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
Vvi4g622 . . . . Bpe02g01271 . . . . Cmo12g00328 . . . Car12g00359 Sed03g1658 Cpe07g00333 . Bhi04g00073 Tan02g2784 Cmetu03g0254 . Hepe10g0203 . Lcy13g1848 . . . . . . . Cone4ag1726 . . . . . . Cme03g01558 . . . . . . . . . . . . Cma12g00376 . . . . . . . . . . . Cla08g01381 Cam08g1852 Cec08g1430 Cco08g1563 Clacu08g1547 . Cre08g1330 Lsi08g01265 . . .
Vvi4g623 . Blo12g01039 Bda01g00652 Bda03g00114 . Bpe02g00524 Bma04g00107 Bma01g02182 . . Cma01g01606 . Car09g00337 . . . Cpe06g00276 . . . . . . . Cla05g01655 Cam05g1766 Cec05g1772 Cco05g1832 Clacu05g1756 Cmu05g1641 Cre05g1771 Cone4ag1725 Cone7ag1645 . . Lsi04g01361 Csa03g04445 Chy04g00256 . . . . . . Bpe04g00100 . . Sed05g1602 Cmo01g01732 Cmo09g00390 Cma09g00557 . Car01g01296 . . Cpe02g00310 Bhi09g02432 Tan01g3787 Cmetu04g0081 . Hepe01g2126 Mch11g0664 . . . . . . . . . . . Cme07g00150
Vvi4g624 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g625 . . . . Bpe02g01272 . . . Cmo05g00340 Cmo12g00329 . Cma05g00338 . . Sed11g1127 Cpe07g00334 . Bhi04g00075 Tan02g2785 Cmetu03g0258 . Hepe10g0202 . Lcy13g1849 . . . . . . . Cone4ag1724 Cone7ag1644 . . . . . Cme03g01557 . . . . . . Bma01g01259 . . . . . Cma12g00377 . Car05g00282 Cpe11g00283 . . . . . . . . Cla08g01382 Cam08g1853 Cec08g1431 Cco08g1564 Clacu08g1548 . Cre08g1331 Lsi08g01266 . Chy03g01067 .
Vvi4g626 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g627 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g628 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g629 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g630 . . . . . . . . Cmo05g00338 . . Cma05g00336 . . . . . Bhi04g00078 Tan02g2789 . . . . Lcy13g1851 . . . . . . . . . Cone17ag0963 Cone20ag0304 . . . Cme03g01554 . . . . . . . . . . . . . . Car05g00280 Cpe11g00281 . . . . . . . . Cla08g01384 Cam08g1855 Cec08g1434 Cco08g1567 Clacu08g1551 . Cre08g1334 Lsi08g01268 . Chy03g01065 .
Vvi4g631 . . . . . . . . . Cmo12g00332 . . . . . Cpe07g00336 . Bhi04g00081 Tan02g2792 . . Hepe10g0197 . Lcy13g1866 . . . . . . . . . . . . . . Cme03g01551 . . Bda01g01359 . . . . . . . . . Cma12g00380 . . . . . . . . . . . . . . . . . . . . Chy03g01064 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 33517281 33521353 - Bda032910 Bda01g00652 652
1 49406524 49408871 + Bda003598.1 Bda01g01359 1359
3 1021779 1024108 + Bda016053.1 Bda03g00114 114
4 1951052 1962113 + XM_039028725.1 Bhi04g00073 73
4 1964514 1966217 - XM_039028729.1 Bhi04g00075 75
4 2105849 2110869 + XM_039028162.1 Bhi04g00078 78
4 2131784 2136902 - XM_039028879.1 Bhi04g00081 81
9 66347130 66351151 + XM_039043813.1 Bhi09g02432 2432
12 28238832 28243077 - BLOR05058 Blo12g01039 1039
1 16771404 16772494 + Bma001572.1 Bma01g01259 1259
1 78713791 78718235 + Bma003028.1 Bma01g02182 2182
4 839888 842250 + Bma018553.1 Bma04g00107 107
2 3410677 3414783 - Bpe008364.1 Bpe02g00524 524
