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
Vvi18g160 . . . . . . . . . . . Cma09g00083 . . . Cpe06g00047 . . . . . . . . . . . . . . . . . . . Lsi04g01780 . Chy04g00390 . . Blo18g00762 . Bda01g01547 Bpe02g01743 . Bma01g00715 . Sed12g1477 . Cmo09g00082 . . . Car09g00072 . Cpe02g00582 Bhi09g02717 Tan01g4064 Cmetu07g2081 . . Mch11g0857 . Cla05g01596 Cam05g1707 Cec05g1707 Cco05g1763 Clacu05g1694 Cmu05g1583 Cre05g1701 . . . .
Vvi18g161 . . . . Bpe02g00334 . . Bma01g02386 . . . Cma09g00084 . . . Cpe06g00048 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo09g00083 . . . Car09g00073 . . . . . . . . . Cla05g01597 Cam05g1708 Cec05g1708 Cco05g1765 Clacu05g1695 Cmu05g1584 Cre05g1702 . . . .
Vvi18g162 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag0842 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g163 . Blo12g00872 . Bda03g00025 . Bpe04g00261 Bma04g00262 . . . Cma01g01991 Cma09g00086 Car01g01562 . . Cpe06g00049 . . . . . . . . . . . . . . . . . . . Lsi04g01778 . Chy04g00392 . . . . . . . . . . Cmo01g02049 Cmo09g00084 . . . Car09g00075 . . . . . . . . . . . . . . . . . . . .
Vvi18g164 . Blo12g00873 . Bda03g00299 . Bpe04g00260 Bma04g00261 . . . . . Car01g01561 . . . . . . . . . . . . . . . . . . . Cone7ag1913 . . Lsi04g01777 . Chy04g00393 . . . . . . Bpe14g00404 . . . . . . . . . . . . . . . . . . Cla05g01599 Cam05g1710 Cec05g1710 Cco05g1767 Clacu05g1697 Cmu05g1586 Cre05g1705 . . . .
Vvi18g165 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g166 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone17ag1428 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g167 . . . . . . . . . . . . . . . . . . . . . . . . Cla08g01399 Cam08g1878 Cec08g1455 Cco08g1589 Clacu08g1570 . Cre08g1354 . Cone7ag1911 . . . . . Cme03g01534 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi08g01295 . Chy03g01043 .
Vvi18g168 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g169 . Blo12g00874 . Bda03g00298 . Bpe04g00259 Bma04g00260 . . . Cma01g01990 Cma09g00087 Car01g01560 . . Cpe06g00050 . . . . . . . . . . . . . . . . . Cone17ag1427 . Lsi04g02418 . Chy04g00394 . . . . . . . . . . Cmo01g02048 Cmo09g00085 . . . . . Cpe02g00056 . . . . . . . Cla05g01600 Cam05g1711 Cec05g1711 Cco05g1768 Clacu05g1698 Cmu05g1587 Cre05g1706 . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 51381130 51382215 - Bda003814.1 Bda01g01547 1547
3 445212 446682 + Bda015958.1 Bda03g00025 25
3 2634355 2636585 + Bda016256.1 Bda03g00298 298
3 2636899 2638518 + Bda016257.1 Bda03g00299 299
9 72821237 72824721 - XM_039040853.1 Bhi09g02717 2717
12 26942429 26942829 + BLOR04891 Blo12g00872 872
12 26944042 26945664 - BLOR04892 Blo12g00873 873
12 26945987 26948267 - BLOR04893 Blo12g00874 874
