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
Vvi2g352 . . . . . . . . . . Cma02g01071 . Car02g00816 . . . Cpe05g00647 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi12g00493 . . . . . Lcy12g0039 . . . . . . . . . . .
Vvi2g353 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g354 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g355 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g356 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g357 . . . . . . . . . Cmo16g00635 . . . . . Cpe14g00496 . . . . . . . . Cla07g00760 Cam07g0816 Cec07g0876 Cco07g0851 Clacu07g0794 Cmu07g0802 Cre07g1156 . . . . . . . . . . . . . . . . . . . . Cma16g00586 . . . . . . . . . . . . . . . . . . . . Chy07g01207 .
Vvi2g358 . . Bda06g00082 . . Bpe07g00117 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme07g01621 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00604 . .
Vvi2g359 . . . . . . Bma07g01642 . . . Cma02g01094 . . Car15g01094 . . Cpe05g00622 . . . . . . . . . . . . . . . . . . . . . . . Blo19g00316 . Bda09g00047 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g360 . . . . . . . Bma14g00589 . . Cma02g01473 Cma15g01214 Car02g01234 . . . Cpe05g00316 . . . . . . . . . . . . . . Cone8ag0319 . . . . . Chy09g01203 . Blo03g00366 . . . . Bpe11g00678 . . . Cmo02g01508 Cmo15g01278 . . . . . Cpe13g00166 Bhi12g00222 . . Lac11g2117 Hepe06g1566 . Lcy12g1674 Cla01g00284 Cam01g0295 Cec01g0288 Cco01g0301 Clacu01g0295 Cmu01g0281 Cre09g2228 Lsi09g00284 . . Cme09g01740
Vvi2g361 . . . . . . . . . . . . Car02g01235 . . . Cpe05g00315 . . . . . . . . . . . . . . . Cone12ag0318 . . . Csa05g00302 Chy09g01202 . . . . . . . . . . Cmo02g01509 . . . . . . . Bhi12g00221 . . Lac11g2118 Hepe06g1567 . Lcy12g1675 . . . . . . . Lsi09g00285 . . Cme09g01739
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 812210 813553 + Bda023253.1 Bda06g00082 82
9 701926 704283 + Bda030570.1 Bda09g00047 47
12 7260119 7266804 + XM_039018792.1 Bhi12g00221 221
12 7272277 7276996 + XM_039020206.1 Bhi12g00222 222
12 15573403 15580360 - XM_039018314.1 Bhi12g00493 493
3 8321695 8328108 + BLOR11547 Blo03g00366 366
19 20408957 20413138 + BLOR09659 Blo19g00316 316
7 52009572 52013793 - Bma026938.1 Bma07g01642 1642
14 6381034 6383874 - Bma011025.1 Bma14g00589 589
7 839337 840628 - Bpe020930.1 Bpe07g00117 117
11 5228278 5231088 + Bpe004034.1 Bpe11g00678 678
1 3314772 3320532 - CaPI482276_01g002950.1 Cam01g0295 295
7 20522231 20529062 + CaPI482276_07g008160.1 Cam07g0816 816
2 5902584 5908384 + Carg08405-RA Car02g00816 816
2 8355120 8358766 - Carg02514-RA Car02g01234 1234
2 8359171 8364904 - Carg02513-RA Car02g01235 1235
15 8617391 8621654 - Carg16648-RA Car15g01094 1094
1 2950245 2955989 - CcPI632755_01g003010.1 Cco01g0301 301
7 19786118 19792782 + CcPI632755_07g008510.1 Cco07g0851 851
1 2917018 2922778 - CePI673135_01g002880.1 Cec01g0288 288
