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
Vvi5g629 . Blo12g00362 Bda03g00847 . Bpe04g00801 . Bma04g00747 . Cmo08g01075 . . . . . . . . . . . . . . . Cla06g00641 Cam06g0686 Cec06g0688 Cco06g0695 Clacu06g0672 . Cre06g1431 . . . . . . Chy05g00346 . . . . . . . . . . . . Cma08g01102 . Car08g00976 . . Cpe17g00180 Bhi12g01653 . . Lac12g2204 Hepe03g0259 . Lcy13g0345 . . . . . . . Lsi09g01258 . . Cme05g00537
Vvi5g630 . . . . . Bpe14g01234 . . . . . Cma14g01788 Car06g01154 Car14g01608 . Cpe08g00316 Cpe03g01496 . . . . . . . . . . . . . . . Cone15ag0145 Cone7ag0302 Cone4ag0302 Lsi05g01689 . . Cme06g00531 Blo02g00618 Blo07g00248 Bda11g00616 Bda13g00083 . Bpe13g00570 Bma02g00802 Bma06g01587 . Cmo06g01350 Cmo14g01824 . . . . . . . . . . . . . Cla05g00474 Cam05g0515 Cec05g0529 Cco05g0529 Clacu05g0516 Cmu05g0490 Cre05g0556 . Csa03g01250 Chy06g00504 .
Vvi5g631 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g632 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g633 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g634 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g635 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g636 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g637 . . . . . . . . . . . . . . . . . . . . . . . . Cla06g00642 Cam06g0687 Cec06g0689 Cco06g0696 Clacu06g0673 Cmu06g0664 Cre06g1432 . . . . Lsi05g01692 . . . . . . . . . . . . . . . . . . . . Bhi12g01651 . . Lac12g2203 . . Lcy13g0346 . . . . . . . . . . .
Vvi5g638 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 7315922 7330312 - Bda016837.1 Bda03g00847 847
11 6221698 6230728 - Bda005360.1 Bda11g00616 616
13 1057155 1063467 + Bda000931.1 Bda13g00083 83
12 53316653 53322568 - XM_039020253.1 Bhi12g01651 1651
12 53325749 53344810 - XM_039019745.1 Bhi12g01653 1653
2 12595007 12615581 - BLOR10348 Blo02g00618 618
7 3047060 3061118 - BLOR18180 Blo07g00248 248
12 19780395 19786885 + BLOR04381 Blo12g00362 362
2 43218272 43224630 + Bma015536.2 Bma02g00802 802
4 8034865 8042884 - Bma019259.2 Bma04g00747 747
6 52105385 52119455 - Bma024703.2 Bma06g01587 1587
4 5259449 5264164 - Bpe015461.1 Bpe04g00801 801
13 12879792 12888561 + Bpe010273.1 Bpe13g00570 570
14 9260101 9271206 - Bpe014595.2 Bpe14g01234 1234
5 4574969 4587617 + CaPI482276_05g005150.1 Cam05g0515 515
6 9200717 9207166 + CaPI482276_06g006860.1 Cam06g0686 686
6 9209040 9212503 + CaPI482276_06g006870.1 Cam06g0687 687
6 8537449 8545221 + Carg06203-RA Car06g01154 1154
8 6479032 6484668 - Carg10946-RA Car08g00976 976
14 12987642 12996507 - Carg16579-RA Car14g01608 1608
5 4239518 4247350 + CcPI632755_05g005290.1 Cco05g0529 529
6 7777400 7783662 + CcPI632755_06g006950.1 Cco06g0695 695
6 7785848 7792446 + CcPI632755_06g006960.1 Cco06g0696 696
5 4232033 4241806 + CePI673135_05g005290.1 Cec05g0529 529
6 7794234 7798164 + CePI673135_06g006880.1 Cec06g0688 688
6 7800017 7803789 + CePI673135_06g006890.1 Cec06g0689 689
5 3564494 3569929 - Chy5G093920.1 Chy05g00346 346
6 3411340 3419059 + Chy6G110320.1 Chy06g00504 504
5 4293444 4301304 + ClG42_05g0051600.10 Clacu05g0516 516
6 7753080 7759538 + ClG42_06g0067200.10 Clacu06g0672 672
6 7761304 7764794 + ClG42_06g0067300.10 Clacu06g0673 673
5 4305590 4316036 + ClCG05G004530.2 Cla05g00474 474
6 7911884 7918491 + ClCG06G006760.2 Cla06g00641 641
6 7919865 7923343 + ClCG06G006770.2 Cla06g00642 642
8 6839396 6844441 - CmaCh08G011020.1 Cma08g01102 1102
14 12915729 12920541 - CmaCh14G017880.1 Cma14g01788 1788
5 5195463 5201890 + MELO3C026783.2.1 Cme05g00537 537
6 3337714 3346836 + MELO3C006460.2.1 Cme06g00531 531
6 9995309 10003218 + CmoCh06G013500.1 Cmo06g01350 1350
8 6923212 6928574 - CmoCh08G010750.1 Cmo08g01075 1075
14 13896277 13907140 - CmoCh14G018240.1 Cmo14g01824 1824
5 4129532 4137395 + CmPI595203_05g004900.1 Cmu05g0490 490
6 7567016 7570522 + CmPI595203_06g006640.1 Cmu06g0664 664
4 1380945 1386572 - Conep04aG0031400.1 Cone4ag0302 302
7 1306693 1312268 - Conep07aG0031000.1 Cone7ag0302 302
15 683262 689042 - Conep15aG0014800.1 Cone15ag0145 145
3 11798217 11808312 - Cp4.1LG03g09940.1 Cpe03g01496 1496
8 1995463 2003620 - Cp4.1LG08g03490.1 Cpe08g00316 316
17 1162982 1168618 + Cp4.1LG17g01730.1 Cpe17g00180 180
5 4923501 4931456 + CrPI670011_05g005560.1 Cre05g0556 556
6 8660733 8664187 + CrPI670011_06g014310.1 Cre06g1431 1431
6 8666421 8669693 + CrPI670011_06g014320.1 Cre06g1432 1432
3 9575112 9582738 + CsaV3_3G012500.1 Csa03g01250 1250
3 3396130 3402421 + Hsped.03g02590.1 Hepe03g0259 259
12 39125619 39133704 - Lag0016575.1 Lac12g2203 2203
12 39152550 39159667 - Lag0016576.1 Lac12g2204 2204
13 3860571 3873023 + Maker00023420 Lcy13g0345 345
13 3893192 3900591 + Maker00024102 Lcy13g0346 346
5 24444895 24453956 - Lsi05G016890.1 Lsi05g01689 1689
5 24471802 24477861 + Lsi05G016920.1 Lsi05g01692 1692
9 20231651 20244438 - Lsi09G012580.1 Lsi09g01258 1258
5 6849120 6865111 - Vvi5g629 Vvi5g629 629
5 6896711 6914835 + Vvi5g630 Vvi5g630 630
5 6954595 6960201 - Vvi5g631 Vvi5g631 631
5 6960754 6966891 - Vvi5g632 Vvi5g632 632
5 6967401 6967893 - Vvi5g633 Vvi5g633 633
5 6985772 6986088 - Vvi5g634 Vvi5g634 634
5 6989195 6989776 - Vvi5g635 Vvi5g635 635
5 7004076 7020364 + Vvi5g636 Vvi5g636 636
5 7020778 7024063 + Vvi5g637 Vvi5g637 637
5 7030505 7031307 + Vvi5g638 Vvi5g638 638
       

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