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
Vvi17g866 . . Bda06g00624 . Bpe12g00685 . . Bma12g01062 . . Cma10g00083 Cma11g00062 Car10g00075 Car11g00056 Sed08g0071 . Cpe04g01590 Bhi02g00588 Tan09g2319 Cmetu02g0952 . Hepe09g0089 . . Cla06g01709 Cam06g1898 Cec06g1947 Cco06g1951 Clacu06g1854 Cmu06g1795 Cre06g2610 . . Cone13ag0188 . . . . . Blo13g00155 Blo15g00244 . . Bpe07g00865 . . . . Cmo10g00085 Cmo11g00064 . . . . . Cpe18g00878 . . . . . . . . . . . . . . Lsi06g01603 Csa01g00094 Chy02g02627 Cme02g02026
Vvi17g867 . . Bda06g00625 Bda15g00531 Bpe12g00677 . . . . . Cma10g00082 Cma11g00061 Car10g00074 Car11g00055 Sed08g0070 . Cpe04g01591 Bhi02g00585 Tan09g2322 Cmetu02g0735 . . . . Cla06g01710 Cam06g1899 Cec06g1948 Cco06g1952 Clacu06g1855 Cmu06g1796 Cre06g2611 Cone2ag0941 Cone16ag0061 . . . . . . Blo13g00156 Blo15g00243 . . . . . Bma08g00074 . Cmo10g00084 Cmo11g00063 . . . . . . . . . . . . . . . . . . . . Lsi06g01604 Csa01g00093 Chy02g02628 Cme02g02027
Vvi17g868 . . . . . . . . . . . Cma11g00060 . Car11g00054 . . Cpe04g01592 Bhi02g00582 . . . . . . Cla06g01711 Cam06g1900 Cec06g1949 Cco06g1953 Clacu06g1856 Cmu06g1797 Cre06g2612 . . Cone13ag0189 . . . . . . . . . . . . . . . Cmo11g00062 . . . . . . . . . . . . . . . . . . . . Lsi06g01605 Csa01g00092 Chy02g02629 Cme02g02028
Vvi17g869 . . . . Bpe12g00678 . . . . . . Cma11g00059 Car10g00073 Car11g00053 . . Cpe04g01593 Bhi02g00579 . . . . . . Cla06g01712 . . . . . . . . Cone13ag0190 Cone19ag0183 . . . . . . . . . . . . . Cmo10g00083 Cmo11g00061 . . . . . Cpe18g00880 . . . . . . . . . . . . . . Lsi06g01606 Csa01g00091 Chy02g02630 Cme02g02029
Vvi17g870 . . . . . . . . . . Cma10g00081 . Car10g00072 . . . . Bhi02g00578 . . . Hepe09g0083 . . Cla06g01713 Cam06g1902 Cec06g1952 Cco06g1955 Clacu06g1858 Cmu06g1800 Cre06g2614 . . . . . . . . . . . . Bpe07g00866 . . . . Cmo10g00082 . . . . . . . . . . . . . . . . . . . . . Lsi06g01608 Csa01g00090 . Cme02g02030
Vvi17g871 . . . . . Bpe13g00263 . . . . . . . . . . . Bhi02g00576 Tan09g2327 Cmetu02g1365 . . . . Cla06g01714 . . Cco06g1956 . . Cre06g2615 . . . . . . . . . . . . . . . . . Cmo10g00081 . . . . . . . . . . . . . . Cla01g01398 Cam01g1460 Cec01g1499 . Clacu01g1484 Cmu01g1379 Cre01g1294 . Csa01g00089 Chy02g02631 .
