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
Vvi5g249 . Blo12g00376 Bda03g00833 . Bpe04g00789 . Bma04g00732 . . . . . . . . . . . . . . . . . Cla06g00396 Cam06g0417 Cec06g0425 Cco06g0425 Clacu06g0404 Cmu06g0404 Cre06g1183 Cone14ag0683 Cone15ag0695 . . . . . . . . . . . . . . Sed09g0597 . . . . . . Cpe12g00347 . Bhi12g01993 Tan06g2812 Cmetu11g0485 Lac11g1038 Hepe03g0014 . Lcy12g0899 . . . . . . . . . . .
Vvi5g250 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g251 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g252 . . . . . Bpe14g01077 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo07g00096 Bda11g00468 . . Bpe13g00731 Bma02g00954 Bma06g01427 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g253 . . . . . . . . . . . . . . . . . . . . . . . . Cla06g00395 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe12g00348 . Bhi12g01995 . . . . . Lcy12g0901 . . . . . . . . . . .
Vvi5g254 . . . . . Bpe14g01076 . . . . . Cma14g01561 Car06g01346 Car14g01376 Sed02g1112 Cpe08g00134 Cpe03g01305 Bhi01g01124 Tan10g1118 Cmetu06g2697 . . . Lcy11g1307 . . . . . . . Cone4ag1796 Cone7ag1704 Cone17ag1026 . Lsi05g01390 . . Cme06g00827 . Blo07g00099 Bda11g00486 . . . Bma02g00955 Bma06g01450 . Cmo06g01580 Cmo14g01596 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g255 Blo01g00024 Blo12g00374 Bda03g00835 . Bpe04g00791 . Bma04g00734 Bma05g00986 . . . . . . . . . . . . . . . . Cla06g00393 Cam06g0415 Cec06g0423 Cco06g0423 Clacu06g0402 Cmu06g0402 Cre06g1181 Cone14ag0681 Cone15ag0693 . . . . . . . . . . . . . . . . . . . . . Cpe12g00349 . Bhi12g01996 . . . Hepe03g0009 . . . . . . . . . . . . .
Vvi5g256 . Blo12g00373 Bda03g00837 . Bpe04g00792 . Bma04g00735 . . . . Cma14g01560 . Car14g01375 . . Cpe03g01304 Bhi01g01126 Tan10g1120 . . Hepe05g1346 . . . . . . . . . Cone14ag0680 Cone15ag0692 . . Lsi05g01389 . . Cme06g00829 . . . . . . . . . . Cmo14g01595 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g257 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g258 Blo01g00023 . . . . . . Bma05g00985 . . . Cma14g01559 . Car14g01374 . . Cpe03g01303 Bhi01g01128 . . . Hepe05g1345 . Lcy11g1304 . . . . . . . . . . . Lsi05g01387 . . Cme06g00830 . . . . Bpe05g00794 . . . . . Cmo14g01593 . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 7138913 7141211 - Bda033502 Bda03g00833 833
3 7152409 7157230 - Bda033503 Bda03g00835 835
3 7172574 7174917 + Bda016822.1 Bda03g00837 837
11 4929788 4932265 - Bda005206.1 Bda11g00468 468
11 5141085 5145224 - Bda005222.1 Bda11g00486 486
1 21896047 21902136 + XM_039050700.1 Bhi01g01124 1124
1 21907185 21910745 + XM_039038169.1 Bhi01g01126 1126
1 21922644 21927447 - XM_039026113.1 Bhi01g01128 1128
12 62601574 62604081 - XM_039019896.1 Bhi12g01993 1993
12 62606932 62613391 - XM_039019897.1 Bhi12g01995 1995
12 62650682 62657535 - XM_039019635.1 Bhi12g01996 1996
1 336142 339468 + BLOR00023 Blo01g00023 23
1 340483 346219 + BLOR00024 Blo01g00024 24
7 1376738 1391962 - BLOR18028 Blo07g00096 96
7 1448859 1459549 - BLOR18031 Blo07g00099 99
12 20107309 20109715 - BLOR04392 Blo12g00373 373
12 20122809 20133032 + BLOR04393 Blo12g00374 374
12 20161122 20163570 + BLOR04395 Blo12g00376 376
2 49575252 49577187 + Bma015752.1 Bma02g00954 954
2 49580189 49586608 + Bma015753.1 Bma02g00955 955
4 7649501 7651923 - Bma019240.1 Bma04g00732 732
4 7663352 7670241 - Bma019242.1 Bma04g00734 734
4 7715193 7717543 + Bma019243.1 Bma04g00735 735
5 48346363 48350137 + Bma022135.1 Bma05g00985 985
5 48351016 48355431 + Bma022136.2 Bma05g00986 986
6 50993322 50995926 - Bma024541.1 Bma06g01427 1427
6 51199093 51203969 - Bma024564.1 Bma06g01450 1450
4 5142017 5144432 - Bpe015450.4 Bpe04g00789 789
4 5161671 5166501 - Bpe015452.2 Bpe04g00791 791
4 5174363 5176707 + Bpe015453.1 Bpe04g00792 792
5 21276003 21279763 + Bpe018207.1 Bpe05g00794 794
13 13876432 13878865 + Bpe010428.1 Bpe13g00731 731
14 8057867 8062814 - Bpe014450.1 Bpe14g01076 1076
14 8064746 8066501 - Bpe014451.1 Bpe14g01077 1077
