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
Vvi5g899 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g900 . . . . . . . . . . . Cma14g01896 . Car14g01698 Sed02g1501 Cpe08g00399 Cpe03g01595 Bhi01g00229 Tan10g0517 Cmetu06g0717 . Hepe05g1763 . Lcy11g1777 . . . . . . . . . . . Lsi05g01844 . . Cme06g00379 . . . . . . . Bma06g01282 . Cmo06g01251 Cmo14g01948 . . . . . . . . . . . . . . . . . . . . . Csa03g01093 Chy06g00362 .
Vvi5g901 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g902 Blo01g00329 . . Bda08g00034 Bpe04g01069 . Bma04g01053 Bma05g01290 Cmo08g00997 . . . . . . . . . . . . . . . Cla06g00753 Cam06g0805 Cec06g0816 . Clacu06g0808 Cmu06g0781 Cre06g1559 . . Cone7ag0393 . . . Chy05g00556 . . . . . Bpe05g01140 . . . Sed09g0187 . . Cma08g01025 . Car08g00902 . . Cpe17g00251 Bhi12g01502 Tan06g2304 Cmetu04g1927 Lac12g2048 Hepe03g0356 . Lcy13g0460 . . . . . . . Lsi09g01146 . . Cme05g00713
Vvi5g903 . . Bda03g01124 Bda08g00035 . . . Bma05g01291 Cmo08g00995 . . . . . . . . . . . . . . . Cla06g00758 Cam06g0808 Cec06g0821 Cco06g0826 Clacu06g0810 Cmu06g0784 Cre06g1562 . . Cone7ag0394 . . . Chy05g00558 . . . . . Bpe05g01141 . . . Sed04g2065 . . Cma08g01023 . Car08g00900 . . . Bhi12g01500 Tan06g2302 Cmetu05g0661 Lac12g2046 Hepe03g0358 . Lcy13g0462 . . . . . . . Lsi09g01142 . . Cme05g00716
Vvi5g904 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g905 Blo01g00331 . . Bda08g00036 . . . Bma05g01292 . Cmo17g00103 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe05g01142 . . . . . . . Cma17g00100 . Car17g00090 Cpe12g00089 . . . . . . . . . . . . . . . . . . .
Vvi5g906 . Blo12g00115 Bda03g01126 . . . Bma04g01055 . Cmo08g00991 . . . . . . . . . . . . . . . Cla06g00760 . Cec06g0822 . Clacu06g0812 Cmu06g0786 . . . . . . . Chy05g00560 . . . . . . . . . Sed04g2068 . . Cma08g01021 . Car08g00898 . . Cpe17g00255 Bhi12g01498 Tan06g2300 Cmetu05g0712 Lac12g2044 Hepe03g0359 . Lcy13g0466 . . . . . . . Lsi09g01139 . . Cme05g00718
Vvi5g907 . . Bda03g01128 . . . Bma04g01056 . . Cmo17g00102 . . . . . . . . . . . . . . Cla06g00762 Cam06g0811 Cec06g0823 Cco06g0829 Clacu06g0813 Cmu06g0787 Cre06g1565 . . . . . . Chy05g00561 . . . . . . . . . Sed09g0186 . . . Cma17g00099 . Car17g00088 Cpe12g00088 . Bhi12g01497 Tan06g2299 Cmetu05g0011 . Hepe03g0361 . . . . . . . . . Lsi09g01138 . . Cme05g00719
Vvi5g908 . . . . . . . . . . Cma06g01231 Cma14g01897 . Car14g01712 . Cpe08g00400 Cpe03g01596 Bhi01g00227 Tan10g0516 . . Hepe05g1764 . . . . . . . . . . . Cone7ag0396 . Lsi05g01845 . . . . . . . . . . . . Cmo06g01250 Cmo14g01949 . . . . . . . . . . . . . . . . . . . . . Csa03g01091 Chy06g00361 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 11808012 11809064 - Bda017176.1 Bda03g01124 1124
3 11813173 11813670 + Bda017177.1 Bda03g01126 1126
3 11830793 11833447 - Bda017179.1 Bda03g01128 1128
8 290244 291940 + Bda024425.1 Bda08g00034 34
8 292221 292820 - Bda024426.1 Bda08g00035 35
8 296797 298743 + Bda024427.2 Bda08g00036 36
1 4249636 4254931 - XM_039044535.1 Bhi01g00227 227
1 4353108 4357037 - XM_039037672.1 Bhi01g00229 229
12 48348678 48354249 + XM_039019904.1 Bhi12g01497 1497
12 48354637 48358962 - XM_039019907.1 Bhi12g01498 1498
12 48382317 48384214 + XM_039019239.1 Bhi12g01500 1500
12 48452704 48458488 - XM_039020083.1 Bhi12g01502 1502
1 3990205 3991899 + BLOR00329 Blo01g00329 329
1 4001263 4003475 + BLOR00331 Blo01g00331 331
12 8294357 8294758 - BLOR04134 Blo12g00115 115
