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
Vvi5g919 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g920 . . . Bda08g00061 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g921 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g922 . . . . . . . . . . . . Car06g01051 . Sed02g1532 Cpe08g00414 . Bhi01g00195 Tan10g0489 Cmetu04g0875 . Hepe05g1779 . Lcy11g1794 . . . . . . . . . Cone7ag0412 . Lsi05g01862 . . Cme06g00364 . . Bda11g00322 . . Bpe13g00871 . . . Cmo06g01236 . . . . . . . . . . . . . . Cla05g00328 Cam05g0358 Cec05g0361 Cco05g0364 Clacu05g0354 Cmu05g0339 Cre05g0402 . Csa03g01074 Chy06g00344 .
Vvi5g923 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g924 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g925 . . . . . Bpe14g00853 . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0247 . Cone7ag0411 . . . . . . . Bda11g00323 . . Bpe13g00870 Bma02g01195 Bma06g01271 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g926 . . . . . . . . . . . Cma14g01953 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g927 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g928 . Blo12g00103 Bda03g01140 . Bpe04g01083 . . . . Cmo17g00092 . Cma14g01909 . . Sed02g1530 . Cpe03g01609 Bhi01g00196 Tan10g0491 Cmetu06g0292 Lac12g2013 Hepe05g1778 . Lcy11g1793 Cla06g00774 Cam06g0824 Cec06g0839 Cco06g0845 Clacu06g0827 Cmu06g0799 Cre06g1581 Cone14ag0246 Cone15ag0264 . . Lsi05g01861 . Chy05g00576 Cme06g00365 . . . . . . . . Sed09g0171 . Cmo14g01963 . Cma17g00086 . Car17g00081 Cpe12g00079 . Bhi12g01479 Tan06g2285 Cmetu05g0427 . . . . Cla05g00329 Cam05g0359 Cec05g0363 Cco05g0365 Clacu05g0356 Cmu05g0341 Cre05g0404 Lsi09g01125 Csa03g01075 Chy06g00345 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 12015098 12016425 - Bda017188.1 Bda03g01140 1140
8 491731 493834 - Bda024452.1 Bda08g00061 61
11 3566250 3569210 + Bda005048.1 Bda11g00322 322
11 3570926 3571977 - Bda005049.1 Bda11g00323 323
1 3782896 3788473 + XM_039041729.1 Bhi01g00195 195
1 3797606 3801494 + XM_039041740.1 Bhi01g00196 196
12 47797736 47807223 - XM_039019428.1 Bhi12g01479 1479
12 7436155 7446775 + BLOR04122 Blo12g00103 103
2 54043935 54045046 + Bma016037.1 Bma02g01195 1195
6 49806530 49807496 - Bma024379.1 Bma06g01271 1271
4 8346870 8350227 - Bpe015756.1 Bpe04g01083 1083
13 14863010 14864049 + Bpe025254 Bpe13g00870 870
13 14865962 14868678 - Bpe010557.2 Bpe13g00871 871
14 6375160 6380028 - Bpe014229.2 Bpe14g00853 853
5 3321292 3325962 + CaPI482276_05g003580.1 Cam05g0358 358
5 3331744 3334029 + CaPI482276_05g003590.1 Cam05g0359 359
6 11487167 11494053 + CaPI482276_06g008240.1 Cam06g0824 824
6 7899040 7902738 + Carg06308-RA Car06g01051 1051
17 461032 467116 - Carg10151-RA Car17g00081 81
5 2955554 2957927 + CcPI632755_05g003640.1 Cco05g0364 364
5 2963605 2965861 + CcPI632755_05g003650.1 Cco05g0365 365
6 10289413 10296294 + CcPI632755_06g008450.1 Cco06g0845 845
5 2967454 2969826 + CePI673135_05g003610.1 Cec05g0361 361
5 2975727 2977982 + CePI673135_05g003630.1 Cec05g0363 363
6 10443362 10450289 + CePI673135_06g008390.1 Cec06g0839 839
5 6517173 6524170 + Chy5G096220.1 Chy05g00576 576