7 21690022 21696684 + CePI673135_07g008760.1 Cec07g0876 876
7 16900650 16902880 + Chy7G140370.1 Chy07g01207 1207
9 14173813 14179347 + Chy9G169180.1 Chy09g01202 1202
9 14183748 14186466 + Chy9G169190.1 Chy09g01203 1203
1 2931213 2936969 - ClG42_01g0029500.10 Clacu01g0295 295
7 20236270 20243002 + ClG42_07g0079400.10 Clacu07g0794 794
1 2995230 3009395 - ClCG01G002940.1 Cla01g00284 284
7 21345886 21354979 + ClCG07G007970.1 Cla07g00760 760
2 6378437 6392694 + CmaCh02G010710.1 Cma02g01071 1071
2 6510262 6519507 - CmaCh02G010940.1 Cma02g01094 1094
2 8438421 8447964 - CmaCh02G014730.1 Cma02g01473 1473
15 7674904 7678800 + CmaCh15G012140.1 Cma15g01214 1214
16 3025406 3030691 + CmaCh16G005860.1 Cma16g00586 586
7 21992668 21995287 + MELO3C016345.2.1 Cme07g01621 1621
9 21927320 21933431 + MELO3C005651.2.1 Cme09g01739 1739
9 21935239 21939462 + MELO3C005652.2.1 Cme09g01740 1740
2 8802067 8805582 - CmoCh02G015080.1 Cmo02g01508 1508
2 8806016 8812804 - CmoCh02G015090.1 Cmo02g01509 1509
15 8757309 8762218 + CmoCh15G012780.1 Cmo15g01278 1278
16 3127828 3133321 + CmoCh16G006350.1 Cmo16g00635 635
1 2887249 2893006 - CmPI595203_01g002810.1 Cmu01g0281 281
7 20450094 20456847 + CmPI595203_07g008020.1 Cmu07g0802 802
8 1849829 1851007 + Conep08aG0033400.1 Cone8ag0319 319
12 1740683 1744951 + Conep12aG0033300.1 Cone12ag0318 318
5 1759853 1764769 + Cp4.1LG05g03550.1 Cpe05g00315 315
5 1766808 1770384 + Cp4.1LG05g03580.1 Cpe05g00316 316
5 3774051 3780046 + Cp4.1LG05g06110.1 Cpe05g00622 622
5 3949716 3956149 - Cp4.1LG05g06590.1 Cpe05g00647 647
13 1246938 1251780 - Cp4.1LG13g01680.1 Cpe13g00166 166
14 3145917 3152367 + Cp4.1LG14g02310.1 Cpe14g00496 496
7 23770011 23776751 + CrPI670011_07g011560.1 Cre07g1156 1156
9 41432101 41436376 + CrPI670011_09g022280.1 Cre09g2228 2228
4 3987987 3991548 - CsaV3_4G006040.1 Csa04g00604 604
5 1907440 1923444 - CsaV3_5G003020.1 Csa05g00302 302
6 66392751 66396824 - Hsped.06g15660.1 Hepe06g1566 1566
6 66400145 66411344 - Hsped.06g15670.1 Hepe06g1567 1567
11 37156936 37160992 - Lag0032755.1 Lac11g2117 2117
11 37164884 37171661 - Lag0032756.1 Lac11g2118 2118
12 651534 664039 + Maker00038769 Lcy12g0039 39
12 37196312 37200889 - Maker00029313 Lcy12g1674 1674
12 37202728 37209724 - Maker00029333 Lcy12g1675 1675
9 2968356 2969932 - Lsi09G002840.1 Lsi09g00284 284
9 2974533 2981378 - Lsi09G002850.1 Lsi09g00285 285
2 3382879 3384672 + Vvi2g352 Vvi2g352 352
2 3392460 3394348 - Vvi2g353 Vvi2g353 353
2 3408483 3412272 + Vvi2g354 Vvi2g354 354
2 3441921 3442763 + Vvi2g355 Vvi2g355 355
2 3445600 3447792 - Vvi2g356 Vvi2g356 356
2 3454312 3457988 + Vvi2g357 Vvi2g357 357
2 3458408 3464102 + Vvi2g358 Vvi2g358 358
2 3470704 3475501 - Vvi2g359 Vvi2g359 359
2 3480174 3487061 - Vvi2g360 Vvi2g360 360
2 3488172 3496025 - Vvi2g361 Vvi2g361 361
       

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