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
Vvi4g652 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g653 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi04g02032 . . . . . . . Bpe14g00062 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g654 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g655 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1717 Cone7ag1635 . . . . . . . Blo18g00245 Bda01g01339 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g656 Blo01g01429 . Bda01g00649 . . Bpe02g00521 . Bma01g02184 . . Cma01g01683 . Car09g00334 . . . Cpe06g00274 . . . . . . . Cla05g01652 Cam05g1764 Cec05g1770 Cco05g1829 Clacu05g1754 Cmu05g1639 Cre05g1767 Cone4ag1716 Cone7ag1634 . . Lsi04g01364 . . . . . . . . . . . Sed05g1812 Cmo01g01734 Cmo09g00388 Cma09g00387 . Car01g01298 . . Cpe02g00308 Bhi09g03051 Tan01g3520 Cmetu07g0647 . . . . . . . . . . . . . . Cme07g00153
Vvi4g657 Blo01g01430 . . . . Bpe02g00520 . . . . Cma01g01686 . Car09g00333 . . . Cpe06g00273 . . . . . . . Cla05g01650 Cam05g1763 Cec05g1769 Cco05g1826 Clacu05g1752 Cmu05g1637 Cre05g1765 Cone4ag1715 Cone7ag1633 . . Lsi04g01366 . . . . . . . . . . . Sed05g1809 Cmo01g01737 Cmo09g00386 Cma09g00384 . Car01g01300 . . Cpe02g00307 Bhi09g03052 Tan01g3517 Cmetu07g0488 . Hepe01g1936 Mch11g0472 . . . . . . . . . . . Cme07g00155
Vvi4g658 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g659 . Blo12g00999 . Bda03g00159 . Bpe02g00225 . Bma01g02228 . . Cma01g01581 . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g04414 Chy04g00287 . . . . . . Bpe04g00141 . . Sed13g2106 . . Cma09g00534 . . . . . Bhi09g02382 Tan01g3749 Cmetu04g0694 . Hepe01g2097 Mch11g0635 . . . . . . . . . . . Cme04g00326
Vvi4g660 . . . . . Bpe02g00224 . . . . Cma01g01579 . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g04413 Chy04g00288 . . . . . . . . . . . . . . . . . . Bhi09g02381 Tan01g3748 . . Hepe01g2096 Mch11g0634 . . . . . . . . . . . Cme04g00327
Vvi4g661 . . . . . Bpe02g00223 . . . . Cma01g01578 . . . . . . . . . . . . . . . . . . . . Cone4ag1864 Cone7ag1771 . . . Csa03g04411 Chy04g00289 . . . . . . . . . . . . Cma09g00533 . . . . . . . . . . . . . . . . . . . . . . Cme04g00330
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 33503972 33510587 + Bda002677.1 Bda01g00649 649
1 49068838 49071085 + Bda003575.1 Bda01g01339 1339
3 1314886 1317379 + Bda016101.1 Bda03g00159 159
9 64955975 64960831 + XM_039040646.1 Bhi09g02381 2381
9 64961583 64965618 - XM_039042749.1 Bhi09g02382 2382
9 78962302 78972376 - XM_039043432.1 Bhi09g03051 3051
9 79021088 79027320 + XM_039043226.1 Bhi09g03052 3052
1 53123294 53129159 - BLOR01429 Blo01g01429 1429
1 53142318 53147751 + BLOR01430 Blo01g01430 1430
12 27995952 27998445 - BLOR05018 Blo12g00999 999
18 2464399 2467795 - BLOR08733 Blo18g00245 245
1 78756518 78762759 - Bma003031.1 Bma01g02184 2184
1 79288701 79290495 + Bma003077.1 Bma01g02228 2228
2 1545664 1547107 + Bpe008070.1 Bpe02g00223 223
2 1549514 1553085 + Bpe008071.1 Bpe02g00224 224
2 1554122 1556530 - Bpe025066 Bpe02g00225 225
2 3384165 3388951 - Bpe008360.1 Bpe02g00520 520
2 3397178 3403390 + Bpe008361.1 Bpe02g00521 521
4 951974 954450 + Bpe014860.1 Bpe04g00141 141
14 1002195 1003166 + Bpe024957 Bpe14g00062 62
5 26266041 26271738 - CaPI482276_05g017630.1 Cam05g1763 1763
5 26355462 26363637 + CaPI482276_05g017640.1 Cam05g1764 1764
1 11683969 11689718 - Carg10739-RA Car01g01298 1298
1 11700849 11706554 + Carg10737-RA Car01g01300 1300
9 1831385 1835749 - Carg02812-RA Car09g00333 333
9 1846239 1853402 + Carg02814-RA Car09g00334 334
5 27058911 27064637 - CcPI632755_05g018260.1 Cco05g1826 1826
5 27141792 27150043 + CcPI632755_05g018290.1 Cco05g1829 1829
5 29380430 29385972 - CePI673135_05g017690.1 Cec05g1769 1769
5 29453913 29462127 + CePI673135_05g017700.1 Cec05g1770 1770
4 2598661 2601467 + Chy4G070050.1 Chy04g00287 287
