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
Vvi2g282 . . . Bda08g00749 . . . . . . Cma02g00955 . Car02g00704 Car15g01201 . . . . . . . . . . . . . . . . . . . . . . . Chy09g01350 . . . . . . . . . . Cmo02g00963 . . . . . . . Bhi12g00062 . . . . . . . . . . . . . . . . .
Vvi2g283 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0578 . . . . Csa05g00135 . . . . . . . . . . . . . . . . . . . . . . . . . . Cla01g00119 Cam01g0122 Cec01g0122 Cco01g0123 Clacu01g0118 Cmu01g0120 Cre09g2386 Lsi09g00107 . . .
Vvi2g284 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g285 . . . . . . . . . . . . . . . . Cpe05g00754 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g286 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo03g00786 . . Bda09g00624 . Bpe11g00384 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g287 . . . . . . Bma07g01051 Bma14g00086 . . Cma02g00962 . Car02g00709 . . . . . . . . . . . . . . . . . . . . . . . . Chy09g01356 . Blo03g00785 . Bda07g00164 . Bpe08g00918 . . . . Cmo02g00969 . . . . . . . Bhi12g00056 . . Lac11g1844 Hepe06g1407 . Lcy12g1474 . . . . . . . . . . Cme09g01902
Vvi2g288 . . . Bda08g00490 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo15g01403 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g289 . . . . . . . . . . . Cma15g01342 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda07g00165 . . . . . . . Cmo15g01404 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g290 . . . . . . . . . . . Cma15g01343 . Car15g01207 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo15g01405 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g291 . . . Bda08g00748 Bpe05g00397 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma05g00548 Bma12g00417 . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 2044506 2045200 - Bda025234.1 Bda07g00164 164
7 2048804 2050859 + Bda025235.1 Bda07g00165 165
8 5011608 5013603 + Bda024941.1 Bda08g00490 490
8 9236247 9243151 - Bda029232.1 Bda08g00748 748
8 9272087 9273849 + Bda029235.1 Bda08g00749 749
9 9143197 9145167 + Bda031251.1 Bda09g00624 624
12 1457766 1462421 + XM_039020409.1 Bhi12g00056 56
12 1815464 1819003 - XM_039019379.1 Bhi12g00062 62
3 32702091 32718241 + BLOR11966 Blo03g00785 785
3 32718302 32727181 + BLOR11967 Blo03g00786 786
5 29945633 29954703 + Bma021518.1 Bma05g00548 548
7 42237598 42239557 - Bma026247.1 Bma07g01051 1051
12 9384421 9390372 - Bma007395.1 Bma12g00417 417
14 1203837 1206315 + Bma010491.1 Bma14g00086 86
5 18261561 18268496 + Bpe017814.2 Bpe05g00397 397
8 11617237 11619288 - Bpe023041.2 Bpe08g00918 918
11 2921264 2923760 - Bpe003758.1 Bpe11g00384 384
1 1504119 1529963 - CaPI482276_01g001220.1 Cam01g0122 122
2 5212727 5215289 + Carg08519-RA Car02g00704 704
2 5244869 5248838 - Carg08514-RA Car02g00709 709
15 9342011 9344901 + Carg21325-RA Car15g01201 1201
15 9375172 9377288 + Carg21331-RA Car15g01207 1207
1 1047072 1072964 - CcPI632755_01g001230.1 Cco01g0123 123
1 1081917 1100790 - CePI673135_01g001220.1 Cec01g0122 122
9 15344569 15346957 + Chy9G170660.1 Chy09g01350 1350
9 15396659 15400670 - Chy9G170720.1 Chy09g01356 1356
1 1113943 1139713 - ClG42_01g0011800.10 Clacu01g0118 118
1 1090035 1116575 - ClCG01G001230.1 Cla01g00119 119
2 5679159 5684382 + CmaCh02G009550.1 Cma02g00955 955
2 5722571 5726297 - CmaCh02G009620.1 Cma02g00962 962
15 8415672 8418268 + CmaCh15G013420.1 Cma15g01342 1342
15 8423171 8425404 + CmaCh15G013430.1 Cma15g01343 1343
9 23162589 23168938 - MELO3C005809.2.1 Cme09g01902 1902
2 5907809 5910513 + CmoCh02G009630.1 Cmo02g00963 963
2 5943970 5948756 - CmoCh02G009690.1 Cmo02g00969 969
15 9545809 9548834 + CmoCh15G014030.1 Cmo15g01403 1403
15 9557270 9559835 + CmoCh15G014040.1 Cmo15g01404 1404
15 9569938 9572108 + CmoCh15G014050.1 Cmo15g01405 1405
1 1058745 1084543 - CmPI595203_01g001200.1 Cmu01g0120 120
8 4650238 4679398 - Conep08aG0059900.1 Cone8ag0578 578
5 4660068 4663518 + Cp4.1LG05g07550.1 Cpe05g00754 754
9 43216803 43242940 + CrPI670011_09g023860.1 Cre09g2386 2386
5 715454 733731 - CsaV3_5G001350.1 Csa05g00135 135
6 64383035 64385886 + Hsped.06g14070.1 Hepe06g1407 1407
11 33161640 33164755 + Lag0032482.1 Lac11g1844 1844
12 33560678 33564608 + Maker00029436 Lcy12g1474 1474
9 983403 1015329 - Lsi09G001070.1 Lsi09g00107 107
2 2582737 2584192 - Vvi2g282 Vvi2g282 282
2 2585170 2615383 - Vvi2g283 Vvi2g283 283
2 2624683 2626283 - Vvi2g284 Vvi2g284 284
2 2627587 2631485 + Vvi2g285 Vvi2g285 285
2 2634297 2636865 + Vvi2g286 Vvi2g286 286
2 2637036 2644475 + Vvi2g287 Vvi2g287 287
2 2652620 2654496 - Vvi2g288 Vvi2g288 288
2 2655930 2659710 - Vvi2g289 Vvi2g289 289
2 2660188 2662100 - Vvi2g290 Vvi2g290 290
2 2662966 2685728 - Vvi2g291 Vvi2g291 291
       

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