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
Vvi4g1142 . . . Bda10g00191 . . . . . . . Cma07g00415 . Car07g00364 Sed14g1204 . Cpe10g00675 Bhi03g00842 Tan03g2099 Cmetu04g2642 . Hepe04g1607 . . . . . . . . . . . . Cone9ag1616 . . . Cme08g00947 . . . . Bpe10g00163 . . . . . Cmo07g00412 . . . . . . . . . . . . . . . . . . . . . Csa06g03345 . .
Vvi4g1143 . . . Bda10g00192 . . . . . . . . . . Sed14g1205 . Cpe10g00676 Bhi03g00841 Tan03g2100 Cmetu04g0811 . Hepe04g1608 . . Cla01g01992 Cam01g2091 Cec04g1748 Cco04g1813 Clacu01g2109 Cmu01g1985 Cre04g1662 . . . . . . . Cme08g00948 . . . . Bpe10g00164 . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa06g03346 . .
Vvi4g1144 . . . Bda10g00208 . . . . . . Cma03g00674 . Car03g00619 . . Cpe19g00869 . . . . . . . . . . . . . . . . . . . Lsi01g00585 . . . . Blo06g00290 . . . . . . . Cmo03g00698 . . . . . . . . . . . . . . . . . . . . . . . Chy02g00556 .
Vvi4g1145 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1146 . . . . . . . . . . Cma03g00672 . Car03g00618 . . . . . . . . . . . . . . . . . . . . Cone6ag1693 Cone9ag1617 Lsi01g00584 . . . . Blo06g00285 . . . . . . . Cmo03g00697 . . . . . . . . . . . . . . . . . . . . . . . Chy02g00555 .
Vvi4g1147 . . . . . . . . . . Cma03g00671 Cma07g00413 Car03g00617 Car07g00363 . Cpe19g00870 Cpe10g00677 Bhi03g00838 . . . . . . Cla01g01993 Cam01g2092 Cec04g1749 Cco04g1814 . Cmu01g1986 Cre04g1663 Cone8ag0861 Cone12ag0824 . . Lsi01g00583 . . Cme08g00949 Blo05g00705 . . . . Bpe06g00133 . . . Cmo03g00696 Cmo07g00409 . Cma20g00739 . . . . . . . . . . . . . . . . . . . Csa06g03347 Chy02g00554 .
Vvi4g1148 . . . . Bpe15g00480 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma03g00953 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1149 . . . . . . . . . . Cma03g00670 . Car03g00616 . Sed10g1021 . Cpe10g00678 Bhi03g00837 Tan03g2102 Cmetu04g0142 . Hepe04g1610 . . Cla01g01994 . Cec04g1750 Cco04g1815 Clacu01g2110 Cmu01g1987 . . Cone12ag0825 Cone6ag1694 Cone9ag1618 Lsi01g00582 . . Cme08g00950 . Blo06g00275 . . Bpe10g00166 . . . . Cmo03g00695 . . . . . . . . . . . . . . . . . . . . . . Csa06g03348 Chy02g00553 .
