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
Vvi17g646 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g647 . Blo16g00171 . . . Bpe13g00309 Bma06g00154 . Cmo13g01125 . . . . . . Cpe20g00069 . . . . . . . . . . . . . . . Cone2ag0807 . . . Lsi02g00115 Csa01g00593 Chy12g01505 Cme12g01949 . . Bda11g01720 . . . . . . . . Cma13g01078 . Car13g00915 . . . Bhi08g01095 . . . . . . Cla04g01159 Cam04g1218 Cec01g1729 Cco01g1775 Clacu04g1245 Cmu04g1224 Cre01g1520 . . . .
Vvi17g648 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g649 . Blo16g00170 Bda06g00526 . . Bpe13g00310 . Bma12g00970 . . . . . Car11g00180 Sed12g1997 . Cpe04g01466 Bhi02g00692 Tan09g2050 Cmetu02g1984 . . . . Cla06g01545 Cam06g1705 Cec06g1766 Cco06g1766 Clacu06g1672 Cmu06g1618 Cre06g2431 Cone2ag0806 Cone16ag0202 Cone13ag0038 . Lsi02g00116 Csa01g00594 Chy12g01504 Cme12g01948 . . Bda11g01721 Bda14g00876 Bpe07g00760 . Bma03g00848 . . . Cmo11g00205 . . . Car18g00006 . Cpe18g00701 Bhi08g01093 . . Lac10g0143 . . . Cla04g01158 Cam04g1217 Cec01g1728 Cco01g1773 Clacu04g1244 Cmu04g1223 Cre01g1519 Lsi06g01420 Csa01g00286 Chy02g02449 Cme02g01836
Vvi17g650 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g651 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone2ag0805 Cone16ag0203 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g652 . . . Bda15g00620 Bpe12g00526 . . . . . . Cma11g00075 . . Sed08g0265 . . Bhi02g00691 Tan09g2049 Cmetu02g2011 . . . . Cla06g01544 Cam06g1704 . Cco06g1765 Clacu06g1671 Cmu06g1617 Cre06g2430 . Cone16ag0204 . . . . . . . . . . . . . . . . . . . . . . Cpe18g00702 . . . . . . . . . . . . . . Lsi06g01419 Csa01g00287 Chy02g02448 Cme02g01835
Vvi17g653 . . Bda06g00525 . . . . Bma12g00968 . . . . . Car11g00182 . . Cpe04g01464 Bhi02g00689 . . . . . . Cla06g01542 Cam06g1702 Cec06g1764 Cco06g1763 Clacu06g1669 Cmu06g1615 Cre06g2428 . . . . . . . . . Blo15g00333 . . Bpe07g00758 . . . . . Cmo11g00207 . . . . . Cpe18g00704 . . . . . . . . . . . . . . Lsi06g01417 Csa01g00290 Chy02g02445 Cme02g01833
Vvi17g654 . . Bda06g00524 Bda15g00621 Bpe12g00525 . . Bma12g00967 Cmo13g01124 . . . . . . Cpe20g00071 . . . . . . . . . . . . . . . Cone2ag0804 . . . Lsi02g00117 Csa01g00596 Chy12g01502 Cme12g01946 . Blo15g00334 . . . . . . Sed01g2299 . . Cma13g01077 . Car13g00913 . . . Bhi08g01087 Tan05g2365 Cmetu12g0105 Lac10g0145 Hepe07g2467 . . Cla04g01157 Cam04g1215 Cec01g1726 Cco01g1771 Clacu04g1242 Cmu04g1221 Cre01g1517 . . . .
