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
Vvi5g709 Blo01g00091 . . . Bpe04g00956 . . Bma05g01066 . . . Cma14g01813 . . . . . . . . . . . . Cla06g00665 . . . . . . . Cone15ag0162 . . . Csa02g01062 Chy05g00321 . . Blo07g00264 Bda11g00632 . Bpe05g01039 . . . . . Cmo14g01851 . . . . . . Bhi12g01617 . . . . . Lcy13g0376 . . . . . . . . . . .
Vvi5g710 . . . . . . . . . . Cma06g01320 Cma14g01814 Car06g01138 Car14g01627 . Cpe08g00335 Cpe03g01518 . . . . . . . . . . . . . . . . . . Lsi05g01733 . . Cme06g00493 . . . . . . . . . Cmo06g01329 Cmo14g01853 . . . . . . . . . . . . . Cla05g00444 Cam05g0484 Cec05g0493 Cco05g0492 Clacu05g0479 . Cre05g0520 . Csa03g01209 Chy06g00472 .
Vvi5g711 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g712 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g713 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g714 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g715 . . . . . Bpe14g01257 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone7ag0324 . . . . . . . . Bda13g00060 . . Bma02g00780 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g716 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g717 . . . . . Bpe14g01258 . . . Cmo17g00160 Cma06g01318 Cma14g01815 Car06g01136 . . . . . . . . . . . Cla06g00667 Cam06g0716 . Cco06g0731 Clacu06g0707 Cmu06g0694 Cre06g1464 . . . . Lsi05g01735 Csa02g01059 Chy05g00319 Cme06g00486 . Blo07g00266 Bda11g00635 Bda13g00059 . . Bma02g00778 . . Cmo06g01328 Cmo14g01854 . Cma17g00162 . Car17g00143 . . Bhi12g01615 . . . . . Lcy13g0378 Cla05g00442 Cam05g0480 Cec05g0490 Cco05g0490 Clacu05g0476 Cmu05g0455 Cre05g0517 Lsi09g01232 Csa03g01204 Chy06g00467 Cme05g00571
Vvi5g718 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 6338490 6339791 + Bda005378.1 Bda11g00632 632
11 6347556 6351165 + Bda005381.1 Bda11g00635 635
13 855669 864010 - Bda000906.1 Bda13g00059 59
13 865012 870577 - Bda000907.1 Bda13g00060 60
12 52195931 52200546 + XM_039051158.1 Bhi12g01615 1615
12 52216813 52218787 - XM_039019610.1 Bhi12g01617 1617
1 1263477 1265121 + BLOR00091 Blo01g00091 91
7 3182324 3183408 + BLOR18196 Blo07g00264 264
7 3191569 3195323 + BLOR18198 Blo07g00266 266
2 41368533 41372083 - Bma015501.1 Bma02g00778 778
2 41377884 41381974 - Bma030901 Bma02g00780 780
5 49388396 49389714 + Bma022231.1 Bma05g01066 1066
4 6452056 6453011 - Bpe015620.1 Bpe04g00956 956
5 22963764 22964716 - Bpe018451.1 Bpe05g01039 1039
14 9497953 9502202 + Bpe025549 Bpe14g01257 1257
14 9503048 9506509 + Bpe014617.1 Bpe14g01258 1258
5 4259337 4263199 - CaPI482276_05g004800.1 Cam05g0480 480
5 4272363 4276840 - CaPI482276_05g004840.1 Cam05g0484 484
6 9703960 9713810 - CaPI482276_06g007160.1 Cam06g0716 716
6 8443312 8447486 - Carg06221-RA Car06g01136 1136
6 8450902 8455082 - Carg06219-RA Car06g01138 1138
14 13070935 13080518 + Carg16560-RA Car14g01627 1627
17 887009 892340 + Carg10088-RA Car17g00143 143
5 3921048 3925685 - CcPI632755_05g004900.1 Cco05g0490 490
5 3934059 3938605 - CcPI632755_05g004920.1 Cco05g0492 492