4 19598462 19599788 + Bma019686.1 Bma04g01053 1053
4 19698362 19698754 + Bma019690.1 Bma04g01055 1055
4 19707798 19710506 - Bma019691.1 Bma04g01056 1056
5 52272695 52274185 + Bma022480.1 Bma05g01290 1290
5 52274680 52275687 - Bma022481.1 Bma05g01291 1291
5 52283736 52285620 + Bma031245 Bma05g01292 1292
6 49905907 49907980 - Bma024390.1 Bma06g01282 1282
4 8141966 8143881 + Bpe015739.2 Bpe04g01069 1069
5 23684783 23686514 + Bpe018558.1 Bpe05g01140 1140
5 23686796 23687392 - Bpe018559.1 Bpe05g01141 1141
5 23690568 23692577 + Bpe018560.1 Bpe05g01142 1142
6 11101004 11101697 + CaPI482276_06g008050.1 Cam06g0805 805
6 11141398 11142672 - CaPI482276_06g008080.1 Cam06g0808 808
6 11185423 11189742 - CaPI482276_06g008110.1 Cam06g0811 811
8 6026819 6029053 - Carg11026-RA Car08g00898 898
8 6037984 6039183 + Carg11024-RA Car08g00900 900
8 6042778 6045823 - Carg11022-RA Car08g00902 902
14 13492552 13501691 + Carg24765-RA Car14g01698 1698
14 13585132 13587164 - Carg14911-RA Car14g01712 1712
17 514072 517504 - Carg10144-RA Car17g00088 88
17 521155 522059 + Carg10142-RA Car17g00090 90
6 9945995 9947272 - CcPI632755_06g008260.1 Cco06g0826 826
6 9992314 9996682 - CcPI632755_06g008290.1 Cco06g0829 829
6 10014987 10019907 + CePI673135_06g008160.1 Cec06g0816 816
6 10069849 10071123 - CePI673135_06g008210.1 Cec06g0821 821
6 10109730 10114486 + CePI673135_06g008220.1 Cec06g0822 822
6 10114492 10118811 - CePI673135_06g008230.1 Cec06g0823 823
5 6082640 6087513 + Chy5G096020.1 Chy05g00556 556
5 6109318 6110520 - Chy5G096040.1 Chy05g00558 558
5 6137469 6139954 + Chy5G096060.1 Chy05g00560 560
5 6142010 6151219 - Chy5G096070.1 Chy05g00561 561
6 2417886 2422163 - Chy6G108890.1 Chy06g00361 361
6 2425505 2428505 - Chy6G108900.1 Chy06g00362 362
6 9752638 9757229 + ClG42_06g0080800.10 Clacu06g0808 808
6 9798998 9800278 - ClG42_06g0081000.10 Clacu06g0810 810
6 9849500 9849874 + ClG42_06g0081200.10 Clacu06g0812 812
6 9852937 9858510 - ClG42_06g0081300.10 Clacu06g0813 813
6 10036298 10042815 + ClCG06G007770.2 Cla06g00753 753
6 10087805 10089085 - ClCG06G007820.2 Cla06g00758 758
6 10140412 10140786 + ClCG06G007840.2 Cla06g00760 760
6 10143849 10149703 - ClCG06G007850.2 Cla06g00762 762
6 8207458 8212254 + CmaCh06G012310.1 Cma06g01231 1231
8 6389036 6391082 - CmaCh08G010210.1 Cma08g01021 1021
8 6400594 6401793 + CmaCh08G010230.1 Cma08g01023 1023
8 6405677 6411251 - CmaCh08G010250.1 Cma08g01025 1025
14 13410652 13414771 + CmaCh14G018960.1 Cma14g01896 1896
14 13415635 13420809 + CmaCh14G018970.1 Cma14g01897 1897
17 483372 487018 - CmaCh17G000990.1 Cma17g00099 99
17 488237 491230 + CmaCh17G001000.1 Cma17g00100 100
5 8358680 8361813 + MELO3C020449.2.1 Cme05g00713 713
5 8372399 8373820 - MELO3C020448.2.1 Cme05g00716 716
5 8402269 8405820 + MELO3C020446.2.1 Cme05g00718 718
5 8406345 8415039 - MELO3C020444.2.1 Cme05g00719 719
6 2373935 2385186 - MELO3C006310.2.1 Cme06g00379 379
4 8854961 8862061 + PI0024573.1 Cmetu04g1927 1927
5 16424929 16432446 + PI0020609.1 Cmetu05g0011 11
5 16460760 16461963 + PI0008058.1 Cmetu05g0661 661
5 16432858 16437649 - PI0004036.1 Cmetu05g0712 712
6 2598534 2602764 - PI0026582.1 Cmetu06g0717 717
6 9451992 9457353 - CmoCh06G012500.1 Cmo06g01250 1250
6 9458147 9462679 - CmoCh06G012510.1 Cmo06g01251 1251
8 6446115 6446642 - CmoCh08G009910.1 Cmo08g00991 991
8 6455586 6456785 + CmoCh08G009950.1 Cmo08g00995 995
8 6460455 6465617 - CmoCh08G009970.1 Cmo08g00997 997
