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
Vvi1g491 . . Bda01g01798 . . . . . . . . . . . . . Cpe01g01830 . . . . . . . . . . . . . . . . . Cone9ag0398 . . . . . . . . . Bpe02g01972 Bma01g00486 . . . . . . . . . . Bhi12g00940 . . . Hepe02g2622 . . Cla01g00638 Cam01g0666 Cec01g0658 Cco01g0684 Clacu01g0655 Cmu01g0628 Cre09g1877 Lsi09g00687 . . Cme09g01345
Vvi1g492 . Blo16g00752 . . Bpe13g01009 . . . . . . . . . . . Cpe01g01828 . . . . . . . . . . . . . . Cone13ag0731 . . . . . . . . . . . . . . Bma06g01129 . . Cmo15g01027 . Cma15g00980 . . Cpe13g00347 . Bhi12g00943 . . . Hepe02g2620 . . Cla01g00640 Cam01g0668 Cec01g0660 Cco01g0686 Clacu01g0657 Cmu01g0630 Cre09g1875 Lsi09g00689 . . .
Vvi1g493 Blo01g00771 Blo16g00753 Bda01g01796 Bda11g00185 Bpe13g01008 . . . Cmo04g01097 . Cma04g01022 Cma04g00076 Car04g00956 Car04g00072 Sed06g0157 . . Bhi07g00384 Tan04g1517 Cmetu10g0436 Lac13g1343 . . . Cla07g00543 Cam07g0582 Cec07g0645 Cco07g0610 Clacu07g0585 Cmu07g0620 Cre07g0956 . . Cone6ag0363 Cone9ag0394 Lsi04g01105 . . Cme10g01616 . . . Bda11g00185 . . Bma01g00488 Bma06g01130 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g494 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g495 . . . . . . Bma14g01933 Bma15g00028 . . . . . . . . . Bhi07g00386 . . . . . . Cla07g00539 Cam07g0580 Cec07g0641 Cco07g0607 Clacu07g0584 Cmu07g0619 Cre07g0955 . . . . Lsi04g01104 . . Cme10g01618 . . Bda07g01751 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g496 . . . . . . . . Cmo04g01098 . Cma04g01023 . Car04g00958 . Sed06g0156 . . Bhi07g00387 Tan04g1515 Cmetu10g1305 Lac13g1337 . . . . . . . . . . . . . . . . . . Blo06g01028 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01250 . .
Vvi1g497 . . . . . Bpe10g00998 . . Cmo04g01101 . Cma04g01027 . Car04g00960 . . . . Bhi07g00393 . . . . . . . . . . . . . . . Cone6ag0362 Cone9ag0393 Lsi04g01102 . . . Blo06g01029 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01254 . .
Vvi1g498 . . . . . Bpe10g00999 Bma14g01932 Bma15g00027 . . . . . . . . Cpe01g01827 . . . . . . . Cla05g02670 Cam05g2867 Cec05g2904 Cco05g2936 Clacu05g2871 Cmu05g2717 Cre05g2834 Cone13ag0728 . . . . . . . Blo06g01030 . . . . . . . . . Cmo15g01028 . Cma15g00981 . . Cpe13g00346 . Bhi12g00945 . . . . . . Cla01g00642 Cam01g0669 Cec01g0661 Cco01g0687 Clacu01g0658 Cmu01g0631 Cre09g1874 Lsi09g00690 . . .
Vvi1g499 . . . . . Bpe10g01000 . . . . . . . . . . Cpe01g01664 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car04g01889 . . . . . . . . . . . . . . . . . . . . .
