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
Vvi18g1210 Blo01g01328 . Bda01g00693 . Bpe02g00613 . . . . . Cma01g00998 Cma09g01088 . . . Cpe06g00889 . . . . . . . . . . . . . . . . . . Cone20ag0403 . . . . . . . . . . Bma01g00875 . . Cmo01g01034 Cmo09g01096 . . . Car09g00986 . Cpe02g00897 Bhi09g01488 Tan01g3362 Cmetu01g2220 . . Mch11g1416 . Cla09g00912 Cam09g0964 Cec09g0969 Cco09g0975 . . Cre09g0933 . . Chy03g00637 .
Vvi18g1211 . . . . . . . . . Cmo15g00633 . . . . Sed11g1327 . . Bhi04g01822 Tan11g1193 Cmetu03g1802 . Hepe02g2761 . Lcy10g1311 . . . . . . . . . Cone17ag0799 Cone20ag0401 . . . Cme03g00403 Blo17g00223 . . Bda13g01536 . . . . . . . . . Car05g00738 Car15g00574 . . . . . . . . . . . . . . . . Lsi08g00520 . Chy03g00586 .
Vvi18g1212 . . . . . . . . . . . . Car01g00885 . . . . . . . . . . . . . . . . . . Cone4ag1521 . . . . . . . . . . . . . . . . Cmo01g01032 . . . . . . Cpe02g00898 Bhi09g01514 . . . . . . Cla09g00915 Cam09g0967 Cec09g0972 Cco09g0978 . . Cre09g0936 . . . .
Vvi18g1213 . Blo12g01108 . Bda03g00030 . Bpe04g00020 Bma04g00028 . . Cmo12g00334 . Cma09g01089 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo09g01097 . . . Car09g00987 . . Bhi09g01512 . . . . . . Cla09g00917 . . . . . . . . . .
Vvi18g1214 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1215 . . . . . . . . Cmo04g02540 Cmo15g00631 . Cma09g01090 . . Sed11g1328 Cpe06g00890 . Bhi04g01820 Tan11g1189 Cmetu01g2322 . Hepe02g2767 . Lcy10g1313 Cla08g00662 Cam08g1093 Cec08g0678 Cco08g0787 Clacu08g0798 . Cre08g0601 . Cone7ag1433 . Cone20ag0399 . . . Cme03g00398 . Blo18g00222 . . . . Bma01g00874 . . . Cmo09g01099 . . Car04g02338 Car09g00988 Cpe01g02099 . Bhi09g01511 . . . . Mch11g1423 . Cla09g00918 Cam09g0970 Cec09g0975 Cco09g0981 . . Cre09g0939 Lsi08g00522 . Chy03g00587 .
Vvi18g1216 Blo01g01787 . . . . . . Bma01g02573 . Cmo15g00630 . . . . Sed03g0457 . Cpe13g00664 Bhi04g01819 Tan11g1188 Cmetu03g1258 . Hepe02g2768 . Lcy10g1314 Cla08g00663 Cam08g1094 Cec08g0679 Cco08g0788 Clacu08g0799 . Cre08g0602 . . . . . . . Cme03g00397 Blo17g00222 . . . . Bpe14g00329 . Bma02g00281 . . . . . . . . . . . . . . . . . . . . . . . Lsi08g00523 . . .
Vvi18g1217 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda13g01440 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1218 . . . . . . . . Cmo04g02541 . . . . . Sed03g0458 . . Bhi04g01818 Tan11g1187 Cmetu03g0054 . . . . Cla08g00664 . Cec08g0680 Cco08g0789 Clacu08g0800 . Cre08g0603 . . . . . . . Cme03g00396 . Blo18g00221 . Bda01g01385 Bpe02g01600 . Bma01g00873 . . . . . . Car04g02339 . Cpe01g02100 . . . . . . . . . . . . . . . Lsi08g00524 . Chy03g00588 .
