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
Vvi2g232 . . . . . . . Bma14g00105 . . Cma02g00941 . Car02g00689 . . . Cpe05g00773 . . . . . . . . . . . . . . . . . . . Csa05g00169 Chy09g01329 . . . Bda07g01951 . . . . . . Cmo02g00950 . . . . . . . Bhi12g00091 . . Lac11g1930 Hepe06g1441 . . Cla01g00150 Cam01g0155 Cec01g0151 Cco01g0157 Clacu01g0150 Cmu01g0150 Cre09g2356 Lsi09g00141 . . Cme09g01876
Vvi2g233 . . . . . . . . Cmo06g00591 Cmo16g01275 . . . . . Cpe14g01015 . . . . . . . . Cla10g00086 Cam10g0085 Cec10g0089 Cco10g0091 Clacu10g0086 Cmu10g0933 Cre10g0347 Cone8ag0554 Cone12ag0553 . . Lsi07g01112 . . Cme06g02392 . . . . . . . Bma12g00254 . . . Cma06g00588 . Car06g00520 Car16g01157 Cpe08g00914 . . . . . . . . . . . . . . . . . . .
Vvi2g234 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda07g01953 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g235 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g236 . . . . . . . Bma14g00104 . . . Cma15g01313 . Car15g01181 . . . . . . . . . . . . . . . . . . Cone12ag0554 . . . Csa05g00168 Chy09g01330 . Blo03g00807 . Bda07g00149 . . Bpe11g00366 . . . . Cmo15g01378 . . . . . . Bhi12g00090 . . Lac11g1929 Hepe06g1440 . Lcy12g1526 Cla01g00149 Cam01g0154 Cec01g0150 Cco01g0156 Clacu01g0149 Cmu01g0149 Cre09g2357 Lsi09g00140 . . Cme09g01878
Vvi2g237 . . . . . . . . . . Cma02g00942 . Car02g00690 . . . Cpe05g00772 . . . . . . . . . . . . . . Cone8ag0597 Cone12ag0591 . . . Csa05g00167 Chy09g01331 . . . . Bda09g00645 Bpe08g00896 . . . . . . . . . . . . Bhi12g00089 . . Lac11g1928 Hepe06g1439 . Lcy12g1523 Cla01g00148 Cam01g0153 Cec01g0149 Cco01g0155 Clacu01g0148 Cmu01g0148 Cre09g2358 Lsi09g00139 . . Cme09g01879
Vvi2g238 . . . . . . . Bma14g00102 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo03g00804 . Bda07g00151 Bda09g00643 Bpe08g00898 Bpe11g00368 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g239 . . . . . . . . . Cmo16g01276 . . . . . Cpe14g01016 . . . . . . . . Cla10g00084 Cam10g0081 Cec10g0085 Cco10g0088 Clacu10g0083 Cmu10g0929 Cre10g0344 . Cone12ag0590 . . Lsi07g01110 . . Cme06g02390 . . . . . . . . . . . Cma06g00584 Cma16g01230 . Car16g01159 Cpe08g00915 . . . . . . . . . . . . . . . . . . .
