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
Vvi17g46 . . . Bda15g00687 Bpe12g00466 . . . . . Cma10g00034 . Car10g00024 . Sed12g2540 . . Bhi02g00643 Tan09g2420 Cmetu02g0270 . . . . Cla06g01771 Cam06g1963 Cec06g2014 Cco06g2021 Clacu06g1921 Cmu06g1862 Cre06g2675 . . Cone13ag0249 Cone19ag0229 . . . . . Blo15g00101 . . . . . Bma08g00271 . Cmo10g00030 . . . . . . . . . . . . . . . . . . . . . Lsi06g01668 Csa01g00023 Chy02g02690 Cme02g02097
Vvi17g47 . Blo16g00286 . . . Bpe13g00189 . . . Cmo18g00235 . . . . . Cpe20g00292 . . . . . . . . . . . . . . . . . Cone13ag0248 Cone19ag0228 Lsi02g00524 Csa01g00986 Chy12g01147 Cme12g01566 . . Bda11g01584 . . . . . . . . Cma13g00826 Cma18g00299 Car13g00669 . Cpe09g00946 . Bhi08g01533 . . . . . . Cla03g00375 Cam03g0395 Cec03g0381 Cco03g0396 Clacu03g0394 Cmu03g0999 Cre03g0691 . . . .
Vvi17g48 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g49 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g50 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g51 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g52 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g53 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g54 . . . . . . . . . . Cma10g00035 . Car10g00025 . Sed12g2539 . . Bhi02g00645 Tan09g2414 Cmetu02g0435 . . . . Cla06g01770 Cam06g1962 Cec06g2013 Cco06g2020 Clacu06g1920 Cmu06g1861 Cre06g2674 . . . . . . . . . . . . . . . . . Cmo10g00031 . . . . . . Cpe18g00925 . . . . . . . . . . . . . . Lsi06g01667 Csa01g00024 Chy02g02689 Cme02g02096
Vvi17g55 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 49137799 49149137 + Bda008456.1 Bda11g01584 1584
15 10277595 10279853 - Bda012538.1 Bda15g00687 687
2 12460365 12463055 + XM_039023693.1 Bhi02g00643 643
2 12479965 12488136 + XM_039023472.1 Bhi02g00645 645
8 43960560 43964646 - XM_039039590.1 Bhi08g01533 1533
15 853914 855984 - BLOR06495 Blo15g00101 101
16 6831496 6834524 - BLOR07534 Blo16g00286 286
8 3690263 3692633 - Bma027291.1 Bma08g00271 271
12 10421175 10423558 + Bpe005726.1 Bpe12g00466 466
13 9839632 9842780 + Bpe006309.1 Bpe13g00189 189
3 5064311 5067916 - CaPI482276_03g003950.1 Cam03g0395 395
6 30468512 30473849 - CaPI482276_06g019620.1 Cam06g1962 1962
6 30477632 30479790 - CaPI482276_06g019630.1 Cam06g1963 1963
10 117873 120507 + Carg10256-RA Car10g00024 24
10 121353 127409 + Carg10257-RA Car10g00025 25
13 8163219 8166987 - Carg07619-RA Car13g00669 669
3 4291563 4295131 - CcPI632755_03g003960.1 Cco03g0396 396
6 30217753 30223205 - CcPI632755_06g020200.1 Cco06g2020 2020
6 30227134 30229292 - CcPI632755_06g020210.1 Cco06g2021 2021
3 4241619 4245215 - CePI673135_03g003810.1 Cec03g0381 381
6 33296090 33301427 - CePI673135_06g020130.1 Cec06g2013 2013
6 33305336 33307503 - CePI673135_06g020140.1 Cec06g2014 2014
2 29789171 29795440 - Chy2G049560.1 Chy02g02689 2689
