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
Vvi18g1740 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1741 Blo01g01683 . . . Bpe02g00258 Bpe04g00324 Bma04g00340 Bma01g02450 . . . . . . Sed11g2309 . . Bhi04g02541 Tan11g0052 Cmetu03g0350 . Hepe02g3462 . Lcy10g2354 . . . . . . . . . . . . . . . . . Bda11g00920 . . . . . . . . . . . . . . . . . . . . . Cla11g00792 Cam11g0826 Cec11g0809 Cco11g0813 Clacu11g1032 Cmu11g0893 Cre11g1270 . . . .
Vvi18g1742 Blo01g01684 . . . Bpe02g00257 . . Bma01g02451 . . . . . . . . . . . . . . . . Cla08g00173 . Cec08g0078 Cco08g0238 . Cmu08g0165 Cre08g0156 . . . . . . . Cme09g00119 . . Bda11g00919 . . . . . . . Cmo09g01209 . . . Car09g01078 . . Bhi06g00121 . . . . . . . . . . . . . Lsi08g00175 . . .
Vvi18g1743 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1744 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1745 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1746 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1747 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1748 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1749 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 9010633 9015299 + Bda005674.2 Bda11g00919 919
11 9016216 9017998 + Bda005675.1 Bda11g00920 920
4 68307608 68311702 - XM_039030130.1 Bhi04g02541 2541
6 3168411 3173371 - XM_039034973.1 Bhi06g00121 121
1 56545813 56547742 + BLOR01683 Blo01g01683 1683
1 56548533 56555117 - BLOR01684 Blo01g01684 1684
1 82114475 82117776 - Bma003320.1 Bma01g02450 2450
1 82119484 82123557 - Bma003321.3 Bma01g02451 2451
4 2763620 2765544 + Bma018799.1 Bma04g00340 340
2 1741313 1745950 + Bpe008102.1 Bpe02g00257 257
2 1746853 1748628 + Bpe008103.1 Bpe02g00258 258
4 2061654 2063592 + Bpe015021.1 Bpe04g00324 324
11 10500898 10501170 - CaPI482276_11g008260.1 Cam11g0826 826
9 10004719 10013698 - Carg27052-RA Car09g01078 1078
8 4148063 4154797 + CcPI632755_08g002380.1 Cco08g0238 238
11 9315040 9318482 - CcPI632755_11g008130.1 Cco11g0813 813
8 1311290 1318062 - CePI673135_08g000780.1 Cec08g0078 78
11 9572905 9573177 - CePI673135_11g008090.1 Cec11g0809 809
11 12791675 12795128 + ClG42_11g0103200.10 Clacu11g1032 1032
8 3516591 3523351 + ClCG08G001730.2 Cla08g00173 173
11 11401007 11404408 - ClCG11G008280.2 Cla11g00792 792
9 885510 889710 + MELO3C022124.2.1 Cme09g00119 119
3 26043281 26047411 - PI0018078.1 Cmetu03g0350 350
9 9220278 9229348 - CmoCh09G012090.1 Cmo09g01209 1209
8 3475731 3482094 + CmPI595203_08g001650.1 Cmu08g0165 165
11 12120732 12124186 + CmPI595203_11g008930.1 Cmu11g0893 893
8 3435867 3442673 + CrPI670011_08g001560.1 Cre08g0156 156
11 11206894 11207166 - CrPI670011_11g012700.1 Cre11g1270 1270
2 83936058 83940374 - Hsped.02g34620.1 Hepe02g3462 3462
10 47144902 47149012 - Maker00039529 Lcy10g2354 2354
8 3614502 3615236 + Lsi08G001750.1 Lsi08g00175 175
11 36111935 36113933 - Sed0011254.1 Sed11g2309 2309
11 787292 791207 + Tan0007793.1 Tan11g0052 52
18 28430030 28430552 - Vvi18g1740 Vvi18g1740 1740
18 28439006 28443747 - Vvi18g1741 Vvi18g1741 1741
18 28445582 28452592 + Vvi18g1742 Vvi18g1742 1742
18 28461771 28464940 + Vvi18g1743 Vvi18g1743 1743
18 28472200 28499501 + Vvi18g1744 Vvi18g1744 1744
18 28508787 28511552 + Vvi18g1745 Vvi18g1745 1745
18 28516116 28528636 + Vvi18g1746 Vvi18g1746 1746
18 28531706 28533746 + Vvi18g1747 Vvi18g1747 1747
18 28596635 28597566 - Vvi18g1748 Vvi18g1748 1748
18 28610014 28612509 - Vvi18g1749 Vvi18g1749 1749
       

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