6 6259026 6277025 + CaPI482276_06g004150.1 Cam06g0415 415
6 6292943 6295204 + CaPI482276_06g004170.1 Cam06g0417 417
6 9653225 9657057 + Carg25655-RA Car06g01346 1346
14 11590347 11596019 + Carg19595-RA Car14g01374 1374
14 11598013 11601322 - Carg19596-RA Car14g01375 1375
14 11602871 11608768 - Carg19597-RA Car14g01376 1376
6 4620896 4638998 + CcPI632755_06g004230.1 Cco06g0423 423
6 4655779 4657581 + CcPI632755_06g004250.1 Cco06g0425 425
6 4770123 4785761 + CePI673135_06g004230.1 Cec06g0423 423
6 4802677 4804941 + CePI673135_06g004250.1 Cec06g0425 425
6 4796962 4815050 + ClG42_06g0040200.10 Clacu06g0402 402
6 4831742 4833544 + ClG42_06g0040400.10 Clacu06g0404 404
6 4822889 4836671 + ClCG06G004215.1 Cla06g00393 393
6 4846508 4849272 + ClCG06G004240.2 Cla06g00395 395
6 4850255 4856295 + ClCG06G004250.2 Cla06g00396 396
14 11712457 11716952 + CmaCh14G015590.1 Cma14g01559 1559
14 11719833 11723180 - CmaCh14G015600.1 Cma14g01560 1560
14 11724495 11734651 - CmaCh14G015610.1 Cma14g01561 1561
6 5654212 5661914 + MELO3C006748.2.1 Cme06g00827 827
6 5663738 5667144 + MELO3C006749.2.1 Cme06g00829 829
6 5670615 5678822 - MELO3C006750.2.1 Cme06g00830 830
6 5747547 5752311 + PI0014726.1 Cmetu06g2697 2697
11 3420937 3425208 + PI0005809.2 Cmetu11g0485 485
6 11104803 11108322 + CmoCh06G015800.1 Cmo06g01580 1580
14 12636908 12641667 + CmoCh14G015930.1 Cmo14g01593 1593
14 12645904 12648387 - CmoCh14G015950.1 Cmo14g01595 1595
14 12649981 12655521 - CmoCh14G015960.1 Cmo14g01596 1596
6 4592160 4610251 + CmPI595203_06g004020.1 Cmu06g0402 402
6 4626946 4629206 + CmPI595203_06g004040.1 Cmu06g0404 404
4 13054929 13056518 + Conep04aG0185500.1 Cone4ag1796 1796
7 11354826 11356765 + Conep07aG0175700.1 Cone7ag1704 1704
14 3512390 3514407 - Conep14aG0069500.1 Cone14ag0680 680
14 3515451 3519760 + Conep14aG0069600.1 Cone14ag0681 681
14 3526425 3528693 + Conep14aG0069800.1 Cone14ag0683 683
15 3731348 3733429 - Conep15aG0070600.1 Cone15ag0692 692
15 3737487 3741874 + Conep15aG0070700.1 Cone15ag0693 693
15 3747225 3749573 + Conep15aG0070900.1 Cone15ag0695 695
17 7809057 7809752 + Conep17aG0105400.1 Cone17ag1026 1026
3 10565046 10572348 + Cp4.1LG03g12160.1 Cpe03g01303 1303
3 10574291 10577778 - Cp4.1LG03g12050.1 Cpe03g01304 1304
3 10579423 10585311 - Cp4.1LG03g12090.1 Cpe03g01305 1305
8 868721 873367 - Cp4.1LG08g05430.1 Cpe08g00134 134
12 2344586 2347731 - Cp4.1LG12g03500.1 Cpe12g00347 347
12 2348377 2352926 - Cp4.1LG12g03460.1 Cpe12g00348 348
12 2357650 2364697 - Cp4.1LG12g03470.1 Cpe12g00349 349
6 5659170 5665995 + CrPI670011_06g011810.1 Cre06g1181 1181
6 5682635 5684909 + CrPI670011_06g011830.1 Cre06g1183 1183
3 125090 132446 + Hsped.03g00090.1 Hepe03g0009 9
3 164078 166584 + Hsped.03g00140.1 Hepe03g0014 14
5 61859498 61865134 + Hsped.05g13450.1 Hepe05g1345 1345
5 61868229 61871643 - Hsped.05g13460.1 Hepe05g1346 1346
11 11751115 11753023 - Lag0031676.1 Lac11g1038 1038
11 36529915 36530745 + Maker00031825 Lcy11g1304 1304
11 36568900 36574879 - Maker00031419 Lcy11g1307 1307
12 12985847 12987752 - Maker00024674 Lcy12g0899 899
12 13013602 13017371 - Maker00025040 Lcy12g0901 901
5 21755829 21760147 + Lsi05G013870.1 Lsi05g01387 1387
5 21767640 21771095 - Lsi05G013890.1 Lsi05g01389 1389
5 21774561 21780831 - Lsi05G013900.1 Lsi05g01390 1390
2 48370499 48374332 - Sed0015802.2 Sed02g1112 1112
9 6794879 6797366 + Sed0024001.1 Sed09g0597 597
6 80226249 80228236 - Tan0007730.2 Tan06g2812 2812
10 10807299 10813931 + Tan0002128.1 Tan10g1118 1118
10 10848677 10852471 + Tan0003542.2 Tan10g1120 1120
5 2561354 2563987 - Vvi5g249 Vvi5g249 249
5 2565342 2574143 - Vvi5g250 Vvi5g250 250
5 2574443 2574879 + Vvi5g251 Vvi5g251 251
5 2586108 2591430 + Vvi5g252 Vvi5g252 252
5 2592612 2596009 - Vvi5g253 Vvi5g253 253
5 2606492 2622986 + Vvi5g254 Vvi5g254 254
5 2622990 2635488 - Vvi5g255 Vvi5g255 255
5 2640363 2644421 + Vvi5g256 Vvi5g256 256
5 2644681 2648982 - Vvi5g257 Vvi5g257 257
5 2650044 2654801 - Vvi5g258 Vvi5g258 258
       

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