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
Vvi19g514 Blo03g00556 . Bda07g00365 Bda09g00402 . Bpe08g01121 . . . . Cma01g01129 Cma09g00955 . Car09g00869 Sed07g2681 Cpe06g00771 Cpe02g00773 Bhi09g01647 Tan01g4554 Cmetu01g2001 . Hepe01g1272 Mch11g1191 . . . . . . . . . . . . Lsi02g01903 Csa07g01094 . . . . . . Bpe11g00551 . Bma07g01294 Bma14g00335 . Cmo01g01180 Cmo09g00953 . . . Car16g00540 . . . . . . . . . Cla09g01010 . . . . . Cre09g1031 . . . Cme01g01033
Vvi19g515 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g516 Blo03g00555 . Bda07g00366 . . . . . . . Cma01g01128 . . . . . Cpe02g00774 Bhi09g01649 . . . . Mch11g1192 . . . . . . . . . . . . Lsi02g01902 Csa07g01095 . . . . . . . . . Bma14g00334 . Cmo01g01179 . . . . Car16g00539 . . . . . . . . . Cla09g01011 Cam09g1068 Cec09g1068 Cco09g1086 . . Cre09g1032 . . . Cme01g01032
Vvi19g517 . Blo03g01453 . . . Bpe08g01120 . . . . Cma01g01127 . . . Sed04g3213 . Cpe02g00775 Bhi09g01650 Tan01g4558 Cmetu01g1354 . Hepe01g1269 Mch11g1193 . . . . . . . . . . . . Lsi02g01901 Csa07g01096 . . . . . . . . Bma07g01293 . . Cmo01g01178 . . . . . . . . . . . . . . Cla09g01012 Cam09g1069 Cec09g1069 Cco09g1087 . . Cre09g1033 . . . Cme01g01030
Vvi19g518 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1148 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g519 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0056 Cone9ag0068 . . . . . . . . . . . . . . . . . . . . . . . Bhi11g00614 . . . . . . . . . . . . . . . . .
Vvi19g520 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g521 . . . . Bpe09g00173 . Bma10g00550 . . . Cma01g01126 . . Car09g00871 Sed07g2679 Cpe06g00772 Cpe02g00776 Bhi09g01651 Tan01g4559 Cmetu01g2194 . Hepe01g1267 Mch11g1195 . . . . . . . . Cone6ag0054 Cone9ag0065 . . Lsi02g01900 Csa07g01097 . . Blo07g00903 Blo10g00835 Bda05g00719 Bda12g00911 . Bpe03g00791 . . . Cmo01g01177 Cmo09g00954 . . . . . . . . . . . . . Cla09g01013 Cam09g1070 Cec09g1070 Cco09g1088 . . Cre09g1034 . . . Cme01g01027
Vvi19g522 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g523 . . . . Bpe09g00172 . . Bma13g01062 . Cmo04g01037 . . . . . . . . . . . . . . Cla10g00497 Cam10g0489 Cec10g0507 Cco10g0492 Clacu10g0509 Cmu10g1336 Cre10g0741 . . Cone14ag1149 Cone15ag1165 . Csa03g00503 . Cme06g02241 . Blo10g00837 . . . . . . Sed01g3775 . . Cma04g00961 . . . . Cpe01g00874 Bhi11g00604 Tan01g1716 Cmetu06g0651 . . Mch10g1289 . . . . . . . . Lsi05g00585 . Chy06g01823 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 55586103 55590381 - Bda021861.2 Bda05g00719 719
7 4661914 4662252 - Bda025451.1 Bda07g00365 365
7 4663869 4668318 - Bda025452.1 Bda07g00366 366
9 5042126 5042464 - Bda030982.1 Bda09g00402 402
12 39816064 39825874 + Bda009447.1 Bda12g00911 911
9 44277848 44279630 - XM_039043454.1 Bhi09g01647 1647
9 44287335 44295298 - XM_039044177.1 Bhi09g01649 1649
9 44335787 44339235 + XM_039040720.1 Bhi09g01650 1650
9 44387277 44388200 + XM_039042841.1 Bhi09g01651 1651
11 13932011 13936323 - XM_039049594.1 Bhi11g00604 604
11 14354065 14358469 + XM_039047247.1 Bhi11g00614 614
3 21895483 21899835 + BLOR11736 Blo03g00555 555
3 21901163 21901501 + BLOR11737 Blo03g00556 556