Vvi17g872 . . . . Bpe12g00679 . . Bma12g01282 . . Cma10g00080 Cma11g00058 Car10g00071 Car11g00052 Sed08g0062 . . Bhi02g00575 Tan09g2328 Cmetu02g1969 . Hepe09g0082 . . . . . . . . . . Cone16ag0060 . . . . . . Blo13g00157 . . . Bpe07g01087 . . . . Cmo10g00080 Cmo11g00060 . . . . . Cpe18g00881 . . . . . . . . . . . . . . . Csa01g00088 Chy02g02632 Cme02g02031
Vvi17g873 . . Bda06g00626 . . . . Bma12g01063 . . . . . . Sed08g0061 . Cpe04g01594 Bhi02g00574 Tan09g2330 Cmetu06g0240 . Hepe09g0081 . . Cla06g01715 Cam06g1904 Cec06g1954 Cco06g1958 Clacu06g1860 Cmu06g1802 Cre06g2617 Cone2ag0942 Cone16ag0059 . . . . . . . Blo15g00241 . . Bpe07g00867 . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi06g01609 Csa01g00087 Chy02g02633 Cme02g02032
Vvi17g874 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g875 . Blo16g00242 . . . . Bma06g00236 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone19ag0184 . . . . . . Bda11g01632 . . Bpe15g00130 Bma03g01289 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 8531279 8532754 + Bda023895.1 Bda06g00624 624
6 8533154 8534442 - Bda023896.1 Bda06g00625 625
6 8538822 8541086 + Bda023897.1 Bda06g00626 626
11 50045413 50047237 - Bda008521.1 Bda11g01632 1632
15 8347495 8349761 + Bda012362.1 Bda15g00531 531
2 10907616 10910364 - XM_039023407.1 Bhi02g00574 574
2 10911278 10914433 - XM_039024113.1 Bhi02g00575 575
2 10934513 10937228 + XM_039024397.1 Bhi02g00576 576
2 10983214 10984908 + XM_039023268.1 Bhi02g00578 578
2 10985463 10987856 - XM_039023266.1 Bhi02g00579 579
2 11012887 11016182 - XM_039024221.1 Bhi02g00582 582
2 11027445 11030501 + XM_039023073.1 Bhi02g00585 585
2 11030577 11032719 - XM_039023069.1 Bhi02g00588 588
13 5210835 5212869 + BLOR05436 Blo13g00155 155
13 5238320 5240781 - BLOR05437 Blo13g00156 156
13 5268760 5271780 + BLOR05438 Blo13g00157 157
15 2527415 2529606 - BLOR06635 Blo15g00241 241
15 2543254 2543535 + BLOR06637 Blo15g00243 243
15 2543901 2545438 - BLOR06638 Blo15g00244 244
16 5606060 5607552 + BLOR07490 Blo16g00242 242
3 24086479 24087455 - Bma017770.1 Bma03g01289 1289
6 3153876 3155393 + Bma022862.1 Bma06g00236 236
8 925069 927339 + Bma027073.1 Bma08g00074 74
12 42806983 42808461 + Bma008411.1 Bma12g01062 1062
12 42811460 42816681 + Bma030530 Bma12g01063 1063
12 45808296 45810602 - Bma008646.1 Bma12g01282 1282
7 14749891 14768237 + Bpe021708.1 Bpe07g00865 865
7 14772737 14774000 - Bpe021709.1 Bpe07g00866 866
7 14774461 14776732 + Bpe021710.1 Bpe07g00867 867
7 16234319 16235150 - Bpe021927.1 Bpe07g01087 1087
12 12399926 12402190 - Bpe005936.1 Bpe12g00677 677
12 12404316 12406196 + Bpe005937.3 Bpe12g00678 678
12 12410661 12413440 + Bpe005938.2 Bpe12g00679 679
12 12443224 12445506 - Bpe005944.2 Bpe12g00685 685