Vvi1g500 . . . . . Bpe10g01001 Bma14g01927 Bma15g00026 Cmo04g01102 . Cma04g01029 Cma04g00077 Car04g00961 Car04g00073 Sed04g3001 . . Bhi07g00400 Tan04g1510 Cmetu10g0919 Lac13g1329 Hepe01g0590 . . Cla07g00538 Cam07g0579 Cec07g0638 Cco07g0604 Clacu07g0582 Cmu07g0618 Cre07g0954 . Cone19ag0733 Cone6ag0360 Cone9ag0390 Lsi04g01101 . . . Blo06g01031 . Bda07g01745 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01255 . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 54169958 54177376 + Bda004087.2 Bda01g01796 1796
1 54192571 54196748 + Bda032980 Bda01g01798 1798
7 32829690 32833783 + Bda028660.2 Bda07g01745 1745
7 32935495 32940994 - Bda028671.2 Bda07g01751 1751
11 2385915 2392663 - Bda004902.1 Bda11g00185 185
7 17248902 17267251 - XM_039036274.1 Bhi07g00384 384
7 17348384 17360804 - XM_039036080.1 Bhi07g00386 386
7 17348933 17360804 - XM_039036081.1 Bhi07g00387 387
7 17529935 17567814 + XM_039036122.1 Bhi07g00393 393
7 17827788 17834390 + XM_039036619.1 Bhi07g00400 400
12 28378068 28383233 - XM_039020284.1 Bhi12g00940 940
12 28514996 28518965 + XM_039018896.1 Bhi12g00943 943
12 28521866 28532029 - XM_039018824.1 Bhi12g00945 945
1 11029995 11039915 - BLOR00771 Blo01g00771 771
6 33607974 33618743 - BLOR17611 Blo06g01028 1028
6 33619104 33622226 + BLOR17612 Blo06g01029 1029
6 33623785 33627229 - BLOR17613 Blo06g01030 1030
6 33628442 33642696 - BLOR17614 Blo06g01031 1031
16 31135020 31138580 + BLOR21539 Blo16g00752 752
16 31151007 31161822 - BLOR21540 Blo16g00753 753
1 3974147 3978267 - Bma000662.1 Bma01g00486 486
1 3985389 4002795 - Bma000664.3 Bma01g00488 488
6 48162266 48165741 + Bma031317 Bma06g01129 1129
6 48167331 48174942 - Bma024223.1 Bma06g01130 1130
14 41119125 41121735 - Bma012719.1 Bma14g01927 1927
14 41238035 41241073 + Bma012724.1 Bma14g01932 1932
14 41254035 41278219 + Bma012726.1 Bma14g01933 1933
15 279938 284138 + Bma012995.1 Bma15g00026 26
15 285755 296799 + Bma012996.1 Bma15g00027 27
15 302134 316607 + Bma012997.1 Bma15g00028 28
2 21571477 21575620 + Bpe009795.1 Bpe02g01972 1972
10 15407620 15410910 + Bpe003304.1 Bpe10g00998 998
10 15412528 15415040 - Bpe003305.1 Bpe10g00999 999
10 15415289 15423860 - Bpe003306.1 Bpe10g01000 1000
10 15425605 15429777 - Bpe024726 Bpe10g01001 1001
13 15838937 15845395 + Bpe010690.1 Bpe13g01008 1008
13 15847453 15850897 - Bpe010691.1 Bpe13g01009 1009
1 7351148 7356637 - CaPI482276_01g006660.1 Cam01g0666 666
1 7366063 7369596 + CaPI482276_01g006680.1 Cam01g0668 668
1 7370625 7374399 - CaPI482276_01g006690.1 Cam01g0669 669
5 35662568 35665535 + CaPI482276_05g028670.1 Cam05g2867 2867
7 9349981 9360538 + CaPI482276_07g005790.1 Cam07g0579 579
7 9481818 9495779 + CaPI482276_07g005800.1 Cam07g0580 580
7 9553694 9570856 + CaPI482276_07g005820.1 Cam07g0582 582
4 374880 390072 - Carg22020-RA Car04g00072 72
4 392579 395585 - Carg22021-RA Car04g00073 73
4 5507512 5509635 - Carg00131-RA Car04g00956 956
4 5526657 5537707 - Carg00133-RA Car04g00958 958
4 5546708 5553722 + Carg00135-RA Car04g00960 960
4 5554706 5560243 - Carg00136-RA Car04g00961 961
