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
Vvi4g992 . . . Bda10g00138 . . . Bma15g00995 . . Cma03g00739 . Car03g00675 . . . Cpe10g00621 Bhi03g01316 . . . Hepe04g1524 . . Cla01g01917 Cam01g2004 Cec04g1661 Cco04g1722 Clacu01g2023 Cmu01g1899 Cre04g1576 . . Cone6ag1634 . Lsi01g00668 . . Cme08g00856 . Blo06g00135 . . . . . . . Cmo03g00768 . . . . . . . . . . . . . . . . . . . . . . Csa06g03249 Chy02g00639 .
Vvi4g993 Blo04g00911 . . . Bpe15g00423 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag1635 . . . Chy07g01233 . . . . . . . . . . . . . . . . . Cpe14g00520 . . . . . . . . . . . . . . . Csa04g00575 . .
Vvi4g994 . . . Bda10g00139 . . . . . . . Cma07g00480 . Car07g00423 . Cpe19g00815 . Bhi03g01318 Tan03g1994 . . Hepe04g1525 . . Cla01g01919 Cam01g2005 Cec04g1663 Cco04g1725 Clacu01g2026 Cmu01g1901 Cre04g1577 . . Cone6ag1636 Cone9ag1557 . . . Cme08g00857 . Blo06g00136 . . Bpe10g00121 . . . . . Cmo07g00479 . . . . . . . . . . . . . . . . . . . . . Csa06g03254 Chy02g00635 .
Vvi4g995 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g996 . . . . Bpe15g00322 . . . . . . . . . . . . Bhi03g00961 Tan03g1574 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed01g0296 . . . Cma20g00843 . . . . Bhi10g01993 Tan05g1292 Cmetu11g1816 . . . . . . . . . . . . . . .
Vvi4g997 . Blo16g00052 . . . Bpe13g00439 . . . . Cma03g00738 Cma07g00478 Car03g00674 Car07g00421 Sed14g1131 Cpe19g00816 Cpe10g00622 Bhi03g01322 Tan03g1998 Cmetu08g1280 . . . . . . . . . . . Cone8ag0818 Cone12ag0770 . . Lsi01g00667 . . Cme08g00859 . . Bda11g01859 . . . . Bma06g00117 . Cmo03g00767 Cmo07g00478 . . . . . . . . . . . . . . . . . . . . . Csa06g03255 Chy02g00634 .
Vvi4g998 . . . . . Bpe13g00438 . . Cmo04g00810 Cmo16g00681 . . . . . . . . . . . . . . . . . . . . . . . Cone6ag1637 . . . Chy07g01248 . . . Bda11g01858 . . . . Bma06g00116 . . . Cma16g00625 . . . . Cpe14g00534 . . . . . . . Cla07g00818 Cam07g0882 Cec07g0935 Cco07g0923 Clacu07g0857 . . Lsi07g00249 Csa04g00555 . .
Vvi4g999 Blo04g00910 Blo16g00053 . . Bpe15g00422 Bpe13g00437 . . . . . Cma07g00477 Car03g00673 Car07g00420 Sed14g1132 Cpe19g00817 Cpe10g00623 Bhi03g01324 Tan03g1999 Cmetu08g1509 . . . . Cla01g01920 . . . Clacu01g2027 Cmu01g1902 . . Cone12ag0778 Cone6ag1638 Cone9ag1558 Lsi01g00666 . . Cme08g00860 . . Bda11g01857 . . . Bma03g00985 Bma06g00115 . . Cmo07g00477 . . . . . . . . . . . . . . . . . . . . . Csa06g03256 Chy02g00633 .
