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
Vvi18g210 Blo01g01309 . Bda01g00677 . Bpe02g00628 . . Bma01g02091 . . Cma01g01364 Cma09g00767 . . . Cpe06g00604 . . . . . . . . . . . . . . . Cone4ag1434 Cone7ag1501 . . . Csa04g01774 . . . . . . . . . . . Cmo01g01417 Cmo09g00759 . . . Car09g00677 . Cpe02g00572 Bhi09g02716 . . . . . . Cla11g01560 Cam11g1625 Cec11g1651 . Clacu11g1781 Cmu11g1597 . . . Chy07g00602 Cme07g00806
Vvi18g211 Blo01g01308 . Bda01g00676 . Bpe02g00629 . . Bma01g02090 Cmo04g02507 Cmo15g00659 . . . . . . . Bhi04g01862 Tan11g1236 . . Hepe02g2211 . Lcy10g1258 Cla08g00625 Cam08g1044 Cec08g0630 Cco08g0742 Clacu08g0751 . Cre08g0560 . . Cone17ag0818 Cone20ag0423 . . . Cme03g00490 . . . . . . . . . . . . . Car04g02314 Car15g00596 Cpe01g02076 . . . . . . . . . . . . . . . Lsi08g00466 . Chy03g00750 .
Vvi18g212 Blo01g01307 . Bda01g00675 . Bpe02g00630 Bpe04g00229 . Bma01g02089 . . Cma01g01365 Cma09g00768 . . . Cpe06g00605 . . . . . . . . . . . . . . . . Cone7ag1502 . . . Csa04g01775 . . . . . . . . . . Sed14g1017 Cmo01g01418 Cmo09g00760 . . . Car09g00678 . Cpe02g00571 Bhi09g02715 Tan01g4063 Cmetu11g1957 . Hepe01g1587 Mch11g0856 . Cla11g01559 Cam11g1624 Cec11g1650 Cco11g1650 Clacu11g1780 . Cre11g2015 . . . Cme07g00807
Vvi18g213 . Blo12g01118 . Bda03g00023 . Bpe04g00014 . . . . . Cma09g00769 . . . Cpe06g00606 . . . . . . . . . . . . . . . . . Cone17ag0819 . . . . . . . . . . . . . Sed05g2401 . Cmo09g00761 . . . Car09g00679 . . Bhi09g02714 Tan01g4062 Cmetu07g0118 . Hepe01g1588 Mch11g0855 . Cla11g01557 Cam11g1621 Cec11g1648 Cco11g1649 Clacu11g1778 Cmu11g1594 Cre11g2012 . . . Cme07g00813
Vvi18g214 . . . . . . . . Cmo04g02506 Cmo15g00661 . . . . . . . Bhi04g01866 . . . Hepe02g2212 . Lcy10g1255 Cla08g00624 Cam08g1038 Cec08g0628 Cco08g0738 Clacu08g0748 . Cre08g0556 . . Cone17ag0820 Cone20ag0424 . . . . Blo17g00168 Blo18g00174 . Bda13g01467 Bpe02g01656 Bpe14g00398 Bma01g00799 Bma02g00203 . . . . . Car04g02312 Car15g00598 Cpe01g02075 . . . . . . . . . . . . . . . Lsi08g00463 . Chy03g00754 .
Vvi18g215 . . . . . . . . . . . Cma09g00770 . . . Cpe06g00607 . . . . . . . . . . . . . . . . Cone7ag1503 . . Lsi04g02416 Csa04g01777 . . . . . . . . . . . . Cmo09g00762 . . . Car09g00680 . Cpe02g00570 Bhi09g02711 . . . . Mch11g0853 . Cla11g01556 Cam11g1620 Cec11g1647 Cco11g1648 Clacu11g1777 Cmu11g1593 Cre11g2011 . . Chy07g00604 Cme07g00814
Vvi18g216 . . . . . . . . Cmo04g02505 Cmo15g00662 . . . . Sed01g3084 . . Bhi04g01869 Tan11g1240 Cmetu03g0963 . Hepe02g2213 . Lcy10g1253 Cla08g00622 Cam08g1036 Cec08g0626 Cco08g0737 Clacu08g0746 . Cre08g0554 Cone4ag1431 Cone7ag1504 . . . . . Cme03g00495 Blo17g00169 . . Bda13g01468 . Bpe14g00397 . Bma02g00204 . . . . . Car04g02311 Car15g00599 Cpe01g02074 . . . . . . . . . . . . . . . Lsi08g00462 . Chy03g00755 .