4 10974692 10976873 + Carg25927-RA Car04g01889 1889
1 7124362 7132951 - CcPI632755_01g006840.1 Cco01g0684 684
1 7142352 7145876 + CcPI632755_01g006860.1 Cco01g0686 686
1 7146901 7150683 - CcPI632755_01g006870.1 Cco01g0687 687
5 36834322 36837356 + CcPI632755_05g029360.1 Cco05g2936 2936
7 8831754 8837488 + CcPI632755_07g006040.1 Cco07g0604 604
7 9021948 9041037 + CcPI632755_07g006070.1 Cco07g0607 607
7 9192391 9209505 + CcPI632755_07g006100.1 Cco07g0610 610
1 7180070 7185623 - CePI673135_01g006580.1 Cec01g0658 658
1 7196822 7200354 + CePI673135_01g006600.1 Cec01g0660 660
1 7201385 7205186 - CePI673135_01g006610.1 Cec01g0661 661
5 39147580 39150634 + CePI673135_05g029040.1 Cec05g2904 2904
7 9518905 9526453 + CePI673135_07g006380.1 Cec07g0638 638
7 9725926 9739526 + CePI673135_07g006410.1 Cec07g0641 641
7 9804705 9819732 + CePI673135_07g006450.1 Cec07g0645 645
1 7000457 7005931 - ClG42_01g0065500.10 Clacu01g0655 655
1 7015160 7018695 + ClG42_01g0065700.10 Clacu01g0657 657
1 7019727 7023544 - ClG42_01g0065800.10 Clacu01g0658 658
5 35890430 35893387 + ClG42_05g0287100.10 Clacu05g2871 2871
7 8273843 8279566 + ClG42_07g0058200.10 Clacu07g0582 582
7 8438397 8456084 + ClG42_07g0058400.10 Clacu07g0584 584
7 8510341 8528667 + ClG42_07g0058500.10 Clacu07g0585 585
1 7380316 7385257 - ClCG01G006540.1 Cla01g00638 638
1 7394415 7397950 + ClCG01G006560.2 Cla01g00640 640
1 7398148 7403271 - ClCG01G006570.1 Cla01g00642 642
5 37876542 37879499 + ClCG05G026670.2 Cla05g02670 2670
7 8466459 8472626 + ClCG07G005600.2 Cla07g00538 538
7 8663697 8678765 + ClCG07G005610.1 Cla07g00539 539
7 8740225 8759724 + ClCG07G005650.2 Cla07g00543 543
4 358586 373391 - CmaCh04G000760.1 Cma04g00076 76
4 375771 383595 - CmaCh04G000770.1 Cma04g00077 77
4 5296664 5312664 - CmaCh04G010220.1 Cma04g01022 1022
4 5312693 5327089 - CmaCh04G010230.1 Cma04g01023 1023
4 5335667 5338800 + CmaCh04G010270.1 Cma04g01027 1027
4 5343300 5348918 - CmaCh04G010290.1 Cma04g01029 1029
15 5537896 5540285 + CmaCh15G009800.1 Cma15g00980 980
15 5540924 5543018 - CmaCh15G009810.1 Cma15g00981 981
9 18637669 18642217 + MELO3C005273.2.1 Cme09g01345 1345
10 21437738 21457643 - MELO3C026439.2.1 Cme10g01616 1616
10 21505678 21519037 - MELO3C026441.2.1 Cme10g01618 1618
10 2226627 2249726 + PI0003069.1 Cmetu10g0436 436
10 2030401 2037504 + PI0018292.1 Cmetu10g0919 919
10 2176324 2189478 + PI0002197.1 Cmetu10g1305 1305
4 5561494 5579105 - CmoCh04G010970.1 Cmo04g01097 1097
4 5583423 5595113 - CmoCh04G010980.1 Cmo04g01098 1098
4 5603933 5611670 + CmoCh04G011010.1 Cmo04g01101 1101
4 5613066 5618712 - CmoCh04G011020.1 Cmo04g01102 1102
15 6125549 6127850 + CmoCh15G010270.1 Cmo15g01027 1027
15 6128617 6130641 - CmoCh15G010280.1 Cmo15g01028 1028
1 6970311 6975785 - CmPI595203_01g006280.1 Cmu01g0628 628
1 6984998 6988533 + CmPI595203_01g006300.1 Cmu01g0630 630
1 6988729 6993369 - CmPI595203_01g006310.1 Cmu01g0631 631
5 35628779 35631735 + CmPI595203_05g027170.1 Cmu05g2717 2717
7 8433252 8438975 + CmPI595203_07g006180.1 Cmu07g0618 618
7 8597656 8615335 + CmPI595203_07g006190.1 Cmu07g0619 619