13 10574481 10575569 - Bpe006386.1 Bpe13g00263 263
15 11233300 11235213 - Bpe001069.1 Bpe15g00130 130
1 28176908 28178080 - CaPI482276_01g014600.1 Cam01g1460 1460
6 29981866 29983634 + CaPI482276_06g018980.1 Cam06g1898 1898
6 29984108 29986921 - CaPI482276_06g018990.1 Cam06g1899 1899
6 29988847 29991558 + CaPI482276_06g019000.1 Cam06g1900 1900
6 30001714 30007174 - CaPI482276_06g019020.1 Cam06g1902 1902
6 30021078 30023513 + CaPI482276_06g019040.1 Cam06g1904 1904
10 319031 321717 - Carg10303-RA Car10g00071 71
10 325727 327929 + Carg10304-RA Car10g00072 72
10 327999 330050 - Carg10305-RA Car10g00073 73
10 332477 335199 + Carg10306-RA Car10g00074 74
10 335745 337358 - Carg10307-RA Car10g00075 75
11 290299 296040 - Carg20190-RA Car11g00052 52
11 300719 302632 - Carg20191-RA Car11g00053 53
11 303891 306684 - Carg20192-RA Car11g00054 54
11 308102 311279 + Carg20193-RA Car11g00055 55
11 311655 313861 - Carg20194-RA Car11g00056 56
6 29717704 29719480 + CcPI632755_06g019510.1 Cco06g1951 1951
6 29719961 29722813 - CcPI632755_06g019520.1 Cco06g1952 1952
6 29724763 29727463 + CcPI632755_06g019530.1 Cco06g1953 1953
6 29737285 29738629 - CcPI632755_06g019550.1 Cco06g1955 1955
6 29739814 29741742 - CcPI632755_06g019560.1 Cco06g1956 1956
6 29755616 29758047 + CcPI632755_06g019580.1 Cco06g1958 1958
1 29612936 29614072 - CePI673135_01g014990.1 Cec01g1499 1499
6 32789837 32791595 + CePI673135_06g019470.1 Cec06g1947 1947
6 32792086 32794902 - CePI673135_06g019480.1 Cec06g1948 1948
6 32796842 32799544 + CePI673135_06g019490.1 Cec06g1949 1949
6 32811577 32817098 - CePI673135_06g019520.1 Cec06g1952 1952
6 32830981 32833404 + CePI673135_06g019540.1 Cec06g1954 1954
2 29385409 29392088 + Chy2G048940.1 Chy02g02627 2627
2 29392512 29394853 - Chy2G048950.1 Chy02g02628 2628
2 29397253 29399943 + Chy2G048960.1 Chy02g02629 2629
2 29404259 29406247 + Chy2G048970.1 Chy02g02630 2630
2 29407143 29410643 - Chy2G048980.1 Chy02g02631 2631
2 29419565 29422046 + Chy2G048990.1 Chy02g02632 2632
2 29423404 29425844 + Chy2G049000.1 Chy02g02633 2633
1 26934159 26935298 - ClG42_01g0148400.10 Clacu01g1484 1484
6 29032706 29034474 + ClG42_06g0185400.10 Clacu06g1854 1854
6 29034948 29037761 - ClG42_06g0185500.10 Clacu06g1855 1855
6 29039687 29042398 + ClG42_06g0185600.10 Clacu06g1856 1856
6 29052542 29058002 - ClG42_06g0185800.10 Clacu06g1858 1858
6 29071938 29074378 + ClG42_06g0186000.10 Clacu06g1860 1860
1 28415235 28416862 - ClCG01G014125.1 Cla01g01398 1398
6 30653399 30661420 + ClCG06G017500.2 Cla06g01709 1709
6 30661453 30664504 - ClCG06G017520.1 Cla06g01710 1710
6 30665931 30669051 + ClCG06G017530.1 Cla06g01711 1711
6 30677277 30679190 + ClCG06G017540.1 Cla06g01712 1712
6 30680304 30681648 - ClCG06G017550.1 Cla06g01713 1713
