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
Vvi4g1272 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1273 Blo04g00967 . . . Bpe15g00400 . . . Cmo02g00627 Cmo20g01075 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda14g01056 . . Bma03g01031 . . . . . Cma20g01067 . . Cpe05g01065 Cpe16g00078 Bhi10g01661 . . . . . . Cla02g00064 Cam02g0065 Cec02g0067 Cco02g0060 Clacu02g0064 Cmu02g0064 Cre02g0403 . . . Cme11g00068
Vvi4g1274 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1275 . . . . . . . . Cmo02g00628 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe05g01064 . Bhi10g01662 Tan07g0871 Cmetu11g0434 . Hepe08g1250 . . . . . . . . . Lsi10g00715 . . Cme11g00067
Vvi4g1276 . . . . . . . . . . Cma03g01087 . Car03g00977 . Sed14g0216 . . Bhi03g01372 Tan03g1320 Cmetu08g1085 . . . . Cla01g01524 Cam01g1594 Cec04g1238 Cco04g1308 . . Cre04g1183 . . . . Lsi01g01140 . . Cme08g01075 . . . . . . . . . Cmo03g01073 . . . . . . . . . . . . . . . . . . . . . . Csa06g02791 Chy02g01044 .
Vvi4g1277 . . . . . . . Bma15g00800 . . . Cma07g00793 . Car07g00779 . Cpe19g00536 . Bhi03g01370 . . . . . . Cla01g01523 Cam01g1593 Cec04g1237 Cco04g1307 Clacu01g1617 Cmu01g1503 Cre04g1182 . . Cone6ag1291 . Lsi01g01141 . . Cme08g01076 . . . . . . . . . . Cmo07g00816 . . . . . . . . . . . . . . . . . . . . . Csa06g02790 Chy02g01045 .
Vvi4g1278 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1279 Blo04g00966 . . . Bpe15g00401 . . . . Cmo20g01074 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma20g01066 . . . Cpe16g00079 Bhi10g01664 Tan07g0869 Cmetu11g0034 . Hepe08g1248 . . Cla02g00061 Cam02g0062 Cec02g0064 Cco02g0057 Clacu02g0061 Cmu02g0060 Cre02g0400 Lsi10g00718 . . Cme11g00066
Vvi4g1280 . . Bda04g00329 Bda10g00372 . . Bma09g00395 . . . Cma03g01089 Cma07g00796 Car03g00980 Car07g00781 Sed14g0223 Cpe19g00534 Cpe10g00343 Bhi03g01358 Tan03g1315 Cmetu11g1734 . Hepe04g1118 . . Cla01g01522 Cam01g1591 Cec04g1234 Cco04g1305 Clacu01g1616 Cmu01g1502 Cre04g1180 . . Cone8ag1461 . Lsi01g01144 . . Cme08g01078 . Blo06g00200 . . Bpe10g00254 Bpe06g00258 . . . Cmo03g01075 Cmo07g00819 . . . . . . . . . . . . . . . . . . . . . Csa06g02787 Chy02g01048 .
Vvi4g1281 Blo04g00965 . . . Bpe15g00402 . . . Cmo02g00629 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda14g01054 . . Bma03g01030 . . . . . . . . Cpe05g01063 . Bhi10g01666 . . . . . . Cla02g00060 Cam02g0061 Cec02g0063 Cco02g0056 Clacu02g0060 Cmu02g0059 Cre02g0399 Lsi10g00720 . . Cme11g00064
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 47712302 47712913 + Bda019217.1 Bda04g00329 329
10 35118386 35119117 + Bda007187.1 Bda10g00372 372
14 9006505 9009541 - Bda027868.1 Bda14g01054 1054
14 9017007 9020473 - Bda027870.1 Bda14g01056 1056
3 28323433 28326900 - XM_039026364.1 Bhi03g01358 1358
3 28350919 28354317 - XM_039025285.1 Bhi03g01370 1370
3 28357881 28361804 - XM_039024998.1 Bhi03g01372 1372
10 41998363 42002196 + XM_039044583.1 Bhi10g01661 1661
10 42004621 42006164 + XM_039044899.1 Bhi10g01662 1662
10 42126902 42130176 - XM_039044627.1 Bhi10g01664 1664
10 42182999 42187700 + XM_039045406.1 Bhi10g01666 1666
4 11902307 11910161 - BLOR13877 Blo04g00965 965
4 11941301 11946666 + BLOR13878 Blo04g00966 966
4 11952974 11956357 - BLOR13879 Blo04g00967 967
6 8478312 8478932 - BLOR16783 Blo06g00200 200
