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
Vvi5g909 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g910 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g911 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g912 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g913 Blo01g00337 Blo12g00102 Bda03g01142 Bda08g00042 Bpe04g01084 . . Bma05g01299 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy05g00570 . . . . . . . . . . . . . . . Car17g00083 . . . . . . . . . . . . . . . . . . . Cme05g00731
Vvi5g914 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g915 Blo01g00338 Blo12g00101 . Bda08g00043 Bpe04g01085 . Bma04g01161 Bma05g01300 . Cmo17g00096 Cma06g01198 Cma14g01913 . . Sed02g1534 Cpe08g00415 Cpe03g01611 Bhi01g00191 Tan10g0486 Cmetu06g1562 . Hepe05g1781 . Lcy11g1796 Cla06g00769 Cam06g0819 Cec06g0832 Cco06g0838 Clacu06g0820 Cmu06g0794 Cre06g1575 . . . . Lsi05g01864 . Chy05g00572 Cme06g00362 . . Bda11g00666 . Bpe05g01148 Bpe13g00872 . Bma06g01269 Sed09g0173 Cmo06g01235 Cmo14g01966 . Cma17g00091 . . Cpe12g00083 . Bhi12g01487 Tan06g2289 Cmetu05g0404 . Hepe03g0372 . . Cla05g00325 Cam05g0355 Cec05g0357 Cco05g0361 Clacu05g0351 Cmu05g0337 Cre05g0399 Lsi09g01129 Csa03g01072 Chy06g00342 .
Vvi5g916 . . . . . Bpe14g00850 . . . . Cma06g01196 Cma14g01914 . Car14g01712 Sed12g0352 Cpe08g00417 Cpe03g01613 Bhi01g00185 Tan10g0484 Cmetu06g1519 . . . Lcy11g1801 . . . . . . . . . . . Lsi05g01869 . . Cme06g00359 . . . Bda13g00480 . . Bma02g01198 . . Cmo06g01233 Cmo14g01968 . . . . . . . . . . . . . Cla05g00322 Cam05g0353 Cec05g0355 Cco05g0358 . Cmu05g0334 Cre05g0397 . Csa03g01069 Chy06g00340 .
Vvi5g917 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g918 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 12249530 12252128 - Bda017196.1 Bda03g01142 1142
8 324555 327377 - Bda024433.1 Bda08g00042 42
8 327898 329675 + Bda033787 Bda08g00043 43
11 6567573 6569427 + Bda005414.1 Bda11g00666 666
13 5711853 5714050 - Bda001386.1 Bda13g00480 480
1 3699733 3703000 + XM_039050776.1 Bhi01g00185 185
1 3717014 3719531 - XM_039022830.1 Bhi01g00191 191
12 48094236 48096568 + XM_039018475.1 Bhi12g01487 1487
1 4032346 4035121 - BLOR00337 Blo01g00337 337
1 4036308 4039612 + BLOR00338 Blo01g00338 338
12 7334484 7336232 - BLOR04120 Blo12g00101 101
12 7371193 7373879 + BLOR04121 Blo12g00102 102
2 54072709 54074723 - Bma016039.1 Bma02g01198 1198
4 29994211 29995970 - Bma019896.1 Bma04g01161 1161
5 52312388 52315169 - Bma022488.2 Bma05g01299 1299
5 52315544 52317356 + Bma022489.1 Bma05g01300 1300
6 49798578 49799850 - Bma024377.3 Bma06g01269 1269
4 8389882 8392471 - Bpe015758.1 Bpe04g01084 1084
4 8393853 8395608 + Bpe025676 Bpe04g01085 1085
5 23731496 23733290 + Bpe018568.1 Bpe05g01148 1148
13 14874492 14876346 + Bpe010558.1 Bpe13g00872 872
14 6354011 6356039 + Bpe014226.1 Bpe14g00850 850
5 3279533 3281666 + CaPI482276_05g003530.1 Cam05g0353 353
5 3300567 3302627 - CaPI482276_05g003550.1 Cam05g0355 355
6 11306012 11307891 - CaPI482276_06g008190.1 Cam06g0819 819
14 13585132 13587164 - Carg14911-RA Car14g01712 1712
17 480322 482739 - Carg10149-RA Car17g00083 83
5 2903919 2906052 + CcPI632755_05g003580.1 Cco05g0358 358
5 2932550 2934593 - CcPI632755_05g003610.1 Cco05g0361 361
6 10109324 10111204 - CcPI632755_06g008380.1 Cco06g0838 838
5 2916664 2918797 + CePI673135_05g003550.1 Cec05g0355 355