Vvi18g217 Blo01g01306 Blo12g01119 . Bda03g00022 Bpe02g00631 . Bma04g00019 Bma01g02087 . . Cma01g01368 Cma09g00772 . . . Cpe06g00608 . . . . . . . . . . . . . . . . . Cone17ag0821 Cone20ag0425 Lsi04g02415 Csa04g01778 . . Blo17g00170 . . Bda13g01469 Bpe02g01655 Bpe14g00396 . Bma02g00205 . Cmo01g01420 Cmo09g00764 . . . Car09g00682 . Cpe02g00569 Bhi09g02709 . . . . Mch11g0852 . Cla11g01554 Cam11g1619 Cec11g1646 Cco11g1647 Clacu11g1776 Cmu11g1592 Cre11g2010 . . . Cme07g00816
Vvi18g218 . . . Bda03g00021 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1430 Cone7ag1506 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g219 . . . Bda03g00020 . Bpe04g00013 . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1429 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 33914706 33916876 + Bda002711.1 Bda01g00675 675
1 33936651 33953623 + Bda002713.1 Bda01g00676 676
1 33954955 33955950 - Bda002714.1 Bda01g00677 677
3 390805 400682 + Bda015952.1 Bda03g00020 20
3 401044 403107 - Bda015953.1 Bda03g00021 21
3 404599 405676 + Bda015954.1 Bda03g00022 22
3 406114 407782 + Bda015955.1 Bda03g00023 23
13 37562427 37564494 + Bda000309.1 Bda13g01467 1467
13 37595017 37602950 + Bda000311.1 Bda13g01468 1468
13 37604178 37605318 - Bda000312.1 Bda13g01469 1469
4 46979582 47006258 - XM_039029073.1 Bhi04g01862 1862
4 47051768 47066675 + XM_039029141.1 Bhi04g01866 1866
4 47071209 47076994 + XM_039028830.1 Bhi04g01869 1869
9 72681777 72685816 + XM_039042830.1 Bhi09g02709 2709
9 72690256 72707224 - XM_039042829.1 Bhi09g02711 2711
9 72758367 72761100 + XM_039040842.1 Bhi09g02714 2714
9 72787432 72792187 + XM_039044007.1 Bhi09g02715 2715
9 72821237 72824753 - XM_039040856.1 Bhi09g02716 2716
1 50167169 50168272 + BLOR01306 Blo01g01306 1306
1 50189791 50191989 + BLOR01307 Blo01g01307 1307
1 50199694 50225332 + BLOR01308 Blo01g01308 1308
1 50226364 50227351 - BLOR01309 Blo01g01309 1309
12 28830925 28832593 - BLOR05137 Blo12g01118 1118
12 28833122 28834260 - BLOR05138 Blo12g01119 1119
17 1689093 1696670 + BLOR15989 Blo17g00168 168
17 1697414 1703436 + BLOR15990 Blo17g00169 169
17 1704995 1706106 - BLOR15991 Blo17g00170 170
18 1672219 1679231 + BLOR08662 Blo18g00174 174
1 7499868 7503937 + Bma001017.2 Bma01g00799 799
1 76576605 76577704 + Bma002905.1 Bma01g02087 2087
1 76663749 76665847 + Bma002910.1 Bma01g02089 2089
1 76962592 76981819 + Bma002913.1 Bma01g02090 2090
1 76981972 76984102 - Bma030282 Bma01g02091 2091
2 2205393 2213361 + Bma014661.1 Bma02g00203 203
2 2220765 2223674 + Bma014662.1 Bma02g00204 204
2 2227031 2228147 - Bma014663.1 Bma02g00205 205
4 252685 253795 + Bma018467.1 Bma04g00019 19
2 4082905 4083905 + Bpe008468.1 Bpe02g00628 628
2 4085197 4100738 - Bpe008469.1 Bpe02g00629 629
2 4110782 4112724 - Bpe008470.1 Bpe02g00630 630
2 4118167 4119266 - Bpe008471.1 Bpe02g00631 631
2 19264726 19265840 + Bpe025164 Bpe02g01655 1655
2 19266888 19273921 - Bpe009497.1 Bpe02g01656 1656
4 129892 139933 + Bpe014739.1 Bpe04g00013 13
4 144578 146235 + Bpe014740.1 Bpe04g00014 14
4 1552256 1553747 + Bpe014945.1 Bpe04g00229 229
14 3702655 3703786 + Bpe007049.1 Bpe14g00396 396