6 8333698 8342200 - CcPI632755_06g007310.1 Cco06g0731 731
5 3911585 3915495 - CePI673135_05g004900.1 Cec05g0490 490
5 3922777 3929158 - CePI673135_05g004930.1 Cec05g0493 493
5 3176257 3180339 + Chy5G093650.1 Chy05g00319 319
5 3206452 3207935 - Chy5G093670.1 Chy05g00321 321
6 3125182 3129635 - Chy6G109950.1 Chy06g00467 467
6 3148681 3152466 - Chy6G110000.1 Chy06g00472 472
5 3965426 3969282 - ClG42_05g0047600.10 Clacu05g0476 476
5 3978411 3982831 - ClG42_05g0047900.10 Clacu05g0479 479
6 8259088 8263085 - ClG42_06g0070700.10 Clacu06g0707 707
5 3947041 3950897 - ClCG05G004300.1 Cla05g00442 442
5 3959939 3965902 - ClCG05G004310.1 Cla05g00444 444
6 8407905 8409441 - ClCG06G006995.1 Cla06g00665 665
6 8455931 8460349 - ClCG06G007010.1 Cla06g00667 667
6 8704757 8711032 - CmaCh06G013180.1 Cma06g01318 1318
6 8714611 8719112 - CmaCh06G013200.1 Cma06g01320 1320
14 12996925 12999234 + CmaCh14G018130.1 Cma14g01813 1813
14 12999277 13003754 + CmaCh14G018140.1 Cma14g01814 1814
14 13003980 13011324 + CmaCh14G018150.1 Cma14g01815 1815
17 827734 832798 + CmaCh17G001620.1 Cma17g00162 162
5 5785991 5790527 - MELO3C022999.2.1 Cme05g00571 571
6 3067172 3071950 - MELO3C006418.2.1 Cme06g00486 486
6 3097094 3102289 - MELO3C006424.2.1 Cme06g00493 493
6 9896077 9900376 - CmoCh06G013280.1 Cmo06g01328 1328
6 9903995 9908079 - CmoCh06G013290.1 Cmo06g01329 1329
14 13981425 13982380 + CmoCh14G018510.1 Cmo14g01851 1851
14 13983807 13988445 + CmoCh14G018530.1 Cmo14g01853 1853
14 13990368 13997627 + CmoCh14G018540.1 Cmo14g01854 1854
17 931998 936059 + CmoCh17G001600.1 Cmo17g00160 160
5 3801610 3805466 - CmPI595203_05g004550.1 Cmu05g0455 455
6 8071261 8075258 - CmPI595203_06g006940.1 Cmu06g0694 694
7 1414639 1417954 + Conep07aG0033200.1 Cone7ag0324 324
15 783705 784895 + Conep15aG0016600.1 Cone15ag0162 162
3 11884322 11890058 + Cp4.1LG03g10090.1 Cpe03g01518 1518
8 2090456 2093870 + Cp4.1LG08g03370.1 Cpe08g00335 335
5 4597252 4601158 - CrPI670011_05g005170.1 Cre05g0517 517
5 4608477 4614941 - CrPI670011_05g005200.1 Cre05g0520 520
6 9177567 9181563 - CrPI670011_06g014640.1 Cre06g1464 1464
2 10277417 10282247 + CsaV3_2G012750.1 Csa02g01059 1059
2 10293412 10295640 - CsaV3_2G012780.1 Csa02g01062 1062
3 9309726 9314622 - CsaV3_3G012040.1 Csa03g01204 1204
3 9333260 9338381 - CsaV3_3G012090.1 Csa03g01209 1209
13 4301843 4303857 + Maker00023648 Lcy13g0376 376
13 4316660 4321831 - Maker00023702 Lcy13g0378 378
5 24766758 24772810 + Lsi05G017330.1 Lsi05g01733 1733
5 24782512 24787905 + Lsi05G017350.1 Lsi05g01735 1735
9 19773050 19777987 + Lsi09G012320.1 Lsi09g01232 1232
5 8046844 8048416 + Vvi5g709 Vvi5g709 709
5 8075612 8090454 + Vvi5g710 Vvi5g710 710
5 8104350 8105282 + Vvi5g711 Vvi5g711 711
5 8137443 8138375 + Vvi5g712 Vvi5g712 712
5 8158982 8170034 + Vvi5g713 Vvi5g713 713
5 8170773 8171806 + Vvi5g714 Vvi5g714 714
5 8179521 8185638 + Vvi5g715 Vvi5g715 715
5 8186955 8196949 + Vvi5g716 Vvi5g716 716
5 8218851 8229689 + Vvi5g717 Vvi5g717 717
5 8239470 8240265 + Vvi5g718 Vvi5g718 718
       

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