2 29797367 29800678 - Chy2G049570.1 Chy02g02690 2690
12 16403329 16424786 + Chy12G217470.1 Chy12g01147 1147
3 4379818 4383731 - ClG42_03g0039400.10 Clacu03g0394 394
6 29511758 29515929 - ClG42_06g0192000.10 Clacu06g1920 1920
6 29519243 29521397 - ClG42_06g0192100.10 Clacu06g1921 1921
3 4339570 4343677 - ClCG03G003980.2 Cla03g00375 375
6 31171226 31175674 - ClCG06G018190.1 Cla06g01770 1770
6 31179575 31182147 - ClCG06G018200.1 Cla06g01771 1771
10 123234 126017 + CmaCh10G000340.1 Cma10g00034 34
10 127323 133114 + CmaCh10G000350.1 Cma10g00035 35
13 6918269 6922344 - CmaCh13G008260.1 Cma13g00826 826
18 1596685 1601262 + CmaCh18G002990.1 Cma18g00299 299
2 26781721 26788265 - MELO3C026178.2.1 Cme02g02096 2096
2 26789740 26793452 - MELO3C026177.2.1 Cme02g02097 2097
12 23051938 23056013 + MELO3C002382.2.1 Cme12g01566 1566
2 25115407 25118957 - PI0023293.1 Cmetu02g0270 270
2 25113108 25114706 - PI0015988.1 Cmetu02g0435 435
10 159460 162092 + CmoCh10G000300.1 Cmo10g00030 30
10 163965 170003 + CmoCh10G000310.1 Cmo10g00031 31
18 1536998 1541439 - CmoCh18G002350.1 Cmo18g00235 235
3 4593933 4597845 - CmPI595203_03g009990.1 Cmu03g0999 999
6 29422264 29426436 - CmPI595203_06g018610.1 Cmu06g1861 1861
6 29429762 29431916 - CmPI595203_06g018620.1 Cmu06g1862 1862
13 1682016 1688851 - Conep13aG0025900.1 Cone13ag0248 248
13 1694783 1696955 - Conep13aG0026000.1 Cone13ag0249 249
19 1478009 1482274 - Conep19aG0023500.1 Cone19ag0228 228
19 1491286 1493693 - Conep19aG0023600.1 Cone19ag0229 229
9 8476261 8484995 + Cp4.1LG09g09500.1 Cpe09g00946 946
18 8201402 8212189 - Cp4.1LG18g09390.1 Cpe18g00925 925
20 1630422 1634652 + Cp4.1LG20g02910.1 Cpe20g00292 292
3 5808259 5811850 - CrPI670011_03g006910.1 Cre03g0691 691
6 34255179 34260496 - CrPI670011_06g026740.1 Cre06g2674 2674
6 34262687 34264852 - CrPI670011_06g026750.1 Cre06g2675 2675
1 152752 156335 + CsaV3_1G000230.1 Csa01g00023 23
1 157881 166502 + CsaV3_1G000240.1 Csa01g00024 24
1 6137843 6141959 - CsaV3_1G009860.1 Csa01g00986 986
2 4517223 4521322 - Lsi02G005240.1 Lsi02g00524 524
6 26917365 26924452 - Lsi06G016670.1 Lsi06g01667 1667
6 26926387 26937552 - Lsi06G016680.1 Lsi06g01668 1668
12 34700856 34708078 - Sed0008346.2 Sed12g2539 2539
12 34710017 34711777 - Sed0004769.1 Sed12g2540 2540
9 73757154 73762460 - Tan0018971.1 Tan09g2414 2414
9 73801755 73804554 - Tan0011782.2 Tan09g2420 2420
17 394285 397861 + Vvi17g46 Vvi17g46 46
17 406867 413574 + Vvi17g47 Vvi17g47 47
17 419128 419605 + Vvi17g48 Vvi17g48 48
17 423989 428203 + Vvi17g49 Vvi17g49 49
17 433720 440709 + Vvi17g50 Vvi17g50 50
17 443115 443631 + Vvi17g51 Vvi17g51 51
17 443669 454615 - Vvi17g52 Vvi17g52 52
17 455236 455699 + Vvi17g53 Vvi17g53 53
17 467821 477779 + Vvi17g54 Vvi17g54 54
17 478198 483524 + Vvi17g55 Vvi17g55 55
       

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