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
Vvi18g120 Blo01g01621 Blo12g00862 . . Bpe02g00321 . Bma04g00278 . Cmo05g01008 Cmo12g00607 Cma01g02006 Cma09g00064 Car01g01575 Car12g00649 Sed11g0838 Cpe06g00031 Cpe07g00583 Bhi04g01561 Tan02g1535 Cmetu03g2046 . Hepe08g1486 . Lcy13g2250 Cla08g00961 . . . . . . . . . . Lsi04g01795 Csa04g02689 . Cme03g01355 . . Bda11g00959 . . . . . Sed01g2448 Cmo01g02064 . Cma12g00668 Cma05g00990 Car05g00872 Car09g00056 Cpe11g00799 Cpe02g00043 Bhi09g02922 Tan01g5088 Cmetu07g1010 . Hepe01g2329 Mch11g0066 . Cla11g01814 Cam11g1880 Cec11g1903 Cco11g1911 Clacu11g2044 Cmu11g1849 Cre11g2254 Lsi08g00801 . Chy07g00380 Cme07g00067
Vvi18g121 . . . . . . . . Cmo05g01009 . . . . . Sed11g0843 . . Bhi04g01560 Tan02g1536 Cmetu03g1244 . Hepe08g1485 . Lcy13g2249 Cla08g00962 . . . . . . . . Cone17ag1442 Cone20ag0035 . . . Cme03g01356 . . . . . . . . . . . . Cma05g00991 Car05g00873 . Cpe11g00800 . . . . . . . . . . . . . . . Lsi08g00802 . Chy03g00631 .
Vvi18g122 . Blo12g00863 . Bda03g00310 Bpe02g00322 Bpe04g00271 Bma04g00277 Bma01g02396 Cmo05g01010 Cmo12g00606 Cma01g02004 Cma09g00065 Car01g01574 Car12g00648 . Cpe06g00032 Cpe07g00582 Bhi04g01558 . . . . . Lcy13g2248 Cla08g00963 . . . . . . Cone4ag2009 Cone7ag1925 Cone17ag1441 Cone20ag0036 Lsi04g01794 Csa04g02688 . Cme03g01357 . . Bda11g00958 . . . . . . Cmo01g02063 Cmo09g00065 Cma12g00667 Cma05g00992 Car05g00874 Car09g00057 Cpe11g00801 Cpe02g00044 Bhi09g02923 . . . . Mch11g0067 . Cla05g01573 Cam05g1682 . Cco05g1732 . . . Lsi08g00803 . Chy07g00379 Cme07g00068
Vvi18g123 . . . . . . . . . . Cma01g02003 Cma09g00066 Car01g01573 . . Cpe06g00033 . . . . . . . . . . . . . . . . . Cone17ag1440 Cone20ag0037 Lsi04g01793 Csa04g02687 . . Blo17g00712 . . . Bpe02g01752 . . . . Cmo01g02062 Cmo09g00066 . . . Car09g00058 . Cpe02g00045 Bhi09g02924 . . . . Mch11g0068 . Cla05g01574 . . . . . . . . Chy07g00378 Cme07g00069
Vvi18g124 . . . . . . . . Cmo05g01011 . . . . . . . . Bhi04g01557 . . . . . . Cla08g00964 . . . . . . . . . . . . . Cme03g01358 Blo17g00713 . Bda08g01175 . . . . . . . . . Cma05g00993 Car05g00875 . . . . . . . . . . . . . . . . . Lsi08g00804 . Chy03g00633 .
