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
Vvi5g209 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g210 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g211 . . . . . . . . . Cmo17g00377 . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy11g01596 . . . . . . . . . . . . . Cma17g00388 . Car17g00358 . . . . . . . . . . . . . . . . . . . .
Vvi5g212 . . . . . . . Bma05g01011 . . . . . . . . . . . . . . . . Cla06g00407 Cam06g0429 Cec06g0436 Cco06g0435 Clacu06g0415 Cmu06g0415 Cre06g1195 . . . . . . . . . . . . Bpe05g00809 . . . . . . . . . . Cpe12g00339 . Bhi12g01957 . . . . . Lcy12g0885 . . . . . . . Lsi09g01511 . . Cme11g02101
Vvi5g213 Blo01g00043 . . . . . . Bma05g01010 . Cmo17g00376 . . . . . . . . . . . . . . Cla06g00408 Cam06g0430 Cec06g0437 Cco06g0436 Clacu06g0416 Cmu06g0416 Cre06g1196 Cone14ag0699 . . . . . . . . . . . Bpe05g00808 . . . . . . . Cma17g00387 . Car17g00357 . . . . . . . . . . . . . . . . . . . Cme11g02100
Vvi5g214 . Blo12g00384 Bda03g00824 . Bpe04g00781 . Bma04g00724 . . . . . . . . . . . . . . . . . Cla06g00405 Cam06g0427 Cec06g0435 Cco06g0434 Clacu06g0413 Cmu06g0413 Cre06g1193 . . . . . . . . . . . . . . . . Sed09g0622 . . . . . . Cpe12g00341 . Bhi12g01966 Tan06g2801 Cmetu11g1241 . . . Lcy12g0887 . . . . . . . . . . .
Vvi5g215 . . . . . . . . . . . Cma14g01573 . Car14g01386 . . Cpe03g01314 Bhi01g01102 . . . . . . . . . . . . . . . . . Lsi05g01409 . . Cme06g00753 . . . . . . . . . . Cmo14g01606 . . . . . . . . . . . . . Cla05g00718 Cam05g0787 Cec05g0792 Cco05g0790 Clacu05g0777 Cmu05g0741 Cre05g0817 . Csa03g01537 Chy06g00774 .
Vvi5g216 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g217 Blo01g00027 . . . . . . Bma05g00989 . . . . . . . . . . . . . . . . Cla06g00404 Cam06g0426 Cec06g0434 Cco06g0433 Clacu06g0412 Cmu06g0412 Cre06g1192 Cone14ag0692 Cone15ag0706 . . . . . . . . . . Bpe05g00796 . . . . . . . . . . Cpe12g00342 . Bhi12g01968 . . . . . Lcy12g0888 . . . . . . . . . . .
Vvi5g218 Blo01g00026 Blo12g00383 Bda03g00825 . Bpe04g00782 Bpe14g01083 . Bma05g00988 . . Cma06g01577 . Car06g01340 . Sed02g1122 Cpe08g00139 . Bhi01g01108 Tan10g1094 Cmetu11g2009 . Hepe05g1359 . Lcy11g1321 . . . . . . . Cone14ag0691 Cone15ag0737 . . Lsi05g01404 . . Cme06g00816 . . . . . . Bma02g00941 . . Cmo06g01571 . . . . . . . Bhi12g01970 Tan06g2802 Cmetu11g1368 Lac11g0925 Hepe03g0023 . Lcy12g0795 . . . . . . . . Csa03g01536 Chy06g00773 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 7015709 7018636 + Bda016811.1 Bda03g00824 824
3 7019046 7021557 - Bda016812.1 Bda03g00825 825
1 21185435 21186711 + XM_039024753.1 Bhi01g01102 1102
1 21373699 21376055 + XM_039037408.1 Bhi01g01108 1108
12 62215943 62228912 + XM_039051183.1 Bhi12g01957 1957
12 62325727 62327846 + XM_039050969.1 Bhi12g01966 1966
12 62328750 62332543 + XM_039050971.1 Bhi12g01968 1968
12 62338719 62341556 - XM_039019918.1 Bhi12g01970 1970
1 364811 367497 + BLOR00026 Blo01g00026 26
1 368372 369677 - BLOR00027 Blo01g00027 27
