Hierarchical alignments

  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 two 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.
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Select Download 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
Vvi8g1092 . . . . . Bpe03g01265 . Bma10g00061 Cmo06g00419 . . . . . . . Cpe08g01064 . . . . . . . . . . . . . . . . . Cone19ag1216 . . . Cme04g02461 Blo07g01374 . . Bda05g01203 . . . . Sed02g0591 . . Cma06g00423 . Car06g00364 . . . Bhi11g02021 Tan08g1812 Cmetu04g3159 Lac10g2943 . . . Cla10g01866 Cam10g1923 Cec10g1978 Cco10g1950 Clacu10g1940 Cmu10g2684 Cre10g2072 Lsi03g01962 . . .
Vvi8g1093 . . . . . . . Bma10g00060 Cmo06g00418 Cmo14g00241 . . . . . . Cpe08g01065 . . . . . . . . . . . . . . . Cone10ag0198 Cone13ag1232 Cone19ag1218 . . . Cme04g02462 Blo07g01375 Blo09g00528 Bda03g01698 . . . . . Sed02g0593 . . Cma06g00421 Cma14g00250 Car06g00363 Car14g00228 Cpe03g00217 . Bhi11g02022 Tan08g1814 Cmetu04g0330 Lac10g2944 Hepe05g0313 . . Cla10g01867 Cam10g1924 Cec10g1979 Cco10g1951 Clacu10g1941 Cmu10g2685 Cre10g2073 Lsi03g01963 . . .
Vvi8g1094 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme04g02471 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi8g1095 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme04g02472 . . . . . . . . Sed04g1413 . . . . . . . . Bhi11g02031 Tan08g1823 Cmetu04g2275 . . . . . . . . . . . Lsi03g01970 . . .
Vvi8g1096 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1002 . . . . . . . . . Cmo18g00244 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi8g1097 . . . . . . . . . Cmo14g00237 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo09g00530 Bda03g01700 . . . . . . . . . Cma14g00247 . Car14g00225 Cpe03g00214 . . . . . . . . Cla10g01872 Cam10g1929 Cec10g1984 Cco10g1956 Clacu10g1946 Cmu10g2690 Cre10g2078 . Csa03g03347 Chy04g01990 .
Vvi8g1098 . . . . . . . Bma10g00057 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g03346 Chy04g01991 .
Vvi8g1099 . . . Bda03g00633 . . . . . . . Cma07g00885 Car03g01074 Car07g00874 Sed14g0032 . . Bhi03g02494 Tan03g0497 Cmetu08g0067 . Hepe04g0503 . . Cla04g00576 . . Cco04g0720 . . Cre04g0653 . . . . Lsi01g01277 Csa06g02632 Chy08g00890 . . . . . Bpe04g00596 . . Bma04g00502 . . Cmo07g00917 . . . . . Cpe19g00440 . . . . . . . . . . . . . . . . . Cme08g01406
Vvi8g1100 . . . . . Bpe03g01266 Bma04g01612 . Cmo06g00021 . . . . . . . Cpe08g01068 . . . . . . . . . . . . . . . . . . . . . Cme04g02112 Blo07g01376 . . . . . . . Sed02g0799 . . Cma06g00024 . Car06g00359 . . . Bhi11g02799 Tan08g1266 Cmetu04g1536 . . . . Cla10g01554 Cam10g1603 Cec10g1650 Cco10g1617 Clacu10g1617 Cmu10g2373 Cre10g1753 Lsi03g01618 Csa03g03345 . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 5304378 5307473 - Bda016610.1 Bda03g00633 633
3 56403737 56413670 - Bda018259.1 Bda03g01698 1698
3 56419615 56425237 + Bda018260.2 Bda03g01700 1700
5 60011340 60012907 + Bda022373.1 Bda05g01203 1203
3 59591271 59595719 - XM_039025709.1 Bhi03g02494 2494
11 57443827 57446007 + XM_039048222.1 Bhi11g02021 2021
11 57447222 57453124 - XM_039048221.1 Bhi11g02022 2022
11 57655962 57664719 + XM_039047981.1 Bhi11g02031 2031
11 75134587 75141269 + XM_039048562.1 Bhi11g02799 2799
7 33861542 33871038 + BLOR19306 Blo07g01374 1374
