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
Vvi5g1079 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo02g00415 . . Bda13g00293 . Bpe13g00748 Bma02g00999 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1080 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo02g00416 . . . . . . Bma06g01408 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1081 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1082 . . . . . . . . . Cmo17g00545 . . . . . . . Bhi01g02663 . . . Hepe05g1249 . . . . . . . . . . . . . . . . . Blo02g00417 . . Bda13g00292 . . Bma02g00998 . . . . . Cma17g00564 . Car17g00518 Cpe12g00478 . . . . . . . . . . . . . . . . . . .
Vvi5g1083 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1084 . . Bda03g01080 . Bpe04g00995 . Bma04g00994 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone18ag0895 Cone11ag0609 . . . . Blo02g00418 Blo07g00077 . . . . Bma02g00997 Bma06g01409 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1085 . . Bda03g01081 . Bpe04g00994 . Bma04g00995 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone18ag0894 . . . . . Blo02g00421 Blo07g00078 . . . . . Bma06g01410 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1086 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone18ag0893 Cone11ag0610 . . . . . Blo07g00079 . . . Bpe13g00745 . Bma06g01411 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1087 . . Bda03g01082 . . . Bma04g00996 . . . . . . . . . . . . . . . . . Cla08g00382 Cam08g0802 Cec08g0372 Cco08g0472 Clacu08g0515 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1088 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 10836574 10838856 + Bda017125.1 Bda03g01080 1080
3 10840197 10843298 + Bda017126.1 Bda03g01081 1081
3 10843743 10844408 - Bda017127.1 Bda03g01082 1082
13 3663462 3664916 - Bda001178.3 Bda13g00292 292
13 3672559 3680908 + Bda001179.1 Bda13g00293 293
1 66308189 66311552 + XM_039048337.1 Bhi01g02663 2663
2 5441375 5441789 - BLOR10145 Blo02g00415 415
2 5470941 5472418 - BLOR10146 Blo02g00416 416
2 5475788 5476897 + BLOR10147 Blo02g00417 417
2 5485857 5492717 + BLOR10148 Blo02g00418 418
2 5510053 5511420 + BLOR10151 Blo02g00421 421
7 1127675 1131923 + BLOR18009 Blo07g00077 77
7 1135218 1138334 + BLOR18010 Blo07g00078 78
7 1140088 1143842 - BLOR18011 Blo07g00079 79
2 50599691 50608178 - Bma015809.10 Bma02g00997 997
2 50611816 50613270 - Bma015810.1 Bma02g00998 998
2 50616426 50618110 + Bma015811.1 Bma02g00999 999
4 16120005 16122881 + Bma019599.1 Bma04g00994 994
4 16141302 16144404 + Bma019600.1 Bma04g00995 995
4 16144772 16145550 - Bma019601.1 Bma04g00996 996
6 50839823 50842090 - Bma024523.1 Bma06g01408 1408
6 50850261 50853996 + Bma024524.1 Bma06g01409 1409
6 50856720 50858912 + Bma024525.1 Bma06g01410 1410
6 50859574 50863332 - Bma024526.1 Bma06g01411 1411
4 6938037 6940743 - Bpe015662.1 Bpe04g00994 994
4 6942577 6945198 - Bpe025672 Bpe04g00995 995
13 14007790 14011484 + Bpe025241 Bpe13g00745 745
13 14019587 14021816 + Bpe010441.1 Bpe13g00748 748
8 10189270 10191701 - CaPI482276_08g008020.1 Cam08g0802 802
17 4751250 4752635 + Carg22640-RA Car17g00518 518
8 11994149 12008256 - CcPI632755_08g004720.1 Cco08g0472 472
8 10497631 10500025 - CePI673135_08g003720.1 Cec08g0372 372
8 10001972 10004431 - ClG42_08g0051500.10 Clacu08g0515 515
8 10163287 10168760 - ClCG08G003690.2 Cla08g00382 382
17 4602049 4605337 + CmaCh17G005640.1 Cma17g00564 564
17 5539202 5540587 + CmoCh17G005450.1 Cmo17g00545 545
11 3763079 3767323 + Conep11aG0062500.1 Cone11ag0609 609
11 3779261 3784989 - Conep11aG0062600.1 Cone11ag0610 610
18 6307747 6312021 + Conep18aG0091900.1 Cone18ag0893 893
18 6312411 6315829 - Conep18aG0092000.1 Cone18ag0894 894
18 6332936 6338746 - Conep18aG0092100.1 Cone18ag0895 895
12 4613225 4614610 + Cp4.1LG12g04780.1 Cpe12g00478 478
5 59513565 59516971 - Hsped.05g12490.1 Hepe05g1249 1249
5 19600418 19604497 - Vvi5g1079 Vvi5g1079 1079
5 19608326 19610244 - Vvi5g1080 Vvi5g1080 1080
5 19619814 19631614 + Vvi5g1081 Vvi5g1081 1081
5 19637028 19638486 + Vvi5g1082 Vvi5g1082 1082
5 19643899 19662114 + Vvi5g1083 Vvi5g1083 1083
5 19681837 19700399 + Vvi5g1084 Vvi5g1084 1084
5 19716798 19720405 + Vvi5g1085 Vvi5g1085 1085
5 19721252 19736794 - Vvi5g1086 Vvi5g1086 1086
5 19742596 19743497 - Vvi5g1087 Vvi5g1087 1087
5 19746229 19750105 - Vvi5g1088 Vvi5g1088 1088
       

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