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
Vvi5g1129 . . . . . . . . . . . . . . . . . Bhi01g02587 . . . . . . . . . . . . . . . . . . . . . Blo02g00441 . . Bda13g00261 . . Bma02g00976 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1130 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1131 . . . Bda08g00105 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1132 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1133 . . . . . . . . . . Cma06g01634 Cma14g01495 Car06g01389 Car14g01328 . Cpe08g00094 Cpe03g01256 Bhi01g02638 . . . . . . . . . . . . . . . Cone18ag0886 Cone11ag0626 . . . Cme07g01857 . Blo07g00098 Bda11g00469 . . Bpe13g00729 . Bma06g01430 . Cmo06g01633 Cmo14g01531 . . . . . . . . . . . . . Cla07g01580 Cam07g1677 Cec07g1772 Cco07g1735 Clacu07g1661 Cmu07g1627 Cre07g2001 . . . .
Vvi5g1134 . . . . . . Bma04g01002 . Cmo08g00089 . . Cma14g01492 . Car14g01327 Sed02g1039 . Cpe03g01255 Bhi01g02639 Tan10g1241 Cmetu07g0051 . Hepe05g1271 . Lcy11g1222 . . . . . . . . Cone15ag0601 . . . . . . . . . . . . . . . . Cmo14g01530 . . Car08g00071 . . Cpe17g00996 . . . . . . . . . . . . . . . . . .
Vvi5g1135 . . . . . . . . . Cmo17g00569 . . . . . . . Bhi01g02640 . . . . . . Cla08g00439 Cam08g0872 Cec08g0450 Cco08g0573 Clacu08g0588 . Cre08g0411 . . . . . . . Cme07g01858 . . . . . . . . . . . . Cma17g00587 . Car17g00543 Cpe12g00499 . . . . . . . . Cla07g01579 Cam07g1676 Cec07g1771 Cco07g1734 Clacu07g1660 Cmu07g1626 Cre07g2000 . . . .
Vvi5g1136 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1137 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1138 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 914614 922212 + Bda024508.1 Bda08g00105 105
11 4940788 4950138 - Bda005208.2 Bda11g00469 469
13 3274217 3277875 + Bda001140.1 Bda13g00261 261
1 63578046 63587535 - XM_039043890.1 Bhi01g02587 2587
1 65373298 65382930 + XM_039042251.1 Bhi01g02638 2638
1 65397678 65405999 - XM_039026437.1 Bhi01g02639 2639
1 65397679 65405894 - XM_039026433.1 Bhi01g02640 2640
2 5971134 5979745 - BLOR10171 Blo02g00441 441
7 1414445 1420050 - BLOR18030 Blo07g00098 98
2 50126160 50129461 + Bma015779.1 Bma02g00976 976
4 16430071 16432123 - Bma019608.2 Bma04g01002 1002
6 51010765 51022915 - Bma024544.2 Bma06g01430 1430
13 13851166 13862869 + Bpe010426.1 Bpe13g00729 729
7 31374738 31383402 + CaPI482276_07g016760.1 Cam07g1676 1676
7 31384450 31393953 - CaPI482276_07g016770.1 Cam07g1677 1677
8 12717378 12722501 - CaPI482276_08g008720.1 Cam08g0872 872
6 9987496 9994220 + Carg15487-RA Car06g01389 1389
8 419918 425718 + Carg04913-RA Car08g00071 71
14 11221695 11225353 + Carg22438-RA Car14g01327 1327
14 11225847 11232521 - Carg22439-RA Car14g01328 1328
17 5048756 5052705 - Carg22615-RA Car17g00543 543
7 31364159 31372848 + CcPI632755_07g017340.1 Cco07g1734 1734
