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
Vvi2g542 . . . Bda08g00594 Bpe05g00563 . . . Cmo06g00822 Cmo16g01170 Cma02g01561 . Car02g01321 . . Cpe14g00927 Cpe05g00232 . . . . . . . Cla10g00233 Cam10g0239 Cec10g0246 Cco10g0246 Clacu10g0241 Cmu10g1084 Cre10g0492 . . Cone6ag0652 Cone9ag0655 Lsi07g01276 Csa05g00449 Chy09g01062 Cme06g02548 . . . . . . Bma05g00745 . . Cmo02g01600 . Cma06g00801 Cma16g01119 . Car16g01056 Cpe08g00725 . . . . . . . . Cla01g00418 Cam01g0438 Cec01g0429 Cco01g0451 Clacu01g0439 Cmu01g0421 Cre09g2092 Lsi09g00448 Csa03g00251 Chy06g02073 Cme09g01595
Vvi2g543 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g544 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g545 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g546 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g547 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g548 . Blo03g00135 Bda06g01307 . Bpe05g00546 Bpe07g00199 . . Cmo06g00844 . . . . . Sed07g0533 . . Bhi11g00085 Tan01g2109 Cmetu06g1674 . Hepe06g1082 Mch10g1601 . Cla10g00208 Cam10g0216 Cec10g0221 Cco10g0221 . . Cre10g0470 . . Cone6ag0632 . Lsi07g01250 . . Cme06g02522 . . . . . . . Bma12g00189 . . . Cma06g00821 . . . . . . . . . . . . . . . . . . . . Csa03g00225 Chy06g02096 .
Vvi2g549 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g550 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g551 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 43739839 43742066 + Bda023161.2 Bda06g01307 1307
8 6063102 6067703 - Bda029059.1 Bda08g00594 594
11 2026303 2029696 - XM_039047236.1 Bhi11g00085 85
3 3873065 3875341 + BLOR11316 Blo03g00135 135
5 43835191 43840483 + Bma021843.1 Bma05g00745 745
12 2566258 2568532 - Bma007074.1 Bma12g00189 189
5 19646889 19648852 + Bpe017963.1 Bpe05g00546 546
5 19766969 19771468 + Bpe017979.1 Bpe05g00563 563
7 1363696 1365889 - Bpe021009.1 Bpe07g00199 199
1 4786103 4786396 - CaPI482276_01g004380.1 Cam01g0438 438
10 3861118 3866776 + CaPI482276_10g002160.1 Cam10g0216 216
10 4171962 4176482 + CaPI482276_10g002390.1 Cam10g0239 239
2 8774543 8777666 - Carg08788-RA Car02g01321 1321
16 9089663 9092948 + Carg24867-RA Car16g01056 1056
1 4481744 4482037 - CcPI632755_01g004510.1 Cco01g0451 451
10 2300911 2303111 + CcPI632755_10g002210.1 Cco10g0221 221
10 2627806 2632370 + CcPI632755_10g002460.1 Cco10g0246 246
1 4513380 4513673 - CePI673135_01g004290.1 Cec01g0429 429
10 2417568 2420962 + CePI673135_10g002210.1 Cec10g0221 221
10 2738078 2742620 + CePI673135_10g002460.1 Cec10g0246 246
6 24910818 24913845 - Chy6G126010.1 Chy06g02073 2073
6 25153531 25156730 - Chy6G126240.1 Chy06g02096 2096
9 13016284 13023502 + Chy9G167780.1 Chy09g01062 1062
1 4429738 4430031 - ClG42_01g0043900.10 Clacu01g0439 439
10 2926805 2931340 + ClG42_10g0024100.10 Clacu10g0241 241
1 4596355 4600579 - ClCG01G004280.2 Cla01g00418 418
10 2424527 2432940 + ClCG10G002150.2 Cla10g00208 208
10 2761381 2766444 + ClCG10G002480.2 Cla10g00233 233
2 8858774 8864735 - CmaCh02G015610.1 Cma02g01561 1561
6 4210050 4216509 - CmaCh06G008010.1 Cma06g00801 801
6 4408161 4420381 - CmaCh06G008210.1 Cma06g00821 821
16 8604218 8607788 + CmaCh16G011190.1 Cma16g01119 1119
6 32267316 32271377 + MELO3C013896.2.1 Cme06g02522 2522
6 32484982 32489537 + MELO3C013920.2.1 Cme06g02548 2548
9 20767362 20771745 + MELO3C005511.2.1 Cme09g01595 1595
6 29162988 29167137 - PI0007245.2 Cmetu06g1674 1674
2 9231696 9234697 - CmoCh02G016000.1 Cmo02g01600 1600
6 4464635 4467562 - CmoCh06G008220.1 Cmo06g00822 822
6 4697035 4699467 - CmoCh06G008440.1 Cmo06g00844 844
16 8341742 8345333 + CmoCh16G011700.1 Cmo16g01170 1170
1 4386553 4386846 - CmPI595203_01g004210.1 Cmu01g0421 421
10 3075653 3080187 + CmPI595203_10g010840.1 Cmu10g1084 1084
6 3199294 3201553 + Conep06aG0065100.1 Cone6ag0632 632
6 3293748 3296336 + Conep06aG0067400.1 Cone6ag0652 652
9 3120078 3122159 + Conep09aG0067200.1 Cone9ag0655 655
5 1309248 1314731 + Cp4.1LG05g02350.1 Cpe05g00232 232
8 5707039 5714898 + Cp4.1LG08g07280.1 Cpe08g00725 725
14 7805666 7808555 + Cp4.1LG14g09270.1 Cpe14g00927 927
9 39925286 39928931 + CrPI670011_09g020920.1 Cre09g2092 2092
10 3720170 3723583 + CrPI670011_10g004700.1 Cre10g0470 470
10 4049666 4054243 + CrPI670011_10g004920.1 Cre10g0492 492
3 1800704 1805112 + CsaV3_3G002250.1 Csa03g00225 225
3 2010781 2020181 + CsaV3_3G002510.1 Csa03g00251 251
5 2962209 2965903 - CsaV3_5G004490.1 Csa05g00449 449
6 59273399 59277275 + Hsped.06g10820.1 Hepe06g1082 1082
7 18237393 18241890 + Lsi07G012500.1 Lsi07g01250 1250
7 18604639 18609733 + Lsi07G012760.1 Lsi07g01276 1276
9 4739202 4743387 - Lsi09G004480.1 Lsi09g00448 448
10 16103686 16107673 - MC10g1268 Mch10g1601 1601
7 3992125 3996564 - Sed0019172.1 Sed07g0533 533
1 24266477 24270202 - Tan0020590.1 Tan01g2109 2109
2 5400660 5409494 + Vvi2g542 Vvi2g542 542
2 5409886 5410351 - Vvi2g543 Vvi2g543 543
2 5412974 5419596 - Vvi2g544 Vvi2g544 544
2 5432503 5432686 + Vvi2g545 Vvi2g545 545
2 5436280 5437031 - Vvi2g546 Vvi2g546 546
2 5444668 5445461 - Vvi2g547 Vvi2g547 547
2 5471748 5475214 - Vvi2g548 Vvi2g548 548
2 5475215 5475660 - Vvi2g549 Vvi2g549 549
2 5483802 5484545 - Vvi2g550 Vvi2g550 550
2 5504704 5507912 - Vvi2g551 Vvi2g551 551
       

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