Vvi2g240 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda07g01954 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g241 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0186 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 1814192 1814656 + Bda025216.2 Bda07g00149 149
7 1866974 1868589 - Bda025218.1 Bda07g00151 151
7 36934946 36937500 + Bda028931.2 Bda07g01951 1951
7 36939837 36943506 - Bda028932.3 Bda07g01953 1953
7 36946040 36946800 - Bda028933.1 Bda07g01954 1954
9 9669577 9671422 + Bda031283.1 Bda09g00643 643
9 9695998 9700505 - Bda031286.1 Bda09g00645 645
12 3031353 3036327 - XM_039020053.1 Bhi12g00089 89
12 3039827 3040576 - XM_039020088.1 Bhi12g00090 90
12 3052599 3058046 - XM_039019623.1 Bhi12g00091 91
3 33317713 33319408 + BLOR11985 Blo03g00804 804
3 33407158 33407622 - BLOR11988 Blo03g00807 807
12 3287423 3302588 + Bma007148.1 Bma12g00254 254
14 1425675 1427239 + Bma010508.1 Bma14g00102 102
14 1445264 1445728 - Bma010509.1 Bma14g00104 104
14 1446625 1449765 - Bma010510.1 Bma14g00105 105
8 11334151 11341193 + Bpe026156 Bpe08g00896 896
8 11361155 11362961 - Bpe023021.1 Bpe08g00898 898
11 2764109 2764573 + Bpe003741.1 Bpe11g00366 366
11 2784746 2786427 - Bpe003742.1 Bpe11g00368 368
1 1914857 1919689 - CaPI482276_01g001530.1 Cam01g0153 153
1 1923810 1924274 - CaPI482276_01g001540.1 Cam01g0154 154
1 1926302 1930507 - CaPI482276_01g001550.1 Cam01g0155 155
10 2397176 2400383 - CaPI482276_10g000810.1 Cam10g0081 81
10 2438802 2449433 + CaPI482276_10g000850.1 Cam10g0085 85
2 5110865 5114205 + Carg08534-RA Car02g00689 689
2 5114896 5118330 + Carg08533-RA Car02g00690 690
6 2917121 2925724 + Carg16272-RA Car06g00520 520
15 9215601 9216065 + Carg21305-RA Car15g01181 1181
16 9862646 9871557 - Carg19484-RA Car16g01157 1157
16 9882065 9888789 + Carg19482-RA Car16g01159 1159
1 1485565 1490133 - CcPI632755_01g001550.1 Cco01g0155 155
1 1494442 1494906 - CcPI632755_01g001560.1 Cco01g0156 156
1 1499683 1504091 - CcPI632755_01g001570.1 Cco01g0157 157
10 801716 816050 - CcPI632755_10g000880.1 Cco10g0088 88
10 843819 854485 + CcPI632755_10g000910.1 Cco10g0091 91
1 1482687 1487473 - CePI673135_01g001490.1 Cec01g0149 149
1 1491556 1492020 - CePI673135_01g001500.1 Cec01g0150 150
1 1494046 1498373 - CePI673135_01g001510.1 Cec01g0151 151
10 829404 832608 - CePI673135_10g000850.1 Cec10g0085 85
10 870493 881448 + CePI673135_10g000890.1 Cec10g0089 89
9 15156370 15161042 + Chy9G170450.1 Chy09g01329 1329
9 15161276 15161740 + Chy9G170460.1 Chy09g01330 1330
9 15163118 15167188 + Chy9G170470.1 Chy09g01331 1331
1 1534478 1539324 - ClG42_01g0014800.10 Clacu01g0148 148
1 1543495 1543959 - ClG42_01g0014900.10 Clacu01g0149 149
1 1545990 1550251 - ClG42_01g0015000.10 Clacu01g0150 150
10 1120015 1122405 - ClG42_10g0008300.10 Clacu10g0083 83
10 1161444 1171988 + ClG42_10g0008600.10 Clacu10g0086 86
1 1531077 1536165 - ClCG01G001520.1 Cla01g00148 148
1 1540320 1540784 - ClCG01G001530.1 Cla01g00149 149
1 1542637 1547125 - ClCG01G001540.2 Cla01g00150 150
10 836218 841652 - ClCG10G000810.2 Cla10g00084 84
10 867478 891804 + ClCG10G000820.2 Cla10g00086 86
2 5580942 5584935 + CmaCh02G009410.1 Cma02g00941 941
2 5585122 5588530 + CmaCh02G009420.1 Cma02g00942 942
6 2808723 2811693 - CmaCh06G005840.1 Cma06g00584 584
6 2820082 2828399 + CmaCh06G005880.1 Cma06g00588 588