7 31374669 31383539 - CcPI632755_07g017350.1 Cco07g1735 1735
8 14713981 14719074 - CcPI632755_08g005730.1 Cco08g0573 573
7 33285383 33293603 + CePI673135_07g017710.1 Cec07g1771 1771
7 33294041 33304605 - CePI673135_07g017720.1 Cec07g1772 1772
8 13221899 13227034 - CePI673135_08g004500.1 Cec08g0450 450
7 31220700 31229688 + ClG42_07g0166000.10 Clacu07g1660 1660
7 31230141 31240218 - ClG42_07g0166100.10 Clacu07g1661 1661
8 12950584 12955708 - ClG42_08g0058800.10 Clacu08g0588 588
7 32989572 32998879 + ClCG07G016550.2 Cla07g01579 1579
7 32995053 33009659 - ClCG07G016560.2 Cla07g01580 1580
8 13429470 13435366 - ClCG08G004210.2 Cla08g00439 439
6 10174478 10181268 + CmaCh06G016340.1 Cma06g01634 1634
14 11307834 11313728 + CmaCh14G014920.1 Cma14g01492 1492
14 11314852 11320856 - CmaCh14G014950.1 Cma14g01495 1495
17 4844916 4848657 - CmaCh17G005870.1 Cma17g00587 587
7 24037115 24043457 + MELO3C017686.2.1 Cme07g01857 1857
7 24044976 24051913 - MELO3C017687.2.1 Cme07g01858 1858
7 2866981 2874055 + PI0005347.1 Cmetu07g0051 51
6 11388006 11394892 + CmoCh06G016330.1 Cmo06g01633 1633
8 461124 468130 + CmoCh08G000890.1 Cmo08g00089 89
14 12217952 12223695 + CmoCh14G015300.1 Cmo14g01530 1530
14 12224439 12230581 - CmoCh14G015310.1 Cmo14g01531 1531
17 5844687 5848491 - CmoCh17G005690.1 Cmo17g00569 569
7 31472486 31481468 + CmPI595203_07g016260.1 Cmu07g1626 1626
7 31481921 31491998 - CmPI595203_07g016270.1 Cmu07g1627 1627
11 3964629 3975067 - Conep11aG0064300.1 Cone11ag0626 626
15 3092173 3094536 + Conep15aG0061400.1 Cone15ag0601 601
18 6247377 6253326 - Conep18aG0091200.1 Cone18ag0886 886
3 10167111 10172528 + Cp4.1LG03g12630.1 Cpe03g01255 1255
3 10172029 10179503 - Cp4.1LG03g12560.1 Cpe03g01256 1256
8 583649 589877 - Cp4.1LG08g05860.1 Cpe08g00094 94
12 4890428 4895146 - Cp4.1LG12g04990.1 Cpe12g00499 499
17 7557445 7564436 + Cp4.1LG17g09990.1 Cpe17g00996 996
7 35486551 35495313 + CrPI670011_07g020000.1 Cre07g2000 2000
7 35496326 35505801 - CrPI670011_07g020010.1 Cre07g2001 2001
8 13698710 13703834 - CrPI670011_08g004110.1 Cre08g0411 411
5 60082686 60088894 + Hsped.05g12710.1 Hepe05g1271 1271
11 34846353 34852027 + Maker00005224 Lcy11g1222 1222
2 47754968 47760807 + Sed0024636.1 Sed02g1039 1039
10 13629802 13635323 - Tan0013202.1 Tan10g1241 1241
5 20721905 20730141 - Vvi5g1129 Vvi5g1129 1129
5 20732550 20735315 - Vvi5g1130 Vvi5g1130 1130
5 20741173 20798303 - Vvi5g1131 Vvi5g1131 1131
5 20808221 20809533 + Vvi5g1132 Vvi5g1132 1132
5 20813450 20843565 + Vvi5g1133 Vvi5g1133 1133
5 20844844 20853619 - Vvi5g1134 Vvi5g1134 1134
5 20858098 20873278 - Vvi5g1135 Vvi5g1135 1135
5 20881429 20884073 + Vvi5g1136 Vvi5g1136 1136
5 20911869 20913529 + Vvi5g1137 Vvi5g1137 1137
5 20913562 20914372 + Vvi5g1138 Vvi5g1138 1138
       

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