Vvi18g1219 . . . . . . . . Cmo04g02542 Cmo15g00629 . . . . Sed01g3642 . Cpe13g00665 Bhi04g01816 Tan11g1186 Cmetu03g0425 . Hepe02g2770 . Lcy10g1316 . . . . . . . . . Cone17ag0798 Cone20ag0397 . . . Cme03g00395 Blo17g00221 . . Bda13g01531 . Bpe14g00330 . Bma02g00280 . . . . . Car04g02340 Car15g00571 Cpe01g02102 . . . . . . . . . . . . . . . Lsi08g00525 . Chy03g00589 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 34098353 34105351 + Bda002730.1 Bda01g00693 693
1 49748248 49751483 - Bda003626.1 Bda01g01385 1385
3 466011 468953 - Bda015963.1 Bda03g00030 30
13 37152359 37155727 - Bda000273.1 Bda13g01440 1440
13 38356724 38367048 - Bda000380.2 Bda13g01531 1531
13 38596439 38597715 + Bda000390.1 Bda13g01536 1536
4 44662804 44669303 - XM_039029454.1 Bhi04g01816 1816
4 44673141 44677177 + XM_039030226.1 Bhi04g01818 1818
4 44684331 44687651 + XM_039028477.1 Bhi04g01819 1819
4 44689859 44696175 + XM_039028096.1 Bhi04g01820 1820
4 44699647 44702179 - XM_039028394.1 Bhi04g01822 1822
9 38634853 38637101 + XM_039040611.1 Bhi09g01488 1488
9 39992258 39995840 + XM_039040958.1 Bhi09g01511 1511
9 39998347 40001687 - XM_039043979.1 Bhi09g01512 1512
9 40068160 40068945 + XM_039040528.1 Bhi09g01514 1514
1 50743003 50745586 + BLOR01328 Blo01g01328 1328
1 57593969 57596204 + BLOR01787 Blo01g01787 1787
12 28765729 28768668 + BLOR05127 Blo12g01108 1108
17 2270128 2282583 - BLOR16042 Blo17g00221 221
17 2297615 2299849 + BLOR16043 Blo17g00222 222
17 2302105 2303380 + BLOR16044 Blo17g00223 223
18 2180234 2183502 + BLOR08709 Blo18g00221 221
18 2186715 2189966 + BLOR08710 Blo18g00222 222
1 8212770 8216753 + Bma001095.1 Bma01g00873 873
1 8220071 8223813 + Bma001096.1 Bma01g00874 874
1 8226135 8228200 + Bma001097.1 Bma01g00875 875
1 83344417 83347710 - Bma003455.1 Bma01g02573 2573
2 3235933 3270273 - Bma030871 Bma02g00280 280
2 3242822 3244635 + Bma014732.1 Bma02g00281 281
4 324933 327875 - Bma018480.1 Bma04g00028 28
2 3990572 3996593 - Bpe008452.2 Bpe02g00613 613
2 18904467 18907526 - Bpe009446.1 Bpe02g01600 1600
4 201046 203988 - Bpe014747.1 Bpe04g00020 20
14 3208006 3211766 - Bpe006981.1 Bpe14g00329 329
14 3212247 3217316 + Bpe006982.1 Bpe14g00330 330
8 17303823 17308955 - CaPI482276_08g010930.1 Cam08g1093 1093
8 17312649 17321598 - CaPI482276_08g010940.1 Cam08g1094 1094
9 9994466 9997022 - CaPI482276_09g009640.1 Cam09g0964 964
9 10007447 10009811 + CaPI482276_09g009670.1 Cam09g0967 967
9 10027488 10030575 - CaPI482276_09g009700.1 Cam09g0970 970
1 8113144 8114680 + Carg25048-RA Car01g00885 885
4 18819312 18822346 - Carg15772-RA Car04g02338 2338
4 18823743 18827838 - Carg15773-RA Car04g02339 2339
4 18828990 18834780 + Carg15774-RA Car04g02340 2340
5 5257562 5261964 - Carg21456-RA Car05g00738 738
9 6339319 6341453 + Carg27258-RA Car09g00986 986
9 6344340 6347334 + Carg27259-RA Car09g00987 987
9 6348708 6351783 - Carg27260-RA Car09g00988 988
15 3163738 3166270 - Carg01584-RA Car15g00571 571
15 3174588 3175937 - Carg01581-RA Car15g00574 574
8 19690589 19695810 - CcPI632755_08g007870.1 Cco08g0787 787
8 19699478 19702882 - CcPI632755_08g007880.1 Cco08g0788 788