14 14402780 14407237 + CmoCh14G019480.1 Cmo14g01948 1948
14 14407766 14412996 + CmoCh14G019490.1 Cmo14g01949 1949
17 553460 557149 - CmoCh17G001020.1 Cmo17g00102 102
17 558572 561380 + CmoCh17G001030.1 Cmo17g00103 103
6 9569876 9570571 + CmPI595203_06g007810.1 Cmu06g0781 781
6 9616416 9617696 - CmPI595203_06g007840.1 Cmu06g0784 784
6 9667049 9667423 + CmPI595203_06g007860.1 Cmu06g0786 786
6 9670489 9676061 - CmPI595203_06g007870.1 Cmu06g0787 787
7 1752040 1754782 + Conep07aG0040200.1 Cone7ag0393 393
7 1756379 1757290 - Conep07aG0040300.1 Cone7ag0394 394
7 1767262 1771450 + Conep07aG0040500.1 Cone7ag0396 396
3 12306680 12311005 + Cp4.1LG03g17980.1 Cpe03g01595 1595
3 12311767 12316980 + Cp4.1LG03g17970.1 Cpe03g01596 1596
8 2538766 2541850 + Cp4.1LG08g02760.1 Cpe08g00399 399
8 2546244 2550562 + Cp4.1LG08g02790.1 Cpe08g00400 400
12 527227 532354 - Cp4.1LG12g00950.1 Cpe12g00088 88
12 533710 542607 + Cp4.1LG12g00850.1 Cpe12g00089 89
17 1660205 1665958 + Cp4.1LG17g03310.1 Cpe17g00251 251
17 1680845 1682861 + Cp4.1LG17g03320.1 Cpe17g00255 255
6 10764119 10764812 + CrPI670011_06g015590.1 Cre06g1559 1559
6 10812133 10813410 - CrPI670011_06g015620.1 Cre06g1562 1562
6 10849577 10853888 - CrPI670011_06g015650.1 Cre06g1565 1565
3 8658465 8664071 - CsaV3_3G010910.1 Csa03g01091 1091
3 8665307 8670413 - CsaV3_3G010930.1 Csa03g01093 1093
3 5115783 5121262 + Hsped.03g03560.1 Hepe03g0356 356
3 5131763 5133068 - Hsped.03g03580.1 Hepe03g0358 358
3 5164567 5165975 + Hsped.03g03590.1 Hepe03g0359 359
3 5169788 5175966 - Hsped.03g03610.1 Hepe03g0361 361
5 67934382 67938833 + Hsped.05g17630.1 Hepe05g1763 1763
5 67942787 67947833 + Hsped.05g17640.1 Hepe05g1764 1764
12 37514969 37518662 - Lag0016416.1 Lac12g2044 2044
12 37547846 37549120 + Lag0016418.1 Lac12g2046 2046
12 37560497 37563442 - Lag0016420.1 Lac12g2048 2048
11 41568145 41580440 + Maker00031955 Lcy11g1777 1777
13 5509030 5514328 + Maker00023328 Lcy13g0460 460
13 5524487 5525767 - Maker00023249 Lcy13g0462 462
13 5562947 5567402 + Maker00023730 Lcy13g0466 466
5 25693622 25697562 + Lsi05G018440.1 Lsi05g01844 1844
5 25699448 25704770 + Lsi05G018450.1 Lsi05g01845 1845
9 18274317 18278516 + Lsi09G011380.1 Lsi09g01138 1138
9 18277785 18284498 - Lsi09G011390.1 Lsi09g01139 1139
9 18328018 18329280 + Lsi09G011420.1 Lsi09g01142 1142
9 18362625 18367942 - Lsi09G011460.1 Lsi09g01146 1146
2 50900149 50904348 + Sed0025050.6 Sed02g1501 1501
4 35017164 35018697 - Sed0021235.1 Sed04g2065 2065
4 35044957 35049861 + Sed0007925.1 Sed04g2068 2068
9 1464659 1471663 + Sed0004631.1 Sed09g0186 186
9 1478192 1485096 - Sed0026703.1 Sed09g0187 187
6 74112939 74117846 + Tan0015767.1 Tan06g2299 2299
6 74118247 74123833 - Tan0020375.1 Tan06g2300 2300
6 74168551 74170089 + Tan0022393.1 Tan06g2302 2302
6 74192862 74199577 - Tan0005927.1 Tan06g2304 2304
10 4134727 4139585 - Tan0001842.2 Tan10g0516 516
10 4141748 4146072 - Tan0014841.1 Tan10g0517 517
5 14190412 14193748 + Vvi5g899 Vvi5g899 899
5 14230836 14235424 + Vvi5g900 Vvi5g900 900
5 14235487 14238846 + Vvi5g901 Vvi5g901 901
5 14282920 14291181 + Vvi5g902 Vvi5g902 902
5 14295822 14297895 - Vvi5g903 Vvi5g903 903
5 14352479 14355765 + Vvi5g904 Vvi5g904 904
5 14365852 14385345 + Vvi5g905 Vvi5g905 905
5 14513413 14516745 + Vvi5g906 Vvi5g906 906
5 14517472 14521074 - Vvi5g907 Vvi5g907 907
5 14531097 14546195 - Vvi5g908 Vvi5g908 908
       

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