2 16121001 16125816 + Bpe009127.1 Bpe02g01271 1271
2 16126093 16127207 - Bpe009128.1 Bpe02g01272 1272
4 714252 717989 + Bpe014821.3 Bpe04g00100 100
5 26427285 26440329 - CaPI482276_05g017660.1 Cam05g1766 1766
8 24579772 24586500 + CaPI482276_08g018520.1 Cam08g1852 1852
8 24589546 24590677 - CaPI482276_08g018530.1 Cam08g1853 1853
8 24616165 24621949 + CaPI482276_08g018550.1 Cam08g1855 1855
1 11667146 11670945 + Carg10741-RA Car01g01296 1296
5 1550265 1558229 - Carg09379-RA Car05g00280 280
5 1566450 1567778 + Carg09377-RA Car05g00282 282
9 1867742 1871134 - Carg02817-RA Car09g00337 337
12 2274781 2281716 + Carg03966-RA Car12g00359 359
5 27225870 27230722 - CcPI632755_05g018320.1 Cco05g1832 1832
8 27243710 27251777 + CcPI632755_08g015630.1 Cco08g1563 1563
8 27253434 27254565 - CcPI632755_08g015640.1 Cco08g1564 1564
8 27280573 27284927 + CcPI632755_08g015670.1 Cco08g1567 1567
5 29554023 29566841 - CePI673135_05g017720.1 Cec05g1772 1772
8 26100463 26108934 + CePI673135_08g014300.1 Cec08g1430 1430
8 26111922 26113050 - CePI673135_08g014310.1 Cec08g1431 1431
8 26139609 26143964 + CePI673135_08g014340.1 Cec08g1434 1434
3 14069020 14075054 - Chy3G060440.1 Chy03g01064 1064
3 14076272 14084142 - Chy3G060450.1 Chy03g01065 1065
3 14104800 14106311 + Chy3G060470.1 Chy03g01067 1067
4 2272719 2278392 - Chy4G069740.1 Chy04g00256 256
5 26642957 26650799 - ClG42_05g0175600.10 Clacu05g1756 1756
8 25320666 25327374 + ClG42_08g0154700.10 Clacu08g1547 1547
8 25330386 25331517 - ClG42_08g0154800.10 Clacu08g1548 1548
8 25358424 25362761 + ClG42_08g0155100.10 Clacu08g1551 1551
5 28135087 28146125 - ClCG05G016040.2 Cla05g01655 1655
8 26665391 26677458 + ClCG08G013850.2 Cla08g01381 1381
8 26678492 26679793 - ClCG08G013860.2 Cla08g01382 1382
8 26706565 26711523 + ClCG08G013880.1 Cla08g01384 1384
1 11067033 11070018 + CmaCh01G016060.1 Cma01g01606 1606
5 1462726 1469993 - CmaCh05G003360.1 Cma05g00336 336
5 1477963 1479772 + CmaCh05G003380.1 Cma05g00338 338
9 2534104 2537616 + CmaCh09G005570.1 Cma09g00557 557
12 1939311 1943921 + CmaCh12G003760.1 Cma12g00376 376
12 1944414 1946056 - CmaCh12G003770.1 Cma12g00377 377
12 1953960 1959829 + CmaCh12G003800.1 Cma12g00380 380
3 24604918 24613795 + MELO3C011325.2.1 Cme03g01551 1551
3 24631660 24636516 - MELO3C011320.2.1 Cme03g01554 1554
3 24667861 24669935 + MELO3C011317.2.1 Cme03g01557 1557
3 24672418 24679721 - MELO3C011316.2.1 Cme03g01558 1558
7 961248 965541 + MELO3C016939.2.1 Cme07g00150 150
3 4734199 4745014 + PI0001306.1 Cmetu03g0254 254
3 4747349 4749614 - PI0027954.1 Cmetu03g0258 258
4 31099210 31102832 + PI0028991.1 Cmetu04g0081 81
1 12942300 12946490 + CmoCh01G017320.1 Cmo01g01732 1732
5 1507671 1511573 - CmoCh05G003380.1 Cmo05g00338 338
5 1519922 1521739 + CmoCh05G003400.1 Cmo05g00340 340
9 1719359 1723794 - CmoCh09G003900.1 Cmo09g00390 390
12 2043155 2049349 + CmoCh12G003280.1 Cmo12g00328 328
