsi08g01365 1365
8 21974057 21978410 + Lsi08G013680.1 Lsi08g01368 1368
8 21978120 21980859 - Lsi08G013690.1 Lsi08g01369 1369
18 11166502 11167953 + Vvi18g1000 Vvi18g1000 1000
18 11169564 11174095 - Vvi18g1001 Vvi18g1001 1001
18 11175009 11180097 - Vvi18g1002 Vvi18g1002 1002
18 11184160 11185662 - Vvi18g1003 Vvi18g1003 1003
18 11188321 11195618 - Vvi18g1004 Vvi18g1004 1004
18 11196525 11198339 - Vvi18g1005 Vvi18g1005 1005
18 11199294 11200843 + Vvi18g1006 Vvi18g1006 1006
18 11201409 11205044 - Vvi18g1007 Vvi18g1007 1007
18 11213319 11229319 - Vvi18g1008 Vvi18g1008 1008
18 11241270 11245493 - Vvi18g1009 Vvi18g1009 1009
       

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