7 33864144 33869949 - BLOR19307 Blo07g01375 1375
7 33877725 33879306 - BLOR19308 Blo07g01376 1376
9 16488356 16492615 - BLOR21443 Blo09g00528 528
9 16510416 16515963 + BLOR21445 Blo09g00530 530
4 4406594 4411006 + Bma018971.1 Bma04g00502 502
4 52067343 52069380 - Bma020541.1 Bma04g01612 1612
10 569953 571276 - Bma003676.1 Bma10g00057 57
10 592505 594369 + Bma003679.2 Bma10g00060 60
10 595146 596691 - Bma003680.1 Bma10g00061 61
3 31224829 31226380 + Bpe013161.1 Bpe03g01265 1265
3 31227514 31238544 - Bpe013162.1 Bpe03g01266 1266
4 3797412 3801497 + Bpe025640 Bpe04g00596 596
10 29829635 29832880 - CaPI482276_10g016030.1 Cam10g1603 1603
10 33273481 33275186 + CaPI482276_10g019230.1 Cam10g1923 1923
10 33277609 33282455 - CaPI482276_10g019240.1 Cam10g1924 1924
10 33341257 33348925 + CaPI482276_10g019290.1 Cam10g1929 1929
3 8724348 8725427 + Carg10449-RA Car03g01074 1074
6 1976430 1978055 + Carg00949-RA Car06g00359 359
6 1991329 1996744 + Carg00945-RA Car06g00363 363
6 1997264 1999206 - Carg00944-RA Car06g00364 364
7 4693798 4699731 + Carg25570-RA Car07g00874 874
14 1056604 1061417 - Carg03730-RA Car14g00225 225
14 1073343 1075636 + Carg03727-RA Car14g00228 228
4 22188397 22188960 + CcPI632755_04g007200.1 Cco04g0720 720
10 29540879 29544124 - CcPI632755_10g016170.1 Cco10g1617 1617
10 33052039 33054179 + CcPI632755_10g019500.1 Cco10g1950 1950
10 33056496 33061282 - CcPI632755_10g019510.1 Cco10g1951 1951
10 33120886 33136875 + CcPI632755_10g019560.1 Cco10g1956 1956
10 30999917 31003159 - CePI673135_10g016500.1 Cec10g1650 1650
10 34549625 34551323 + CePI673135_10g019780.1 Cec10g1978 1978
10 34553684 34558384 - CePI673135_10g019790.1 Cec10g1979 1979
10 34620890 34628485 + CePI673135_10g019840.1 Cec10g1984 1984
4 25730218 25736112 - Chy4G087080.1 Chy04g01990 1990
4 25739079 25741608 - Chy4G087090.1 Chy04g01991 1991
8 16316270 16321498 - Chy8G154950.1 Chy08g00890 890
10 29543271 29546512 - ClG42_10g0161700.10 Clacu10g1617 1617
10 32985721 32987442 + ClG42_10g0194000.10 Clacu10g1940 1940
10 32989707 32995713 - ClG42_10g0194100.10 Clacu10g1941 1941
10 33052304 33068378 + ClG42_10g0194600.10 Clacu10g1946 1946
4 19454399 19455175 - ClCG04G005640.1 Cla04g00576 576
10 30943300 30952618 - ClCG10G016270.1 Cla10g01554 1554
10 34561189 34562910 + ClCG10G019640.2 Cla10g01866 1866
10 34564899 34571541 - ClCG10G019650.2 Cla10g01867 1867
10 34631682 34639931 + ClCG10G019700.2 Cla10g01872 1872
6 156257 156838 + CmaCh06G000240.1 Cma06g00024 24
6 1945861 1951094 + CmaCh06G004210.1 Cma06g00421 421
6 1951400 1953810 - CmaCh06G004230.1 Cma06g00423 423
7 4177829 4185454 + CmaCh07G008850.1 Cma07g00885 885
14 1075607 1081060 - CmaCh14G002470.1 Cma14g00247 247
14 1090696 1095130 + CmaCh14G002500.1 Cma14g00250 250
4 28476211 28494629 - MELO3C030717.2.1 Cme04g02112 2112
4 31147743 31149904 + MELO3C009408.2.1 Cme04g02461 2461
4 31152818 31158241 - MELO3C009407.2.1 Cme04g02462 2462
4 31220936 31223383 - MELO3C009396.2.1 Cme04g02471 2471
4 31223673 31233828 - MELO3C009393.2.1 Cme04g02472 2472
8 12085103 12091143 - MELO3C019099.2.1 Cme08g01406 1406
4 4645454 4650443 + PI0010265.1 Cmetu04g0330 330
4 7462100 7466967 - PI0022201.5 Cmetu04g1536 1536
4 4574614 4582933 + PI0025886.1 Cmetu04g2275 2275
4 4651568 4653858 - PI0024797.1 Cmetu04g3159 3159