18 21214284 21215369 + BLOR09250 Blo18g00762 762
1 6536310 6537395 + Bma000925.1 Bma01g00715 715
1 81453907 81454821 + Bma003257.1 Bma01g02386 2386
4 2176588 2178816 + Bma018712.1 Bma04g00260 260
4 2179118 2180755 + Bma018713.1 Bma04g00261 261
4 2181673 2182036 - Bma018714.1 Bma04g00262 262
2 2174822 2175550 - Bpe008175.1 Bpe02g00334 334
2 19821567 19822649 - Bpe009574.1 Bpe02g01743 1743
4 1716806 1719049 + Bpe014970.1 Bpe04g00259 259
4 1719372 1720991 + Bpe014971.1 Bpe04g00260 260
4 1721910 1722311 - Bpe025591 Bpe04g00261 261
14 3793009 3794762 + Bpe007058.1 Bpe14g00404 404
5 25438199 25439281 + CaPI482276_05g017070.1 Cam05g1707 1707
5 25454750 25455415 - CaPI482276_05g017080.1 Cam05g1708 1708
5 25466747 25468351 - CaPI482276_05g017100.1 Cam05g1710 1710
5 25469429 25473176 - CaPI482276_05g017110.1 Cam05g1711 1711
8 24790870 24794561 - CaPI482276_08g018780.1 Cam08g1878 1878
1 13012821 13015768 + Carg17215-RA Car01g01560 1560
1 13016230 13019222 + Carg17216-RA Car01g01561 1561
1 13018356 13018766 - Carg17217-RA Car01g01562 1562
9 357324 358406 + Carg08655-RA Car09g00072 72
9 360771 361463 - Carg08656-RA Car09g00073 73
9 363647 364051 + Carg08658-RA Car09g00075 75
5 26093835 26094917 + CcPI632755_05g017630.1 Cco05g1763 1763
5 26121484 26122149 - CcPI632755_05g017650.1 Cco05g1765 1765
5 26131216 26132820 - CcPI632755_05g017670.1 Cco05g1767 1767
5 26133950 26137681 - CcPI632755_05g017680.1 Cco05g1768 1768
8 27457035 27460718 - CcPI632755_08g015890.1 Cco08g1589 1589
5 28403456 28404538 + CePI673135_05g017070.1 Cec05g1707 1707
5 28417473 28418129 - CePI673135_05g017080.1 Cec05g1708 1708
5 28426942 28428546 - CePI673135_05g017100.1 Cec05g1710 1710
5 28429655 28433409 - CePI673135_05g017110.1 Cec05g1711 1711
8 26313711 26317406 - CePI673135_08g014550.1 Cec08g1455 1455
3 13925236 13929883 + Chy3G060230.1 Chy03g01043 1043
4 3464787 3465869 + Chy4G071080.1 Chy04g00390 390
4 3480465 3480793 + Chy4G071100.1 Chy04g00392 392
4 3481791 3483395 - Chy4G071110.1 Chy04g00393 393
4 3484289 3488762 - Chy4G071120.1 Chy04g00394 394
5 25633084 25634166 + ClG42_05g0169400.10 Clacu05g1694 1694
5 25649476 25650141 - ClG42_05g0169500.10 Clacu05g1695 1695
5 25658915 25660519 - ClG42_05g0169700.10 Clacu05g1697 1697
5 25661658 25665411 - ClG42_05g0169800.10 Clacu05g1698 1698
8 25538061 25542334 - ClG42_08g0157000.10 Clacu08g1570 1570
5 27082477 27083559 + ClCG05G015400.1 Cla05g01596 1596
5 27100506 27101171 - ClCG05G015410.1 Cla05g01597 1597
5 27109950 27111554 - ClCG05G015430.1 Cla05g01599 1599
5 27112513 27116501 - ClCG05G015440.1 Cla05g01600 1600
8 26893805 26897033 - ClCG08G014040.2 Cla08g01399 1399
1 12786139 12791643 + CmaCh01G019900.1 Cma01g01990 1990
1 12790275 12792706 - CmaCh01G019910.1 Cma01g01991 1991
