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
Vvi2g592 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g593 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda07g00844 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g594 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g595 . . . . . . . Bma14g00091 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo19g00258 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g596 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g597 . . . . . . . Bma14g00129 . . Cma02g01584 . Car02g01347 . . . Cpe05g00207 . . . . . . . . . . . . . . . . Cone6ag0621 . . . Chy04g00045 . Blo03g00824 . Bda07g00116 . . Bpe11g00355 . . . Cmo02g01626 . . . . . . . . . . . . . . Cla09g01183 Cam09g1247 Cec09g1264 . . . Cre09g1211 . Csa03g04655 . Cme04g00056
Vvi2g598 Blo02g01004 . . Bda08g00617 Bpe05g00539 . . . . Cmo16g01138 . . . . . Cpe14g00899 . . . . . . . . Cla10g00191 Cam10g0197 Cec10g0203 Cco10g0204 Clacu10g0201 Cmu10g1045 Cre10g0451 . . . Cone9ag0624 . . . Cme06g02504 . . . . . . Bma05g00396 . . . . . Cma16g01088 . Car16g01030 . . . . . . . . . . . . . . . . . . Chy06g02111 .
Vvi2g599 . . . . . . Bma07g00979 Bma14g00130 Cmo06g00686 Cmo16g01137 . . . . . Cpe14g00898 . Bhi11g00106 . . . . Mch10g1617 . Cla10g00190 Cam10g0195 Cec10g0201 Cco10g0202 Clacu10g0199 Cmu10g1044 Cre10g0450 Cone8ag0446 Cone12ag0435 . . Lsi07g01234 . . Cme06g02503 Blo03g00825 Blo19g00160 Bda07g00115 Bda09g00693 Bpe08g00863 Bpe11g00354 . . . . . Cma06g00659 Cma16g01087 . Car16g01029 . . . . . . . . . . . . . . . . . Csa03g00208 Chy06g02112 .
Vvi2g600 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g601 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 1372310 1383920 + Bda025175.2 Bda07g00115 115
7 1387626 1430287 + Bda025176.2 Bda07g00116 116
7 9888113 9890047 + Bda025981.1 Bda07g00844 844
8 6320752 6321429 + Bda029079.1 Bda08g00617 617
9 10916528 10933833 - Bda034123 Bda09g00693 693
11 2585484 2598148 - XM_039047570.1 Bhi11g00106 106
2 39028235 39028909 - BLOR10734 Blo02g01004 1004
3 33795824 33831987 - BLOR12005 Blo03g00824 824
3 33841142 33850958 - BLOR12006 Blo03g00825 825
19 6420274 6440766 - BLOR09503 Blo19g00160 160
5 12313452 12314126 - Bma021222.1 Bma05g00396 396
7 37745529 37755678 + Bma026132.1 Bma07g00979 979
14 1281302 1282342 + Bma010496.1 Bma14g00091 91
14 1852423 1896178 - Bma030645 Bma14g00129 129
14 1899583 1909370 - Bma010533.1 Bma14g00130 130
5 19577767 19578441 - Bpe017956.2 Bpe05g00539 539
8 10981753 10991798 + Bpe022986.1 Bpe08g00863 863
11 2564767 2574044 + Bpe003728.1 Bpe11g00354 354
11 2577123 2618209 + Bpe003729.1 Bpe11g00355 355
9 14297070 14319879 + CaPI482276_09g012470.1 Cam09g1247 1247
10 3602390 3613631 + CaPI482276_10g001950.1 Cam10g0195 195
10 3614560 3615231 - CaPI482276_10g001970.1 Cam10g0197 197
2 8913499 8924802 - Carg08814-RA Car02g01347 1347