3 41156899 41160963 + BLOR12634 Blo03g01453 1453
7 27959587 27960135 - BLOR18835 Blo07g00903 903
10 26643893 26647062 + BLOR02625 Blo10g00835 835
10 26665348 26672558 + BLOR02627 Blo10g00837 837
7 48534837 48536687 - Bma026565.1 Bma07g01293 1293
7 48567148 48567498 + Bma026569.1 Bma07g01294 1294
10 6663790 6667637 + Bma004250.1 Bma10g00550 550
13 43331255 43334077 + Bma010182.1 Bma13g01062 1062
14 4174443 4179415 + Bma030657 Bma14g00334 334
14 4182271 4182639 + Bma010756.1 Bma14g00335 335
3 27877294 27881636 - Bpe012703.1 Bpe03g00791 791
8 13176333 13178187 - Bpe023246.1 Bpe08g01120 1120
8 13180832 13181173 + Bpe023247.1 Bpe08g01121 1121
9 1185460 1188342 - Bpe023843.1 Bpe09g00172 172
9 1192932 1193498 - Bpe023844.1 Bpe09g00173 173
11 4222231 4222569 - Bpe003918.1 Bpe11g00551 551
9 11028201 11036938 - CaPI482276_09g010680.1 Cam09g1068 1068
9 11038751 11042236 + CaPI482276_09g010690.1 Cam09g1069 1069
9 11049900 11050463 + CaPI482276_09g010700.1 Cam09g1070 1070
10 7340777 7344114 - CaPI482276_10g004890.1 Cam10g0489 489
9 5316227 5317286 - Carg12823-RA Car09g00869 869
9 5325232 5325792 + Carg12825-RA Car09g00871 871
16 3425355 3427527 + Carg05624-RA Car16g00539 539
16 3428428 3429726 + Carg05625-RA Car16g00540 540
9 10359758 10368477 - CcPI632755_09g010860.1 Cco09g1086 1086
9 10370270 10373714 + CcPI632755_09g010870.1 Cco09g1087 1087
9 10381724 10382293 + CcPI632755_09g010880.1 Cco09g1088 1088
10 5898204 5901543 - CcPI632755_10g004920.1 Cco10g0492 492
9 10394552 10403299 - CePI673135_09g010680.1 Cec09g1068 1068
9 10405086 10408534 + CePI673135_09g010690.1 Cec09g1069 1069
9 10416157 10416720 + CePI673135_09g010700.1 Cec09g1070 1070
10 6105439 6114657 - CePI673135_10g005070.1 Cec10g0507 507
6 21982859 21986129 + Chy6G123510.1 Chy06g01823 1823
10 6174181 6177522 - ClG42_10g0050900.10 Clacu10g0509 509
9 10620803 10621141 - ClCG09G010810.1 Cla09g01010 1010
9 10625014 10629537 - ClCG09G010820.2 Cla09g01011 1011
9 10631110 10634806 + ClCG09G010830.2 Cla09g01012 1012
9 10643025 10643588 + ClCG09G010840.1 Cla09g01013 1013
10 6568795 6573063 - ClCG10G005320.1 Cla10g00497 497
1 8258212 8258772 - CmaCh01G011260.1 Cma01g01126 1126
1 8263043 8269923 - CmaCh01G011270.1 Cma01g01127 1127
1 8270641 8276215 + CmaCh01G011280.1 Cma01g01128 1128
1 8277250 8278581 + CmaCh01G011290.1 Cma01g01129 1129
4 4932627 4936234 - CmaCh04G009610.1 Cma04g00961 961
9 4806670 4807328 - CmaCh09G009550.1 Cma09g00955 955
1 12680776 12681578 - MELO3C013159.2.1 Cme01g01027 1027
1 12714292 12717431 - MELO3C013160.2.1 Cme01g01030 1030
1 12726533 12734549 + MELO3C013162.2.1 Cme01g01032 1032
1 12741259 12742555 + MELO3C013163.2.1 Cme01g01033 1033
6 29314905 29319140 - MELO3C025365.2.1 Cme06g02241 2241
1 10853192 10856568 + PI0012140.1 Cmetu01g1354 1354
1 10818275 10819892 - PI0009521.2 Cmetu01g2001 2001
1 10871334 10872247 + PI0008665.1 Cmetu01g2194 2194
6 26317777 26321033 + PI0027504.1 Cmetu06g0651 651
1 9589343 9589870 - CmoCh01G011770.1 Cmo01g01177 1177
1 9593221 9598896 - CmoCh01G011780.1 Cmo01g01178 1178
1 9599515 9606590 + CmoCh01G011790.1 Cmo01g01179 1179
1 9608583 9609570 + CmoCh01G011800.1 Cmo01g01180 1180
