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
Vvi18g60 . Blo12g00847 . . . Bpe04g00289 . . . . Cma01g02032 Cma09g00033 Car01g01600 . . . . . . . . . . . . . . . . . . Cone4ag2035 Cone7ag1948 Cone17ag1471 Cone20ag0008 Lsi04g01831 Csa04g02728 . . . . . . . . . . . Cmo01g02087 Cmo09g00034 . . . Car09g00028 . Cpe02g00021 Bhi09g02839 Tan01g5137 . . . Mch11g0040 . Cla11g01841 Cam11g1909 Cec11g1934 Cco11g1946 Clacu11g2072 Cmu11g1878 Cre11g2286 . . Chy07g00414 Cme07g00035
Vvi18g61 . . . . . . . . Cmo05g00986 Cmo12g00624 . . . Car12g00665 . . Cpe07g00598 Bhi04g01216 . . . . . . Cla08g00933 Cam08g1379 Cec08g0960 Cco08g1080 Clacu08g1086 . Cre08g0869 . . . . . . . Cme03g01331 . Blo18g00737 . Bda01g01569 Bpe02g01763 . . . . . . Cma12g00690 . Car05g00849 . Cpe11g00778 . . . . . . . . . . . . . . . Lsi08g00774 . Chy03g00606 .
Vvi18g62 . . . . Bpe02g00298 . . Bma01g02418 Cmo05g00987 Cmo12g00623 . . . Car12g00664 . . Cpe07g00597 Bhi04g01217 . . . . . . . . . . . . . . . Cone17ag1469 Cone20ag0010 . . . Cme03g01332 . . Bda11g00984 . . . . . . . . Cma12g00688 Cma05g00967 Car05g00851 . Cpe11g00779 . . . . . . . . . . . . . . . Lsi08g00775 . Chy03g00607 .
Vvi18g63 Blo01g01645 . . . Bpe02g00299 . . Bma01g02417 . . Cma01g02031 . Car01g01598 . . . . . . . . . . . . . . . . . . Cone4ag2033 Cone7ag1947 . . Lsi04g01829 Csa04g02725 . . . . Bda11g00983 . . . . . Sed01g2411 Cmo01g02086 . . . . . . Cpe02g00023 Bhi09g02841 Tan01g5134 Cmetu07g1872 . Hepe01g2357 Mch11g0041 . Cla11g01840 Cam11g1907 Cec11g1933 Cco11g1943 Clacu11g2070 Cmu11g1876 Cre11g2284 . . Chy07g00411 Cme07g00037
Vvi18g64 . . . . . . . . Cmo05g00988 . . . . . . . . . . . . . . . Cla08g00934 Cam08g1381 Cec08g0962 Cco08g1081 Clacu08g1088 . Cre08g0871 Cone4ag2032 . . . . . . . . Blo18g00738 . Bda01g01568 Bpe02g01762 Bpe05g00178 Bma01g00695 . . . . . . Car05g00852 . Cpe11g00780 . . . . . . . . . . . . . . . . . . .
Vvi18g65 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo18g00739 . Bda01g01567 Bpe02g01761 . Bma01g00696 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g66 . . . . . . . . . . . . . . . . . Bhi04g01218 . . . . . . . . . . . . . . . Cone17ag1467 . . . . Cme03g01333 . . . . . . . . . . . . Cma05g00968 . . . . . . . . . . . . . . . . . . Lsi08g00776 . Chy03g00608 .