16 8821283 8831874 + Carg23233-RA Car16g01029 1029
16 8831968 8832642 - Carg23234-RA Car16g01030 1030
10 2043539 2054743 + CcPI632755_10g002020.1 Cco10g0202 202
10 2055673 2056344 - CcPI632755_10g002040.1 Cco10g0204 204
9 14401137 14438014 + CePI673135_09g012640.1 Cec09g1264 1264
10 2123313 2134567 + CePI673135_10g002010.1 Cec10g0201 201
10 2135496 2136165 - CePI673135_10g002030.1 Cec10g0203 203
4 500346 531176 - Chy4G067630.1 Chy04g00045 45
6 25315016 25329081 + Chy6G126390.1 Chy06g02111 2111
6 25330110 25340121 - Chy6G126400.1 Chy06g02112 2112
10 2352937 2364158 + ClG42_10g0019900.10 Clacu10g0199 199
10 2365085 2365756 - ClG42_10g0020100.10 Clacu10g0201 201
9 14331195 14369455 + ClCG09G012450.1 Cla09g01183 1183
10 2151110 2162741 + ClCG10G001940.2 Cla10g00190 190
10 2163668 2164339 - ClCG10G001950.1 Cla10g00191 191
2 8999987 9014026 - CmaCh02G015840.1 Cma02g01584 1584
6 3268699 3270297 - CmaCh06G006590.1 Cma06g00659 659
16 8352928 8367772 + CmaCh16G010870.1 Cma16g01087 1087
16 8367693 8368457 - CmaCh16G010880.1 Cma16g01088 1088
4 442870 465094 - MELO3C003362.2.1 Cme04g00056 56
6 32012495 32022344 + MELO3C013879.2.1 Cme06g02503 2503
6 32023261 32024182 - MELO3C013880.2.1 Cme06g02504 2504
2 9374569 9390311 - CmoCh02G016260.1 Cmo02g01626 1626
6 3482481 3485960 - CmoCh06G006860.1 Cmo06g00686 686
16 8089566 8103449 + CmoCh16G011370.1 Cmo16g01137 1137
16 8103537 8104211 - CmoCh16G011380.1 Cmo16g01138 1138
19 1886284 1886991 + CmoCh19G002580.1 Cmo19g00258 258
10 2503907 2515125 + CmPI595203_10g010440.1 Cmu10g1044 1044
10 2516052 2516723 - CmPI595203_10g010450.1 Cmu10g1045 1045
6 3079519 3088284 + Conep06aG0064000.1 Cone6ag0621 621
8 2827246 2838085 - Conep08aG0046300.1 Cone8ag0446 446
9 2961606 2962310 - Conep09aG0063800.1 Cone9ag0624 624
12 2583821 2595847 - Conep12aG0045000.1 Cone12ag0435 435
5 1127570 1140628 + Cp4.1LG05g02150.1 Cpe05g00207 207
14 7530962 7544961 + Cp4.1LG14g09020.1 Cpe14g00898 898
14 7545061 7545735 - Cp4.1LG14g08970.1 Cpe14g00899 899
9 14401113 14429669 + CrPI670011_09g012110.1 Cre09g1211 1211
10 3465631 3476895 + CrPI670011_10g004500.1 Cre10g0450 450
10 3477823 3478494 - CrPI670011_10g004510.1 Cre10g0451 451
3 1635213 1647259 + CsaV3_3G002080.1 Csa03g00208 208
3 40421340 40449919 + CsaV3_3G049610.1 Csa03g04655 4655
7 17996323 18010185 + Lsi07G012340.1 Lsi07g01234 1234
10 16292167 16305174 - MC10g1282 Mch10g1617 1617
2 6184187 6195799 + Vvi2g592 Vvi2g592 592
2 6196285 6199394 + Vvi2g593 Vvi2g593 593
2 6199954 6208988 + Vvi2g594 Vvi2g594 594
2 6208999 6209468 + Vvi2g595 Vvi2g595 595
2 6211850 6213577 + Vvi2g596 Vvi2g596 596
2 6219928 6269739 - Vvi2g597 Vvi2g597 597
2 6285883 6286527 + Vvi2g598 Vvi2g598 598
2 6287438 6318076 - Vvi2g599 Vvi2g599 599
2 6334168 6334784 - Vvi2g600 Vvi2g600 600
2 6343551 6352827 - Vvi2g601 Vvi2g601 601
       

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