Vvi4g1150 . . Bda04g00238 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma03g00952 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1151 . . . . Bpe15g00481 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma16g01245 . . . . . . . . . . . . . . . . . . . Lsi07g01092 . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 17736587 17738468 - Bda018832.1 Bda04g00238 238
10 6714464 6716080 + Bda033108 Bda10g00191 191
10 6720009 6722563 - Bda006696.1 Bda10g00192 192
10 7224728 7226344 - Bda006718.2 Bda10g00208 208
3 15340294 15345077 + XM_039024873.1 Bhi03g00837 837
3 15345552 15349549 - XM_039025029.1 Bhi03g00838 838
3 15406225 15410124 + XM_039025143.1 Bhi03g00841 841
3 15410696 15412729 - XM_039025519.1 Bhi03g00842 842
5 24300346 24303106 - BLOR15667 Blo05g00705 705
6 15083378 15087656 - BLOR16858 Blo06g00275 275
6 16013506 16016077 + BLOR16868 Blo06g00285 285
6 16088271 16089871 - BLOR16873 Blo06g00290 290
3 10137582 10139394 - Bma017291.1 Bma03g00952 952
3 10142379 10143380 + Bma017292.2 Bma03g00953 953
6 2316684 2319406 + Bpe019584.1 Bpe06g00133 133
10 4008170 4009788 + Bpe002474.1 Bpe10g00163 163
10 4011412 4014075 - Bpe024645 Bpe10g00164 164
10 4069082 4073258 - Bpe002476.1 Bpe10g00166 166
15 16121488 16122501 - Bpe001414.2 Bpe15g00480 480
15 16123857 16125737 + Bpe001415.1 Bpe15g00481 481
1 33929674 33933989 - CaPI482276_01g020910.1 Cam01g2091 2091
1 33936969 33939745 + CaPI482276_01g020920.1 Cam01g2092 2092
3 5667531 5672427 + Carg00576-RA Car03g00616 616
3 5673124 5675802 - Carg00577-RA Car03g00617 617
3 5677709 5680741 + Carg00578-RA Car03g00618 618
3 5681405 5683333 - Carg00579-RA Car03g00619 619
7 1822220 1824664 - Carg07943-RA Car07g00363 363
7 1828395 1830199 - Carg07944-RA Car07g00364 364
4 33006412 33010307 - CcPI632755_04g018130.1 Cco04g1813 1813
4 33010610 33016505 + CcPI632755_04g018140.1 Cco04g1814 1814
4 33017593 33022142 - CcPI632755_04g018150.1 Cco04g1815 1815
4 36491517 36495858 - CePI673135_04g017480.1 Cec04g1748 1748
4 36498777 36501803 + CePI673135_04g017490.1 Cec04g1749 1749
4 36502319 36507132 - CePI673135_04g017500.1 Cec04g1750 1750
2 3324058 3329459 + Chy2G028200.1 Chy02g00553 553
2 3330461 3333097 - Chy2G028210.1 Chy02g00554 554
2 3336023 3339280 + Chy2G028220.1 Chy02g00555 555
2 3340245 3342013 - Chy2G028230.1 Chy02g00556 556
1 32781139 32785613 - ClG42_01g0210900.10 Clacu01g2109 2109
1 32792419 32796975 - ClG42_01g0211000.10 Clacu01g2110 2110
1 34574476 34581454 - ClCG01G020440.2 Cla01g01992 1992
1 34584732 34587849 + ClCG01G020450.1 Cla01g01993 1993
1 34588511 34593335 - ClCG01G020460.1 Cla01g01994 1994
3 5575491 5580486 + CmaCh03G006700.1 Cma03g00670 670
3 5581029 5584286 - CmaCh03G006710.1 Cma03g00671 671
3 5585762 5588774 + CmaCh03G006720.1 Cma03g00672 672
3 5589638 5591446 - CmaCh03G006740.1 Cma03g00674 674
7 1788521 1791191 - CmaCh07G004130.1 Cma07g00413 413
7 1794431 1799538 - CmaCh07G004150.1 Cma07g00415 415
16 9410986 9413514 + CmaCh16G012450.1 Cma16g01245 1245
20 3463463 3466735 - CmaCh20G007390.1 Cma20g00739 739
8 6224502 6226545 + MELO3C007922.2.1 Cme08g00947 947
8 6226898 6231282 - MELO3C007923.2.1 Cme08g00948 948