15 8258784 8259248 + CmaCh15G013130.1 Cma15g01313 1313
16 9327015 9330190 + CmaCh16G012300.1 Cma16g01230 1230
6 31068303 31073664 - MELO3C013773.2.1 Cme06g02390 2390
6 31087498 31096336 + MELO3C013775.2.1 Cme06g02392 2392
9 22907252 22908457 + MELO3C027095.2.1 Cme09g01876 1876
9 22913955 22914419 + MELO3C005784.2.1 Cme09g01878 1878
9 22915819 22919693 + MELO3C005785.2.1 Cme09g01879 1879
2 5802855 5810249 + CmoCh02G009500.1 Cmo02g00950 950
6 2901368 2910059 + CmoCh06G005910.1 Cmo06g00591 591
15 9381158 9381622 + CmoCh15G013780.1 Cmo15g01378 1378
16 9088882 9099739 - CmoCh16G012750.1 Cmo16g01275 1275
16 9104712 9112378 + CmoCh16G012760.1 Cmo16g01276 1276
1 1488018 1492863 - CmPI595203_01g001480.1 Cmu01g0148 148
1 1497036 1497500 - CmPI595203_01g001490.1 Cmu01g0149 149
1 1499531 1503787 - CmPI595203_01g001500.1 Cmu01g0150 150
10 1271559 1273931 - CmPI595203_10g009290.1 Cmu10g0929 929
10 1313012 1323555 + CmPI595203_10g009330.1 Cmu10g0933 933
8 4163888 4183215 - Conep08aG0057500.1 Cone8ag0554 554
8 5087967 5092954 - Conep08aG0061800.1 Cone8ag0597 597
12 3968105 3983043 - Conep12aG0057400.1 Cone12ag0553 553
12 3989883 3990533 - Conep12aG0057500.1 Cone12ag0554 554
12 5104440 5107081 - Conep12aG0061100.1 Cone12ag0590 590
12 5138724 5144714 - Conep12aG0061200.1 Cone12ag0591 591
13 1153997 1155869 + Conep13aG0019100.1 Cone13ag0186 186
5 4793079 4796860 - Cp4.1LG05g07770.1 Cpe05g00772 772
5 4797230 4800757 - Cp4.1LG05g07760.1 Cpe05g00773 773
8 7198460 7207375 - Cp4.1LG08g09100.1 Cpe08g00914 914
8 7215630 7221228 + Cp4.1LG08g09230.1 Cpe08g00915 915
14 8558479 8567392 - Cp4.1LG14g10240.1 Cpe14g01015 1015
14 8579935 8584169 + Cp4.1LG14g10160.1 Cpe14g01016 1016
9 42808920 42813229 + CrPI670011_09g023560.1 Cre09g2356 2356
9 42815299 42815763 + CrPI670011_09g023570.1 Cre09g2357 2357
9 42819960 42824721 + CrPI670011_09g023580.1 Cre09g2358 2358
10 2241615 2244817 - CrPI670011_10g003440.1 Cre10g0344 344
10 2282783 2293496 + CrPI670011_10g003470.1 Cre10g0347 347
5 973367 978112 - CsaV3_5G001670.1 Csa05g00167 167
5 979234 979698 - CsaV3_5G001680.1 Csa05g00168 168
5 980408 984045 - CsaV3_5G001690.1 Csa05g00169 169
6 64958720 64963529 - Hsped.06g14390.1 Hepe06g1439 1439
6 64966542 64967003 - Hsped.06g14400.1 Hepe06g1440 1440
6 64969171 64976036 - Hsped.06g14410.1 Hepe06g1441 1441
11 34743996 34748380 - Lag0032566.1 Lac11g1928 1928
11 34754047 34754517 - Lag0032567.1 Lac11g1929 1929
11 34769239 34775540 - Lag0032568.1 Lac11g1930 1930
12 35053920 35058128 - Maker00029427 Lcy12g1523 1523
12 35071484 35071951 - Maker00029390 Lcy12g1526 1526
7 16524291 16529135 - Lsi07G011100.1 Lsi07g01110 1110
7 16557155 16567146 + Lsi07G011120.1 Lsi07g01112 1112
9 1425681 1430336 - Lsi09G001390.1 Lsi09g00139 139
9 1435436 1435900 - Lsi09G001400.1 Lsi09g00140 140
9 1437241 1446052 - Lsi09G001410.1 Lsi09g00141 141
2 2178574 2181567 + Vvi2g232 Vvi2g232 232
2 2182863 2194766 - Vvi2g233 Vvi2g233 233
2 2196015 2200712 - Vvi2g234 Vvi2g234 234
2 2200730 2201170 - Vvi2g235 Vvi2g235 235
2 2205553 2206193 + Vvi2g236 Vvi2g236 236
2 2206313 2212270 + Vvi2g237 Vvi2g237 237
2 2231720 2233589 - Vvi2g238 Vvi2g238 238
2 2239746 2248426 + Vvi2g239 Vvi2g239 239
2 2249074 2251461 - Vvi2g240 Vvi2g240 240
2 2265422 2267057 + Vvi2g241 Vvi2g241 241
       

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