Vvi4g1000 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1001 . Blo16g00054 . . . Bpe13g00436 . . . . . Cma07g00476 Car03g00672 Car07g00419 Sed14g1133 . . Bhi03g01325 Tan03g2000 Cmetu08g1336 . Hepe04g1527 . . Cla01g01921 Cam01g2007 Cec04g1666 Cco04g1727 Clacu01g2028 Cmu01g1903 Cre04g1578 . . . . . . . Cme08g00861 . . . . . . . . . Cmo03g00766 Cmo07g00476 . . . . . . . . . . . . . . . . . . . . . . Chy02g00632 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
10 3974309 3976654 - Bda006604.1 Bda10g00138 138
10 3995373 3998408 + Bda006605.1 Bda10g00139 139
11 53702338 53708242 - Bda008795.1 Bda11g01857 1857
11 53710625 53712705 - Bda008796.1 Bda11g01858 1858
11 53713713 53715447 - Bda008797.1 Bda11g01859 1859
3 18256954 18259674 - XM_039024996.1 Bhi03g00961 961
3 27052176 27054925 - XM_039027961.1 Bhi03g01316 1316
3 27116510 27120550 + XM_039027924.1 Bhi03g01318 1318
3 27123998 27126810 + XM_039025207.1 Bhi03g01322 1322
3 27155414 27161580 + XM_039027199.1 Bhi03g01324 1324
3 27161945 27162758 + XM_039027200.1 Bhi03g01325 1325
10 49877560 49880578 + XM_039044465.1 Bhi10g01993 1993
4 10683239 10689118 - BLOR13822 Blo04g00910 910
4 10698661 10700755 - BLOR13823 Blo04g00911 911
6 5447666 5449928 - BLOR16718 Blo06g00135 135
6 5482303 5486898 + BLOR16719 Blo06g00136 136
16 1905530 1909618 + BLOR07300 Blo16g00052 52
16 1913155 1918213 + BLOR07301 Blo16g00053 53
16 1919282 1919638 + BLOR07302 Blo16g00054 54
3 10546960 10551259 - Bma017329.2 Bma03g00985 985
6 1599957 1605449 - Bma022734.1 Bma06g00115 115
6 1608007 1608845 - Bma022735.1 Bma06g00116 116
6 1610767 1612500 - Bma022736.1 Bma06g00117 117
15 38614858 38617104 + Bma014278.2 Bma15g00995 995
10 2248262 2251273 + Bpe002424.2 Bpe10g00121 121
13 11928206 11931438 - Bpe006560.1 Bpe13g00436 436
13 11932668 11938508 - Bpe006561.1 Bpe13g00437 437
13 11941781 11943630 - Bpe006562.1 Bpe13g00438 438
13 11944520 11946206 - Bpe006563.1 Bpe13g00439 439
15 14762568 14764090 + Bpe001259.1 Bpe15g00322 322
15 15763796 15769546 - Bpe001358.2 Bpe15g00422 422
15 15773248 15774878 - Bpe001359.1 Bpe15g00423 423
1 33268374 33275102 - CaPI482276_01g020040.1 Cam01g2004 2004
1 33282938 33286704 + CaPI482276_01g020050.1 Cam01g2005 2005
1 33300403 33307264 + CaPI482276_01g020070.1 Cam01g2007 2007
7 21867140 21867367 + CaPI482276_07g008820.1 Cam07g0882 882
3 5987541 5988011 - Carg00632-RA Car03g00672 672
3 5988162 5994390 - Carg00633-RA Car03g00673 673
3 5996604 5999763 - Carg00634-RA Car03g00674 674
3 6002856 6005745 + Carg00635-RA Car03g00675 675
7 2135541 2135882 - Carg16056-RA Car07g00419 419
7 2136421 2142337 - Carg16055-RA Car07g00420 420
7 2144445 2146973 - Carg16054-RA Car07g00421 421
7 2149019 2152275 - Carg16052-RA Car07g00423 423
4 32322285 32323019 - CcPI632755_04g017220.1 Cco04g1722 1722
4 32337077 32340829 + CcPI632755_04g017250.1 Cco04g1725 1725
4 32342844 32361306 + CcPI632755_04g017270.1 Cco04g1727 1727