8 6208012 6211004 - PI0006393.1 Cmetu08g0067 67
6 139954 143146 - CmoCh06G000210.1 Cmo06g00021 21
6 2003918 2014725 + CmoCh06G004180.1 Cmo06g00418 418
6 2014800 2017239 - CmoCh06G004190.1 Cmo06g00419 419
7 4397355 4403028 + CmoCh07G009170.1 Cmo07g00917 917
14 1091997 1096462 - CmoCh14G002370.1 Cmo14g00237 237
14 1109096 1113038 + CmoCh14G002410.1 Cmo14g00241 241
18 1611522 1613282 - CmoCh18G002440.1 Cmo18g00244 244
10 30161569 30164830 - CmPI595203_10g023730.1 Cmu10g2373 2373
10 33604788 33606523 + CmPI595203_10g026840.1 Cmu10g2684 2684
10 33608789 33613611 - CmPI595203_10g026850.1 Cmu10g2685 2685
10 33671460 33684275 + CmPI595203_10g026900.1 Cmu10g2690 2690
10 987633 988922 - Conep10aG0020400.1 Cone10ag0198 198
13 9438678 9441134 - Conep13aG0126500.1 Cone13ag1232 1232
19 8465636 8467248 - Conep19aG0125100.1 Cone19ag1216 1216
19 8468647 8471226 - Conep19aG0125300.1 Cone19ag1218 1218
3 1069213 1075490 - Cp4.1LG03g01470.1 Cpe03g00214 214
3 1085775 1089746 + Cp4.1LG03g01560.1 Cpe03g00217 217
8 8106286 8109053 + Cp4.1LG08g10480.1 Cpe08g01064 1064
8 8107943 8114015 - Cp4.1LG08g10730.1 Cpe08g01065 1065
8 8126840 8128184 - Cp4.1LG08g10780.1 Cpe08g01068 1068
19 3917919 3924539 - Cp4.1LG19g03680.1 Cpe19g00440 440
4 24375532 24376096 + CrPI670011_04g006530.1 Cre04g0653 653
10 31933695 31936940 - CrPI670011_10g017530.1 Cre10g1753 1753
10 35398261 35400000 + CrPI670011_10g020720.1 Cre10g2072 2072
10 35402468 35408546 - CrPI670011_10g020730.1 Cre10g2073 2073
10 35466640 35474308 + CrPI670011_10g020780.1 Cre10g2078 2078
3 30321621 30324826 + CsaV3_3G036510.1 Csa03g03345 3345
3 30330263 30333021 + CsaV3_3G036520.1 Csa03g03346 3346
3 30334895 30342598 + CsaV3_3G036530.1 Csa03g03347 3347
6 23173773 23180857 - CsaV3_6G040180.1 Csa06g02632 2632
4 57053000 57057211 - Hsped.04g05030.1 Hepe04g0503 503
5 3889688 3895863 + Hsped.05g03130.1 Hepe05g0313 313
10 44027931 44029782 + Lag0026988.1 Lac10g2943 2943
10 44032128 44037743 - Lag0026989.1 Lac10g2944 2944
1 11033086 11040625 + Lsi01G012770.1 Lsi01g01277 1277
3 27294493 27297490 - Lsi03G016180.1 Lsi03g01618 1618
3 31026974 31029097 + Lsi03G019620.1 Lsi03g01962 1962
3 31030971 31037059 - Lsi03G019630.1 Lsi03g01963 1963
3 31110745 31125900 + Lsi03G019700.1 Lsi03g01970 1970
2 43570521 43579851 + Sed0004549.1 Sed02g0591 591
2 43581092 43586015 - Sed0015688.1 Sed02g0593 593
2 45665055 45670896 - Sed0021719.1 Sed02g0799 799
4 28630787 28655474 - Sed0019421.2 Sed04g1413 1413
14 392580 404048 - Sed0018260.5 Sed14g0032 32
3 58863283 58867409 - Tan0006734.2 Tan03g0497 497
8 41283058 41288114 + Tan0006791.1 Tan08g1266 1266
8 70035845 70039132 + Tan0019897.2 Tan08g1812 1812
8 70044636 70050939 - Tan0000534.1 Tan08g1814 1814
8 70210383 70218875 + Tan0005111.1 Tan08g1823 1823
1 15722217 15727580 + Vvi1g1002 Vvi1g1002 1002
8 18394969 18396458 + Vvi8g1092 Vvi8g1092 1092
8 18396650 18401473 - Vvi8g1093 Vvi8g1093 1093
8 18402844 18412633 - Vvi8g1094 Vvi8g1094 1094
8 18415969 18425901 - Vvi8g1095 Vvi8g1095 1095
8 18427576 18427678 - Vvi8g1096 Vvi8g1096 1096
8 18427703 18443167 - Vvi8g1097 Vvi8g1097 1097
8 18446518 18449828 - Vvi8g1098 Vvi8g1098 1098
8 18452453 18458036 - Vvi8g1099 Vvi8g1099 1099
8 18459915 18461377 - Vvi8g1100 Vvi8g1100 1100
       

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