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
Vvi18g1360 . Blo12g00781 . . . . . . . . . Cma09g01181 . . . . . . . . . . . . . . . . . . . Cone4ag1486 Cone7ag1458 . . . . . . . . . . . . . . . . Cmo09g01185 . . . Car09g01056 . . . . . . . . . . . . . . . . . . Chy03g00248 .
Vvi18g1361 Blo01g01731 Blo12g00782 . . . . Bma04g00376 Bma01g02510 . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1489 Cone7ag1455 . . . . . . . . Bda11g00871 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1362 . . . Bda03g00397 . Bpe04g00358 Bma04g00375 . . . . Cma09g01177 . . . . . Bhi04g02202 . . . . . . . . . . . . . Cone4ag1490 . . . . . . . . . . . . . . . . . . . . . Car09g01052 . . . . . . . . . . . . . . . . . . Chy03g00252 .
Vvi18g1363 . Blo12g00783 . Bda03g00395 . Bpe04g00357 Bma04g00373 . . . . Cma09g01174 . . . . . . . . . . . . . . . . . . . . . . Cone20ag0373 . . . . . . . . . . . . . . Cmo09g01181 . . . . . . . . . . . . . . . . . . . . . . Chy03g00253 .
Vvi18g1364 . Blo12g00784 . Bda03g00394 . Bpe04g00356 Bma04g00372 . . . . . . . . . . . . . . . . . Cla08g00249 Cam08g0690 . Cco08g0328 Clacu08g0396 . Cre08g0219 Cone4ag1491 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi08g00221 . Chy03g00261 .
Vvi18g1365 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1366 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1494 Cone7ag1454 . Cone20ag0374 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1367 . . Bda01g00860 . . . . . . . . . . . . . . Bhi04g01770 . . . . . . Cla08g00714 Cam08g1142 Cec08g0731 Cco08g0839 Clacu08g0850 . Cre08g0650 . . Cone17ag0781 Cone20ag0375 . . . . Blo17g00144 Blo18g00154 . Bda13g01430 . Bpe14g00430 Bma01g01439 Bma02g00166 . . . . . . . . . . . . . . . . . . . . . . . Lsi08g00556 . . .
Vvi18g1368 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1369 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 41265018 41270827 + Bda002990.1 Bda01g00860 860
3 3255114 3257380 + Bda033484 Bda03g00394 394
3 3258072 3260185 + Bda016357.1 Bda03g00395 395
3 3304977 3315450 + Bda016361.1 Bda03g00397 397
11 8584600 8584997 - Bda005624.1 Bda11g00871 871
13 37000149 37003631 - Bda000256.2 Bda13g01430 1430
4 43050939 43063268 + XM_039029451.1 Bhi04g01770 1770
4 60708611 60712112 + XM_039030483.1 Bhi04g02202 2202
1 57030286 57030689 + BLOR01731 Blo01g01731 1731
12 26213649 26218533 - BLOR04800 Blo12g00781 781
12 26227288 26227758 - BLOR04801 Blo12g00782 782
12 26236149 26239646 - BLOR04802 Blo12g00783 783
12 26240783 26243018 - BLOR04803 Blo12g00784 784
17 1335156 1340933 - BLOR15965 Blo17g00144 144
18 1403715 1411468 - BLOR08642 Blo18g00154 154
1 24467021 24472237 - Bma001813.1 Bma01g01439 1439
1 82783178 82783581 + Bma003390.1 Bma01g02510 2510
2 1453824 1464618 - Bma014621.1 Bma02g00166 166
4 2981722 2983910 + Bma018830.1 Bma04g00372 372
4 2984589 2986804 + Bma018831.1 Bma04g00373 373