5 2937288 2939339 - CePI673135_05g003570.1 Cec05g0357 357
6 10227682 10229565 - CePI673135_06g008320.1 Cec06g0832 832
5 6338737 6341172 - Chy5G096160.1 Chy05g00570 570
5 6411221 6413075 + Chy5G096180.1 Chy05g00572 572
6 2255449 2257476 + Chy6G108680.1 Chy06g00340 340
6 2266057 2267646 - Chy6G108700.1 Chy06g00342 342
5 3014592 3016653 - ClG42_05g0035100.10 Clacu05g0351 351
6 9976539 9978418 - ClG42_06g0082000.10 Clacu06g0820 820
5 2931206 2938034 + ClCG05G003060.1 Cla05g00322 322
5 2956372 2958433 - ClCG05G003090.1 Cla05g00325 325
6 10270228 10272107 - ClCG06G007930.1 Cla06g00769 769
6 8005463 8009666 + CmaCh06G011960.1 Cma06g01196 1196
6 8013328 8015411 - CmaCh06G011980.1 Cma06g01198 1198
14 13509373 13510423 + CmaCh14G019130.1 Cma14g01913 1913
14 13512373 13519962 - CmaCh14G019140.1 Cma14g01914 1914
17 459399 461623 + CmaCh17G000910.1 Cma17g00091 91
5 8676123 8679061 + MELO3C020429.2.1 Cme05g00731 731
6 2219235 2222909 + MELO3C006288.2.1 Cme06g00359 359
6 2230428 2232420 - MELO3C006291.2.1 Cme06g00362 362
5 16159954 16162246 + PI0025456.1 Cmetu05g0404 404
6 2413703 2416733 + PI0002114.1 Cmetu06g1519 1519
6 2436655 2438954 - PI0001343.1 Cmetu06g1562 1562
6 9329887 9333367 + CmoCh06G012330.1 Cmo06g01233 1233
6 9336539 9339119 - CmoCh06G012350.1 Cmo06g01235 1235
14 14505868 14508286 + CmoCh14G019660.1 Cmo14g01966 1966
14 14515610 14518497 - CmoCh14G019680.1 Cmo14g01968 1968
17 527871 529683 + CmoCh17G000960.1 Cmo17g00096 96
5 2832460 2834592 + CmPI595203_05g003340.1 Cmu05g0334 334
5 2850001 2855168 - CmPI595203_05g003370.1 Cmu05g0337 337
6 9793696 9795575 - CmPI595203_06g007940.1 Cmu06g0794 794
3 12403379 12406039 + Cp4.1LG03g17810.1 Cpe03g01611 1611
3 12411534 12414477 - Cp4.1LG03g17720.1 Cpe03g01613 1613
8 2665192 2667589 + Cp4.1LG08g02650.1 Cpe08g00415 415
8 2671282 2674819 - Cp4.1LG08g02580.1 Cpe08g00417 417
12 500071 506199 + Cp4.1LG12g00840.1 Cpe12g00083 83
5 3611546 3613800 + CrPI670011_05g003970.1 Cre05g0397 397
5 3632066 3634126 - CrPI670011_05g003990.1 Cre05g0399 399
6 10948676 10952350 - CrPI670011_06g015750.1 Cre06g1575 1575
3 8504904 8508856 + CsaV3_3G010690.1 Csa03g01069 1069
3 8515280 8517444 - CsaV3_3G010720.1 Csa03g01072 1072
3 5300198 5302476 - Hsped.03g03720.1 Hepe03g0372 372
5 68122828 68123595 + Hsped.05g17810.1 Hepe05g1781 1781
11 41760304 41762731 + Maker00031453 Lcy11g1796 1796
11 41835701 41838717 - Maker00031924 Lcy11g1801 1801
5 25872656 25874611 + Lsi05G018640.1 Lsi05g01864 1864
5 25912314 25915116 + Lsi05G018690.1 Lsi05g01869 1869
9 18146710 18149307 + Lsi09G011290.1 Lsi09g01129 1129
2 51062476 51064962 + Sed0020775.1 Sed02g1534 1534
9 1408311 1411059 + Sed0012181.1 Sed09g0173 173
12 2153535 2157276 + Sed0020550.1 Sed12g0352 352
6 73990453 73992824 + Tan0000183.1 Tan06g2289 2289
10 3908775 3911612 + Tan0013822.1 Tan10g0484 484
10 3922746 3925162 - Tan0011434.1 Tan10g0486 486
5 14562375 14563204 + Vvi5g909 Vvi5g909 909
5 14591198 14603052 + Vvi5g910 Vvi5g910 910
5 14610219 14614850 + Vvi5g911 Vvi5g911 911
5 14661980 14664993 - Vvi5g912 Vvi5g912 912
5 14756066 14759491 - Vvi5g913 Vvi5g913 913
5 14776361 14776686 - Vvi5g914 Vvi5g914 914
5 14827684 14829753 + Vvi5g915 Vvi5g915 915
5 14874064 14903057 + Vvi5g916 Vvi5g916 916
5 14942826 14946221 + Vvi5g917 Vvi5g917 917
5 14955236 14956390 - Vvi5g918 Vvi5g918 918
       

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