Vvi17g655 . . Bda06g00523 . . . . Bma12g00966 . . . . . Car11g00184 . . Cpe04g01462 Bhi02g00097 . . . Hepe09g0271 . . Cla06g01541 Cam06g1700 Cec06g1762 Cco06g1761 Clacu06g1667 Cmu06g1613 Cre06g2426 . . Cone13ag0037 Cone19ag0046 . . . . . Blo15g00335 . . Bpe07g00757 . . . . . Cmo11g00208 . . . . . . . . . . . . . . . . . . . . Lsi06g01414 Csa01g00292 Chy02g02443 Cme02g01831
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 7487885 7490318 - Bda023778.1 Bda06g00523 523
6 7491628 7494672 - Bda023779.1 Bda06g00524 524
6 7495859 7499536 + Bda023780.1 Bda06g00525 525
6 7511661 7513612 - Bda023782.1 Bda06g00526 526
11 51631306 51646207 - Bda008617.2 Bda11g01720 1720
11 51677149 51679522 + Bda008618.1 Bda11g01721 1721
14 6792007 6794754 + Bda027654.1 Bda14g00876 876
15 9375880 9381834 + Bda012464.2 Bda15g00620 620
15 9382778 9385808 + Bda012465.1 Bda15g00621 621
2 1900642 1904605 - XM_039022450.1 Bhi02g00097 97
2 13861378 13865620 + XM_039024659.1 Bhi02g00689 689
2 13914238 13922927 - XM_039022412.1 Bhi02g00691 691
2 13949895 13952586 - XM_039022630.1 Bhi02g00692 692
8 35078387 35081914 - XM_039037743.1 Bhi08g01087 1087
8 35224299 35230673 - XM_039039583.1 Bhi08g01093 1093
8 35302752 35338215 + XM_039037842.1 Bhi08g01095 1095
15 3955856 3963673 - BLOR06727 Blo15g00333 333
15 3972939 3976098 + BLOR06728 Blo15g00334 334
15 3978200 3987131 + BLOR06729 Blo15g00335 335
16 3822679 3823191 - BLOR07418 Blo16g00170 170
16 3835216 3867947 + BLOR07419 Blo16g00171 171
3 8171992 8174378 + Bma017164.1 Bma03g00848 848
6 2001096 2016988 + Bma022773.1 Bma06g00154 154
12 41635818 41638119 - Bma008308.1 Bma12g00966 966
12 41663442 41667124 - Bma008309.1 Bma12g00967 967
12 41669085 41672141 + Bma008310.1 Bma12g00968 968
12 41688295 41694324 - Bma008312.1 Bma12g00970 970
7 14087433 14089508 - Bpe021603.1 Bpe07g00757 757
7 14093954 14097094 + Bpe021604.1 Bpe07g00758 758
7 14108427 14110531 - Bpe021606.1 Bpe07g00760 760
12 11130742 11133814 - Bpe005790.1 Bpe12g00525 525
12 11134637 11148116 - Bpe005791.1 Bpe12g00526 526
13 10931093 10965682 - Bpe006436.1 Bpe13g00309 309
13 10974512 10974790 + Bpe006437.1 Bpe13g00310 310
4 26169482 26172660 - CaPI482276_04g012150.1 Cam04g1215 1215
4 26189403 26195699 - CaPI482276_04g012170.1 Cam04g1217 1217
4 26199124 26235874 + CaPI482276_04g012180.1 Cam04g1218 1218
6 28379957 28383884 - CaPI482276_06g017000.1 Cam06g1700 1700
6 28401047 28404572 + CaPI482276_06g017020.1 Cam06g1702 1702
6 28408710 28417953 - CaPI482276_06g017040.1 Cam06g1704 1704
6 28417992 28423313 - CaPI482276_06g017050.1 Cam06g1705 1705
11 1044686 1047381 + Carg09209-RA Car11g00180 180
11 1050577 1054333 - Carg09207-RA Car11g00182 182
11 1063709 1068074 + Carg09205-RA Car11g00184 184
13 9427283 9431028 - Carg04758-RA Car13g00913 913
13 9441699 9464592 + Carg04756-RA Car13g00915 915
18 21027 23847 - Carg22780-RA Car18g00006 6
1 30420665 30423811 - CcPI632755_01g017710.1 Cco01g1771 1771
1 30440895 30441251 - CcPI632755_01g017730.1 Cco01g1773 1773
1 30457325 30493890 + CcPI632755_01g017750.1 Cco01g1775 1775
6 28083840 28087653 - CcPI632755_06g017610.1 Cco06g1761 1761
6 28104688 28108220 + CcPI632755_06g017630.1 Cco06g1763 1763