8 19710754 19714242 - CcPI632755_08g007890.1 Cco08g0789 789
9 9249689 9252205 - CcPI632755_09g009750.1 Cco09g0975 975
9 9262534 9264852 + CcPI632755_09g009780.1 Cco09g0978 978
9 9286364 9289448 - CcPI632755_09g009810.1 Cco09g0981 981
8 18515272 18520471 - CePI673135_08g006780.1 Cec08g0678 678
8 18524107 18527764 - CePI673135_08g006790.1 Cec08g0679 679
8 18531719 18535165 - CePI673135_08g006800.1 Cec08g0680 680
9 9287286 9289835 - CePI673135_09g009690.1 Cec09g0969 969
9 9300502 9302724 + CePI673135_09g009720.1 Cec09g0972 972
9 9318198 9321286 - CePI673135_09g009750.1 Cec09g0975 975
3 8397782 8399515 + Chy3G055660.1 Chy03g00586 586
3 8403567 8408902 - Chy3G055670.1 Chy03g00587 587
3 8426353 8433976 - Chy3G055680.1 Chy03g00588 588
3 8438406 8443774 + Chy3G055690.1 Chy03g00589 589
3 8880512 8888896 - Chy3G056170.1 Chy03g00637 637
8 18043574 18048696 - ClG42_08g0079800.10 Clacu08g0798 798
8 18052356 18055160 - ClG42_08g0079900.10 Clacu08g0799 799
8 18060595 18064083 - ClG42_08g0080000.10 Clacu08g0800 800
8 18905283 18911839 - ClCG08G006450.1 Cla08g00662 662
8 18915243 18918443 - ClCG08G006460.1 Cla08g00663 663
8 18923484 18927505 - ClCG08G006470.1 Cla08g00664 664
9 9527379 9529457 - ClCG09G009780.1 Cla09g00912 912
9 9540657 9543146 + ClCG09G009810.2 Cla09g00915 915
9 9553752 9558978 + ClCG09G009830.2 Cla09g00917 917
9 9558533 9562065 - ClCG09G009840.2 Cla09g00918 918
1 7192934 7194911 - CmaCh01G009980.1 Cma01g00998 998
9 5860605 5862783 + CmaCh09G010880.1 Cma09g01088 1088
9 5864608 5867616 + CmaCh09G010890.1 Cma09g01089 1089
9 5868859 5872063 - CmaCh09G010900.1 Cma09g01090 1090
3 5508313 5514239 - MELO3C008406.2.1 Cme03g00395 395
3 5528355 5532412 + MELO3C008407.2.1 Cme03g00396 396
3 5535748 5538982 + MELO3C008408.2.1 Cme03g00397 397
3 5578694 5583339 + MELO3C008410.2.1 Cme03g00398 398
3 5611211 5613788 - MELO3C008413.2.1 Cme03g00403 403
1 17884881 17886870 + PI0019928.1 Cmetu01g2220 2220
1 17768571 17771707 - PI0024392.1 Cmetu01g2322 2322
3 10081729 10085268 + PI0026315.1 Cmetu03g0054 54
3 10058228 10063554 - PI0027353.1 Cmetu03g0425 425
3 10086867 10090585 + PI0012547.1 Cmetu03g1258 1258
3 10121114 10123168 - PI0025578.1 Cmetu03g1802 1802
1 8078823 8080550 + CmoCh01G010320.1 Cmo01g01032 1032
1 8082928 8084961 + CmoCh01G010340.1 Cmo01g01034 1034
4 18651098 18653985 - CmoCh04G025400.1 Cmo04g02540 2540
4 18655552 18659579 - CmoCh04G025410.1 Cmo04g02541 2541
4 18660831 18667071 + CmoCh04G025420.1 Cmo04g02542 2542
9 6085628 6087773 + CmoCh09G010960.1 Cmo09g01096 1096
9 6092502 6098486 + CmoCh09G010970.1 Cmo09g01097 1097
9 6097855 6100769 - CmoCh09G010990.1 Cmo09g01099 1099
12 2094430 2096562 + CmoCh12G003340.1 Cmo12g00334 334
15 3047350 3053068 - CmoCh15G006290.1 Cmo15g00629 629
15 3053207 3055915 + CmoCh15G006300.1 Cmo15g00630 630
15 3056255 3059502 + CmoCh15G006310.1 Cmo15g00631 631
15 3060341 3063044 - CmoCh15G006330.1 Cmo15g00633 633
4 11783028 11784489 + Conep04aG0157300.1 Cone4ag1521 1521
7 10173412 10176160 - Conep07aG0147500.1 Cone7ag1433 1433
17 6267546 6269549 - Conep17aG0081600.1 Cone17ag0798 798