6 30682872 30684807 - ClCG06G017555.1 Cla06g01714 1714
6 30699833 30706234 + ClCG06G017560.2 Cla06g01715 1715
10 329896 332822 - CmaCh10G000800.1 Cma10g00080 80
10 335128 338309 + CmaCh10G000810.1 Cma10g00081 81
10 342983 346462 + CmaCh10G000820.1 Cma10g00082 82
10 346447 348394 - CmaCh10G000830.1 Cma10g00083 83
11 290516 297405 - CmaCh11G000580.1 Cma11g00058 58
11 301170 303080 - CmaCh11G000590.1 Cma11g00059 59
11 304185 307165 - CmaCh11G000600.1 Cma11g00060 60
11 307695 311440 + CmaCh11G000610.1 Cma11g00061 61
11 311645 321280 - CmaCh11G000620.1 Cma11g00062 62
2 26390976 26393565 + MELO3C026246.2.1 Cme02g02026 2026
2 26392805 26396051 - MELO3C026245.2.1 Cme02g02027 2027
2 26397525 26400419 + MELO3C026244.2.1 Cme02g02028 2028
2 26403848 26406018 + MELO3C026243.2.1 Cme02g02029 2029
2 26403848 26407789 - MELO3C026242.2.1 Cme02g02030 2030
2 26418283 26421515 + MELO3C026240.2.1 Cme02g02031 2031
2 26422340 26425053 + MELO3C026239.2.1 Cme02g02032 2032
2 24691335 24693690 - PI0007678.1 Cmetu02g0735 735
2 24689133 24690890 + PI0011324.1 Cmetu02g0952 952
2 24707532 24708575 - PI0023871.1 Cmetu02g1365 1365
2 24716139 24719307 + PI0023571.1 Cmetu02g1969 1969
6 5367356 5375754 - PI0021957.1 Cmetu06g0240 240
10 361895 364398 - CmoCh10G000800.1 Cmo10g00080 80
10 366994 368226 + CmoCh10G000810.1 Cmo10g00081 81
10 368458 370156 + CmoCh10G000820.1 Cmo10g00082 82
10 371698 373749 - CmoCh10G000830.1 Cmo10g00083 83
10 376037 379063 + CmoCh10G000840.1 Cmo10g00084 84
10 378908 380841 - CmoCh10G000850.1 Cmo10g00085 85
11 279849 285947 - CmoCh11G000600.1 Cmo11g00060 60
11 290504 292417 - CmoCh11G000610.1 Cmo11g00061 61
11 293663 296613 - CmoCh11G000620.1 Cmo11g00062 62
11 298073 301367 + CmoCh11G000630.1 Cmo11g00063 63
11 301615 303744 - CmoCh11G000640.1 Cmo11g00064 64
1 27277958 27279097 - CmPI595203_01g013790.1 Cmu01g1379 1379
6 28937013 28938781 + CmPI595203_06g017950.1 Cmu06g1795 1795
6 28939255 28942065 - CmPI595203_06g017960.1 Cmu06g1796 1796
6 28943963 28946659 + CmPI595203_06g017970.1 Cmu06g1797 1797
6 28956683 28962178 - CmPI595203_06g018000.1 Cmu06g1800 1800
6 28976126 28978556 + CmPI595203_06g018020.1 Cmu06g1802 1802
2 35110671 35112956 - Conep02aG0197500.1 Cone2ag0941 941
2 35114856 35117124 + Conep02aG0197600.1 Cone2ag0942 942
13 1168381 1170461 + Conep13aG0019300.1 Cone13ag0188 188
13 1175283 1178484 + Conep13aG0019400.1 Cone13ag0189 189
13 1182897 1185142 + Conep13aG0019500.1 Cone13ag0190 190
16 311376 314107 - Conep16aG0005900.1 Cone16ag0059 59
16 316749 319037 - Conep16aG0006000.1 Cone16ag0060 60
16 321212 323332 + Conep16aG0006200.1 Cone16ag0061 61
19 1158498 1160604 + Conep19aG0018900.1 Cone19ag0183 183
19 1168187 1169692 + Conep19aG0019000.1 Cone19ag0184 184
4 12392068 12394970 + Cp4.1LG04g15880.1 Cpe04g01590 1590
