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
Vvi2g722 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g723 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g724 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0486 . . . . . . . . . . Bda09g00755 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g725 . . Bda06g01257 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone5ag1840 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g726 Blo02g00978 Blo03g00105 . . . Bpe07g00236 . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0487 . . . . . . . . . . . . . . Bma12g00237 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g727 . . . Bda08g00641 Bpe05g00518 . . . . . . . . . Sed02g0069 . . Bhi11g00009 Tan01g2215 Cmetu06g1490 . . Mch10g1683 . . . . . . . . . . . . . . . . . . . . . . Bma05g00703 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g728 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g729 . . . . . . . . Cmo06g00635 Cmo16g01238 . . . . . Cpe14g00986 . . . . . . . . Cla10g00126 Cam10g0126 . . Clacu10g0131 Cmu10g0978 . Cone8ag0492 Cone12ag0490 . . Lsi07g01161 . . . Blo03g00884 . Bda07g00074 . . Bpe11g00314 . . . . . Cma06g00626 Cma16g01190 Car06g00561 Car16g01122 . . . . . . . . . . . . . . . . . Csa03g00134 Chy06g02173 .
Vvi2g730 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g731 . . . . . . . . . . Cma02g01637 . Car02g01396 . . . . . . . . . . . . . . . . . . Cone8ag0493 Cone12ag0491 . . . . Chy04g00127 . Blo03g00885 . Bda07g00073 . . Bpe11g00313 . . Sed01g4141 Cmo02g01682 Cmo19g00229 . . . . . Cpe15g00189 Bhi05g00443 Tan07g2011 Cmetu04g1552 Lac11g2451 Hepe06g1802 . Lcy12g1974 Cla09g01091 Cam09g1144 Cec09g1154 Cco09g1170 . . Cre09g1107 . Csa03g04578 . Cme04g00150
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 43077047 43079454 + Bda023097.1 Bda06g01257 1257
7 942042 951205 - Bda025131.1 Bda07g00073 73
7 952590 961707 - Bda025132.1 Bda07g00074 74
8 6589154 6589468 + Bda034012 Bda08g00641 641
9 13423733 13428307 + Bda031463.1 Bda09g00755 755
5 9267552 9274524 - XM_039032486.1 Bhi05g00443 443
11 104299 108711 - XM_039048722.1 Bhi11g00009 9
2 37891363 37891851 + BLOR10708 Blo02g00978 978
3 3333165 3333656 + BLOR11286 Blo03g00105 105
3 34703549 34705920 + BLOR12065 Blo03g00884 884
3 34708021 34726345 + BLOR12066 Blo03g00885 885
5 41006041 41006355 - Bma031200 Bma05g00703 703
12 3055177 3059996 - Bma007127.1 Bma12g00237 237
5 19371815 19372135 - Bpe017935.1 Bpe05g00518 518
7 1670032 1674422 - Bpe021047.1 Bpe07g00236 236
11 2282774 2291845 - Bpe003687.1 Bpe11g00313 313
11 2293833 2296146 - Bpe003688.1 Bpe11g00314 314
9 11974174 11981935 - CaPI482276_09g011440.1 Cam09g1144 1144
10 2843070 2846707 - CaPI482276_10g001260.1 Cam10g0126 126
2 9178120 9185647 + Carg08863-RA Car02g01396 1396
6 3181653 3184937 - Carg23402-RA Car06g00561 561
16 9641748 9644388 + Carg23587-RA Car16g01122 1122
9 11357869 11365665 - CcPI632755_09g011700.1 Cco09g1170 1170
9 11390491 11403743 - CePI673135_09g011540.1 Cec09g1154 1154
4 1145934 1151002 + Chy4G068450.1 Chy04g00127 127
6 26008781 26010794 + Chy6G127010.1 Chy06g02173 2173
10 1566565 1570269 - ClG42_10g0013100.10 Clacu10g0131 131
9 11613915 11626402 - ClCG09G011630.2 Cla09g01091 1091
10 1303659 1307364 - ClCG10G001270.2 Cla10g00126 126
2 9278113 9286284 + CmaCh02G016370.1 Cma02g01637 1637
6 3063759 3067341 - CmaCh06G006260.1 Cma06g00626 626
16 9089026 9091924 + CmaCh16G011900.1 Cma16g01190 1190
4 1136907 1147175 + MELO3C003440.2.1 Cme04g00150 150
4 32277206 32283577 - PI0015958.1 Cmetu04g1552 1552
6 29851592 29855731 + PI0023204.1 Cmetu06g1490 1490
2 9652747 9660787 + CmoCh02G016820.1 Cmo02g01682 1682
6 3160939 3164064 - CmoCh06G006350.1 Cmo06g00635 635
16 8869934 8872228 + CmoCh16G012380.1 Cmo16g01238 1238
19 1557034 1566907 - CmoCh19G002290.1 Cmo19g00229 229
10 1717680 1721384 - CmPI595203_10g009780.1 Cmu10g0978 978
5 12933131 12934821 + Conep05aG0189900.1 Cone5ag1840 1840
8 3377935 3384736 - Conep08aG0050700.1 Cone8ag0486 486
8 3411942 3413493 + Conep08aG0050800.1 Cone8ag0487 487
8 3495849 3498832 + Conep08aG0051300.1 Cone8ag0492 492
8 3502901 3510482 + Conep08aG0051400.1 Cone8ag0493 493
12 3281955 3284828 + Conep12aG0051100.1 Cone12ag0490 490
12 3296646 3310862 + Conep12aG0051200.1 Cone12ag0491 491
14 8336209 8339727 + Cp4.1LG14g09770.1 Cpe14g00986 986
15 1536439 1547538 - Cp4.1LG15g01900.1 Cpe15g00189 189
9 11551229 11558975 - CrPI670011_09g011070.1 Cre09g1107 1107
3 1033754 1037211 - CsaV3_3G001340.1 Csa03g00134 134
3 39833339 39839599 - CsaV3_3G048840.1 Csa03g04578 4578
6 69110354 69124051 + Hsped.06g18020.1 Hepe06g1802 1802
11 40704674 40711714 + Lag0033089.1 Lac11g2451 2451
12 41132374 41140689 + Maker00038128 Lcy12g1974 1974
7 17087558 17090664 - Lsi07G011610.1 Lsi07g01161 1161
10 16878172 16878521 + MC10g1338 Mch10g1683 1683
1 70221193 70229413 + Sed0022223.1 Sed01g4141 4141
2 8288171 8291322 + Sed0013912.1 Sed02g0069 69
1 26293905 26299209 + Tan0010915.1 Tan01g2215 2215
7 71831555 71840827 + Tan0008335.2 Tan07g2011 2011
2 8692316 8703054 - Vvi2g722 Vvi2g722 722
2 8734265 8734868 - Vvi2g723 Vvi2g723 723
2 8739163 8746005 + Vvi2g724 Vvi2g724 724
2 8757169 8762765 + Vvi2g725 Vvi2g725 725
2 8764177 8764669 + Vvi2g726 Vvi2g726 726
2 8765672 8766279 - Vvi2g727 Vvi2g727 727
2 8806500 8811165 - Vvi2g728 Vvi2g728 728
2 8849437 8856333 + Vvi2g729 Vvi2g729 729
2 8916389 8916758 - Vvi2g730 Vvi2g730 730
2 8943008 8975937 + Vvi2g731 Vvi2g731 731
       

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