14 3705032 3711045 - Bpe007050.1 Bpe14g00397 397
14 3714870 3726521 - Bpe007051.1 Bpe14g00398 398
8 16622892 16626616 - CaPI482276_08g010360.1 Cam08g1036 1036
8 16636591 16652039 - CaPI482276_08g010380.1 Cam08g1038 1038
8 16684700 16709049 + CaPI482276_08g010440.1 Cam08g1044 1044
11 28965055 28966697 + CaPI482276_11g016190.1 Cam11g1619 1619
11 28968210 28984994 - CaPI482276_11g016200.1 Cam11g1620 1620
11 28988089 28993109 + CaPI482276_11g016210.1 Cam11g1621 1621
11 29002783 29007003 + CaPI482276_11g016240.1 Cam11g1624 1624
11 29008562 29009807 - CaPI482276_11g016250.1 Cam11g1625 1625
4 18603920 18610296 - Carg15745-RA Car04g02311 2311
4 18611386 18626711 - Carg15746-RA Car04g02312 2312
4 18629551 18653001 + Carg15748-RA Car04g02314 2314
9 3975577 3976560 + Carg20084-RA Car09g00677 677
9 3977159 3980243 - Carg20085-RA Car09g00678 678
9 3983932 3987592 - Carg20086-RA Car09g00679 679
9 3988909 3997292 + Carg20087-RA Car09g00680 680
9 3998403 3999914 - Carg20089-RA Car09g00682 682
15 3297937 3315694 - Carg01559-RA Car15g00596 596
15 3318531 3328864 + Carg01557-RA Car15g00598 598
15 3330149 3334994 + Carg01556-RA Car15g00599 599
8 18983722 18994523 - CcPI632755_08g007370.1 Cco08g0737 737
8 18997375 19012758 - CcPI632755_08g007380.1 Cco08g0738 738
8 19046855 19071314 + CcPI632755_08g007420.1 Cco08g0742 742
11 29333111 29334767 + CcPI632755_11g016470.1 Cco11g1647 1647
11 29336287 29349823 - CcPI632755_11g016480.1 Cco11g1648 1648
11 29356144 29363478 + CcPI632755_11g016490.1 Cco11g1649 1649
11 29363717 29374557 + CcPI632755_11g016500.1 Cco11g1650 1650
8 17813617 17817589 - CePI673135_08g006260.1 Cec08g0626 626
8 17827249 17842747 - CePI673135_08g006280.1 Cec08g0628 628
8 17873721 17898531 + CePI673135_08g006300.1 Cec08g0630 630
11 30788391 30790058 + CePI673135_11g016460.1 Cec11g1646 1646
11 30791557 30808480 - CePI673135_11g016470.1 Cec11g1647 1647
11 30811550 30817713 + CePI673135_11g016480.1 Cec11g1648 1648
11 30825720 30829942 + CePI673135_11g016500.1 Cec11g1650 1650
11 30831498 30832743 - CePI673135_11g016510.1 Cec11g1651 1651
3 10047496 10069549 - Chy3G057300.1 Chy03g00750 750
3 10103533 10124956 + Chy3G057340.1 Chy03g00754 754
3 10127774 10133392 + Chy3G057350.1 Chy03g00755 755
7 5362708 5364006 + Chy7G134320.1 Chy07g00602 602
7 5411783 5416068 + Chy7G134340.1 Chy07g00604 604
8 17364232 17368197 - ClG42_08g0074600.10 Clacu08g0746 746
8 17377858 17393320 - ClG42_08g0074800.10 Clacu08g0748 748
8 17423642 17447694 + ClG42_08g0075100.10 Clacu08g0751 751
11 28985553 28987208 + ClG42_11g0177600.10 Clacu11g1776 1776
11 28988723 29005619 - ClG42_11g0177700.10 Clacu11g1777 1777
11 29009176 29014245 + ClG42_11g0177800.10 Clacu11g1778 1778
11 29023710 29027798 + ClG42_11g0178000.10 Clacu11g1780 1780
11 29029345 29030590 - ClG42_11g0178100.10 Clacu11g1781 1781
8 18200325 18211155 - ClCG08G005990.2 Cla08g00622 622
8 18215685 18231644 - ClCG08G006020.2 Cla08g00624 624
8 18263987 18289296 + ClCG08G006030.1 Cla08g00625 625
11 29280900 29282555 + ClCG11G015950.1 Cla11g01554 1554
11 29283771 29301130 - ClCG11G015970.1 Cla11g01556 1556
