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
Vvi5g1059 . Blo12g00158 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0538 Cone15ag0562 Cone18ag0903 . . . . . . Blo07g00197 . . . . . Bma06g01485 . . . Cma08g00873 . . . . . Bhi12g02115 . . . . . Lcy13g0883 . . . . . . . Lsi09g01615 . . Cme11g02213
Vvi5g1060 . . . . . . . . . . Cma06g01602 . . . Sed07g1127 . . Bhi01g01165 Tan01g0396 Cmetu06g1383 . . Mch10g1536 Lcy11g1280 . . . . . . . . . Cone18ag0902 . . . . Cme06g00857 . . . . . . . Bma06g01396 . Cmo06g01598 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1061 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe13g00750 . . . . . . . . . . . . . . . . . . Cla07g01471 Cam07g1571 Cec07g1670 Cco07g1631 Clacu07g1562 Cmu07g1530 Cre07g1906 . . . .
Vvi5g1062 . . . . Bpe04g00997 . . . Cmo08g00094 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car08g00075 . . Cpe17g01000 . . . . . . . . . . . . . . . . . .
Vvi5g1063 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1064 . . Bda03g01077 . . . Bma04g00991 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone11ag0604 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1065 Blo01g00274 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe05g01074 . . . . . . . . . . . . . . . . . . . Cla07g01472 Cam07g1572 Cec07g1671 Cco07g1632 Clacu07g1563 Cmu07g1531 Cre07g1907 . . . .
Vvi5g1066 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone18ag0899 . . . . . . Blo07g00072 . . . . . . . . . . . . . . . . . . . . . . Cla07g01473 Cam07g1573 Cec07g1672 Cco07g1633 Clacu07g1564 Cmu07g1532 Cre07g1908 . . . .
Vvi5g1067 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag1297 Cone10ag1249 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1068 . . . . . . . . . . . Cma14g01522 . Car14g01348 . . Cpe03g01281 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma06g01402 . . Cmo14g01558 . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 10813904 10814772 - Bda017121.1 Bda03g01077 1077
1 22883136 22887993 - XM_039049721.1 Bhi01g01165 1165
12 65893298 65896730 - XM_039018756.1 Bhi12g02115 2115
1 3466377 3472233 + BLOR00274 Blo01g00274 274
7 1083394 1088068 + BLOR18004 Blo07g00072 72
7 2441795 2443465 - BLOR18129 Blo07g00197 197
12 10635191 10638373 + BLOR04177 Blo12g00158 158
4 16106067 16106935 - Bma019596.1 Bma04g00991 991
6 50707483 50708718 - Bma024511.1 Bma06g01396 1396
6 50790500 50800859 + Bma024517.1 Bma06g01402 1402
6 51418306 51421402 + Bma024597.1 Bma06g01485 1485
4 6954123 6958021 - Bpe015663.3 Bpe04g00997 997
5 23253860 23255217 + Bpe018489.1 Bpe05g01074 1074
13 14033470 14034895 - Bpe010443.1 Bpe13g00750 750
7 30416675 30419037 - CaPI482276_07g015710.1 Cam07g1571 1571
7 30422771 30426646 + CaPI482276_07g015720.1 Cam07g1572 1572
7 30436882 30442971 - CaPI482276_07g015730.1 Cam07g1573 1573
8 443420 448260 - Carg04917-RA Car08g00075 75
14 11371068 11389110 - Carg24791-RA Car14g01348 1348
