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
Vvi1g651 . . . . . . . . . . . Cma18g00785 . . . . . Bhi07g01753 . . . . . . Cla05g02559 . . . . . . . . Cone8ag0680 Cone12ag0658 Lsi04g00566 Csa05g02318 Chy10g00886 Cme10g00543 . . . . . . Bma01g00042 . . . . . Cma05g00032 . . . . . . . . . . . . . . . . . . . . . .
Vvi1g652 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0678 . . . . . . . . . . . . Bma06g00608 . . . . Cma05g00031 . . . . . . . . . . . . . . . . . . . . . .
Vvi1g653 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0679 . . . . . . . . . . . . . . . . . . . Car05g00027 . . . . . . . . . . . . . . . . . . . .
Vvi1g654 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g655 . Blo16g01166 . Bda11g01279 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g01279 . . . . . . . . . . Car05g00026 . . . . . . . . . . . . . . . . . . . .
Vvi1g656 . . . . Bpe13g00503 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g657 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g658 . . . . Bpe13g01477 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g659 . Blo16g01165 . Bda11g01278 Bpe13g01476 . . . . Cmo18g00789 . Cma18g00787 . Car18g00717 Sed08g0113 Cpe09g00513 Cpe01g01546 Bhi07g01752 Tan04g1268 Cmetu10g1281 Lac13g0183 Hepe10g0032 . . Cla05g02558 Cam05g2746 Cec05g2778 Cco05g2818 Clacu05g2747 Cmu05g2599 Cre05g2714 Cone13ag1055 Cone19ag1044 . . Lsi04g00565 Csa05g02319 Chy10g00887 Cme10g00541 . . . Bda11g01278 . . . Bma06g00609 . . . Cma04g01746 Cma05g00030 Car04g01779 Car05g00025 . . . . . . . . . . . . . . . . . . . .
Vvi1g660 . Blo16g01164 . Bda11g01277 Bpe13g01475 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0677 . . . . . . . . Bda11g01277 . . Bma01g00560 Bma06g00610 . . . . Cma05g00029 . Car05g00024 . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 13373417 13381032 + Bda007795.2 Bda11g01277 1277
11 13413309 13419843 + Bda007796.1 Bda11g01278 1278
11 13421198 13423059 + Bda007797.1 Bda11g01279 1279
7 48154438 48161425 + XM_039036254.1 Bhi07g01752 1752
7 48161494 48165715 - XM_039036252.1 Bhi07g01753 1753
16 40180205 40188681 + BLOR21951 Blo16g01164 1164
16 40199397 40206642 + BLOR21952 Blo16g01165 1165
16 40207400 40212576 + BLOR21953 Blo16g01166 1166
1 473093 475573 + Bma000210.1 Bma01g00042 42
1 4942020 4944555 - Bma000748.1 Bma01g00560 560
6 32443702 32445558 - Bma023542.1 Bma06g00608 608
6 32446915 32457931 - Bma023543.1 Bma06g00609 609
6 32595869 32598495 - Bma023548.1 Bma06g00610 610
13 12421042 12423544 - Bpe010213.2 Bpe13g00503 503
13 19998380 20006299 + Bpe011139.2 Bpe13g01475 1475
13 20040897 20047453 + Bpe011142.1 Bpe13g01476 1476
13 20049403 20051248 + Bpe011143.1 Bpe13g01477 1477
5 34728066 34734782 + CaPI482276_05g027460.1 Cam05g2746 2746
4 10166478 10172810 + Carg14326-RA Car04g01779 1779
5 131296 133319 + Carg21824-RA Car05g00024 24
5 135513 146019 + Carg21825-RA Car05g00025 25
5 147071 148548 + Carg21826-RA Car05g00026 26
5 149238 155392 - Carg21827-RA Car05g00027 27
18 8364211 8366136 - Carg14481-RA Car18g00717 717
5 35868572 35875907 + CcPI632755_05g028180.1 Cco05g2818 2818
5 38185860 38192572 + CePI673135_05g027780.1 Cec05g2778 2778
10 14646950 14650716 + Chy10G180800.1 Chy10g00886 886
10 14651229 14656749 - Chy10G180810.1 Chy10g00887 887
5 34935468 34942202 + ClG42_05g0274700.10 Clacu05g2747 2747
5 36873530 36881144 + ClCG05G025510.2 Cla05g02558 2558
5 36880979 36884914 - ClCG05G025520.1 Cla05g02559 2559
4 8772054 8779396 + CmaCh04G017460.1 Cma04g01746 1746
5 130684 132717 + CmaCh05G000290.1 Cma05g00029 29
5 135056 146436 + CmaCh05G000300.1 Cma05g00030 30
5 146888 152472 + CmaCh05G000310.1 Cma05g00031 31
5 148546 151929 - CmaCh05G000320.1 Cma05g00032 32
18 6945003 6949067 + CmaCh18G007850.1 Cma18g00785 785
18 6949757 6956576 - CmaCh18G007870.1 Cma18g00787 787
10 3457746 3465335 + MELO3C011979.2.1 Cme10g00541 541
10 3464745 3469001 - MELO3C011978.2.1 Cme10g00543 543
10 18536543 18543572 - PI0013514.1 Cmetu10g1281 1281
18 9414147 9420399 - CmoCh18G007890.1 Cmo18g00789 789
5 34673380 34680111 + CmPI595203_05g025990.1 Cmu05g2599 2599
8 6759164 6762387 + Conep08aG0070000.1 Cone8ag0677 677
8 6767097 6768727 + Conep08aG0070100.1 Cone8ag0678 678
8 6769285 6796406 - Conep08aG0070200.1 Cone8ag0679 679
8 6804886 6808130 - Conep08aG0070300.1 Cone8ag0680 680
12 6028821 6033828 - Conep12aG0068100.1 Cone12ag0658 658
13 8661649 8668692 - Conep13aG0108600.1 Cone13ag1055 1055
19 7712741 7719564 - Conep19aG0107600.1 Cone19ag1044 1044
1 9228197 9230224 + Cp4.1LG01g15490.1 Cpe01g01546 1546
9 3419266 3427130 + Cp4.1LG09g05110.1 Cpe09g00513 513
5 38032045 38039310 + CrPI670011_05g027140.1 Cre05g2714 2714
5 25639895 25644173 + CsaV3_5G031370.1 Csa05g02318 2318
5 25644124 25651196 - CsaV3_5G031380.1 Csa05g02319 2319
10 293584 305263 + Hsped.10g00320.1 Hepe10g0032 32
13 1279830 1281457 - Lag0039979.1 Lac13g0183 183
4 5168784 5176102 + Lsi04G005650.1 Lsi04g00565 565
4 5175720 5180225 - Lsi04G005660.1 Lsi04g00566 566
8 674054 682119 - Sed0018081.1 Sed08g0113 113
4 12193149 12199896 + Tan0000738.1 Tan04g1268 1268
1 7490193 7493506 + Vvi1g651 Vvi1g651 651
1 7494006 7502229 - Vvi1g652 Vvi1g652 652
1 7502367 7512803 + Vvi1g653 Vvi1g653 653
1 7512989 7513366 - Vvi1g654 Vvi1g654 654
1 7520997 7523462 - Vvi1g655 Vvi1g655 655
1 7536463 7537993 + Vvi1g656 Vvi1g656 656
1 7543669 7543982 - Vvi1g657 Vvi1g657 657
1 7544631 7545963 - Vvi1g658 Vvi1g658 658
1 7552214 7562392 - Vvi1g659 Vvi1g659 659
1 7572937 7577645 - Vvi1g660 Vvi1g660 660
       

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