12 2050764 2052174 - CmoCh12G003290.1 Cmo12g00329 329
12 2061235 2067614 + CmoCh12G003320.1 Cmo12g00332 332
5 26357131 26369624 - CmPI595203_05g016410.1 Cmu05g1641 1641
4 12765271 12766606 + Conep04aG0177800.1 Cone4ag1724 1724
4 12767565 12771628 - Conep04aG0178000.1 Cone4ag1725 1725
4 12772776 12778037 - Conep04aG0178100.1 Cone4ag1726 1726
7 11095778 11097227 + Conep07aG0169300.1 Cone7ag1644 1644
7 11098796 11102786 - Conep07aG0169400.1 Cone7ag1645 1645
17 7487368 7489359 - Conep17aG0099000.1 Cone17ag0963 963
20 1355036 1356998 - Conep20aG0031700.1 Cone20ag0304 304
2 1640017 1644169 - Cp4.1LG02g05500.1 Cpe02g00310 310
6 1521860 1525527 - Cp4.1LG06g02880.1 Cpe06g00276 276
7 2156217 2164314 + Cp4.1LG07g03350.1 Cpe07g00333 333
7 2164576 2167022 - Cp4.1LG07g03410.1 Cpe07g00334 334
7 2175457 2190707 + Cp4.1LG07g03340.1 Cpe07g00336 336
11 1524344 1528667 - Cp4.1LG11g02850.1 Cpe11g00281 281
11 1535861 1537575 + Cp4.1LG11g02780.1 Cpe11g00283 283
5 29588318 29597407 - CrPI670011_05g017710.1 Cre05g1771 1771
8 26382186 26388818 + CrPI670011_08g013300.1 Cre08g1330 1330
8 26391862 26392993 - CrPI670011_08g013310.1 Cre08g1331 1331
8 26418951 26423248 + CrPI670011_08g013340.1 Cre08g1334 1334
3 38776312 38780451 + CsaV3_3G047510.1 Csa03g04445 4445
1 85895053 85898970 + Hsped.01g21260.1 Hepe01g2126 2126
10 2000129 2013985 - Hsped.10g01970.1 Hepe10g0197 197
10 2065897 2067412 + Hsped.10g02020.1 Hepe10g0202 202
10 2069543 2076733 - Hsped.10g02030.1 Hepe10g0203 203
13 37420361 37428009 + Maker00034159 Lcy13g1848 1848
13 37431636 37433828 - Maker00034068 Lcy13g1849 1849
13 37463381 37467096 + Maker00034022 Lcy13g1851 1851
13 37547779 37554447 - Maker00034063 Lcy13g1866 1866
4 21361522 21366112 + Lsi04G013610.1 Lsi04g01361 1361
8 21065371 21073639 + Lsi08G012650.1 Lsi08g01265 1265
8 21077088 21078568 - Lsi08G012660.1 Lsi08g01266 1266
8 21106367 21111140 + Lsi08G012680.1 Lsi08g01268 1268
11 4336020 4340051 + MC11g0555 Mch11g0664 664
3 10652596 10658965 + Sed0026921.1 Sed03g1658 1658
5 29810283 29814106 - Sed0026805.2 Sed05g1602 1602
11 27063716 27065345 + Sed0010033.1 Sed11g1127 1127
1 102701702 102705638 + Tan0020942.1 Tan01g3787 3787
2 96123416 96130006 + Tan0004657.1 Tan02g2784 2784
2 96133046 96134945 - Tan0006982.1 Tan02g2785 2785
2 96180042 96184884 + Tan0021592.2 Tan02g2789 2789
2 96193127 96214714 + Tan0020650.1 Tan02g2792 2792
4 7599227 7641472 + Vvi4g622 Vvi4g622 622
4 7643368 7650501 + Vvi4g623 Vvi4g623 623
4 7650582 7651498 + Vvi4g624 Vvi4g624 624
4 7669423 7671321 - Vvi4g625 Vvi4g625 625
4 7698368 7698578 + Vvi4g626 Vvi4g626 626
4 7704571 7722920 - Vvi4g627 Vvi4g627 627
4 7748235 7749085 - Vvi4g628 Vvi4g628 628
4 7749087 7758596 + Vvi4g629 Vvi4g629 629
4 7769836 7809190 + Vvi4g630 Vvi4g630 630
4 7856757 7897638 + Vvi4g631 Vvi4g631 631
       

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