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
Vvi18g300 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone7ag1548 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g301 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g302 . . . . . . . . Cmo04g02457 Cmo15g00710 . . . . . . . . . . . . . . Cla08g00562 Cam08g0979 Cec08g0569 Cco08g0678 Clacu08g0686 . Cre08g0501 . . . Cone20ag0454 . . . . . . . Bda13g01487 . . . Bma02g00224 . . . . . . Car15g00640 Cpe01g02037 . . . . . . . . . . . . . . . Lsi08g00411 . Chy03g00354 .
Vvi18g303 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g304 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g305 . . . . . Bpe04g00480 . . Cmo04g02456 . . . . . . . . . . . . . . . Cla08g00561 Cam08g0978 Cec08g0568 Cco08g0677 Clacu08g0685 . Cre08g0500 . . . . . . . . . Blo18g00190 . Bda01g01416 . . Bma01g00830 . . . . . . Car04g02274 . Cpe01g02036 . . . . . . . . . . . . . . . Lsi08g00410 . Chy03g00353 .
Vvi18g306 . Blo12g00679 . . Bpe02g00077 . . Bma01g02641 . Cmo15g00711 . . . . . . . . . . . . . . . . . . . . . . . . Cone20ag0457 . . . . . . . . . . . . . . . . . . Car15g00641 . . . . . . . . . . . . . . . . . . . .
Vvi18g307 . Blo12g00681 . Bda03g00525 . Bpe04g00479 . . Cmo04g02455 . . . . . . . . . . . . . . . . . . . . . . Cone4ag1382 Cone7ag1549 . . . . . . . . . . . . . . . . . . . Car04g02273 . Cpe01g02035 . . . . . . . . . . . . . . . . . . .
Vvi18g308 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g309 . . . . . . . . Cmo04g02453 Cmo15g00712 . . . . . . . . . . . . . . . . . . . . . . . Cone17ag1268 Cone20ag0459 . . . . Blo17g00185 Blo18g00191 . Bda13g01489 Bpe02g01629 Bpe14g00374 Bma01g00832 Bma02g00226 . . . . . Car04g02272 . Cpe01g02033 . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 50063508 50074246 - Bda003659.1 Bda01g01416 1416
3 4392926 4395425 + Bda016495.1 Bda03g00525 525
13 37809586 37809974 + Bda032812 Bda13g01487 1487
13 37814832 37817327 - Bda032813 Bda13g01489 1489
12 25055345 25056493 - BLOR04698 Blo12g00679 679
12 25071740 25074126 - BLOR04700 Blo12g00681 681
17 1897460 1900016 - BLOR16006 Blo17g00185 185
18 1832564 1834987 + BLOR08678 Blo18g00190 190
18 1853952 1856556 - BLOR08679 Blo18g00191 191
1 7815478 7818166 + Bma001050.1 Bma01g00830 830
1 7823057 7825908 - Bma001052.2 Bma01g00832 832
1 83915758 83916946 - Bma003526.1 Bma01g02641 2641
2 2372591 2373072 + Bma014680.1 Bma02g00224 224
2 2380363 2383529 - Bma014682.1 Bma02g00226 226
2 588661 598592 + Bpe007928.1 Bpe02g00077 77
2 19129805 19132738 + Bpe025158 Bpe02g01629 1629
4 3022363 3024879 + Bpe025627 Bpe04g00479 479
4 3025552 3026741 - Bpe015164.1 Bpe04g00480 480
14 3546543 3548800 + Bpe007028.1 Bpe14g00374 374
8 15730072 15731263 - CaPI482276_08g009780.1 Cam08g0978 978
8 15735739 15738255 - CaPI482276_08g009790.1 Cam08g0979 979
4 18302524 18305723 + Carg24457-RA Car04g02272 2272
4 18312120 18315397 + Carg24456-RA Car04g02273 2273
4 18316356 18318316 - Carg24455-RA Car04g02274 2274
15 3543584 3546005 + Carg01515-RA Car15g00640 640
15 3546306 3547452 + Carg01514-RA Car15g00641 641
8 18092163 18093354 - CcPI632755_08g006770.1 Cco08g0677 677
8 18098334 18100852 - CcPI632755_08g006780.1 Cco08g0678 678
8 16897824 16899015 - CePI673135_08g005680.1 Cec08g0568 568
8 16903673 16906187 - CePI673135_08g005690.1 Cec08g0569 569
3 4790950 4792141 - Chy3G053330.1 Chy03g00353 353
3 4805271 4807370 - Chy3G053340.1 Chy03g00354 354
8 16421746 16422937 - ClG42_08g0068500.10 Clacu08g0685 685
8 16427463 16429980 - ClG42_08g0068600.10 Clacu08g0686 686
8 17142569 17143925 - ClCG08G005380.2 Cla08g00561 561
8 17148075 17150930 - ClCG08G005390.2 Cla08g00562 562
4 18158524 18161874 + CmoCh04G024530.1 Cmo04g02453 2453
4 18168521 18171844 + CmoCh04G024550.1 Cmo04g02455 2455
4 18173623 18175696 - CmoCh04G024560.1 Cmo04g02456 2456
4 18176795 18179658 - CmoCh04G024570.1 Cmo04g02457 2457
15 3451977 3453672 + CmoCh15G007100.1 Cmo15g00710 710
15 3454346 3457487 + CmoCh15G007110.1 Cmo15g00711 711
15 3461361 3464480 - CmoCh15G007120.1 Cmo15g00712 712
4 11192141 11193963 + Conep04aG0143100.1 Cone4ag1382 1382
7 10666698 10668016 + Conep07aG0159400.1 Cone7ag1548 1548
7 10672397 10675651 - Conep07aG0159500.1 Cone7ag1549 1549
17 9138383 9140335 + Conep17aG0129900.1 Cone17ag1268 1268
20 2327300 2329764 - Conep20aG0046900.1 Cone20ag0454 454
20 2367967 2369908 + Conep20aG0047200.1 Cone20ag0457 457
20 2378269 2381222 - Conep20aG0047400.1 Cone20ag0459 459
1 17298508 17301673 + Cp4.1LG01g20210.1 Cpe01g02033 2033
1 17308111 17311590 + Cp4.1LG01g20400.1 Cpe01g02035 2035
1 17310966 17313927 - Cp4.1LG01g20480.1 Cpe01g02036 2036
1 17314974 17315891 - Cp4.1LG01g20510.1 Cpe01g02037 2037
8 17400238 17401429 - CrPI670011_08g005000.1 Cre08g0500 500
8 17406100 17408617 - CrPI670011_08g005010.1 Cre08g0501 501
8 11506602 11508137 - Lsi08G004100.1 Lsi08g00410 410
8 11510485 11512781 - Lsi08G004110.1 Lsi08g00411 411
18 3309836 3311940 - Vvi18g300 Vvi18g300 300
18 3312009 3316888 - Vvi18g301 Vvi18g301 301
18 3320930 3328582 + Vvi18g302 Vvi18g302 302
18 3338309 3340079 + Vvi18g303 Vvi18g303 303
18 3340661 3348874 - Vvi18g304 Vvi18g304 304
18 3349226 3350728 + Vvi18g305 Vvi18g305 305
18 3351204 3359027 + Vvi18g306 Vvi18g306 306
18 3359360 3369305 - Vvi18g307 Vvi18g307 307
18 3369963 3370941 - Vvi18g308 Vvi18g308 308
18 3380426 3383311 - Vvi18g309 Vvi18g309 309
       

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