7 30377188 30379556 - CcPI632755_07g016310.1 Cco07g1631 1631
7 30384286 30387861 + CcPI632755_07g016320.1 Cco07g1632 1632
7 30403937 30409386 - CcPI632755_07g016330.1 Cco07g1633 1633
7 32292046 32294385 - CePI673135_07g016700.1 Cec07g1670 1670
7 32300304 32301446 + CePI673135_07g016710.1 Cec07g1671 1671
7 32311784 32317292 - CePI673135_07g016720.1 Cec07g1672 1672
7 30271275 30273639 - ClG42_07g0156200.10 Clacu07g1562 1562
7 30279822 30280959 + ClG42_07g0156300.10 Clacu07g1563 1563
7 30291098 30297193 - ClG42_07g0156400.10 Clacu07g1564 1564
7 31994158 31996522 - ClCG07G015500.1 Cla07g01471 1471
7 32000199 32003842 + ClCG07G015510.2 Cla07g01472 1472
7 32013709 32019604 - ClCG07G015520.2 Cla07g01473 1473
6 9979458 9981336 - CmaCh06G016020.1 Cma06g01602 1602
8 5399682 5403331 + CmaCh08G008730.1 Cma08g00873 873
14 11518604 11536537 - CmaCh14G015220.1 Cma14g01522 1522
6 5872341 5874195 - MELO3C006777.2.1 Cme06g00857 857
11 29369857 29373316 - MELO3C021159.2.1 Cme11g02213 2213
6 6254801 6255587 - PI0028180.1 Cmetu06g1383 1383
6 11188144 11191483 - CmoCh06G015980.1 Cmo06g01598 1598
8 485302 490344 - CmoCh08G000940.1 Cmo08g00094 94
14 12428174 12446762 - CmoCh14G015580.1 Cmo14g01558 1558
7 30523417 30525784 - CmPI595203_07g015300.1 Cmu07g1530 1530
7 30531975 30533112 + CmPI595203_07g015310.1 Cmu07g1531 1531
7 30543245 30549347 - CmPI595203_07g015320.1 Cmu07g1532 1532
3 31855461 31857916 + Conep03aG0180500.1 Cone3ag1297 1297
10 9487226 9490343 + Conep10aG0128400.1 Cone10ag1249 1249
11 3717599 3718450 - Conep11aG0062000.1 Cone11ag0604 604
14 2684562 2687941 - Conep14aG0054900.1 Cone14ag0538 538
15 2821303 2824676 - Conep15aG0057400.1 Cone15ag0562 562
18 6373434 6378033 - Conep18aG0092500.1 Cone18ag0899 899
18 6398445 6401343 - Conep18aG0092800.1 Cone18ag0902 902
18 6407345 6410464 - Conep18aG0092900.1 Cone18ag0903 903
3 10370896 10390013 - Cp4.1LG03g12320.1 Cpe03g01281 1281
17 7579685 7586247 - Cp4.1LG17g10020.1 Cpe17g01000 1000
7 34526015 34528348 - CrPI670011_07g019060.1 Cre07g1906 1906
7 34534723 34535867 + CrPI670011_07g019070.1 Cre07g1907 1907
7 34546354 34551853 - CrPI670011_07g019080.1 Cre07g1908 1908
11 36105582 36109342 + Maker00005191 Lcy11g1280 1280
13 15333608 15337293 - Maker00026353 Lcy13g0883 883
9 24351370 24355098 - Lsi09G016150.1 Lsi09g01615 1615
10 15293058 15294431 + MC10g1213 Mch10g1536 1536
7 8348158 8349182 + Sed0010718.1 Sed07g1127 1127
1 3363121 3408587 + Tan0000508.2 Tan01g0396 396
5 19047736 19052175 + Vvi5g1059 Vvi5g1059 1059
5 19068827 19070888 + Vvi5g1060 Vvi5g1060 1060
5 19076701 19078272 + Vvi5g1061 Vvi5g1061 1061
5 19079703 19088500 - Vvi5g1062 Vvi5g1062 1062
5 19108995 19111113 + Vvi5g1063 Vvi5g1063 1063
5 19111215 19112436 - Vvi5g1064 Vvi5g1064 1064
5 19191450 19193008 - Vvi5g1065 Vvi5g1065 1065
5 19249663 19262384 - Vvi5g1066 Vvi5g1066 1066
5 19290438 19292702 - Vvi5g1067 Vvi5g1067 1067
5 19303219 19374596 - Vvi5g1068 Vvi5g1068 1068
       

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