Vvi18g125 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag2007 Cone7ag1923 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g126 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g127 . . . . . . . . . . . . . . . Cpe06g00035 . . . . . . . . . . . . . . . Cone4ag2006 Cone7ag1922 . . . . . . . . . . . Bpe05g00171 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g128 . . . . . . . . . . Cma01g02002 Cma09g00069 Car01g01572 . . . . . . . . . . . . . . . . . . . . . . Lsi04g01792 Csa04g02685 . . Blo17g00714 . Bda08g01177 . . . . . Sed08g2452 Cmo01g02061 Cmo09g00069 . . . Car09g00060 . . Bhi09g02929 Tan01g5083 Cmetu05g1135 . Hepe01g2324 Mch11g0071 . Cla05g01577 Cam05g1685 Cec05g1691 Cco05g1735 Clacu05g1675 Cmu05g1567 Cre05g1684 . . Chy07g00376 Cme07g00071
Vvi18g129 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 2685859 2690019 - Bda016270.1 Bda03g00310 310
8 47074234 47075404 - Bda030124.1 Bda08g01175 1175
8 47204989 47206971 - Bda030126.1 Bda08g01177 1177
11 9354369 9358691 - Bda033068 Bda11g00958 958
11 9360413 9361318 - Bda005720.1 Bda11g00959 959
4 39315551 39318735 + XM_039030859.1 Bhi04g01557 1557
4 39365003 39370086 - XM_039030267.1 Bhi04g01558 1558
4 39418841 39421431 - XM_039028601.1 Bhi04g01560 1560
4 39454912 39455769 - XM_039029962.1 Bhi04g01561 1561
9 76323297 76324653 + XM_039042781.1 Bhi09g02922 2922
9 76350851 76355481 + XM_039041784.1 Bhi09g02923 2923
9 76355571 76358506 - XM_039041783.1 Bhi09g02924 2924
9 76403948 76411008 + XM_039042374.1 Bhi09g02929 2929
1 56111921 56112814 - BLOR01621 Blo01g01621 1621
12 26857381 26858268 + BLOR04881 Blo12g00862 862
12 26862607 26866599 + BLOR04882 Blo12g00863 863
17 20497564 20500456 - BLOR08258 Blo17g00712 712
17 20643412 20644613 - BLOR08259 Blo17g00713 713
17 20865662 20867738 - BLOR08260 Blo17g00714 714
1 81544807 81551140 - Bma003268.1 Bma01g02396 2396
4 2254521 2258627 - Bma018731.1 Bma04g00277 277
4 2260149 2261036 - Bma018732.1 Bma04g00278 278
2 2096646 2097539 + Bpe008162.1 Bpe02g00321 321
2 2100145 2104440 + Bpe008163.1 Bpe02g00322 322
2 19877596 19879546 + Bpe009582.1 Bpe02g01752 1752
4 1757517 1761673 - Bpe025593 Bpe04g00271 271
5 5627243 5629228 + Bpe017558.1 Bpe05g00171 171
5 25130878 25134947 + CaPI482276_05g016820.1 Cam05g1682 1682
5 25147594 25153034 + CaPI482276_05g016850.1 Cam05g1685 1685
11 31355879 31356787 - CaPI482276_11g018800.1 Cam11g1880 1880
1 13071467 13074962 - Carg21383-RA Car01g01572 1572
1 13075645 13078346 + Carg21382-RA Car01g01573 1573
1 13078511 13081083 - Carg21381-RA Car01g01574 1574
1 13082093 13082977 - Carg21380-RA Car01g01575 1575
5 8513018 8513848 + Carg21867-RA Car05g00872 872
5 8516870 8518837 + Carg21866-RA Car05g00873 873
5 8522541 8528199 + Carg21865-RA Car05g00874 874
5 8532128 8534212 - Carg21864-RA Car05g00875 875
9 279742 280644 + Carg08639-RA Car09g00056 56
9 282756 285669 + Carg08640-RA Car09g00057 57
9 285668 288820 - Carg08641-RA Car09g00058 58
9 292585 307665 + Carg08643-RA Car09g00060 60
12 4382585 4388477 - Carg17654-RA Car12g00648 648
12 4392140 4392985 - Carg17653-RA Car12g00649 649
5 25684984 25689033 + CcPI632755_05g017320.1 Cco05g1732 1732
5 25701367 25706877 + CcPI632755_05g017350.1 Cco05g1735 1735
11 31812735 31813643 - CcPI632755_11g019110.1 Cco11g1911 1911
5 28083572 28089037 + CePI673135_05g016910.1 Cec05g1691 1691