11 29306646 29308930 + ClCG11G015980.1 Cla11g01557 1557
11 29321179 29325267 + ClCG11G016000.2 Cla11g01559 1559
11 29326605 29329959 - ClCG11G016010.1 Cla11g01560 1560
1 9715391 9719290 + CmaCh01G013640.1 Cma01g01364 1364
1 9719667 9724142 - CmaCh01G013650.1 Cma01g01365 1365
1 9732640 9734145 - CmaCh01G013680.1 Cma01g01368 1368
9 3702010 3703165 + CmaCh09G007670.1 Cma09g00767 767
9 3703771 3706709 - CmaCh09G007680.1 Cma09g00768 768
9 3710773 3714134 - CmaCh09G007690.1 Cma09g00769 769
9 3715225 3723336 + CmaCh09G007700.1 Cma09g00770 770
9 3724176 3725889 - CmaCh09G007720.1 Cma09g00772 772
3 7179647 7204071 - MELO3C008475.2.1 Cme03g00490 490
3 7343726 7350131 - MELO3C010654.2.1 Cme03g00495 495
7 7604871 7608343 + MELO3C010516.2.1 Cme07g00806 806
7 7608414 7612997 - MELO3C010515.2.1 Cme07g00807 807
7 7715512 7718382 - MELO3C010512.2.1 Cme07g00813 813
7 7720721 7729614 + MELO3C010511.2.1 Cme07g00814 814
7 7744179 7746313 - MELO3C010508.2.1 Cme07g00816 816
3 11929020 11934719 + PI0020960.1 Cmetu03g0963 963
7 19987767 19990631 + PI0003897.1 Cmetu07g0118 118
11 1773285 1780524 + PI0028259.1 Cmetu11g1957 1957
1 11126667 11128398 + CmoCh01G014170.1 Cmo01g01417 1417
1 11128669 11133140 - CmoCh01G014180.1 Cmo01g01418 1418
1 11140743 11142003 - CmoCh01G014200.1 Cmo01g01420 1420
4 18424226 18431778 - CmoCh04G025050.1 Cmo04g02505 2505
4 18431820 18447794 - CmoCh04G025060.1 Cmo04g02506 2506
4 18450568 18474899 + CmoCh04G025070.1 Cmo04g02507 2507
9 3840186 3841415 + CmoCh09G007590.1 Cmo09g00759 759
9 3841900 3844789 - CmoCh09G007600.1 Cmo09g00760 760
9 3849854 3853344 - CmoCh09G007610.1 Cmo09g00761 761
9 3854666 3862979 + CmoCh09G007620.1 Cmo09g00762 762
9 3864093 3865516 - CmoCh09G007640.1 Cmo09g00764 764
15 3196833 3214381 - CmoCh15G006590.1 Cmo15g00659 659
15 3217795 3229492 + CmoCh15G006610.1 Cmo15g00661 661
15 3231145 3239896 + CmoCh15G006620.1 Cmo15g00662 662
11 28238935 28240590 + CmPI595203_11g015920.1 Cmu11g1592 1592
11 28242104 28258999 - CmPI595203_11g015930.1 Cmu11g1593 1593
11 28262556 28267625 + CmPI595203_11g015940.1 Cmu11g1594 1594
11 28283229 28283976 - CmPI595203_11g015970.1 Cmu11g1597 1597
4 11378712 11387541 + Conep04aG0148100.1 Cone4ag1429 1429
4 11387687 11390160 - Conep04aG0148200.1 Cone4ag1430 1430
4 11394261 11402209 - Conep04aG0148300.1 Cone4ag1431 1431
4 11403220 11405814 - Conep04aG0148600.1 Cone4ag1434 1434
7 10488228 10490870 + Conep07aG0154400.1 Cone7ag1501 1501
7 10493014 10495335 + Conep07aG0154500.1 Cone7ag1502 1502
7 10496429 10502172 + Conep07aG0154600.1 Cone7ag1503 1503
7 10503150 10508261 + Conep07aG0154700.1 Cone7ag1504 1504
7 10512414 10515049 + Conep07aG0154900.1 Cone7ag1506 1506
17 6522515 6528912 - Conep17aG0083700.1 Cone17ag0818 818
17 6540330 6542733 - Conep17aG0083800.1 Cone17ag0819 819
17 6549269 6555483 + Conep17aG0083900.1 Cone17ag0820 820
17 6559292 6560459 - Conep17aG0084000.1 Cone17ag0821 821
20 2080667 2099749 - Conep20aG0043700.1 Cone20ag0423 423
20 2103465 2109866 + Conep20aG0043800.1 Cone20ag0424 424
20 2110746 2112211 - Conep20aG0043900.1 Cone20ag0425 425
