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
Vvi2g742 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g743 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g744 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g745 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g746 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g747 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g748 Blo02g00975 . . Bda08g00644 Bpe05g00515 . . . Cmo06g00628 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme06g02436 . . . . . . Bma05g00701 . . . . Cma06g00620 . Car06g00554 . . . . . . . . . . . . . . . . . . Csa03g00128 Chy06g02178 .
Vvi2g749 . . . . . . . . Cmo06g00627 . . . . . . . . . . . . . . . Cla10g00123 Cam10g0123 Cec10g0132 Cco10g0132 Clacu10g0128 Cmu10g0975 Cre10g0385 Cone8ag0498 Cone12ag0497 . . Lsi07g01156 . Chy04g00132 . . . Bda07g00072 Bda09g00760 Bpe08g00803 Bpe11g00312 . . Sed02g0043 . Cmo19g00227 Cma06g00619 . Car06g00553 . . Cpe15g00185 Bhi05g00433 Tan07g2028 Cmetu04g1055 Lac11g2456 Hepe06g0983 . Lcy12g1980 Cla09g01084 Cam09g1138 Cec09g1145 Cco09g1163 . . Cre09g1101 . Csa03g04572 . Cme04g00155
Vvi2g750 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0499 . . . . . Chy04g00133 . . . . Bda09g00761 Bpe08g00802 . . . . . Cmo19g00226 . . . . . Cpe15g00184 Bhi05g00432 . . . Hepe06g1808 . Lcy12g1981 Cla09g01083 . . . . . . . . . .
Vvi2g751 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 935814 940553 - Bda025130.2 Bda07g00072 72
8 6603548 6606095 - Bda029104.1 Bda08g00644 644
9 13736431 13741099 + Bda031475.1 Bda09g00760 760
9 13741427 13742539 - Bda034124 Bda09g00761 761
5 9116829 9119282 + XM_039032001.1 Bhi05g00432 432
5 9120025 9125584 - XM_039032002.1 Bhi05g00433 433
2 37764064 37765720 + BLOR10705 Blo02g00975 975
5 40938327 40940930 + Bma021773.1 Bma05g00701 701
5 19358971 19361582 + Bpe025816 Bpe05g00515 515
8 9976623 9978437 + Bpe022922.1 Bpe08g00802 802
8 9978815 9983409 - Bpe022923.1 Bpe08g00803 803
11 2276574 2281151 - Bpe003686.1 Bpe11g00312 312
9 11878940 11883944 - CaPI482276_09g011380.1 Cam09g1138 1138
10 2805900 2809075 - CaPI482276_10g001230.1 Cam10g0123 123
6 3138953 3144415 - Carg23410-RA Car06g00553 553
6 3146204 3149325 + Carg23409-RA Car06g00554 554
9 11255979 11261010 - CcPI632755_09g011630.1 Cco09g1163 1163
10 1209088 1213409 - CcPI632755_10g001320.1 Cco10g0132 132
9 11292520 11298463 - CePI673135_09g011450.1 Cec09g1145 1145
10 1223705 1228128 - CePI673135_10g001320.1 Cec10g0132 132
4 1190483 1200694 + Chy4G068500.1 Chy04g00132 132
4 1201243 1203063 - Chy4G068510.1 Chy04g00133 133
6 26048383 26056799 - Chy6G127060.1 Chy06g02178 2178
10 1524795 1532448 - ClG42_10g0012800.10 Clacu10g0128 128
9 11503962 11505779 + ClCG09G011550.1 Cla09g01083 1083
9 11506107 11511828 - ClCG09G011560.2 Cla09g01084 1084
10 1248242 1266221 - ClCG10G001230.2 Cla10g00123 123
6 3021980 3027565 - CmaCh06G006190.1 Cma06g00619 619
6 3028436 3032832 + CmaCh06G006200.1 Cma06g00620 620
4 1188968 1194096 + MELO3C003445.2.1 Cme04g00155 155
6 31413782 31418011 + MELO3C013816.2.1 Cme06g02436 2436
4 32228820 32236973 - PI0019414.1 Cmetu04g1055 1055
6 3115672 3121107 - CmoCh06G006270.1 Cmo06g00627 627
6 3121949 3126229 + CmoCh06G006280.1 Cmo06g00628 628
19 1524411 1526510 + CmoCh19G002260.1 Cmo19g00226 226
19 1527342 1546008 - CmoCh19G002270.1 Cmo19g00227 227
10 1675816 1683469 - CmPI595203_10g009750.1 Cmu10g0975 975
8 3550792 3553976 + Conep08aG0051900.1 Cone8ag0498 498
8 3553662 3556260 - Conep08aG0052000.1 Cone8ag0499 499
12 3372974 3377649 + Conep12aG0051800.1 Cone12ag0497 497
15 1504820 1507430 + Cp4.1LG15g01850.1 Cpe15g00184 184
15 1507381 1513932 - Cp4.1LG15g01910.1 Cpe15g00185 185
9 11451915 11456953 - CrPI670011_09g011010.1 Cre09g1101 1101
10 2636218 2640718 - CrPI670011_10g003850.1 Cre10g0385 385
3 993217 995377 + CsaV3_3G001280.1 Csa03g00128 128
3 39784170 39792798 - CsaV3_3G048780.1 Csa03g04572 4572
6 57548262 57554899 - Hsped.06g09830.1 Hepe06g0983 983
6 69175764 69177872 - Hsped.06g18080.1 Hepe06g1808 1808
11 40752624 40758079 + Lag0033094.1 Lac11g2456 2456
12 41184542 41190426 + Maker00038125 Lcy12g1980 1980
12 41195629 41197446 - Maker00038135 Lcy12g1981 1981
7 17026221 17037749 - Lsi07G011560.1 Lsi07g01156 1156
2 5116434 5124349 - Sed0001384.1 Sed02g0043 43
7 71894488 71902729 + Tan0015704.1 Tan07g2028 2028
2 9325318 9325519 - Vvi2g742 Vvi2g742 742
2 9372615 9380457 + Vvi2g743 Vvi2g743 743
2 9393861 9395234 - Vvi2g744 Vvi2g744 744
2 9395763 9397535 + Vvi2g745 Vvi2g745 745
2 9406775 9411582 - Vvi2g746 Vvi2g746 746
2 9912737 9926343 + Vvi2g747 Vvi2g747 747
2 9983201 9995416 - Vvi2g748 Vvi2g748 748
2 10033048 10045349 + Vvi2g749 Vvi2g749 749
2 10045637 10047493 - Vvi2g750 Vvi2g750 750
2 10099013 10099295 - Vvi2g751 Vvi2g751 751
       

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