11 33256381 33257289 - CePI673135_11g019030.1 Cec11g1903 1903
3 8826547 8828589 + Chy3G056110.1 Chy03g00631 631
3 8844472 8847584 - Chy3G056130.1 Chy03g00633 633
7 3036561 3039300 - Chy7G132060.1 Chy07g00376 376
7 3044401 3047192 + Chy7G132080.1 Chy07g00378 378
7 3047419 3050672 - Chy7G132090.1 Chy07g00379 379
7 3055430 3056344 - Chy7G132100.1 Chy07g00380 380
5 25327764 25333227 + ClG42_05g0167500.10 Clacu05g1675 1675
11 31394919 31395827 - ClG42_11g0204400.10 Clacu11g2044 2044
5 26729244 26733314 + ClCG05G015150.1 Cla05g01573 1573
5 26733041 26736534 - ClCG05G015160.1 Cla05g01574 1574
5 26748390 26754153 + ClCG05G015210.1 Cla05g01577 1577
8 22196564 22197415 + ClCG08G009560.1 Cla08g00961 961
8 22205556 22207596 + ClCG08G009570.1 Cla08g00962 962
8 22215307 22220483 + ClCG08G009580.1 Cla08g00963 963
8 22233105 22235605 - ClCG08G009590.2 Cla08g00964 964
11 31802462 31803370 - ClCG11G018620.1 Cla11g01814 1814
1 12847571 12850663 - CmaCh01G020020.1 Cma01g02002 2002
1 12851017 12853976 + CmaCh01G020030.1 Cma01g02003 2003
1 12853824 12856568 - CmaCh01G020040.1 Cma01g02004 2004
1 12857239 12858132 - CmaCh01G020060.1 Cma01g02006 2006
5 7949306 7950136 + CmaCh05G009900.1 Cma05g00990 990
5 7951813 7954212 + CmaCh05G009910.1 Cma05g00991 991
5 7957123 7963771 + CmaCh05G009920.1 Cma05g00992 992
5 7967946 7970623 - CmaCh05G009930.1 Cma05g00993 993
9 285935 286810 + CmaCh09G000640.1 Cma09g00064 64
9 288745 291962 + CmaCh09G000650.1 Cma09g00065 65
9 291068 295315 - CmaCh09G000660.1 Cma09g00066 66
9 298453 311820 + CmaCh09G000690.1 Cma09g00069 69
12 3581671 3591595 - CmaCh12G006670.1 Cma12g00667 667
12 3592667 3593692 - CmaCh12G006680.1 Cma12g00668 668
3 23073089 23074088 + MELO3C026545.2.1 Cme03g01355 1355
3 23076228 23078936 + MELO3C026546.2.1 Cme03g01356 1356
3 23084162 23089529 + MELO3C026547.2.1 Cme03g01357 1357
3 23093865 23095895 - MELO3C026548.2.1 Cme03g01358 1358
7 428173 429269 + MELO3C017013.2.1 Cme07g00067 67
7 433822 437731 + MELO3C017012.2.1 Cme07g00068 68
7 437672 440966 - MELO3C017011.2.1 Cme07g00069 69
7 444827 447870 + MELO3C017009.2.1 Cme07g00071 71
3 6312263 6314675 - PI0005423.1 Cmetu03g1244 1244
3 6318182 6319061 - PI0023945.1 Cmetu03g2046 2046
5 10389256 10412310 + PI0025333.1 Cmetu05g1135 1135
7 24362172 24363435 - PI0023943.1 Cmetu07g1010 1010
1 14389013 14392370 - CmoCh01G020610.1 Cmo01g02061 2061
1 14392773 14395628 + CmoCh01G020620.1 Cmo01g02062 2062
1 14395757 14398815 - CmoCh01G020630.1 Cmo01g02063 2063
1 14399329 14400222 - CmoCh01G020640.1 Cmo01g02064 2064
5 8110991 8111821 + CmoCh05G010080.1 Cmo05g01008 1008
5 8113638 8115643 + CmoCh05G010090.1 Cmo05g01009 1009
5 8119199 8125426 + CmoCh05G010100.1 Cmo05g01010 1010
5 8130951 8133095 - CmoCh05G010110.1 Cmo05g01011 1011
9 296581 299813 + CmoCh09G000650.1 Cmo09g00065 65
9 299966 303212 - CmoCh09G000660.1 Cmo09g00066 66
9 306661 309130 + CmoCh09G000690.1 Cmo09g00069 69
12 3780136 3786744 - CmoCh12G006060.1 Cmo12g00606 606
12 3791049 3791894 - CmoCh12G006070.1 Cmo12g00607 607
5 25049289 25054771 + CmPI595203_05g015670.1 Cmu05g1567 1567
11 30644891 30645799 - CmPI595203_11g018490.1 Cmu11g1849 1849
4 13992231 13995012 - Conep04aG0207100.1 Cone4ag2006 2006
4 13995346 13997268 + Conep04aG0207200.1 Cone4ag2007 2007
4 14000251 14003449 - Conep04aG0207400.1 Cone4ag2009 2009
7 12291893 12293924 - Conep07aG0198000.1 Cone7ag1922 1922