7 8670773 8687923 + CmPI595203_07g006200.1 Cmu07g0620 620
6 1758539 1763358 - Conep06aG0036800.1 Cone6ag0360 360
6 1772232 1775973 - Conep06aG0037000.1 Cone6ag0362 362
6 1778550 1785367 + Conep06aG0037100.1 Cone6ag0363 363
9 1785606 1790122 - Conep09aG0040000.1 Cone9ag0390 390
9 1807930 1811569 - Conep09aG0040300.1 Cone9ag0393 393
9 1811695 1819163 + Conep09aG0040400.1 Cone9ag0394 394
9 1830421 1833595 - Conep09aG0040800.1 Cone9ag0398 398
13 7016575 7018678 - Conep13aG0075200.1 Cone13ag0728 728
13 7028804 7031337 + Conep13aG0075500.1 Cone13ag0731 731
19 6025835 6029531 + Conep19aG0075400.1 Cone19ag0733 733
1 10356581 10358830 + Cp4.1LG01g16590.1 Cpe01g01664 1664
1 15552484 15558591 + Cp4.1LG01g18270.1 Cpe01g01827 1827
1 15559384 15562033 - Cp4.1LG01g18330.1 Cpe01g01828 1828
1 15570668 15574438 + Cp4.1LG01g18240.1 Cpe01g01830 1830
13 3434254 3436352 + Cp4.1LG13g03460.1 Cpe13g00346 346
13 3436937 3439443 - Cp4.1LG13g03470.1 Cpe13g00347 347
5 38991537 38994578 + CrPI670011_05g028340.1 Cre05g2834 2834
7 10289246 10294977 + CrPI670011_07g009540.1 Cre07g0954 954
7 10437914 10449904 + CrPI670011_07g009550.1 Cre07g0955 955
7 10535583 10551807 + CrPI670011_07g009560.1 Cre07g0956 956
9 37331551 37335346 + CrPI670011_09g018740.1 Cre09g1874 1874
9 37336392 37339920 - CrPI670011_09g018750.1 Cre09g1875 1875
9 37349265 37354125 + CrPI670011_09g018770.1 Cre09g1877 1877
5 13241920 13260579 - CsaV3_5G015740.1 Csa05g01250 1250
5 13344597 13362784 + CsaV3_5G015780.1 Csa05g01254 1254
5 13370595 13376558 - CsaV3_5G015790.1 Csa05g01255 1255
1 66969843 66975720 - Hsped.01g05900.1 Hepe01g0590 590
2 73528778 73532470 - Hsped.02g26200.1 Hepe02g2620 2620
2 73552465 73559122 + Hsped.02g26220.1 Hepe02g2622 2622
13 12475910 12481663 + Lag0041125.1 Lac13g1329 1329
13 12562954 12586231 + Lag0041133.1 Lac13g1337 1337
13 12682022 12692919 + Lag0041139.1 Lac13g1343 1343
4 13649677 13654678 + Lsi04G011010.1 Lsi04g01101 1101
4 13671606 13719246 - Lsi04G011020.1 Lsi04g01102 1102
4 13817306 13829083 + Lsi04G011040.1 Lsi04g01104 1104
4 13871495 13895801 + Lsi04G011050.1 Lsi04g01105 1105
9 7800301 7810764 - Lsi09G006870.1 Lsi09g00687 687
9 7827653 7831967 + Lsi09G006890.1 Lsi09g00689 689
9 7832170 7837701 - Lsi09G006900.1 Lsi09g00690 690
4 41265501 41271578 + Sed0004797.1 Sed04g3001 3001
6 1077526 1093551 + Sed0010499.1 Sed06g0156 156
6 1096914 1113945 + Sed0013183.1 Sed06g0157 157
4 20654666 20661637 + Tan0008966.1 Tan04g1510 1510
4 20970053 20984696 + Tan0005373.1 Tan04g1515 1515
4 21041796 21063795 + Tan0012607.1 Tan04g1517 1517
1 5390828 5401654 - Vvi1g491 Vvi1g491 491
1 5403227 5412360 + Vvi1g492 Vvi1g492 492
1 5414341 5433963 - Vvi1g493 Vvi1g493 493
1 5434033 5434186 - Vvi1g494 Vvi1g494 494
1 5436774 5450762 - Vvi1g495 Vvi1g495 495
1 5451232 5476280 - Vvi1g496 Vvi1g496 496
1 5477592 5485134 + Vvi1g497 Vvi1g497 497
1 5486106 5493034 - Vvi1g498 Vvi1g498 498
1 5493953 5552597 - Vvi1g499 Vvi1g499 499
1 5559854 5567209 + Vvi1g500 Vvi1g500 500
       

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