Vvi18g67 Blo01g01644 . . . Bpe02g00300 . . . . . Cma01g02030 Cma09g00035 Car01g01597 . . Cpe06g00009 . . . . . . . . . . . . . . . Cone4ag2031 Cone7ag1946 . . . Csa04g02724 . . . . Bda11g00982 . . . . . Sed01g2413 Cmo01g02085 Cmo09g00036 . . . Car09g00030 . Cpe02g00024 Bhi09g02842 Tan01g5132 Cmetu07g1199 . Hepe01g2356 . . Cla11g01839 Cam11g1906 Cec11g1932 Cco11g1942 Clacu11g2069 Cmu11g1875 Cre11g2283 . . Chy07g00410 Cme07g00038
Vvi18g68 Blo01g01643 . . . Bpe02g00301 . . Bma01g02416 . . Cma01g02029 Cma09g00036 Car01g01596 . . Cpe06g00010 . . . . . . . . . . . . . . . . . Cone17ag1465 Cone20ag0011 Lsi04g01828 Csa04g02722 . . . . Bda11g00981 . . . . . Sed01g2415 Cmo01g02084 Cmo09g00037 . . . Car09g00031 . . Bhi09g02843 Tan01g5131 Cmetu07g0789 . Hepe01g2355 Mch11g0042 . Cla11g01837 Cam11g1904 Cec11g1931 Cco11g1940 Clacu11g2068 Cmu11g1874 Cre11g2282 . . Chy07g00409 Cme07g00039
Vvi18g69 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo18g00740 . Bda01g01566 Bpe02g01760 . Bma01g00697 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 51528641 51532276 - Bda003835.1 Bda01g01566 1566
1 51536634 51541465 + Bda003836.1 Bda01g01567 1567
1 51542215 51545694 + Bda003837.1 Bda01g01568 1568
1 51553071 51554547 + Bda032957 Bda01g01569 1569
11 9542585 9544583 - Bda005745.1 Bda11g00981 981
11 9545166 9547250 - Bda033070 Bda11g00982 982
11 9547832 9549207 + Bda005746.2 Bda11g00983 983
11 9549959 9554428 + Bda005747.1 Bda11g00984 984
4 29404106 29407915 - XM_039029003.1 Bhi04g01216 1216
4 29410398 29414992 - XM_039030156.1 Bhi04g01217 1217
4 29484089 29491279 - XM_039029925.1 Bhi04g01218 1218
9 75179944 75184282 - XM_039043851.1 Bhi09g02839 2839
9 75191160 75193981 - XM_039042683.1 Bhi09g02841 2841
9 75311448 75315878 + XM_039044211.1 Bhi09g02842 2842
9 75358129 75360774 + XM_039043839.1 Bhi09g02843 2843
1 56245174 56247226 - BLOR01643 Blo01g01643 1643
1 56247867 56255523 - BLOR01644 Blo01g01644 1644
1 56256267 56263227 + BLOR01645 Blo01g01645 1645
12 26741604 26747482 - BLOR04866 Blo12g00847 847
18 19764579 19777145 - BLOR09225 Blo18g00737 737
18 19903529 19906953 - BLOR09226 Blo18g00738 738
18 19907639 19917208 - BLOR09227 Blo18g00739 739
18 19978075 19982520 + BLOR09228 Blo18g00740 740
1 6380280 6383706 - Bma000905.1 Bma01g00695 695
1 6384387 6389424 - Bma000906.1 Bma01g00696 696
1 6392328 6396079 + Bma000907.1 Bma01g00697 697
1 81767148 81769146 - Bma030302 Bma01g02416 2416
1 81772540 81773802 + Bma003289.1 Bma01g02417 2417
1 81774595 81779458 + Bma003290.2 Bma01g02418 2418
2 1976578 1981179 - Bpe008141.1 Bpe02g00298 298
2 1981983 1983310 - Bpe008142.1 Bpe02g00299 299
2 1983896 1986006 + Bpe008143.1 Bpe02g00300 300
2 1986586 1988582 + Bpe025071 Bpe02g00301 301
2 19925157 19928799 - Bpe009591.1 Bpe02g01760 1760