7 12294882 12296745 + Conep07aG0198100.1 Cone7ag1923 1923
7 12298592 12301786 - Conep07aG0198300.1 Cone7ag1925 1925
17 9816321 9819134 + Conep17aG0148100.1 Cone17ag1440 1440
17 9818822 9822543 - Conep17aG0148200.1 Cone17ag1441 1441
17 9823982 9826250 - Conep17aG0148300.1 Cone17ag1442 1442
20 185490 187688 + Conep20aG0003500.1 Cone20ag0035 35
20 190196 193402 + Conep20aG0003600.1 Cone20ag0036 36
20 193504 196407 - Conep20aG0003700.1 Cone20ag0037 37
2 226046 226939 + Cp4.1LG02g08470.1 Cpe02g00043 43
2 227298 231117 + Cp4.1LG02g08450.1 Cpe02g00044 44
2 230234 233488 - Cp4.1LG02g08300.1 Cpe02g00045 45
6 162594 163499 + Cp4.1LG06g00190.1 Cpe06g00031 31
6 165628 168832 + Cp4.1LG06g00210.1 Cpe06g00032 32
6 168873 172257 - Cp4.1LG06g00320.1 Cpe06g00033 33
6 175728 178200 + Cp4.1LG06g00470.1 Cpe06g00035 35
7 3903789 3912442 - Cp4.1LG07g05910.1 Cpe07g00582 582
7 3916162 3917007 - Cp4.1LG07g05880.1 Cpe07g00583 583
11 6461081 6461911 + Cp4.1LG11g07980.1 Cpe11g00799 799
11 6464739 6467101 + Cp4.1LG11g08000.1 Cpe11g00800 800
11 6470632 6476451 + Cp4.1LG11g08020.1 Cpe11g00801 801
5 28243029 28248549 + CrPI670011_05g016840.1 Cre05g1684 1684
11 34319876 34320784 - CrPI670011_11g022540.1 Cre11g2254 2254
4 26054439 26057668 - CsaV3_4G037110.1 Csa04g02685 2685
4 26062157 26065432 + CsaV3_4G037130.1 Csa04g02687 2687
4 26065433 26069305 - CsaV3_4G037140.1 Csa04g02688 2688
4 26072790 26074421 - CsaV3_4G037150.1 Csa04g02689 2689
1 87826885 87830319 - Hsped.01g23240.1 Hepe01g2324 2324
1 87856154 87857305 - Hsped.01g23290.1 Hepe01g2329 2329
8 18405647 18408827 - Hsped.08g14850.1 Hepe08g1485 1485
8 18441792 18442649 - Hsped.08g14860.1 Hepe08g1486 1486
13 41427446 41432305 - Maker00025206 Lcy13g2248 2248
13 41441293 41443738 - Maker00025253 Lcy13g2249 2249
13 41447268 41448128 - Maker00025146 Lcy13g2250 2250
4 25135071 25151668 - Lsi04G017920.1 Lsi04g01792 1792
4 25156822 25165266 + Lsi04G017930.1 Lsi04g01793 1793
4 25163703 25168346 - Lsi04G017940.1 Lsi04g01794 1794
4 25176145 25177053 - Lsi04G017950.1 Lsi04g01795 1795
8 16384945 16385796 + Lsi08G008010.1 Lsi08g00801 801
8 16390258 16392509 + Lsi08G008020.1 Lsi08g00802 802
8 16400279 16405545 + Lsi08G008030.1 Lsi08g00803 803
8 16414661 16416930 - Lsi08G008040.1 Lsi08g00804 804
11 432505 433386 + MC11g0060 Mch11g0066 66
11 437944 441035 + MC11g0061 Mch11g0067 67
11 439524 444377 - MC11g0062 Mch11g0068 68
11 451915 455833 + MC11g0065 Mch11g0071 71
1 18246576 18247820 + Sed0010871.1 Sed01g2448 2448
8 37492296 37497178 + Sed0009918.1 Sed08g2452 2452
11 19332494 19333755 + Sed0005663.1 Sed11g0838 838
11 19382322 19384705 + Sed0008613.1 Sed11g0843 843
1 116309724 116318318 - Tan0005369.1 Tan01g5083 5083
1 116337490 116338846 - Tan0010129.1 Tan01g5088 5088
2 65638412 65639464 + Tan0017411.1 Tan02g1535 1535
2 65807248 65809472 + Tan0012568.1 Tan02g1536 1536
18 1181543 1182422 + Vvi18g120 Vvi18g120 120
18 1192882 1202960 + Vvi18g121 Vvi18g121 121
18 1204152 1214765 + Vvi18g122 Vvi18g122 122
18 1214781 1221660 - Vvi18g123 Vvi18g123 123
18 1226990 1228749 - Vvi18g124 Vvi18g124 124
18 1239329 1246388 - Vvi18g125 Vvi18g125 125
18 1247945 1248829 - Vvi18g126 Vvi18g126 126
18 1249391 1252271 + Vvi18g127 Vvi18g127 127
18 1252316 1257960 + Vvi18g128 Vvi18g128 128
18 1262259 1262685 + Vvi18g129 Vvi18g129 129
       

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