3 11837414 11840516 - Bma017384.1 Bma03g01030 1030
3 11944121 11947562 - Bma017386.1 Bma03g01031 1031
9 33200662 33201273 + Bma029347.1 Bma09g00395 395
15 17728408 17730016 - Bma013889.2 Bma15g00800 800
6 13313700 13314311 + Bpe019750.1 Bpe06g00258 258
10 9555078 9555692 + Bpe002588.1 Bpe10g00254 254
15 15512866 15516307 + Bpe001337.1 Bpe15g00400 400
15 15519019 15520680 - Bpe001338.1 Bpe15g00401 401
15 15527691 15530800 + Bpe001340.1 Bpe15g00402 402
1 29395786 29397378 - CaPI482276_01g015910.1 Cam01g1591 1591
1 29416706 29428878 - CaPI482276_01g015930.1 Cam01g1593 1593
1 29429209 29432421 - CaPI482276_01g015940.1 Cam01g1594 1594
2 1728004 1731538 - CaPI482276_02g000610.1 Cam02g0061 61
2 1734524 1737766 + CaPI482276_02g000620.1 Cam02g0062 62
2 1753777 1756918 - CaPI482276_02g000650.1 Cam02g0065 65
3 7550860 7554153 + Carg10544-RA Car03g00977 977
3 7568044 7568816 + Carg10541-RA Car03g00980 980
7 4079453 4082650 + Carg05301-RA Car07g00779 779
7 4096880 4097559 + Carg05303-RA Car07g00781 781
2 598179 601710 - CcPI632755_02g000560.1 Cco02g0056 56
2 605782 608931 + CcPI632755_02g000570.1 Cco02g0057 57
2 624667 627810 - CcPI632755_02g000600.1 Cco02g0060 60
4 28325894 28326660 - CcPI632755_04g013050.1 Cco04g1305 1305
4 28351352 28354228 - CcPI632755_04g013070.1 Cco04g1307 1307
4 28359028 28362210 - CcPI632755_04g013080.1 Cco04g1308 1308
2 602085 605772 - CePI673135_02g000630.1 Cec02g0063 63
2 608126 609034 + CePI673135_02g000640.1 Cec02g0064 64
2 625525 628643 - CePI673135_02g000670.1 Cec02g0067 67
4 31887456 31888801 - CePI673135_04g012340.1 Cec04g1234 1234
4 31912977 31920322 - CePI673135_04g012370.1 Cec04g1237 1237
4 31920653 31923837 - CePI673135_04g012380.1 Cec04g1238 1238
2 7154818 7158087 + Chy2G033110.1 Chy02g01044 1044
2 7162702 7165601 + Chy2G033120.1 Chy02g01045 1045
2 7186730 7187495 + Chy2G033150.1 Chy02g01048 1048
1 28189043 28190663 - ClG42_01g0161600.10 Clacu01g1616 1616
1 28197395 28203910 - ClG42_01g0161700.10 Clacu01g1617 1617
2 619816 623329 - ClG42_02g0006000.10 Clacu02g0060 60
2 626146 629318 + ClG42_02g0006100.10 Clacu02g0061 61
2 645190 648299 - ClG42_02g0006400.10 Clacu02g0064 64
1 29721734 29722890 - ClCG01G015500.2 Cla01g01522 1522
1 29731563 29756181 - ClCG01G015510.2 Cla01g01523 1523
1 29755909 29759765 - ClCG01G015530.1 Cla01g01524 1524
2 613984 618559 - ClCG02G000580.2 Cla02g00060 60
2 620728 623942 + ClCG02G000590.2 Cla02g00061 61
2 635635 642914 - ClCG02G000600.2 Cla02g00064 64
3 7441160 7449608 + CmaCh03G010870.1 Cma03g01087 1087
3 7466835 7467545 + CmaCh03G010890.1 Cma03g01089 1089
7 3599565 3602865 + CmaCh07G007930.1 Cma07g00793 793
7 3617126 3623093 + CmaCh07G007960.1 Cma07g00796 796
20 8035512 8038470 + CmaCh20G010660.1 Cma20g01066 1066
20 8047687 8051349 - CmaCh20G010670.1 Cma20g01067 1067
8 7057444 7061784 + MELO3C008044.2.1 Cme08g01075 1075
8 7064580 7068769 + MELO3C008045.2.1 Cme08g01076 1076
8 7087227 7088204 + MELO3C008047.2.1 Cme08g01078 1078
11 540874 544309 - MELO3C023252.2.1 Cme11g00064 64
11 551946 554318 + MELO3C023254.2.1 Cme11g00066 66
11 560167 562175 - MELO3C023255.2.1 Cme11g00067 67
11 564239 567386 - MELO3C023256.2.1 Cme11g00068 68
8 18453536 18458006 - PI0016717.1 Cmetu08g1085 1085
11 30460015 30462273 - PI0013520.1 Cmetu11g0034 34