4 5175703 5179500 - CmoCh04G010370.1 Cmo04g01037 1037
9 5015254 5023210 - CmoCh09G009530.1 Cmo09g00953 953
9 5023313 5023867 + CmoCh09G009540.1 Cmo09g00954 954
10 6298029 6301401 - CmPI595203_10g013360.1 Cmu10g1336 1336
6 301851 303237 - Conep06aG0005400.1 Cone6ag0054 54
6 305863 308073 + Conep06aG0005600.1 Cone6ag0056 56
9 308329 309328 - Conep09aG0006500.1 Cone9ag0065 65
9 318240 320377 + Conep09aG0006800.1 Cone9ag0068 68
14 9501544 9507493 - Conep14aG0117200.1 Cone14ag1148 1148
14 9508548 9512366 + Conep14aG0117300.1 Cone14ag1149 1149
15 9431074 9434607 + Conep15aG0119400.1 Cone15ag1165 1165
1 5142385 5146738 - Cp4.1LG01g07900.1 Cpe01g00874 874
2 4921219 4923871 - Cp4.1LG02g01050.1 Cpe02g00773 773
2 4925947 4931695 - Cp4.1LG02g00990.1 Cpe02g00774 774
2 4932154 4938720 + Cp4.1LG02g01140.1 Cpe02g00775 775
2 4942962 4943486 + Cp4.1LG02g00920.1 Cpe02g00776 776
6 4865024 4872507 - Cp4.1LG06g08880.1 Cpe06g00771 771
6 4874721 4875281 + Cp4.1LG06g08900.1 Cpe06g00772 772
9 10561793 10562131 - CrPI670011_09g010310.1 Cre09g1031 1031
9 10571710 10576103 - CrPI670011_09g010320.1 Cre09g1032 1032
9 10577898 10581323 + CrPI670011_09g010330.1 Cre09g1033 1033
9 10589603 10590166 + CrPI670011_09g010340.1 Cre09g1034 1034
10 7190719 7194042 - CrPI670011_10g007410.1 Cre10g0741 741
3 4189124 4193475 - CsaV3_3G005030.1 Csa03g00503 503
7 10538881 10540789 - CsaV3_7G021830.1 Csa07g01094 1094
7 10549125 10555761 - CsaV3_7G021840.1 Csa07g01095 1095
7 10562879 10566419 + CsaV3_7G021850.1 Csa07g01096 1096
7 10572223 10572774 + CsaV3_7G021860.1 Csa07g01097 1097
1 77961518 77962296 + Hsped.01g12670.1 Hepe01g1267 1267
1 77978633 77981866 - Hsped.01g12690.1 Hepe01g1269 1269
1 77992758 77993096 + Hsped.01g12720.1 Hepe01g1272 1272
2 24934301 24934873 - Lsi02G019000.1 Lsi02g01900 1900
2 24940132 24944269 - Lsi02G019010.1 Lsi02g01901 1901
2 24946562 24951361 + Lsi02G019020.1 Lsi02g01902 1902
2 24954852 24955190 + Lsi02G019030.1 Lsi02g01903 1903
5 7278940 7283089 - Lsi05G005850.1 Lsi05g00585 585
10 10702958 10708309 + MC10g1057 Mch10g1289 1289
11 8371201 8371539 - MC11g0982 Mch11g1191 1191
11 8374783 8379628 - MC11g0983 Mch11g1192 1192
11 8380068 8383910 + MC11g0984 Mch11g1193 1193
11 8397340 8397882 + MC11g0986 Mch11g1195 1195
1 66882211 66888890 + Sed0003194.1 Sed01g3775 3775
4 42735134 42738557 + Sed0013659.1 Sed04g3213 3213
7 42193407 42195848 - Sed0014487.1 Sed07g2679 2679
7 42206324 42208374 + Sed0016288.1 Sed07g2681 2681
1 18268024 18272248 + Tan0022814.1 Tan01g1716 1716
1 111360078 111361668 - Tan0007672.1 Tan01g4554 4554
1 111392926 111398608 + Tan0003502.2 Tan01g4558 4558
1 111424445 111425516 + Tan0005982.1 Tan01g4559 4559
19 6579959 6581211 - Vvi19g514 Vvi19g514 514
19 6584227 6586583 - Vvi19g515 Vvi19g515 515
19 6587060 6593530 - Vvi19g516 Vvi19g516 516
19 6593737 6601198 + Vvi19g517 Vvi19g517 517
19 6601790 6614339 - Vvi19g518 Vvi19g518 518
19 6615173 6623463 - Vvi19g519 Vvi19g519 519
19 6628746 6632800 + Vvi19g520 Vvi19g520 520
19 6634270 6642457 + Vvi19g521 Vvi19g521 521
19 6659402 6661175 - Vvi19g522 Vvi19g522 522
19 6671392 6678633 + Vvi19g523 Vvi19g523 523
       

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