2 19933460 19938309 + Bpe009592.1 Bpe02g01761 1761
2 19938996 19942417 + Bpe009593.1 Bpe02g01762 1762
2 19943831 19945305 + Bpe009594.1 Bpe02g01763 1763
4 1849450 1851470 + Bpe014992.1 Bpe04g00289 289
5 6765765 6767854 + Bpe017568.1 Bpe05g00178 178
8 20082816 20086329 - CaPI482276_08g013790.1 Cam08g1379 1379
8 20095875 20102957 - CaPI482276_08g013810.1 Cam08g1381 1381
11 31554051 31556689 - CaPI482276_11g019040.1 Cam11g1904 1904
11 31558248 31561945 - CaPI482276_11g019060.1 Cam11g1906 1906
11 31562901 31567502 + CaPI482276_11g019070.1 Cam11g1907 1907
11 31572911 31576196 + CaPI482276_11g019090.1 Cam11g1909 1909
1 13175970 13179689 - Carg21359-RA Car01g01596 1596
1 13180457 13183233 - Carg21358-RA Car01g01597 1597
1 13184312 13187168 + Carg21357-RA Car01g01598 1598
1 13191356 13194697 + Carg21355-RA Car01g01600 1600
5 8366662 8369982 - Carg21890-RA Car05g00849 849
5 8372486 8375585 - Carg21888-RA Car05g00851 851
5 8377189 8382279 - Carg21887-RA Car05g00852 852
9 140593 144436 - Carg08611-RA Car09g00028 28
9 151608 154589 + Carg08613-RA Car09g00030 30
9 155021 159318 + Carg08614-RA Car09g00031 31
12 4496798 4500800 + Carg17638-RA Car12g00664 664
12 4503054 4506908 + Carg17637-RA Car12g00665 665
8 22594440 22602071 - CcPI632755_08g010800.1 Cco08g1080 1080
8 22604995 22612196 - CcPI632755_08g010810.1 Cco08g1081 1081
11 32026405 32029013 - CcPI632755_11g019400.1 Cco11g1940 1940
11 32030585 32034197 - CcPI632755_11g019420.1 Cco11g1942 1942
11 32035159 32037640 + CcPI632755_11g019430.1 Cco11g1943 1943
11 32046721 32049965 + CcPI632755_11g019460.1 Cco11g1946 1946
8 21433712 21438692 - CePI673135_08g009600.1 Cec08g0960 960
8 21448093 21455206 - CePI673135_08g009620.1 Cec08g0962 962
11 33472909 33475552 - CePI673135_11g019310.1 Cec11g1931 1931
11 33477103 33480931 - CePI673135_11g019320.1 Cec11g1932 1932
11 33481667 33487233 + CePI673135_11g019330.1 Cec11g1933 1933
11 33491769 33495061 + CePI673135_11g019340.1 Cec11g1934 1934
3 8639141 8639925 - Chy3G055860.1 Chy03g00606 606
3 8641724 8645631 - Chy3G055870.1 Chy03g00607 607
3 8646988 8651997 - Chy3G055880.1 Chy03g00608 608
7 3239184 3241445 - Chy7G132390.1 Chy07g00409 409
7 3242962 3246141 - Chy7G132400.1 Chy07g00410 410
7 3246817 3249241 + Chy7G132410.1 Chy07g00411 411
7 3253962 3259746 + Chy7G132440.1 Chy07g00414 414
8 20857009 20858229 - ClG42_08g0108600.10 Clacu08g1086 1086
8 20867670 20874869 - ClG42_08g0108800.10 Clacu08g1088 1088
11 31592041 31594689 - ClG42_11g0206800.10 Clacu11g2068 2068
11 31594842 31599892 - ClG42_11g0206900.10 Clacu11g2069 2069
11 31599908 31603359 + ClG42_11g0207000.10 Clacu11g2070 2070
11 31610941 31613910 + ClG42_11g0207200.10 Clacu11g2072 2072
8 21853437 21858867 - ClCG08G009240.2 Cla08g00933 933
8 21860892 21879107 - ClCG08G009250.2 Cla08g00934 934
