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
Vvi5g269 . . . . . . . . . . . . Car06g01351 . Sed12g0731 Cpe08g00129 . Bhi01g01139 Tan10g1128 Cmetu06g1150 . Hepe05g1340 . Lcy11g1300 . . . . . . . . . . . . . . Cme06g00837 . Blo07g00125 . . . . . . . Cmo06g01585 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g270 . . . . . Bpe14g01075 . . . . . . . . . Cpe08g00130 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma02g00956 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g271 . . . . . . . . . . . . . . . Cpe08g00131 . . . . . . . . . . . . . . . . . . . . Csa06g01540 . . . . . . . . . . . . . . . . . . Cpe17g00093 . . . . . . . . . . . . . . . . . .
Vvi5g272 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g273 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g274 . . . . . Bpe14g01074 . . . . . Cma14g01549 . Car14g01367 . . Cpe03g01296 . . . . . . . . . . . . . . . . . . Lsi05g01375 . . Cme06g00843 . . . . . Bpe13g00717 Bma02g00958 . . . Cmo14g01585 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g275 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g276 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g277 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g278 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 22026006 22030453 - XM_039046800.1 Bhi01g01139 1139
7 1702026 1705472 - BLOR18057 Blo07g00125 125
2 49587792 49589398 + Bma015754.1 Bma02g00956 956
2 49593239 49594578 - Bma015756.1 Bma02g00958 958
13 13722034 13723194 - Bpe025236 Bpe13g00717 717
14 8053005 8053972 + Bpe014448.1 Bpe14g01074 1074
14 8055258 8056842 - Bpe014449.1 Bpe14g01075 1075
6 9674208 9678196 - Carg25660-RA Car06g01351 1351
14 11558455 11560076 + Carg19588-RA Car14g01367 1367
14 11679667 11682119 + CmaCh14G015490.1 Cma14g01549 1549
6 5706117 5711263 - MELO3C006756.2.1 Cme06g00837 837
6 5759977 5761758 - MELO3C006763.2.1 Cme06g00843 843
6 5797291 5801907 - PI0019760.1 Cmetu06g1150 1150
6 11126084 11130564 - CmoCh06G015850.1 Cmo06g01585 1585
14 12602199 12603852 + CmoCh14G015850.1 Cmo14g01585 1585
3 10536125 10539871 + Cp4.1LG03g12170.1 Cpe03g01296 1296
8 846561 850933 + Cp4.1LG08g05530.1 Cpe08g00129 129
8 851995 854625 + Cp4.1LG08g05490.1 Cpe08g00130 130
8 852899 862112 - Cp4.1LG08g05450.1 Cpe08g00131 131
17 551467 558573 - Cp4.1LG17g00980.1 Cpe17g00093 93
6 12898315 12906335 - CsaV3_6G017380.1 Csa06g01540 1540
5 61800817 61805758 + Hsped.05g13400.1 Hepe05g1340 1340
11 36489520 36493802 + Maker00031752 Lcy11g1300 1300
5 21639263 21655645 + Lsi05G013750.1 Lsi05g01375 1375
12 4362464 4367014 + Sed0000719.2 Sed12g0731 731
10 10917045 10921458 - Tan0021746.1 Tan10g1128 1128
5 2741659 2747844 + Vvi5g269 Vvi5g269 269
5 2749339 2750998 + Vvi5g270 Vvi5g270 270
5 2751283 2771189 - Vvi5g271 Vvi5g271 271
5 2775452 2778471 + Vvi5g272 Vvi5g272 272
5 2780126 2781179 + Vvi5g273 Vvi5g273 273
5 2781821 2783804 - Vvi5g274 Vvi5g274 274
5 2791464 2791901 + Vvi5g275 Vvi5g275 275
5 2799918 2800164 + Vvi5g276 Vvi5g276 276
5 2806227 2806473 + Vvi5g277 Vvi5g277 277
5 2813783 2814029 + Vvi5g278 Vvi5g278 278
       

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