6 2284502 2287351 + Chy6G108720.1 Chy06g00344 344
6 2292132 2294330 + Chy6G108730.1 Chy06g00345 345
5 3035516 3040120 + ClG42_05g0035400.10 Clacu05g0354 354
5 3045762 3048040 + ClG42_05g0035600.10 Clacu05g0356 356
6 10170018 10176843 + ClG42_06g0082700.10 Clacu06g0827 827
5 2979410 2982055 + ClCG05G003120.2 Cla05g00328 328
5 2987542 2990205 + ClCG05G003130.2 Cla05g00329 329
6 10470763 10485887 + ClCG06G007970.2 Cla06g00774 774
14 13486256 13492879 - CmaCh14G019090.1 Cma14g01909 1909
14 13741588 13743708 + CmaCh14G019530.1 Cma14g01953 1953
17 429652 437522 - CmaCh17G000860.1 Cma17g00086 86
6 2249041 2252278 + MELO3C006293.2.1 Cme06g00364 364
6 2255786 2258921 + MELO3C006294.2.1 Cme06g00365 365
4 7444869 7447360 + PI0023550.1 Cmetu04g0875 875
5 15952545 15962869 - PI0014138.2 Cmetu05g0427 427
6 2462554 2466802 + PI0023640.3 Cmetu06g0292 292
6 9341024 9344551 + CmoCh06G012360.1 Cmo06g01236 1236
14 14486633 14489674 - CmoCh14G019630.1 Cmo14g01963 1963
17 497373 504726 - CmoCh17G000920.1 Cmo17g00092 92
5 2874024 2878627 + CmPI595203_05g003390.1 Cmu05g0339 339
5 2884250 2886528 + CmPI595203_05g003410.1 Cmu05g0341 341
6 9986577 9993401 + CmPI595203_06g007990.1 Cmu06g0799 799
7 1829893 1831366 + Conep07aG0042100.1 Cone7ag0411 411
7 1832397 1833829 - Conep07aG0042200.1 Cone7ag0412 412
14 1137327 1142368 - Conep14aG0025100.1 Cone14ag0246 246
14 1143035 1149140 + Conep14aG0025200.1 Cone14ag0247 247
15 1241420 1246301 - Conep15aG0027000.1 Cone15ag0264 264
3 12385339 12389518 - Cp4.1LG03g17750.1 Cpe03g01609 1609
8 2659434 2662947 - Cp4.1LG08g02610.1 Cpe08g00414 414
12 473535 481977 - Cp4.1LG12g00710.1 Cpe12g00079 79
5 3655327 3657698 + CrPI670011_05g004020.1 Cre05g0402 402
5 3663445 3665705 + CrPI670011_05g004040.1 Cre05g0404 404
6 11133904 11143067 + CrPI670011_06g015810.1 Cre06g1581 1581
3 8534384 8538434 + CsaV3_3G010740.1 Csa03g01074 1074
3 8539213 8544449 + CsaV3_3G010750.1 Csa03g01075 1075
5 68089091 68093590 - Hsped.05g17780.1 Hepe05g1778 1778
5 68097396 68101348 - Hsped.05g17790.1 Hepe05g1779 1779
12 37053242 37060746 + Lag0016385.1 Lac12g2013 2013
11 41725564 41729755 - Maker00031579 Lcy11g1793 1793
11 41734404 41738983 - Maker00031911 Lcy11g1794 1794
5 25840830 25845182 - Lsi05G018610.1 Lsi05g01861 1861
5 25849555 25852677 - Lsi05G018620.1 Lsi05g01862 1862
9 18043170 18051314 - Lsi09G011250.1 Lsi09g01125 1125
2 51020226 51024589 - Sed0001070.3 Sed02g1530 1530
2 51027684 51032590 - Sed0013696.2 Sed02g1532 1532
9 1378045 1387670 - Sed0005118.2 Sed09g0171 171
6 73844439 73857267 - Tan0002858.2 Tan06g2285 2285
10 3953006 3956444 + Tan0018400.1 Tan10g0489 489
10 3962281 3966892 + Tan0018901.3 Tan10g0491 491
5 14976880 14979821 - Vvi5g919 Vvi5g919 919
5 15017217 15020147 + Vvi5g920 Vvi5g920 920
5 15022474 15032692 - Vvi5g921 Vvi5g921 921
5 15069724 15086324 - Vvi5g922 Vvi5g922 922
5 15099440 15105228 - Vvi5g923 Vvi5g923 923
5 15127346 15128808 + Vvi5g924 Vvi5g924 924
5 15132754 15137711 - Vvi5g925 Vvi5g925 925
5 15149938 15152005 + Vvi5g926 Vvi5g926 926
5 15181149 15183347 + Vvi5g927 Vvi5g927 927
5 15201476 15223939 + Vvi5g928 Vvi5g928 928
       

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