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
Vvi1g541 . . . . Bpe13g00996 Bpe10g01009 Bma14g01926 Bma15g00020 . . . Cma04g00037 . Car04g00043 . . Cpe01g01860 . . . . . . . . . . . . . . . . . . . Csa05g01960 . . Blo06g01036 Blo11g00909 Bda07g01735 . . . . Bma06g01142 . Cmo04g02240 Cmo15g00923 Cma04g02148 Cma15g00884 Car04g02081 Car15g00831 Cpe13g00431 . Bhi12g00972 . . . Hepe02g2596 . Lcy10g1590 Cla01g00659 Cam01g0689 Cec01g0681 Cco01g0709 Clacu01g0678 Cmu01g0652 Cre09g1855 Lsi09g00712 . . Cme09g01297
Vvi1g542 . . . . . Bpe10g01010 . Bma15g00019 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo06g01037 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g543 . . . . . Bpe10g01011 . Bma15g00018 . . . Cma04g00036 . Car04g00042 . . . . . . . . . . . . . . . . . . . Cone6ag0337 Cone9ag0371 . . . . Blo06g01038 Blo11g00962 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g544 . . . . . Bpe10g01016 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo06g01043 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g545 . . . . Bpe13g00994 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01958 . . . . . . . . . . . . Cmo15g00921 . Cma15g00883 . Car15g00830 Cpe13g00432 . Bhi12g00974 . . . . . Lcy10g1587 Cla01g00660 Cam01g0690 Cec01g0682 Cco01g0710 Clacu01g0679 Cmu01g0653 Cre09g1853 Lsi09g00714 . . .
Vvi1g546 . . . . . . . Bma15g00014 . . . . . . . . . . . . . . . . Cla05g02669 Cam05g2866 Cec05g2903 Cco05g2935 Clacu05g2870 Cmu05g2716 Cre05g2833 Cone13ag0722 Cone19ag0721 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g547 . . . . . . . . . . . . . . . . Cpe01g01861 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo04g02242 . Cma04g02149 Cma15g00882 Car04g02082 Car15g00829 Cpe13g00433 . Bhi12g00977 . . . . . Lcy10g1586 Cla01g00661 Cam01g0692 Cec01g0684 Cco01g0712 Clacu01g0680 Cmu01g0655 Cre09g1851 Lsi09g00715 Csa05g01288 . Cme09g01292
Vvi1g548 . . . . . . Bma14g01929 . . . . . . . . . . Bhi07g00101 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g549 . . . . . . . . . . . . . . . . Cpe01g01663 Bhi07g00102 . . . . . . . . . . . . . Cone13ag0721 Cone19ag0720 . . . . . . . . . . . . . . . . . . . Car04g01888 . . . . . . . . . . . . . . . . . . Csa05g00993 . .
Vvi1g550 . Blo16g01197 . . . . . . . . . . . . . . Cpe01g01863 . . . . . . . . . . . . . . . . Cone6ag0334 Cone9ag0370 . . . . . . . . . . . Bma06g00578 . Cmo04g02243 Cmo15g00917 Cma04g02150 Cma05g00061 Car04g02084 Car05g00051 Cpe13g00434 . Bhi12g00978 . . . Hepe02g2591 . Lcy10g1585 Cla01g00662 Cam01g0693 Cec01g0685 Cco01g0713 Clacu01g0681 Cmu01g0656 Cre09g1850 Lsi09g00716 Csa05g01289 . Cme09g01291
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 32499108 32499536 - Bda028643.1 Bda07g01735 1735
7 6422695 6451383 + XM_039037360.1 Bhi07g00101 101
7 6422695 6451360 + XM_039037359.1 Bhi07g00102 102
12 29533148 29535755 + XM_039019225.1 Bhi12g00972 972
12 29598308 29602134 - XM_039051024.1 Bhi12g00974 974
12 29691491 29697837 + XM_039050582.1 Bhi12g00977 977
12 29757976 29763448 + XM_039020314.1 Bhi12g00978 978
6 33679238 33680774 + BLOR17619 Blo06g01036 1036
6 33681357 33684002 - BLOR17620 Blo06g01037 1037
6 33687700 33693391 + BLOR17621 Blo06g01038 1038
6 33749321 33752956 - BLOR17626 Blo06g01043 1043
11 18704562 18705844 - BLOR03785 Blo11g00909 909
11 21377540 21397555 + BLOR03838 Blo11g00962 962
16 40478405 40484483 - BLOR21984 Blo16g01197 1197
6 31022553 31024923 - Bma023496.1 Bma06g00578 578
6 48349575 48351734 + Bma024241.1 Bma06g01142 1142
14 41071366 41073609 + Bma012716.1 Bma14g01926 1926
14 41150191 41155594 + Bma030751 Bma14g01929 1929
15 184693 187075 - Bma012983.1 Bma15g00014 14
15 243080 247794 - Bma012987.1 Bma15g00018 18
15 251255 253658 + Bma012988.1 Bma15g00019 19
15 254650 256494 - Bma012989.1 Bma15g00020 20
10 15524378 15526335 + Bpe003314.1 Bpe10g01009 1009