11 32000477 32003124 - ClCG11G018880.2 Cla11g01837 1837
11 32004716 32008805 - ClCG11G018900.1 Cla11g01839 1839
11 32008672 32014128 + ClCG11G018910.2 Cla11g01840 1840
11 32014194 32022557 + ClCG11G018920.2 Cla11g01841 1841
1 12948496 12951186 - CmaCh01G020290.1 Cma01g02029 2029
1 12952182 12955893 - CmaCh01G020300.1 Cma01g02030 2030
1 12956160 12959295 + CmaCh01G020310.1 Cma01g02031 2031
1 12962922 12966677 + CmaCh01G020320.1 Cma01g02032 2032
5 7802030 7811517 - CmaCh05G009670.1 Cma05g00967 967
5 7813496 7819212 - CmaCh05G009680.1 Cma05g00968 968
9 151504 156567 - CmaCh09G000330.1 Cma09g00033 33
9 160627 163298 + CmaCh09G000350.1 Cma09g00035 35
9 164102 166483 + CmaCh09G000360.1 Cma09g00036 36
12 3724631 3728404 + CmaCh12G006880.1 Cma12g00688 688
12 3730594 3734924 + CmaCh12G006900.1 Cma12g00690 690
3 22870715 22873695 - MELO3C026523.2.1 Cme03g01331 1331
3 22875772 22880445 - MELO3C026524.2.1 Cme03g01332 1332
3 22883415 22889076 - MELO3C026525.2.1 Cme03g01333 1333
7 228907 232883 - MELO3C017048.2.1 Cme07g00035 35
7 240710 242342 - MELO3C017046.2.1 Cme07g00037 37
7 242439 246034 + MELO3C017045.2.1 Cme07g00038 38
7 246226 250588 + MELO3C017044.2.1 Cme07g00039 39
7 24561098 24563348 - PI0015392.1 Cmetu07g0789 789
7 24564632 24568034 - PI0019140.1 Cmetu07g1199 1199
7 24568832 24575054 + PI0009891.2 Cmetu07g1872 1872
1 14494959 14497795 - CmoCh01G020840.1 Cmo01g02084 2084
1 14498265 14502093 - CmoCh01G020850.1 Cmo01g02085 2085
1 14502359 14505478 + CmoCh01G020860.1 Cmo01g02086 2086
1 14507770 14513158 + CmoCh01G020870.1 Cmo01g02087 2087
5 7943173 7947078 - CmoCh05G009860.1 Cmo05g00986 986
5 7947221 7951711 - CmoCh05G009870.1 Cmo05g00987 987
5 7954924 7959648 - CmoCh05G009880.1 Cmo05g00988 988
9 149396 156449 - CmoCh09G000340.1 Cmo09g00034 34
9 160413 163466 + CmoCh09G000360.1 Cmo09g00036 36
9 163475 167329 + CmoCh09G000370.1 Cmo09g00037 37
12 3903702 3908517 + CmoCh12G006230.1 Cmo12g00623 623
12 3910080 3914143 + CmoCh12G006240.1 Cmo12g00624 624
11 30841614 30844262 - CmPI595203_11g018740.1 Cmu11g1874 1874
11 30844415 30849456 - CmPI595203_11g018750.1 Cmu11g1875 1875
11 30849472 30852922 + CmPI595203_11g018760.1 Cmu11g1876 1876
11 30860505 30863474 + CmPI595203_11g018780.1 Cmu11g1878 1878
4 14101913 14103432 - Conep04aG0209600.1 Cone4ag2031 2031
4 14113354 14116677 + Conep04aG0209700.1 Cone4ag2032 2032
4 14118074 14120253 + Conep04aG0209800.1 Cone4ag2033 2033
4 14122150 14124044 + Conep04aG0210000.1 Cone4ag2035 2035
7 12409270 12411682 - Conep07aG0200400.1 Cone7ag1946 1946
7 12419532 12421700 + Conep07aG0200500.1 Cone7ag1947 1947
7 12422298 12422959 + Conep07aG0200600.1 Cone7ag1948 1948
17 9922290 9924794 - Conep17aG0150600.1 Cone17ag1465 1465
17 9932597 9937276 + Conep17aG0150800.1 Cone17ag1467 1467
17 9942485 9942971 + Conep17aG0151000.1 Cone17ag1469 1469