4 2602983 2607584 - Chy4G070060.1 Chy04g00288 288
4 2612385 2615042 - Chy4G070070.1 Chy04g00289 289
5 26489492 26495186 - ClG42_05g0175200.10 Clacu05g1752 1752
5 26562297 26570481 + ClG42_05g0175400.10 Clacu05g1754 1754
5 27985262 27991497 - ClCG05G015990.1 Cla05g01650 1650
5 28058634 28067049 + ClCG05G016010.2 Cla05g01652 1652
1 10902600 10908483 + CmaCh01G015780.1 Cma01g01578 1578
1 10909946 10914271 + CmaCh01G015790.1 Cma01g01579 1579
1 10915923 10919118 - CmaCh01G015810.1 Cma01g01581 1581
1 11482122 11488084 - CmaCh01G016830.1 Cma01g01683 1683
1 11498023 11503482 + CmaCh01G016860.1 Cma01g01686 1686
9 1605892 1611348 - CmaCh09G003840.1 Cma09g00384 384
9 1623094 1631212 + CmaCh09G003870.1 Cma09g00387 387
9 2376770 2380593 + CmaCh09G005330.1 Cma09g00533 533
9 2381792 2385780 - CmaCh09G005340.1 Cma09g00534 534
4 2611900 2615264 + MELO3C003616.2.1 Cme04g00326 326
4 2616233 2621284 - MELO3C003617.2.1 Cme04g00327 327
4 2625047 2629570 - MELO3C003619.2.1 Cme04g00330 330
7 986984 997638 - MELO3C016937.2.1 Cme07g00153 153
7 1021501 1027732 + MELO3C016935.2.1 Cme07g00155 155
4 30753336 30756161 - PI0001870.1 Cmetu04g0694 694
7 23728681 23734282 - PI0026686.1 Cmetu07g0488 488
7 23764582 23767035 + PI0015359.1 Cmetu07g0647 647
1 12959460 12965238 - CmoCh01G017340.1 Cmo01g01734 1734
1 12976555 12981881 + CmoCh01G017370.1 Cmo01g01737 1737
9 1684591 1690663 - CmoCh09G003860.1 Cmo09g00386 386
9 1701613 1708743 + CmoCh09G003880.1 Cmo09g00388 388
5 26208339 26214032 - CmPI595203_05g016370.1 Cmu05g1637 1637
5 26281155 26289338 + CmPI595203_05g016390.1 Cmu05g1639 1639
4 12706155 12710731 - Conep04aG0176900.1 Cone4ag1715 1715
4 12713507 12717642 + Conep04aG0177000.1 Cone4ag1716 1716
4 12718045 12721784 - Conep04aG0177100.1 Cone4ag1717 1717
4 13363054 13365602 + Conep04aG0192300.1 Cone4ag1864 1864
7 11043917 11048394 - Conep07aG0168200.1 Cone7ag1633 1633
7 11050862 11055104 + Conep07aG0168300.1 Cone7ag1634 1634
7 11055723 11059629 - Conep07aG0168400.1 Cone7ag1635 1635
7 11663010 11665490 + Conep07aG0182400.1 Cone7ag1771 1771
2 1602027 1608063 - Cp4.1LG02g05670.1 Cpe02g00307 307
2 1621064 1627724 + Cp4.1LG02g05740.1 Cpe02g00308 308
6 1487181 1493330 - Cp4.1LG06g02860.1 Cpe06g00273 273
6 1503597 1511115 + Cp4.1LG06g02780.1 Cpe06g00274 274
5 29463171 29468901 - CrPI670011_05g017650.1 Cre05g1765 1765
5 29515973 29524192 + CrPI670011_05g017670.1 Cre05g1767 1767
3 38465750 38470216 + CsaV3_3G047170.1 Csa03g04411 4411
3 38472710 38477560 + CsaV3_3G047190.1 Csa03g04413 4413
3 38476463 38482334 - CsaV3_3G047200.1 Csa03g04414 4414
1 84169148 84176103 - Hsped.01g19360.1 Hepe01g1936 1936
1 85570136 85578054 + Hsped.01g20960.1 Hepe01g2096 2096
1 85578571 85582853 - Hsped.01g20970.1 Hepe01g2097 2097
4 21402488 21411643 - Lsi04G013640.1 Lsi04g01364 1364
4 21441899 21448606 + Lsi04G013660.1 Lsi04g01366 1366
4 27435874 27439090 + Lsi04G020320.1 Lsi04g02032 2032
11 2986499 2993294 - MC11g0379 Mch11g0472 472
11 4089781 4098629 + MC11g0528 Mch11g0634 634
11 4093054 4098669 - MC11g0529 Mch11g0635 635
5 31671333 31678113 - Sed0017854.1 Sed05g1809 1809
5 31715207 31724658 + Sed0022125.1 Sed05g1812 1812
13 25730419 25734616 - Sed0021461.1 Sed13g2106 2106
1 100257672 100264916 - Tan0001935.1 Tan01g3517 3517
1 100332118 100339956 + Tan0000942.1 Tan01g3520 3520
1 102270451 102274629 + Tan0009148.1 Tan01g3748 3748
1 102276965 102280483 - Tan0012715.1 Tan01g3749 3749
4 8627883 8628150 + Vvi4g652 Vvi4g652 652
4 8653855 8658091 + Vvi4g653 Vvi4g653 653
4 8709992 8711285 + Vvi4g654 Vvi4g654 654
4 8723149 8739489 + Vvi4g655 Vvi4g655 655
4 8773509 8788445 - Vvi4g656 Vvi4g656 656
4 8831626 8851182 + Vvi4g657 Vvi4g657 657
4 8856566 8866591 + Vvi4g658 Vvi4g658 658
4 8878294 8882271 + Vvi4g659 Vvi4g659 659
4 8890607 8897634 - Vvi4g660 Vvi4g660 660
4 8906594 8911966 - Vvi4g661 Vvi4g661 661
       

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