1 17567500 17573917 - Cp4.1LG01g20710.1 Cpe01g02074 2074
1 17574696 17589887 - Cp4.1LG01g20730.1 Cpe01g02075 2075
1 17594309 17617803 + Cp4.1LG01g20810.1 Cpe01g02076 2076
2 3394347 3395607 + Cp4.1LG02g03090.1 Cpe02g00569 569
2 3396467 3399572 - Cp4.1LG02g03050.1 Cpe02g00570 570
2 3406131 3410360 + Cp4.1LG02g03120.1 Cpe02g00571 571
2 3411111 3414635 - Cp4.1LG02g02970.1 Cpe02g00572 572
6 3721406 3725158 + Cp4.1LG06g06000.1 Cpe06g00604 604
6 3725574 3728710 - Cp4.1LG06g06100.1 Cpe06g00605 605
6 3732649 3736398 - Cp4.1LG06g06090.1 Cpe06g00606 606
6 3737758 3745954 + Cp4.1LG06g06060.1 Cpe06g00607 607
6 3747174 3748601 - Cp4.1LG06g06110.1 Cpe06g00608 608
8 18275707 18280633 - CrPI670011_08g005540.1 Cre08g0554 554
8 18289359 18304906 - CrPI670011_08g005560.1 Cre08g0556 556
8 18335836 18360225 + CrPI670011_08g005600.1 Cre08g0560 560
11 31889529 31891175 + CrPI670011_11g020100.1 Cre11g2010 2010
11 31892705 31909459 - CrPI670011_11g020110.1 Cre11g2011 2011
11 31912617 31919142 + CrPI670011_11g020120.1 Cre11g2012 2012
11 31927543 31931762 + CrPI670011_11g020150.1 Cre11g2015 2015
4 17398529 17402133 + CsaV3_4G028000.1 Csa04g01774 1774
4 17399610 17406194 - CsaV3_4G028010.1 Csa04g01775 1775
4 17422137 17435718 + CsaV3_4G028030.1 Csa04g01777 1777
4 17434178 17437248 - CsaV3_4G028040.1 Csa04g01778 1778
1 81072728 81076892 - Hsped.01g15870.1 Hepe01g1587 1587
1 81082177 81085949 - Hsped.01g15880.1 Hepe01g1588 1588
2 62513956 62540640 - Hsped.02g22110.1 Hepe02g2211 2211
2 62620599 62638177 + Hsped.02g22120.1 Hepe02g2212 2212
2 62716523 62725249 + Hsped.02g22130.1 Hepe02g2213 2213
10 35195523 35201852 - Maker00008837 Lcy10g1253 1253
10 35212387 35224588 - Maker00008868 Lcy10g1255 1255
10 35254330 35271206 + Maker00008347 Lcy10g1258 1258
4 31289051 31291085 + Lsi04G024150.1 Lsi04g02415 2415
4 31289786 31307069 - Lsi04G024160.1 Lsi04g02416 2416
8 12312432 12324114 - Lsi08G004620.1 Lsi08g00462 462
8 12326225 12344514 - Lsi08G004630.1 Lsi08g00463 463
8 12382357 12383697 + Lsi08G004660.1 Lsi08g00466 466
11 5813090 5816948 + MC11g0717 Mch11g0852 852
11 5813129 5824503 - MC11g0718 Mch11g0853 853
11 5825682 5828524 + MC11g0720 Mch11g0855 855
11 5833313 5838238 + MC11g0721 Mch11g0856 856
1 41470915 41481512 - Sed0025958.1 Sed01g3084 3084
5 36399451 36402881 - Sed0021255.2 Sed05g2401 2401
14 19692247 19699515 + Sed0000564.1 Sed14g1017 1017
1 105560023 105562953 + Tan0014389.1 Tan01g4062 4062
1 105569573 105575479 + Tan0019404.1 Tan01g4063 4063
11 10485826 10522204 - Tan0020858.1 Tan11g1236 1236
11 10560362 10566481 + Tan0008958.1 Tan11g1240 1240
18 2255021 2258087 + Vvi18g210 Vvi18g210 210
18 2259997 2287308 - Vvi18g211 Vvi18g211 211
18 2291788 2294142 - Vvi18g212 Vvi18g212 212
18 2298827 2303531 - Vvi18g213 Vvi18g213 213
18 2306431 2323070 + Vvi18g214 Vvi18g214 214
18 2324024 2335526 + Vvi18g215 Vvi18g215 215
18 2336970 2345266 + Vvi18g216 Vvi18g216 216
18 2346914 2348502 - Vvi18g217 Vvi18g217 217
18 2352062 2359074 + Vvi18g218 Vvi18g218 218
18 2359939 2406066 - Vvi18g219 Vvi18g219 219
       

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