11 30447208 30449408 + PI0013189.1 Cmetu11g0434 434
11 29263595 29264235 - PI0016898.1 Cmetu11g1734 1734
2 3892742 3896073 + CmoCh02G006270.1 Cmo02g00627 627
2 3906752 3908057 + CmoCh02G006280.1 Cmo02g00628 628
2 3911668 3914408 + CmoCh02G006290.1 Cmo02g00629 629
3 8022886 8030495 + CmoCh03G010730.1 Cmo03g01073 1073
3 8046980 8047914 + CmoCh03G010750.1 Cmo03g01075 1075
7 3781436 3784840 + CmoCh07G008160.1 Cmo07g00816 816
7 3798815 3805601 + CmoCh07G008190.1 Cmo07g00819 819
20 9934282 9937224 + CmoCh20G010740.1 Cmo20g01074 1074
20 9949118 9953331 - CmoCh20G010750.1 Cmo20g01075 1075
1 28538282 28539046 - CmPI595203_01g015020.1 Cmu01g1502 1502
1 28545795 28552310 - CmPI595203_01g015030.1 Cmu01g1503 1503
2 619112 623273 - CmPI595203_02g000590.1 Cmu02g0059 59
2 625404 628576 + CmPI595203_02g000600.1 Cmu02g0060 60
2 644455 647564 - CmPI595203_02g000640.1 Cmu02g0064 64
6 10342630 10348105 - Conep06aG0133900.1 Cone6ag1291 1291
8 11240409 11241443 - Conep08aG0150300.1 Cone8ag1461 1461
5 7037914 7041363 - Cp4.1LG05g10620.1 Cpe05g01063 1063
5 7045251 7046227 - Cp4.1LG05g10670.1 Cpe05g01064 1064
5 7047728 7050936 - Cp4.1LG05g10640.1 Cpe05g01065 1065
10 1998127 1999138 - Cp4.1LG10g03410.1 Cpe10g00343 343
16 1571677 1575523 + Cp4.1LG16g00780.1 Cpe16g00078 78
16 1588437 1591477 - Cp4.1LG16g00820.1 Cpe16g00079 79
19 4530320 4533018 - Cp4.1LG19g11930.1 Cpe19g00534 534
19 4546179 4548187 - Cp4.1LG19g11970.1 Cpe19g00536 536
2 1150701 1154222 - CrPI670011_02g003990.1 Cre02g0399 399
2 1160634 1163843 + CrPI670011_02g004000.1 Cre02g0400 400
2 1179779 1182924 - CrPI670011_02g004030.1 Cre02g0403 403
4 30400511 30402129 - CrPI670011_04g011800.1 Cre04g1180 1180
4 30426052 30433468 - CrPI670011_04g011820.1 Cre04g1182 1182
4 30433799 30437014 - CrPI670011_04g011830.1 Cre04g1183 1183
6 24304724 24306996 - CsaV3_6G041730.1 Csa06g02787 2787
6 24327518 24330389 - CsaV3_6G041760.1 Csa06g02790 2790
6 24333822 24338279 - CsaV3_6G041770.1 Csa06g02791 2791
4 66094109 66094889 - Hsped.04g11180.1 Hepe04g1118 1118
8 13291241 13295510 + Hsped.08g12480.1 Hepe08g1248 1248
8 13322690 13324299 - Hsped.08g12500.1 Hepe08g1250 1250
1 9583611 9587817 + Lsi01G011400.1 Lsi01g01140 1140
1 9592625 9596500 + Lsi01G011410.1 Lsi01g01141 1141
1 9621284 9622449 + Lsi01G011440.1 Lsi01g01144 1144
10 10008638 10016446 + Lsi10G007150.1 Lsi10g00715 715
10 10056507 10059556 - Lsi10G007180.1 Lsi10g00718 718
10 10067912 10071827 + Lsi10G007200.1 Lsi10g00720 720
14 2408956 2412476 + Sed0005738.1 Sed14g0216 216
14 2454099 2454986 + Sed0007275.1 Sed14g0223 223
3 69651855 69653295 - Tan0003625.1 Tan03g1315 1315
3 69688853 69692735 - Tan0021662.1 Tan03g1320 1320
7 14777265 14780553 + Tan0014469.1 Tan07g0869 869
7 14950641 14952819 - Tan0001381.1 Tan07g0871 871
4 22216317 22217379 - Vvi4g1272 Vvi4g1272 1272
4 22226308 22252207 + Vvi4g1273 Vvi4g1273 1273
4 22252565 22254371 + Vvi4g1274 Vvi4g1274 1274
4 22259238 22260359 + Vvi4g1275 Vvi4g1275 1275
4 22273571 22279015 + Vvi4g1276 Vvi4g1276 1276
4 22283581 22287943 + Vvi4g1277 Vvi4g1277 1277
4 22297589 22298477 + Vvi4g1278 Vvi4g1278 1278
4 22313151 22315063 - Vvi4g1279 Vvi4g1279 1279
4 22359046 22359457 + Vvi4g1280 Vvi4g1280 1280
4 22391450 22398790 + Vvi4g1281 Vvi4g1281 1281
       

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