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
Vvi4g612 . . . . . . . . Cmo05g00344 . . Cma05g00341 . . . . . Bhi04g00070 . . . . . Lcy13g1845 . . . . . . . . . . Cone20ag0308 . . . Cme03g01561 . . . . . . . . . . . . . . Car05g00286 Cpe11g00286 . . . . . . . . Cla08g01378 . . . . . . Lsi08g01262 . Chy03g01071 .
Vvi4g613 . . . . Bpe02g01269 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1730 Cone7ag1649 . . . . . . . . Bda01g01019 . . . Bma01g01260 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g614 . . . Bda03g00113 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe04g00099 . . Sed05g1816 . . . . . . . . Bhi09g03045 Tan01g3527 Cmetu07g1748 . Hepe01g1942 Mch11g0478 . . . . . . . . . . . Cme07g00147
Vvi4g615 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g616 Blo01g01427 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi04g01358 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g617 . . . . . . . . . . . . Car09g00340 . . . Cpe06g00279 . . . . . . . Cla05g01658 Cam05g1769 Cec05g1777 Cco05g1835 Clacu05g1759 Cmu05g1645 Cre05g1773 Cone4ag1728 Cone7ag1648 Cone17ag0969 . . . . . . . . . . . . . . . Cmo09g00393 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g618 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma09g00391 . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g619 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g620 . . . . Bpe02g01270 . . . Cmo05g00342 Cmo12g00326 . Cma05g00340 Car09g00339 Car12g00357 Sed01g2916 Cpe07g00331 Cpe06g00278 Bhi04g00071 Tan02g2782 Cmetu03g0233 . Hepe10g0204 . Lcy13g1846 Cla05g01657 Cam05g1768 Cec05g1775 Cco05g1834 Clacu05g1758 Cmu05g1643 Cre05g1772 . Cone7ag1647 Cone17ag0966 Cone20ag0307 Lsi04g01359 . . Cme03g01560 . . . . . . . Bma02g00004 . . Cmo09g00392 . Cma12g00373 . Car05g00285 Cpe11g00285 . Bhi09g03046 Tan01g3525 Cmetu07g0269 . Hepe01g1941 Mch11g0477 . Cla08g01379 Cam08g1850 Cec08g1428 Cco08g1561 Clacu08g1545 . Cre08g1328 Lsi08g01263 . Chy03g01070 Cme07g00148
Vvi4g621 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 43754752 43758722 + Bda003176.2 Bda01g01019 1019
3 1014277 1016137 + Bda016052.1 Bda03g00113 113
4 1848063 1851116 + XM_039028565.1 Bhi04g00070 70
4 1852829 1854394 - XM_039030842.1 Bhi04g00071 71
9 78812858 78817573 + XM_039041990.1 Bhi09g03045 3045
9 78862525 78863887 - XM_039043659.1 Bhi09g03046 3046
1 53080047 53091831 + BLOR01427 Blo01g01427 1427
1 16779422 16783642 - Bma001573.1 Bma01g01260 1260
2 170914 171804 + Bma014462.1 Bma02g00004 4
2 16115050 16119101 + Bpe009125.1 Bpe02g01269 1269
2 16119351 16120247 - Bpe009126.1 Bpe02g01270 1270
4 705399 706743 + Bpe014820.1 Bpe04g00099 99
5 26479429 26480307 + CaPI482276_05g017680.1 Cam05g1768 1768
5 26521760 26526016 - CaPI482276_05g017690.1 Cam05g1769 1769
8 24565500 24566417 - CaPI482276_08g018500.1 Cam08g1850 1850
5 1579751 1580566 + Carg09374-RA Car05g00285 285
5 1582200 1584341 - Carg09373-RA Car05g00286 286
9 1876461 1877396 - Carg02819-RA Car09g00339 339
9 1879296 1881957 - Carg02820-RA Car09g00340 340
12 2265971 2266873 - Carg03964-RA Car12g00357 357
5 27272952 27273830 + CcPI632755_05g018340.1 Cco05g1834 1834
5 27316994 27321281 - CcPI632755_05g018350.1 Cco05g1835 1835
8 27229116 27230036 - CcPI632755_08g015610.1 Cco08g1561 1561
5 29606421 29607296 + CePI673135_05g017750.1 Cec05g1775 1775
5 29644612 29648862 - CePI673135_05g017770.1 Cec05g1777 1777
8 26084421 26085347 - CePI673135_08g014280.1 Cec08g1428 1428
3 14127391 14128296 + Chy3G060500.1 Chy03g01070 1070
3 14131231 14133345 - Chy3G060510.1 Chy03g01071 1071
5 26688665 26689543 + ClG42_05g0175800.10 Clacu05g1758 1758