7 21289620 21289847 + CcPI632755_07g009230.1 Cco07g0923 923
4 35817269 35819329 - CePI673135_04g016610.1 Cec04g1661 1661
4 35828824 35832586 + CePI673135_04g016630.1 Cec04g1663 1663
4 35851085 35857946 + CePI673135_04g016660.1 Cec04g1666 1666
7 23132222 23137775 + CePI673135_07g009350.1 Cec07g0935 935
2 3870171 3870527 - Chy2G028990.1 Chy02g00632 632
2 3871269 3877007 - Chy2G029000.1 Chy02g00633 633
2 3881290 3883687 - Chy2G029010.1 Chy02g00634 634
2 3885700 3889008 - Chy2G029020.1 Chy02g00635 635
2 3901951 3906401 + Chy2G029060.1 Chy02g00639 639
7 17123682 17126532 + Chy7G140630.1 Chy07g01233 1233
7 17209240 17212626 + Chy7G140780.1 Chy07g01248 1248
1 32113083 32125964 - ClG42_01g0202300.10 Clacu01g2023 2023
1 32136776 32139227 + ClG42_01g0202600.10 Clacu01g2026 2026
1 32149514 32156659 + ClG42_01g0202700.10 Clacu01g2027 2027
1 32157397 32157753 + ClG42_01g0202800.10 Clacu01g2028 2028
7 21600681 21600908 + ClG42_07g0085700.10 Clacu07g0857 857
1 33882841 33887983 - ClCG01G019670.2 Cla01g01917 1917
1 33898077 33907788 + ClCG01G019690.2 Cla01g01919 1919
1 33917508 33924573 + ClCG01G019710.2 Cla01g01920 1920
1 33924007 33924363 + ClCG01G019715.1 Cla01g01921 1921
7 22762643 22762870 + ClCG07G008605.1 Cla07g00818 818
3 5877909 5881020 - CmaCh03G007380.1 Cma03g00738 738
3 5883727 5886505 + CmaCh03G007390.1 Cma03g00739 739
7 2075112 2080412 - CmaCh07G004760.1 Cma07g00476 476
7 2080968 2086833 - CmaCh07G004770.1 Cma07g00477 477
7 2088913 2091813 - CmaCh07G004780.1 Cma07g00478 478
7 2093288 2096821 - CmaCh07G004800.1 Cma07g00480 480
16 3222668 3226887 + CmaCh16G006250.1 Cma16g00625 625
20 4038993 4043313 + CmaCh20G008430.1 Cma20g00843 843
8 5639415 5641909 - MELO3C007836.2.1 Cme08g00856 856
8 5647780 5651451 + MELO3C007837.2.1 Cme08g00857 857
8 5653653 5656464 + MELO3C007838.2.1 Cme08g00859 859
8 5665035 5671063 + MELO3C007839.2.1 Cme08g00860 860
8 5671279 5672276 + MELO3C007840.2.1 Cme08g00861 861
8 21719213 21722075 + PI0028372.1 Cmetu08g1280 1280
8 21734187 21734543 + PI0009165.1 Cmetu08g1336 1336
8 21727677 21733443 + PI0000264.1 Cmetu08g1509 1509
11 27526606 27531241 - PI0021229.1 Cmetu11g1816 1816
3 6370723 6381697 - CmoCh03G007660.1 Cmo03g00766 766
3 6383818 6387311 - CmoCh03G007670.1 Cmo03g00767 767
3 6390131 6395127 + CmoCh03G007680.1 Cmo03g00768 768
4 4047277 4051296 + CmoCh04G008100.1 Cmo04g00810 810
7 2171002 2171439 - CmoCh07G004760.1 Cmo07g00476 476
7 2171990 2177872 - CmoCh07G004770.1 Cmo07g00477 477
7 2180102 2183070 - CmoCh07G004780.1 Cmo07g00478 478
7 2183312 2188247 - CmoCh07G004790.1 Cmo07g00479 479
16 3364169 3370054 + CmoCh16G006810.1 Cmo16g00681 681
1 32461583 32469788 - CmPI595203_01g018990.1 Cmu01g1899 1899
1 32485260 32487710 + CmPI595203_01g019010.1 Cmu01g1901 1901
1 32498073 32505219 + CmPI595203_01g019020.1 Cmu01g1902 1902
1 32505957 32506313 + CmPI595203_01g019030.1 Cmu01g1903 1903