4 12393908 12397735 - Cp4.1LG04g15990.1 Cpe04g01591 1591
4 12398780 12402073 + Cp4.1LG04g15910.1 Cpe04g01592 1592
4 12403043 12404833 + Cp4.1LG04g15900.1 Cpe04g01593 1593
4 12408763 12415131 + Cp4.1LG04g15930.1 Cpe04g01594 1594
18 7994528 7996143 + Cp4.1LG18g08630.1 Cpe18g00878 878
18 8002077 8004128 + Cp4.1LG18g08820.1 Cpe18g00880 880
18 8010732 8014454 + Cp4.1LG18g08830.1 Cpe18g00881 881
1 26191064 26192203 - CrPI670011_01g012940.1 Cre01g1294 1294
6 33762919 33764676 + CrPI670011_06g026100.1 Cre06g2610 2610
6 33765167 33767976 - CrPI670011_06g026110.1 Cre06g2611 2611
6 33769978 33772686 + CrPI670011_06g026120.1 Cre06g2612 2612
6 33781375 33783495 - CrPI670011_06g026140.1 Cre06g2614 2614
6 33784950 33786892 - CrPI670011_06g026150.1 Cre06g2615 2615
6 33800725 33803158 + CrPI670011_06g026170.1 Cre06g2617 2617
1 527481 530941 - CsaV3_1G000870.1 Csa01g00087 87
1 531278 534858 - CsaV3_1G000880.1 Csa01g00088 88
1 541500 542985 + CsaV3_1G000890.1 Csa01g00089 89
1 543320 548121 + CsaV3_1G000900.1 Csa01g00090 90
1 545619 547550 - CsaV3_1G000910.1 Csa01g00091 91
1 551161 554399 - CsaV3_1G000920.1 Csa01g00092 92
1 555803 559089 + CsaV3_1G000930.1 Csa01g00093 93
1 557862 561197 - CsaV3_1G000940.1 Csa01g00094 94
9 678129 681118 - Hsped.09g00810.1 Hepe09g0081 81
9 681854 684940 - Hsped.09g00820.1 Hepe09g0082 82
9 694957 696796 + Hsped.09g00830.1 Hepe09g0083 83
9 712705 714860 - Hsped.09g00890.1 Hepe09g0089 89
6 26406577 26409338 + Lsi06G016030.1 Lsi06g01603 1603
6 26408676 26411909 - Lsi06G016040.1 Lsi06g01604 1604
6 26413945 26416853 + Lsi06G016050.1 Lsi06g01605 1605
6 26428106 26430019 + Lsi06G016060.1 Lsi06g01606 1606
6 26431146 26432610 - Lsi06G016080.1 Lsi06g01608 1608
6 26449440 26462434 + Lsi06G016090.1 Lsi06g01609 1609
8 347060 349560 - Sed0016445.1 Sed08g0061 61
8 350944 354734 - Sed0021479.1 Sed08g0062 62
8 369887 373237 + Sed0025533.6 Sed08g0070 70
8 375199 377854 - Sed0023054.1 Sed08g0071 71
9 73040360 73042513 + Tan0012820.1 Tan09g2319 2319
9 73042640 73046117 - Tan0006843.3 Tan09g2322 2322
9 73067047 73068171 - Tan0003180.1 Tan09g2327 2327
9 73086034 73089106 + Tan0017320.1 Tan09g2328 2328
9 73090510 73093869 + Tan0011911.2 Tan09g2330 2330
17 11462813 11466176 + Vvi17g866 Vvi17g866 866
17 11466272 11469716 - Vvi17g867 Vvi17g867 867
17 11508740 11511764 + Vvi17g868 Vvi17g868 868
17 11534127 11536699 + Vvi17g869 Vvi17g869 869
17 11538506 11549899 - Vvi17g870 Vvi17g870 870
17 11592927 11594130 - Vvi17g871 Vvi17g871 871
17 11600215 11606424 + Vvi17g872 Vvi17g872 872
17 11606488 11620317 + Vvi17g873 Vvi17g873 873
17 11622795 11629827 - Vvi17g874 Vvi17g874 874
17 11632896 11634953 + Vvi17g875 Vvi17g875 875
       

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