5 26727752 26731944 - ClG42_05g0175900.10 Clacu05g1759 1759
8 25306408 25307328 - ClG42_08g0154500.10 Clacu08g1545 1545
5 28188299 28189177 + ClCG05G016060.1 Cla05g01657 1657
5 28227400 28231998 - ClCG05G016070.1 Cla05g01658 1658
8 26646574 26648691 + ClCG08G013820.1 Cla08g01378 1378
8 26651804 26653471 - ClCG08G013830.1 Cla08g01379 1379
5 1488732 1489547 + CmaCh05G003400.1 Cma05g00340 340
5 1491372 1498040 - CmaCh05G003410.1 Cma05g00341 341
9 1649823 1654650 - CmaCh09G003910.1 Cma09g00391 391
12 1928110 1929012 - CmaCh12G003730.1 Cma12g00373 373
3 24690430 24691985 + MELO3C011315.2.1 Cme03g01560 1560
3 24694429 24696543 - MELO3C011314.2.1 Cme03g01561 1561
7 940916 945756 + MELO3C016942.2.1 Cme07g00147 147
7 947005 948144 - MELO3C016941.2.1 Cme07g00148 148
3 4723345 4726561 - PI0024519.1 Cmetu03g0233 233
7 23806676 23808442 + PI0017647.1 Cmetu07g0269 269
7 23810341 23815638 - PI0021203.1 Cmetu07g1748 1748
5 1534355 1535170 + CmoCh05G003420.1 Cmo05g00342 342
5 1536905 1539025 - CmoCh05G003440.1 Cmo05g00344 344
9 1727811 1728746 - CmoCh09G003920.1 Cmo09g00392 392
9 1730747 1733632 - CmoCh09G003930.1 Cmo09g00393 393
12 2034308 2035210 - CmoCh12G003260.1 Cmo12g00326 326
5 26407442 26408320 + CmPI595203_05g016430.1 Cmu05g1643 1643
5 26446638 26450823 - CmPI595203_05g016450.1 Cmu05g1645 1645
4 12783585 12785520 + Conep04aG0178300.1 Cone4ag1728 1728
4 12791216 12795255 - Conep04aG0178500.1 Cone4ag1730 1730
7 11111002 11111912 + Conep07aG0169600.1 Cone7ag1647 1647
7 11114309 11116662 - Conep07aG0169700.1 Cone7ag1648 1648
7 11118581 11122578 - Conep07aG0169800.1 Cone7ag1649 1649
17 7514868 7515799 + Conep17aG0099300.1 Cone17ag0966 966
17 7522679 7524583 + Conep17aG0099600.1 Cone17ag0969 969
20 1376544 1377263 + Conep20aG0032000.1 Cone20ag0307 307
20 1377345 1379426 - Conep20aG0032100.1 Cone20ag0308 308
6 1530456 1531391 - Cp4.1LG06g02850.1 Cpe06g00278 278
6 1532462 1536312 - Cp4.1LG06g02820.1 Cpe06g00279 279
7 2147559 2148461 - Cp4.1LG07g03420.1 Cpe07g00331 331
11 1549066 1549881 + Cp4.1LG11g02810.1 Cpe11g00285 285
11 1550190 1553772 - Cp4.1LG11g02900.1 Cpe11g00286 286
5 29636825 29637703 + CrPI670011_05g017720.1 Cre05g1772 1772
5 29697469 29701724 - CrPI670011_05g017730.1 Cre05g1773 1773
8 26368130 26369047 - CrPI670011_08g013280.1 Cre08g1328 1328
1 84270787 84271808 + Hsped.01g19410.1 Hepe01g1941 1941
1 84272425 84277342 - Hsped.01g19420.1 Hepe01g1942 1942
10 2088979 2090849 + Hsped.10g02040.1 Hepe10g0204 204
13 37399758 37401875 + Maker00033870 Lcy13g1845 1845
13 37404770 37405684 - Maker00033951 Lcy13g1846 1846
4 21324131 21328781 + Lsi04G013580.1 Lsi04g01358 1358
4 21334540 21335418 - Lsi04G013590.1 Lsi04g01359 1359
8 21046843 21052579 + Lsi08G012620.1 Lsi08g01262 1262
8 21052882 21053793 - Lsi08G012630.1 Lsi08g01263 1263
11 3050582 3051436 + MC11g0384 Mch11g0477 477
11 3052757 3056984 - MC11g0385 Mch11g0478 478
1 25025520 25033538 + Sed0024027.1 Sed01g2916 2916
5 31758392 31762359 - Sed0024771.1 Sed05g1816 1816
1 100414405 100415713 + Tan0017799.1 Tan01g3525 3525
1 100417957 100423228 - Tan0007369.2 Tan01g3527 3527
2 96099919 96101522 - Tan0005866.1 Tan02g2782 2782
4 7150218 7155555 + Vvi4g612 Vvi4g612 612
4 7178803 7188084 + Vvi4g613 Vvi4g613 613
4 7189958 7192597 + Vvi4g614 Vvi4g614 614
4 7205147 7207822 + Vvi4g615 Vvi4g615 615
4 7244097 7247313 + Vvi4g616 Vvi4g616 616
4 7263243 7279815 - Vvi4g617 Vvi4g617 617
4 7315580 7317297 - Vvi4g618 Vvi4g618 618
4 7425296 7426276 - Vvi4g619 Vvi4g619 619
4 7520541 7521754 - Vvi4g620 Vvi4g620 620
4 7584558 7587444 - Vvi4g621 Vvi4g621 621
       

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