6 28112387 28121745 - CcPI632755_06g017650.1 Cco06g1765 1765
6 28121813 28127070 - CcPI632755_06g017660.1 Cco06g1766 1766
1 31847361 31850547 - CePI673135_01g017260.1 Cec01g1726 1726
1 31867671 31873916 - CePI673135_01g017280.1 Cec01g1728 1728
1 31877317 31914023 + CePI673135_01g017290.1 Cec01g1729 1729
6 31152959 31155868 - CePI673135_06g017620.1 Cec06g1762 1762
6 31174761 31178292 + CePI673135_06g017640.1 Cec06g1764 1764
6 31182519 31197063 - CePI673135_06g017660.1 Cec06g1766 1766
2 28069934 28080210 - Chy2G047100.1 Chy02g02443 2443
2 28096033 28099390 + Chy2G047120.1 Chy02g02445 2445
2 28105040 28112661 - Chy2G047150.1 Chy02g02448 2448
2 28116829 28119368 - Chy2G047160.1 Chy02g02449 2449
12 18836503 18839790 - Chy12G221020.1 Chy12g01502 1502
12 18848579 18855100 - Chy12G221040.1 Chy12g01504 1504
12 18857661 18881243 + Chy12G221050.1 Chy12g01505 1505
4 26518745 26521920 - ClG42_04g0124200.10 Clacu04g1242 1242
4 26540882 26547042 - ClG42_04g0124400.10 Clacu04g1244 1244
4 26550384 26593569 + ClG42_04g0124500.10 Clacu04g1245 1245
6 27438626 27441522 - ClG42_06g0166700.10 Clacu06g1667 1667
6 27459671 27463180 + ClG42_06g0166900.10 Clacu06g1669 1669
6 27467036 27476259 - ClG42_06g0167100.10 Clacu06g1671 1671
6 27479020 27481603 - ClG42_06g0167200.10 Clacu06g1672 1672
4 26756680 26760264 - ClCG04G011820.1 Cla04g01157 1157
4 26767050 26785366 - ClCG04G011830.1 Cla04g01158 1158
4 26792545 26829551 + ClCG04G011840.1 Cla04g01159 1159
6 28988051 28991745 - ClCG06G015640.1 Cla06g01541 1541
6 28998557 29013256 + ClCG06G015650.2 Cla06g01542 1542
6 29017629 29025899 - ClCG06G015680.1 Cla06g01544 1544
6 29028344 29032131 - ClCG06G015690.1 Cla06g01545 1545
11 365637 369286 + CmaCh11G000750.1 Cma11g00075 75
13 8124681 8135798 - CmaCh13G010770.1 Cma13g01077 1077
13 8137463 8161341 + CmaCh13G010780.1 Cma13g01078 1078
2 25033666 25037671 - MELO3C017224.2.1 Cme02g01831 1831
2 25050815 25055189 + MELO3C017223.2.1 Cme02g01833 1833
2 25060564 25068611 - MELO3C017221.2.1 Cme02g01835 1835
2 25068447 25075561 - MELO3C017220.2.1 Cme02g01836 1836
12 25376295 25379810 - MELO3C002027.2.1 Cme12g01946 1946
12 25392192 25396367 - MELO3C002024.2.1 Cme12g01948 1948
12 25399175 25423463 + MELO3C002023.2.1 Cme12g01949 1949
2 23389406 23391854 - PI0022759.1 Cmetu02g1984 1984
2 23376086 23384971 - PI0026087.1 Cmetu02g2011 2011
12 756334 759901 + PI0001915.1 Cmetu12g0105 105
11 1011697 1014513 + CmoCh11G002050.1 Cmo11g00205 205
11 1018366 1022020 - CmoCh11G002070.1 Cmo11g00207 207
11 1022345 1035593 + CmoCh11G002080.1 Cmo11g00208 208
13 9141563 9152803 - CmoCh13G011240.1 Cmo13g01124 1124
13 9154080 9178437 + CmoCh13G011250.1 Cmo13g01125 1125
4 26700729 26703889 - CmPI595203_04g012210.1 Cmu04g1221 1221
4 26722837 26729011 - CmPI595203_04g012230.1 Cmu04g1223 1223
4 26732885 26773947 + CmPI595203_04g012240.1 Cmu04g1224 1224
6 27347605 27350501 - CmPI595203_06g016130.1 Cmu06g1613 1613
6 27368653 27372163 + CmPI595203_06g016150.1 Cmu06g1615 1615
6 27376019 27385243 - CmPI595203_06g016170.1 Cmu06g1617 1617
6 27385268 27390584 - CmPI595203_06g016180.1 Cmu06g1618 1618
2 34047874 34052048 - Conep02aG0183200.1 Cone2ag0804 804