4 3001588 3006230 + Bma018833.1 Bma04g00375 375
4 3008962 3009407 + Bma018834.1 Bma04g00376 376
4 2252639 2254876 + Bpe015047.1 Bpe04g00356 356
4 2255669 2257827 + Bpe015048.1 Bpe04g00357 357
4 2258788 2262118 + Bpe015049.1 Bpe04g00358 358
14 3946766 3950667 + Bpe007081.1 Bpe14g00430 430
8 5346216 5351651 - CaPI482276_08g006900.1 Cam08g0690 690
8 17754788 17763670 - CaPI482276_08g011420.1 Cam08g1142 1142
9 8904508 8913576 - Carg28094-RA Car09g01052 1052
9 9352842 9359762 + Carg27431-RA Car09g01056 1056
8 6436114 6439751 - CcPI632755_08g003280.1 Cco08g0328 328
8 20222167 20231036 - CcPI632755_08g008390.1 Cco08g0839 839
8 19032289 19041173 - CePI673135_08g007310.1 Cec08g0731 731
3 2363057 2368498 - Chy3G052280.1 Chy03g00248 248
3 2510054 2513779 - Chy3G052320.1 Chy03g00252 252
3 2519265 2521273 - Chy3G052330.1 Chy03g00253 253
3 2618464 2621611 - Chy3G052410.1 Chy03g00261 261
8 5171356 5176791 - ClG42_08g0039600.10 Clacu08g0396 396
8 18533724 18542577 - ClG42_08g0085000.10 Clacu08g0850 850
8 5104069 5107385 - ClCG08G002400.1 Cla08g00249 249
8 19413774 19425321 - ClCG08G007010.1 Cla08g00714 714
9 7234676 7238957 + CmaCh09G011740.1 Cma09g01174 1174
9 7284035 7297701 + CmaCh09G011770.1 Cma09g01177 1177
9 7489487 7496140 + CmaCh09G011810.1 Cma09g01181 1181
9 8373415 8376361 - CmoCh09G011810.1 Cmo09g01181 1181
9 8679508 8686164 + CmoCh09G011850.1 Cmo09g01185 1185
4 11633123 11638674 - Conep04aG0153800.1 Cone4ag1486 1486
4 11648828 11650176 - Conep04aG0154100.1 Cone4ag1489 1489
4 11653914 11656765 - Conep04aG0154200.1 Cone4ag1490 1490
4 11656825 11659246 - Conep04aG0154300.1 Cone4ag1491 1491
4 11664335 11665149 - Conep04aG0154600.1 Cone4ag1494 1494
7 10267419 10268226 + Conep07aG0149600.1 Cone7ag1454 1454
7 10282471 10283398 + Conep07aG0149700.1 Cone7ag1455 1455
7 10292094 10297657 + Conep07aG0150000.1 Cone7ag1458 1458
17 6006948 6012051 - Conep17aG0079900.1 Cone17ag0781 781
20 1720265 1723270 - Conep20aG0038700.1 Cone20ag0373 373
20 1725721 1726725 + Conep20aG0038800.1 Cone20ag0374 374
20 1727159 1731591 - Conep20aG0038900.1 Cone20ag0375 375
8 5709024 5712180 - CrPI670011_08g002190.1 Cre08g0219 219
8 19447268 19456151 - CrPI670011_08g006500.1 Cre08g0650 650
8 4970936 4974575 - Lsi08G002210.1 Lsi08g00221 221
8 13749780 13761930 - Lsi08G005570.1 Lsi08g00556 556
18 19565381 19573457 - Vvi18g1360 Vvi18g1360 1360
18 19583450 19584514 - Vvi18g1361 Vvi18g1361 1361
18 19587110 19592826 - Vvi18g1362 Vvi18g1362 1362
18 19593286 19597222 - Vvi18g1363 Vvi18g1363 1363
18 19597266 19609925 - Vvi18g1364 Vvi18g1364 1364
18 19617943 19618377 - Vvi18g1365 Vvi18g1365 1365
18 19625487 19626211 + Vvi18g1366 Vvi18g1366 1366
18 19628750 19649753 - Vvi18g1367 Vvi18g1367 1367
18 19674977 19675780 + Vvi18g1368 Vvi18g1368 1368
18 19675812 19677806 + Vvi18g1369 Vvi18g1369 1369
       

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