6 12553552 12555434 - Conep06aG0169800.1 Cone6ag1634 1634
6 12555576 12557495 + Conep06aG0169900.1 Cone6ag1635 1635
6 12558775 12561497 + Conep06aG0170000.1 Cone6ag1636 1636
6 12561813 12564155 + Conep06aG0170100.1 Cone6ag1637 1637
6 12565717 12570492 + Conep06aG0170200.1 Cone6ag1638 1638
8 8187788 8195306 + Conep08aG0084400.1 Cone8ag0818 818
9 11281576 11286781 + Conep09aG0160500.1 Cone9ag1557 1557
9 11288162 11292748 + Conep09aG0160600.1 Cone9ag1558 1558
12 7070015 7071982 + Conep12aG0079300.1 Cone12ag0770 770
12 7124452 7128726 + Conep12aG0080100.1 Cone12ag0778 778
10 3596596 3600960 - Cp4.1LG10g00570.1 Cpe10g00621 621
10 3602473 3605832 + Cp4.1LG10g00680.1 Cpe10g00622 622
10 3607670 3614668 + Cp4.1LG10g00690.1 Cpe10g00623 623
14 3298733 3302313 + Cp4.1LG14g01990.1 Cpe14g00520 520
14 3360077 3364436 + Cp4.1LG14g01980.1 Cpe14g00534 534
19 6100226 6104027 + Cp4.1LG19g09300.1 Cpe19g00815 815
19 6105269 6108613 + Cp4.1LG19g09320.1 Cpe19g00816 816
19 6110756 6117671 + Cp4.1LG19g09260.1 Cpe19g00817 817
4 34311166 34318835 - CrPI670011_04g015760.1 Cre04g1576 1576
4 34324729 34332995 + CrPI670011_04g015770.1 Cre04g1577 1577
4 34341169 34349474 + CrPI670011_04g015780.1 Cre04g1578 1578
4 3692748 3697281 - CsaV3_4G005550.1 Csa04g00555 555
4 3779237 3782329 - CsaV3_4G005750.1 Csa04g00575 575
6 27400985 27403807 - CsaV3_6G046350.1 Csa06g03249 3249
6 27413046 27416362 + CsaV3_6G046400.1 Csa06g03254 3254
6 27418036 27420945 + CsaV3_6G046410.1 Csa06g03255 3255
6 27424959 27430718 + CsaV3_6G046420.1 Csa06g03256 3256
4 70756438 70760454 - Hsped.04g15240.1 Hepe04g1524 1524
4 70779746 70783917 + Hsped.04g15250.1 Hepe04g1525 1525
4 70814379 70814741 + Hsped.04g15270.1 Hepe04g1527 1527
1 5344701 5352060 - Lsi01G006660.1 Lsi01g00666 666
1 5360402 5370495 - Lsi01G006670.1 Lsi01g00667 667
1 5379274 5390042 + Lsi01G006680.1 Lsi01g00668 668
7 2749769 2754674 - Lsi07G002490.1 Lsi07g00249 249
1 2270477 2272290 + Sed0002809.1 Sed01g0296 296
14 20753712 20757651 + Sed0004565.4 Sed14g1131 1131
14 20767193 20773293 + Sed0010746.1 Sed14g1132 1132
14 20773887 20774228 + Sed0008243.1 Sed14g1133 1133
3 71996002 71998793 - Tan0001303.1 Tan03g1574 1574
3 74955891 74960102 + Tan0001810.3 Tan03g1994 1994
3 74962150 74971123 + Tan0018672.3 Tan03g1998 1998
3 74980031 74985859 + Tan0007857.1 Tan03g1999 1999
3 74986610 74986948 + Tan0011981.1 Tan03g2000 2000
5 15085814 15087817 + Tan0018000.1 Tan05g1292 1292
4 18542671 18546815 - Vvi4g992 Vvi4g992 992
4 18547144 18550545 + Vvi4g993 Vvi4g993 993
4 18551003 18557058 + Vvi4g994 Vvi4g994 994
4 18557137 18557335 - Vvi4g995 Vvi4g995 995
4 18558541 18561055 - Vvi4g996 Vvi4g996 996
4 18563503 18568390 + Vvi4g997 Vvi4g997 997
4 18570541 18574335 + Vvi4g998 Vvi4g998 998
4 18579202 18592042 + Vvi4g999 Vvi4g999 999
4 18592599 18593688 - Vvi4g1000 Vvi4g1000 1000
4 18596950 18597674 + Vvi4g1001 Vvi4g1001 1001
       

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