2 34056154 34058522 - Conep02aG0183300.1 Cone2ag0805 805
2 34067696 34072267 - Conep02aG0183400.1 Cone2ag0806 806
2 34079030 34117771 + Conep02aG0183500.1 Cone2ag0807 807
13 225809 228090 - Conep13aG0004000.1 Cone13ag0037 37
13 228804 230544 - Conep13aG0004100.1 Cone13ag0038 38
16 1333894 1336658 + Conep16aG0020600.1 Cone16ag0202 202
16 1337972 1353259 + Conep16aG0020700.1 Cone16ag0203 203
16 1367351 1372616 + Conep16aG0020800.1 Cone16ag0204 204
19 295358 297537 - Conep19aG0005000.1 Cone19ag0046 46
4 11648028 11661051 - Cp4.1LG04g14640.1 Cpe04g01462 1462
4 11661315 11665145 + Cp4.1LG04g14530.1 Cpe04g01464 1464
4 11667711 11671789 - Cp4.1LG04g14810.1 Cpe04g01466 1466
18 6952652 6955832 + Cp4.1LG18g06940.1 Cpe18g00701 701
18 6957198 6963455 + Cp4.1LG18g07000.1 Cpe18g00702 702
18 6965984 6972591 - Cp4.1LG18g07050.1 Cpe18g00704 704
20 350730 373432 - Cp4.1LG20g00690.1 Cpe20g00069 69
20 383670 387317 + Cp4.1LG20g00750.1 Cpe20g00071 71
1 28367134 28370325 - CrPI670011_01g015170.1 Cre01g1517 1517
1 28387818 28394189 - CrPI670011_01g015190.1 Cre01g1519 1519
1 28397679 28435919 + CrPI670011_01g015200.1 Cre01g1520 1520
6 32143332 32146870 - CrPI670011_06g024260.1 Cre06g2426 2426
6 32164458 32167980 + CrPI670011_06g024280.1 Cre06g2428 2428
6 32172179 32181504 - CrPI670011_06g024300.1 Cre06g2430 2430
6 32181529 32186885 - CrPI670011_06g024310.1 Cre06g2431 2431
1 1793964 1796517 + CsaV3_1G002860.1 Csa01g00286 286
1 1800473 1806924 + CsaV3_1G002870.1 Csa01g00287 287
1 1812904 1817088 - CsaV3_1G002900.1 Csa01g00290 290
1 1829922 1833979 + CsaV3_1G002920.1 Csa01g00292 292
1 3799682 3823564 - CsaV3_1G005930.1 Csa01g00593 593
1 3825546 3829446 + CsaV3_1G005940.1 Csa01g00594 594
1 3840589 3843647 + CsaV3_1G005960.1 Csa01g00596 596
7 68978243 68981909 - Hsped.07g24670.1 Hepe07g2467 2467
9 2320698 2323640 + Hsped.09g02710.1 Hepe09g0271 271
10 1088689 1092743 + Lag0024188.1 Lac10g0143 143
10 1108388 1111332 + Lag0024190.1 Lac10g0145 145
2 916139 942623 - Lsi02G001150.1 Lsi02g00115 115
2 944509 952678 + Lsi02G001160.1 Lsi02g00116 116
2 957772 977324 + Lsi02G001170.1 Lsi02g00117 117
6 24703839 24707409 - Lsi06G014140.1 Lsi06g01414 1414
6 24728079 24732166 + Lsi06G014170.1 Lsi06g01417 1417
6 24735401 24738789 - Lsi06G014190.1 Lsi06g01419 1419
6 24743658 24754309 - Lsi06G014200.1 Lsi06g01420 1420
1 17382831 17386721 - Sed0007546.1 Sed01g2299 2299
8 1569198 1577823 + Sed0006061.1 Sed08g0265 265
12 30896513 30901502 + Sed0009906.1 Sed12g1997 1997
5 74987705 74991853 - Tan0012263.1 Tan05g2365 2365
9 70989546 70998901 - Tan0010991.1 Tan09g2049 2049
9 71001486 71006339 - Tan0006708.1 Tan09g2050 2050
17 8040091 8045434 + Vvi17g646 Vvi17g646 646
17 8047114 8103821 - Vvi17g647 Vvi17g647 647
17 8104282 8106302 + Vvi17g648 Vvi17g648 648
17 8111067 8115895 + Vvi17g649 Vvi17g649 649
17 8131828 8135242 + Vvi17g650 Vvi17g650 650
17 8143214 8144054 + Vvi17g651 Vvi17g651 651
17 8144794 8155931 + Vvi17g652 Vvi17g652 652
17 8158121 8165201 - Vvi17g653 Vvi17g653 653
17 8166162 8174076 + Vvi17g654 Vvi17g654 654
17 8174939 8184172 + Vvi17g655 Vvi17g655 655
       

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