17 6274041 6275685 + Conep17aG0081700.1 Cone17ag0799 799
20 1922722 1931785 - Conep20aG0041100.1 Cone20ag0397 397
20 1935815 1939475 + Conep20aG0041300.1 Cone20ag0399 399
20 1942219 1942542 + Conep20aG0041500.1 Cone20ag0401 401
20 1948120 1950580 - Conep20aG0041700.1 Cone20ag0403 403
1 17773447 17776759 - Cp4.1LG01g21020.1 Cpe01g02099 2099
1 17778064 17782080 - Cp4.1LG01g20960.1 Cpe01g02100 2100
1 17785525 17799106 + Cp4.1LG01g20910.1 Cpe01g02102 2102
2 6432500 6434510 - Cp4.1LG02g08830.1 Cpe02g00897 897
2 6435115 6436805 - Cp4.1LG02g08900.1 Cpe02g00898 898
6 5938078 5940234 + Cp4.1LG06g07690.1 Cpe06g00889 889
6 5946395 5949611 - Cp4.1LG06g07640.1 Cpe06g00890 890
13 6263771 6270716 - Cp4.1LG13g04110.1 Cpe13g00664 664
13 6270484 6281774 + Cp4.1LG13g04150.1 Cpe13g00665 665
8 18964790 18969388 - CrPI670011_08g006010.1 Cre08g0601 601
8 18973009 18975858 - CrPI670011_08g006020.1 Cre08g0602 602
8 18981732 18985221 - CrPI670011_08g006030.1 Cre08g0603 603
9 9494755 9497281 - CrPI670011_09g009330.1 Cre09g0933 933
9 9507637 9509761 + CrPI670011_09g009360.1 Cre09g0936 936
9 9526158 9529244 - CrPI670011_09g009390.1 Cre09g0939 939
2 76214945 76218481 + Hsped.02g27610.1 Hepe02g2761 2761
2 76256449 76260810 - Hsped.02g27670.1 Hepe02g2767 2767
2 76262785 76265609 - Hsped.02g27680.1 Hepe02g2768 2768
2 76279803 76286873 + Hsped.02g27700.1 Hepe02g2770 2770
10 36029923 36030525 + Maker00008422 Lcy10g1311 1311
10 36033749 36037784 - Maker00008350 Lcy10g1313 1313
10 36039942 36042804 - Maker00008683 Lcy10g1314 1314
10 36051571 36058121 + Maker00008561 Lcy10g1316 1316
8 13160622 13164315 + Lsi08G005200.1 Lsi08g00520 520
8 13171853 13177093 - Lsi08G005220.1 Lsi08g00522 522
8 13180314 13183390 - Lsi08G005230.1 Lsi08g00523 523
8 13185572 13189577 - Lsi08G005240.1 Lsi08g00524 524
8 13193757 13200870 + Lsi08G005250.1 Lsi08g00525 525
11 10540305 10553025 - MC11g1167 Mch11g1416 1416
11 10675152 10679801 - MC11g1174 Mch11g1423 1423
1 65613829 65630572 + Sed0013991.1 Sed01g3642 3642
3 2752340 2754909 - Sed0007582.1 Sed03g0457 457
3 2756190 2760058 - Sed0013655.1 Sed03g0458 458
11 29020204 29022875 + Sed0006787.1 Sed11g1327 1327
11 29024684 29032012 - Sed0013556.1 Sed11g1328 1328
1 93584985 93586955 + Tan0004266.1 Tan01g3362 3362
11 9783384 9789860 - Tan0018790.1 Tan11g1186 1186
11 9791112 9795161 + Tan0011790.1 Tan11g1187 1187
11 9798005 9800642 + Tan0002477.1 Tan11g1188 1188
11 9803726 9809096 + Tan0017262.1 Tan11g1189 1189
11 9841000 9843670 - Tan0022134.1 Tan11g1193 1193
18 13581890 13585088 + Vvi18g1210 Vvi18g1210 1210
18 13614974 13618325 + Vvi18g1211 Vvi18g1211 1211
18 13650263 13655312 - Vvi18g1212 Vvi18g1212 1212
18 13662477 13665624 - Vvi18g1213 Vvi18g1213 1213
18 13666499 13667021 - Vvi18g1214 Vvi18g1214 1214
18 13667827 13671320 - Vvi18g1215 Vvi18g1215 1215
18 13676033 13681500 - Vvi18g1216 Vvi18g1216 1216
18 13682338 13692522 - Vvi18g1217 Vvi18g1217 1217
18 13700911 13706415 - Vvi18g1218 Vvi18g1218 1218
18 13719616 13730593 + Vvi18g1219 Vvi18g1219 1219
       

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