17 9949472 9950380 + Conep17aG0151200.1 Cone17ag1471 1471
20 68114 70834 - Conep20aG0000800.1 Cone20ag0008 8
20 87030 91200 + Conep20aG0001000.1 Cone20ag0010 10
20 93310 95508 + Conep20aG0001100.1 Cone20ag0011 11
2 114985 120978 - Cp4.1LG02g08510.1 Cpe02g00021 21
2 124972 127897 - Cp4.1LG02g08550.1 Cpe02g00023 23
2 128035 136358 + Cp4.1LG02g08670.1 Cpe02g00024 24
6 33828 37123 + Cp4.1LG06g00090.1 Cpe06g00009 9
6 37214 41101 + Cp4.1LG06g00070.1 Cpe06g00010 10
7 4014692 4018651 + Cp4.1LG07g05870.1 Cpe07g00597 597
7 4020868 4025328 + Cp4.1LG07g05860.1 Cpe07g00598 598
11 6302468 6305732 - Cp4.1LG11g07820.1 Cpe11g00778 778
11 6307056 6311919 - Cp4.1LG11g07800.1 Cpe11g00779 779
11 6313467 6319741 - Cp4.1LG11g07830.1 Cpe11g00780 780
8 21821385 21826368 - CrPI670011_08g008690.1 Cre08g0869 869
8 21835728 21842918 - CrPI670011_08g008710.1 Cre08g0871 871
11 34525914 34528565 - CrPI670011_11g022820.1 Cre11g2282 2282
11 34528718 34533716 - CrPI670011_11g022830.1 Cre11g2283 2283
11 34533732 34537164 + CrPI670011_11g022840.1 Cre11g2284 2284
11 34544619 34548262 + CrPI670011_11g022860.1 Cre11g2286 2286
4 26248609 26250874 - CsaV3_4G037480.1 Csa04g02722 2722
4 26251959 26255702 - CsaV3_4G037500.1 Csa04g02724 2724
4 26256251 26258689 + CsaV3_4G037510.1 Csa04g02725 2725
4 26265091 26268289 + CsaV3_4G037540.1 Csa04g02728 2728
1 88056232 88058874 - Hsped.01g23550.1 Hepe01g2355 2355
1 88059473 88062590 - Hsped.01g23560.1 Hepe01g2356 2356
1 88064727 88067581 + Hsped.01g23570.1 Hepe01g2357 2357
4 25431480 25432784 - Lsi04G018280.1 Lsi04g01828 1828
4 25432642 25436505 + Lsi04G018290.1 Lsi04g01829 1829
4 25448720 25452798 + Lsi04G018310.1 Lsi04g01831 1831
8 16132112 16132969 - Lsi08G007740.1 Lsi08g00774 774
8 16134858 16139958 - Lsi08G007750.1 Lsi08g00775 775
8 16142106 16149568 - Lsi08G007760.1 Lsi08g00776 776
11 255159 258703 - MC11g0035 Mch11g0040 40
11 262779 268583 - MC11g0036 Mch11g0041 41
11 269240 276018 + MC11g0037 Mch11g0042 42
1 18044504 18049203 - Sed0011537.5 Sed01g2411 2411
1 18050836 18058765 + Sed0020344.2 Sed01g2413 2413
1 18060159 18062848 + Sed0007215.2 Sed01g2415 2415
1 116642462 116644741 - Tan0009431.1 Tan01g5131 5131
1 116645474 116649883 - Tan0009236.1 Tan01g5132 5132
1 116650534 116655094 + Tan0010427.2 Tan01g5134 5134
1 116663357 116667557 + Tan0006916.2 Tan01g5137 5137
18 620591 623967 - Vvi18g60 Vvi18g60 60
18 631116 634528 - Vvi18g61 Vvi18g61 61
18 635350 641071 - Vvi18g62 Vvi18g62 62
18 642568 645549 - Vvi18g63 Vvi18g63 63
18 646525 652067 - Vvi18g64 Vvi18g64 64
18 653646 659479 - Vvi18g65 Vvi18g65 65
18 659972 671731 - Vvi18g66 Vvi18g66 66
18 673420 679783 + Vvi18g67 Vvi18g67 67
18 681145 684604 + Vvi18g68 Vvi18g68 68
18 686114 690591 + Vvi18g69 Vvi18g69 69
       

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