8 6234042 6237050 + MELO3C007924.2.1 Cme08g00949 949
8 6237848 6243695 - MELO3C007925.2.1 Cme08g00950 950
4 3600831 3605793 + PI0011587.1 Cmetu04g0142 142
4 3606203 3616447 + PI0010225.2 Cmetu04g0811 811
4 3616930 3618978 - PI0016843.1 Cmetu04g2642 2642
3 6064325 6072234 + CmoCh03G006950.1 Cmo03g00695 695
3 6070292 6073322 - CmoCh03G006960.1 Cmo03g00696 696
3 6074801 6077963 + CmoCh03G006970.1 Cmo03g00697 697
3 6078347 6080484 - CmoCh03G006980.1 Cmo03g00698 698
7 1873815 1876543 - CmoCh07G004090.1 Cmo07g00409 409
7 1880541 1882342 - CmoCh07G004120.1 Cmo07g00412 412
1 33118701 33123185 - CmPI595203_01g019850.1 Cmu01g1985 1985
1 33126122 33128910 + CmPI595203_01g019860.1 Cmu01g1986 1986
1 33129982 33134537 - CmPI595203_01g019870.1 Cmu01g1987 1987
6 12804155 12806151 - Conep06aG0175800.1 Cone6ag1693 1693
6 12806823 12808828 - Conep06aG0175900.1 Cone6ag1694 1694
8 8516559 8519080 + Conep08aG0088700.1 Cone8ag0861 861
9 11538146 11539920 + Conep09aG0166600.1 Cone9ag1616 1616
9 11540097 11542367 - Conep09aG0166700.1 Cone9ag1617 1617
9 11543221 11547153 - Conep09aG0166800.1 Cone9ag1618 1618
12 7490928 7493555 + Conep12aG0084900.1 Cone12ag0824 824
12 7493715 7495673 - Conep12aG0085000.1 Cone12ag0825 825
10 3892765 3894662 + Cp4.1LG10g00120.1 Cpe10g00675 675
10 3895353 3898464 - Cp4.1LG10g00030.1 Cpe10g00676 676
10 3899405 3903399 + Cp4.1LG10g00090.1 Cpe10g00677 677
10 3899405 3908741 - Cp4.1LG10g00020.1 Cpe10g00678 678
19 6397977 6399793 + Cp4.1LG19g08780.1 Cpe19g00869 869
19 6402885 6406468 + Cp4.1LG19g08720.1 Cpe19g00870 870
4 34969056 34976345 - CrPI670011_04g016620.1 Cre04g1662 1662
4 34976448 34979223 + CrPI670011_04g016630.1 Cre04g1663 1663
6 27921892 27924924 + CsaV3_6G047310.1 Csa06g03345 3345
6 27925057 27929144 - CsaV3_6G047320.1 Csa06g03346 3346
6 27930770 27936174 + CsaV3_6G047330.1 Csa06g03347 3347
6 27934942 27940851 - CsaV3_6G047340.1 Csa06g03348 3348
4 71536179 71538491 + Hsped.04g16070.1 Hepe04g1607 1607
4 71538782 71542295 - Hsped.04g16080.1 Hepe04g1608 1608
4 71547921 71552678 - Hsped.04g16100.1 Hepe04g1610 1610
1 4641723 4651344 + Lsi01G005820.1 Lsi01g00582 582
1 4647352 4650847 - Lsi01G005830.1 Lsi01g00583 583
1 4654101 4657907 + Lsi01G005840.1 Lsi01g00584 584
1 4658463 4660239 - Lsi01G005850.1 Lsi01g00585 585
7 16311016 16315333 - Lsi07G010920.1 Lsi07g01092 1092
10 8879768 8885472 - Sed0025600.3 Sed10g1021 1021
14 21297064 21299508 + Sed0013645.2 Sed14g1204 1204
14 21299923 21305860 - Sed0021051.1 Sed14g1205 1205
3 75869669 75871630 + Tan0002522.1 Tan03g2099 2099
3 75872337 75875341 - Tan0020473.1 Tan03g2100 2100
3 75885319 75890431 - Tan0014377.1 Tan03g2102 2102
4 20260683 20262824 + Vvi4g1142 Vvi4g1142 1142
4 20263132 20278688 - Vvi4g1143 Vvi4g1143 1143
4 20279053 20280781 + Vvi4g1144 Vvi4g1144 1144
4 20280809 20281115 - Vvi4g1145 Vvi4g1145 1145
4 20281249 20288177 - Vvi4g1146 Vvi4g1146 1146
4 20288223 20291182 + Vvi4g1147 Vvi4g1147 1147
4 20291206 20293244 - Vvi4g1148 Vvi4g1148 1148
4 20299414 20306280 - Vvi4g1149 Vvi4g1149 1149
4 20310392 20310911 + Vvi4g1150 Vvi4g1150 1150
4 20310935 20311643 + Vvi4g1151 Vvi4g1151 1151
       

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