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
Vvi16g904 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g905 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g906 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme06g01120 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy06g01230 .
Vvi16g907 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g908 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme06g01121 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy06g01229 .
Vvi16g909 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy06g01227 .
Vvi16g910 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme06g01132 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy06g01226 .
Vvi16g911 . . . . Bpe03g00186 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy09g01472 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme09g02021
Vvi16g912 . . . . Bpe03g00237 . . . . . . . . . Sed08g1878 . . Bhi01g01481 Tan01g0112 Cmetu06g2373 . Hepe07g0068 Mch10g0067 . . . . . . . . . . . . . . . Cme06g01133 . . . . . . . . . . . . . . . Cpe09g00030 . Bhi12g00774 . . Lac11g0079 Hepe06g0728 . Lcy12g0061 . . . . . . . . . Chy06g01210 .
Vvi16g913 . . . . Bpe03g00187 . . . . . . . . . Sed01g3497 Cpe05g00603 Cpe14g00043 Bhi01g01482 Tan01g0109 Cmetu06g0712 . . Mch10g0065 . . . . . . . . . . . . . . Chy09g01435 Cme06g01134 . . . . . . . . . . . . . . . Cpe09g00029 Cpe13g00312 Bhi12g00631 . . Lac11g0150 Hepe06g0788 . Lcy12g0128 . . . . . . . . . . Cme09g01980
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 30450173 30459754 - XM_039041045.1 Bhi01g01481 1481
1 30463745 30467365 - XM_039051062.1 Bhi01g01482 1482
12 19255657 19259026 - XM_039020096.1 Bhi12g00631 631
12 23250334 23252149 - XM_039020142.1 Bhi12g00774 774
3 2255031 2259475 + Bpe012032.1 Bpe03g00186 186
3 2261981 2264237 - Bpe012033.1 Bpe03g00187 187
3 3153381 3163956 + Bpe025365 Bpe03g00237 237
6 10813546 10822402 + Chy6G117380.1 Chy06g01210 1210
6 11125670 11130291 + Chy6G117540.1 Chy06g01226 1226
6 11132003 11139903 - Chy6G117550.1 Chy06g01227 1227
6 11149869 11154373 + Chy6G117570.1 Chy06g01229 1229
6 11176456 11186641 + Chy6G117580.1 Chy06g01230 1230
9 15917484 15920010 - Chy9G171510.1 Chy09g01435 1435
9 16142628 16149660 - Chy9G171880.1 Chy09g01472 1472
6 8511897 8522560 - MELO3C008481.2.1 Cme06g01120 1120
6 8542794 8548226 - MELO3C008483.2.1 Cme06g01121 1121
6 8672548 8677242 - MELO3C008489.2.1 Cme06g01132 1132
6 8683159 8691829 - MELO3C008490.2.1 Cme06g01133 1133
6 8696390 8699966 - MELO3C008491.2.1 Cme06g01134 1134
9 23658108 23661592 - MELO3C005883.2.1 Cme09g01980 1980
9 23891816 23897232 - MELO3C005921.2.1 Cme09g02021 2021
6 8216284 8220467 + PI0024521.1 Cmetu06g0712 712
6 8226026 8235613 + PI0006029.1 Cmetu06g2373 2373
5 3667340 3670872 + Cp4.1LG05g06040.1 Cpe05g00603 603
9 158013 161044 + Cp4.1LG09g00220.1 Cpe09g00029 29
9 163417 175758 + Cp4.1LG09g00200.1 Cpe09g00030 30
13 2637830 2640503 - Cp4.1LG13g03110.1 Cpe13g00312 312
14 235241 237914 + Cp4.1LG14g06810.1 Cpe14g00043 43
6 53314997 53316292 + Hsped.06g07280.1 Hepe06g0728 728
6 54525912 54529119 - Hsped.06g07880.1 Hepe06g0788 788
7 644193 653598 + Hsped.07g00680.1 Hepe07g0068 68
11 698579 699818 + Lag0030717.1 Lac11g0079 79
11 1378653 1381276 - Lag0030788.1 Lac11g0150 150
12 922852 924085 + Maker00038445 Lcy12g0061 61
12 1595491 1598578 - Maker00038651 Lcy12g0128 128
10 363374 366894 + MC10g0060 Mch10g0065 65
10 368513 377332 + MC10g0061 Mch10g0067 67
1 64100013 64103117 + Sed0018241.1 Sed01g3497 3497
8 33304369 33317778 - Sed0005718.5 Sed08g1878 1878
1 1097464 1102192 + Tan0020507.2 Tan01g0109 109
1 1103649 1114981 + Tan0000237.1 Tan01g0112 112
16 20648810 20661453 - Vvi16g904 Vvi16g904 904
16 20662034 20665713 + Vvi16g905 Vvi16g905 905
16 20666458 20679303 - Vvi16g906 Vvi16g906 906
16 20694057 20700574 - Vvi16g907 Vvi16g907 907
16 20703874 20708561 - Vvi16g908 Vvi16g908 908
16 20709325 20726862 + Vvi16g909 Vvi16g909 909
16 20727487 20735214 - Vvi16g910 Vvi16g910 910
16 20740370 20751493 + Vvi16g911 Vvi16g911 911
16 20769709 20783861 - Vvi16g912 Vvi16g912 912
16 20787348 20792059 - Vvi16g913 Vvi16g913 913
       

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