1 581043 597888 + BLOR00043 Blo01g00043 43
12 20407290 20409876 + BLOR04402 Blo12g00383 383
12 20410292 20411604 - BLOR04403 Blo12g00384 384
2 49318301 49320251 - Bma015735.1 Bma02g00941 941
4 7484746 7485302 + Bma019230.1 Bma04g00724 724
5 48375682 48378362 + Bma022139.1 Bma05g00988 988
5 48379179 48380275 - Bma022140.1 Bma05g00989 989
5 48579649 48599261 + Bma022165.1 Bma05g01010 1010
5 48601879 48609582 + Bma022166.1 Bma05g01011 1011
4 5033815 5035134 + Bpe015443.1 Bpe04g00781 781
4 5035662 5038180 - Bpe015444.1 Bpe04g00782 782
5 21303972 21305080 - Bpe018209.1 Bpe05g00796 796
5 21390969 21412211 + Bpe018221.1 Bpe05g00808 808
5 21414712 21423177 + Bpe018222.1 Bpe05g00809 809
14 8110634 8115722 + Bpe014457.1 Bpe14g01083 1083
5 6887364 6889090 + CaPI482276_05g007870.1 Cam05g0787 787
6 6386157 6389425 - CaPI482276_06g004260.1 Cam06g0426 426
6 6390933 6392705 - CaPI482276_06g004270.1 Cam06g0427 427
6 6402858 6413354 - CaPI482276_06g004290.1 Cam06g0429 429
6 6419345 6430700 - CaPI482276_06g004300.1 Cam06g0430 430
6 9616840 9620369 + Carg25649-RA Car06g01340 1340
14 11720238 11723601 + Carg19607-RA Car14g01386 1386
17 2273875 2287167 + Carg05564-RA Car17g00357 357
17 2288150 2297793 + Carg05565-RA Car17g00358 358
5 6601355 6603048 + CcPI632755_05g007900.1 Cco05g0790 790
6 4758238 4761518 - CcPI632755_06g004330.1 Cco06g0433 433
6 4763117 4764907 - CcPI632755_06g004340.1 Cco06g0434 434
6 4770042 4786952 - CcPI632755_06g004350.1 Cco06g0435 435
6 4792647 4804311 - CcPI632755_06g004360.1 Cco06g0436 436
5 6620587 6622305 + CePI673135_05g007920.1 Cec05g0792 792
6 4898181 4901506 - CePI673135_06g004340.1 Cec06g0434 434
6 4903112 4904837 - CePI673135_06g004350.1 Cec06g0435 435
6 4909081 4925671 - CePI673135_06g004360.1 Cec06g0436 436
6 4932261 4943624 - CePI673135_06g004370.1 Cec06g0437 437
6 5372565 5374618 + Chy6G113010.1 Chy06g00773 773
6 5375213 5376750 - Chy6G113020.1 Chy06g00774 774
11 22528493 22542645 + Chy11G201760.1 Chy11g01596 1596
5 6592052 6597174 + ClG42_05g0077700.10 Clacu05g0777 777
6 4923779 4927042 - ClG42_06g0041200.10 Clacu06g0412 412
6 4928556 4930326 - ClG42_06g0041300.10 Clacu06g0413 413
6 4940367 4950805 - ClG42_06g0041500.10 Clacu06g0415 415
6 4956869 4968202 - ClG42_06g0041600.10 Clacu06g0416 416
5 6738904 6744153 + ClCG05G006690.2 Cla05g00718 718
6 4952711 4956352 - ClCG06G004330.1 Cla06g00404 404
6 4957797 4960119 - ClCG06G004340.2 Cla06g00405 405
6 4969320 4980209 - ClCG06G004360.1 Cla06g00407 407
6 4985504 4998146 - ClCG06G004370.1 Cla06g00408 408
6 9870910 9873505 + CmaCh06G015770.1 Cma06g01577 1577
14 11842205 11845344 + CmaCh14G015730.1 Cma14g01573 1573
17 2167340 2183333 + CmaCh17G003870.1 Cma17g00387 387
17 2184685 2195012 + CmaCh17G003880.1 Cma17g00388 388
6 4965108 4972348 - MELO3C006684.2.1 Cme06g00753 753
6 5526524 5529280 + MELO3C006734.2.1 Cme06g00816 816
11 28635377 28648190 + MELO3C021252.2.1 Cme11g02100 2100
11 28649049 28659985 + MELO3C021251.2.1 Cme11g02101 2101