9 364250 365332 + CmaCh09G000830.1 Cma09g00083 83
9 367074 367754 - CmaCh09G000840.1 Cma09g00084 84
9 370111 370831 + CmaCh09G000860.1 Cma09g00086 86
9 370848 373972 - CmaCh09G000870.1 Cma09g00087 87
3 24484684 24486878 + MELO3C011342.2.1 Cme03g01534 1534
7 20002093 20003461 - PI0004346.1 Cmetu07g2081 2081
1 14327699 14330940 + CmoCh01G020480.1 Cmo01g02048 2048
1 14331056 14334185 - CmoCh01G020490.1 Cmo01g02049 2049
9 377965 379047 + CmoCh09G000820.1 Cmo09g00082 82
9 381353 382045 - CmoCh09G000830.1 Cmo09g00083 83
9 383817 384840 + CmoCh09G000840.1 Cmo09g00084 84
9 385162 388124 - CmoCh09G000850.1 Cmo09g00085 85
5 25354333 25355415 + CmPI595203_05g015830.1 Cmu05g1583 1583
5 25371045 25371710 - CmPI595203_05g015840.1 Cmu05g1584 1584
5 25380488 25382092 - CmPI595203_05g015860.1 Cmu05g1586 1586
5 25383230 25386979 - CmPI595203_05g015870.1 Cmu05g1587 1587
7 12241825 12244549 + Conep07aG0196800.1 Cone7ag1911 1911
7 12245977 12247213 + Conep07aG0197000.1 Cone7ag1913 1913
12 7595818 7606060 + Conep12aG0086700.1 Cone12ag0842 842
17 9760259 9762896 + Conep17aG0146500.1 Cone17ag1427 1427
17 9762965 9764788 - Conep17aG0146600.1 Cone17ag1428 1428
2 293174 297350 - Cp4.1LG02g08150.1 Cpe02g00056 56
2 3485937 3489845 - Cp4.1LG02g02880.1 Cpe02g00582 582
6 240259 241341 + Cp4.1LG06g00350.1 Cpe06g00047 47
6 243479 244400 - Cp4.1LG06g00510.1 Cpe06g00048 48
6 246108 247322 + Cp4.1LG06g00370.1 Cpe06g00049 49
6 247528 250708 - Cp4.1LG06g00540.1 Cpe06g00050 50
5 28530828 28531910 + CrPI670011_05g017010.1 Cre05g1701 1701
5 28550674 28551339 - CrPI670011_05g017020.1 Cre05g1702 1702
5 28558918 28560522 - CrPI670011_05g017050.1 Cre05g1705 1705
5 28561656 28565448 - CrPI670011_05g017060.1 Cre05g1706 1706
8 26594694 26598958 - CrPI670011_08g013540.1 Cre08g1354 1354
4 24980393 24981997 + Lsi04G017760.1 Lsi04g01777 1777
4 24982235 24983132 - Lsi04G017780.1 Lsi04g01778 1778
4 25001145 25002227 - Lsi04G017800.1 Lsi04g01780 1780
4 31310179 31313197 - Lsi04G024180.1 Lsi04g02418 2418
8 21331974 21335674 - Lsi08G012950.1 Lsi08g01295 1295
11 5837257 5840221 - MC11g0722 Mch11g0857 857
12 17372429 17378000 + Sed0026006.1 Sed12g1477 1477
1 105576686 105580053 - Tan0015861.1 Tan01g4064 4064
18 1565404 1566718 + Vvi18g160 Vvi18g160 160
18 1566763 1576208 - Vvi18g161 Vvi18g161 161
18 1602590 1612334 - Vvi18g162 Vvi18g162 162
18 1615550 1618288 + Vvi18g163 Vvi18g163 163
18 1619216 1620812 - Vvi18g164 Vvi18g164 164
18 1623645 1667296 - Vvi18g165 Vvi18g165 165
18 1670373 1677096 + Vvi18g166 Vvi18g166 166
18 1677717 1683663 - Vvi18g167 Vvi18g167 167
18 1684390 1687018 - Vvi18g168 Vvi18g168 168
18 1691067 1697042 - Vvi18g169 Vvi18g169 169
       

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