11 3506837 3509277 - PI0023150.1 Cmetu11g1241 1241
11 3499704 3502317 + PI0025150.1 Cmetu11g1368 1368
11 3810956 3817438 + PI0016314.1 Cmetu11g2009 2009
6 11076450 11078680 + CmoCh06G015710.1 Cmo06g01571 1571
14 12771084 12774258 + CmoCh14G016060.1 Cmo14g01606 1606
17 2314870 2329638 + CmoCh17G003760.1 Cmo17g00376 376
17 2330844 2340546 + CmoCh17G003770.1 Cmo17g00377 377
5 6448081 6453222 + CmPI595203_05g007410.1 Cmu05g0741 741
6 4719056 4722319 - CmPI595203_06g004120.1 Cmu06g0412 412
6 4723870 4725640 - CmPI595203_06g004130.1 Cmu06g0413 413
6 4735632 4746074 - CmPI595203_06g004150.1 Cmu06g0415 415
6 4752144 4763483 - CmPI595203_06g004160.1 Cmu06g0416 416
14 3641045 3643398 + Conep14aG0070600.1 Cone14ag0691 691
14 3643764 3646285 - Conep14aG0070700.1 Cone14ag0692 692
14 3764678 3774795 + Conep14aG0071500.1 Cone14ag0699 699
15 3830849 3833016 - Conep15aG0072000.1 Cone15ag0706 706
15 4227539 4232622 + Conep15aG0075200.1 Cone15ag0737 737
3 10696668 10701389 + Cp4.1LG03g11930.1 Cpe03g01314 1314
8 898172 900889 - Cp4.1LG08g05260.1 Cpe08g00139 139
12 2266842 2277240 + Cp4.1LG12g03350.1 Cpe12g00339 339
12 2286130 2287985 + Cp4.1LG12g03310.1 Cpe12g00341 341
12 2288619 2293003 + Cp4.1LG12g03420.1 Cpe12g00342 342
5 7245731 7247488 + CrPI670011_05g008170.1 Cre05g0817 817
6 5775521 5778796 - CrPI670011_06g011920.1 Cre06g1192 1192
6 5780366 5782135 - CrPI670011_06g011930.1 Cre06g1193 1193
6 5792410 5802878 - CrPI670011_06g011950.1 Cre06g1195 1195
6 5808828 5820229 - CrPI670011_06g011960.1 Cre06g1196 1196
3 11439184 11441792 + CsaV3_3G015360.1 Csa03g01536 1536
3 11439184 11445628 - CsaV3_3G015370.1 Csa03g01537 1537
3 256236 258873 + Hsped.03g00230.1 Hepe03g0023 23
5 62135964 62138307 - Hsped.05g13590.1 Hepe05g1359 1359
11 10082843 10088322 - Lag0031563.1 Lac11g0925 925
11 36786529 36788994 - Maker00031261 Lcy11g1321 1321
12 10364778 10370878 - Maker00025108 Lcy12g0795 795
12 12620745 12632700 + Maker00025097 Lcy12g0885 885
12 12702299 12703918 + Maker00024738 Lcy12g0887 887
12 12704267 12711181 + Maker00025095 Lcy12g0888 888
5 21940055 21943871 - Lsi05G014040.1 Lsi05g01404 1404
5 22011876 22014070 - Lsi05G014090.1 Lsi05g01409 1409
9 23198554 23223172 + Lsi09G015110.1 Lsi09g01511 1511
2 48411366 48414816 - Sed0001944.1 Sed02g1122 1122
9 7775728 7778160 + Sed0012529.1 Sed09g0622 622
6 80115458 80116736 + Tan0019489.1 Tan06g2801 2801
6 80125410 80127924 - Tan0005855.1 Tan06g2802 2802
10 10423584 10426164 + Tan0020737.1 Tan10g1094 1094
5 2141831 2142422 - Vvi5g209 Vvi5g209 209
5 2142656 2145832 + Vvi5g210 Vvi5g210 210
5 2147654 2150249 + Vvi5g211 Vvi5g211 211
5 2150843 2163230 + Vvi5g212 Vvi5g212 212
5 2164749 2168736 - Vvi5g213 Vvi5g213 213
5 2171259 2173222 + Vvi5g214 Vvi5g214 214
5 2173791 2174477 + Vvi5g215 Vvi5g215 215
5 2181821 2182295 - Vvi5g216 Vvi5g216 216
5 2184078 2194337 + Vvi5g217 Vvi5g217 217
5 2195138 2199442 - Vvi5g218 Vvi5g218 218
       

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