10 15527382 15529927 - Bpe003315.1 Bpe10g01010 1010
10 15537324 15542761 + Bpe003316.1 Bpe10g01011 1011
10 15617768 15621095 - Bpe003322.3 Bpe10g01016 1016
13 15692871 15695355 - Bpe010677.1 Bpe13g00994 994
13 15704312 15706407 - Bpe010679.1 Bpe13g00996 996
1 7675556 7677904 + CaPI482276_01g006890.1 Cam01g0689 689
1 7685278 7689804 - CaPI482276_01g006900.1 Cam01g0690 690
1 7724612 7732231 + CaPI482276_01g006920.1 Cam01g0692 692
1 7757783 7762025 + CaPI482276_01g006930.1 Cam01g0693 693
5 35647818 35652157 - CaPI482276_05g028660.1 Cam05g2866 2866
4 230738 234524 + Carg21990-RA Car04g00042 42
4 235437 237558 - Carg21991-RA Car04g00043 43
4 10968144 10970031 + Carg25928-RA Car04g01888 1888
4 16959045 16961186 + Carg25255-RA Car04g02081 2081
4 16967623 16969450 + Carg25256-RA Car04g02082 2082
4 16981193 16985641 + Carg25258-RA Car04g02084 2084
5 250508 253259 - Carg21851-RA Car05g00051 51
15 4731436 4734319 - Carg01326-RA Car15g00829 829
15 4744907 4748976 + Carg01325-RA Car15g00830 830
15 4748960 4750537 - Carg01324-RA Car15g00831 831
1 7463929 7466315 + CcPI632755_01g007090.1 Cco01g0709 709
1 7472529 7477318 - CcPI632755_01g007100.1 Cco01g0710 710
1 7518831 7523872 + CcPI632755_01g007120.1 Cco01g0712 712
1 7549226 7553847 + CcPI632755_01g007130.1 Cco01g0713 713
5 36819713 36824064 - CcPI632755_05g029350.1 Cco05g2935 2935
1 7518348 7520717 + CePI673135_01g006810.1 Cec01g0681 681
1 7527969 7532776 - CePI673135_01g006820.1 Cec01g0682 682
1 7574746 7579838 + CePI673135_01g006840.1 Cec01g0684 684
1 7612377 7616966 + CePI673135_01g006850.1 Cec01g0685 685
5 39133257 39137555 - CePI673135_05g029030.1 Cec05g2903 2903
1 7352933 7355278 + ClG42_01g0067800.10 Clacu01g0678 678
1 7361787 7366518 - ClG42_01g0067900.10 Clacu01g0679 679
1 7399766 7406801 + ClG42_01g0068000.10 Clacu01g0680 680
1 7432812 7437905 + ClG42_01g0068100.10 Clacu01g0681 681
5 35875822 35880167 - ClG42_05g0287000.10 Clacu05g2870 2870
1 7739113 7741738 + ClCG01G006760.1 Cla01g00659 659
1 7748131 7752864 - ClCG01G006770.2 Cla01g00660 660
1 7789953 7795137 + ClCG01G006780.1 Cla01g00661 661
1 7826148 7834623 + ClCG01G006790.2 Cla01g00662 662
5 37861787 37866279 - ClCG05G026660.2 Cla05g02669 2669
4 202968 207520 + CmaCh04G000360.1 Cma04g00036 36
4 207985 210428 - CmaCh04G000370.1 Cma04g00037 37
4 15020445 15023301 + CmaCh04G021480.1 Cma04g02148 2148
4 15028783 15032051 + CmaCh04G021490.1 Cma04g02149 2149
4 15041402 15045940 + CmaCh04G021500.1 Cma04g02150 2150
5 246040 249176 - CmaCh05G000610.1 Cma05g00061 61
15 4479353 4482374 - CmaCh15G008820.1 Cma15g00882 882
15 4492548 4496081 + CmaCh15G008830.1 Cma15g00883 883
15 4496385 4498274 - CmaCh15G008840.1 Cma15g00884 884
9 17837152 17842288 - MELO3C005241.2.1 Cme09g01291 1291
9 17866548 17870691 - MELO3C005242.2.1 Cme09g01292 1292
9 17959997 17962698 - MELO3C005245.2.1 Cme09g01297 1297
4 16755636 16758293 + CmoCh04G022400.1 Cmo04g02240 2240
4 16764760 16768131 + CmoCh04G022420.1 Cmo04g02242 2242
4 16780230 16784812 + CmoCh04G022430.1 Cmo04g02243 2243
15 4653052 4657559 - CmoCh15G009170.1 Cmo15g00917 917
15 4678326 4682234 + CmoCh15G009210.1 Cmo15g00921 921
15 4683231 4684923 - CmoCh15G009230.1 Cmo15g00923 923
1 7322211 7324557 + CmPI595203_01g006520.1 Cmu01g0652 652
1 7331027 7335765 - CmPI595203_01g006530.1 Cmu01g0653 653
1 7370171 7376958 + CmPI595203_01g006550.1 Cmu01g0655 655
1 7407964 7413058 + CmPI595203_01g006560.1 Cmu01g0656 656
5 35614188 35618528 - CmPI595203_05g027160.1 Cmu05g2716 2716
6 1583591 1589124 + Conep06aG0034000.1 Cone6ag0334 334
6 1597228 1599108 - Conep06aG0034300.1 Cone6ag0337 337
9 1647061 1652597 + Conep09aG0037800.1 Cone9ag0370 370
9 1652969 1661738 - Conep09aG0037900.1 Cone9ag0371 371
13 6981468 6983679 - Conep13aG0074500.1 Cone13ag0721 721
13 6983831 6986087 + Conep13aG0074600.1 Cone13ag0722 722
19 5963388 5964736 - Conep19aG0074100.1 Cone19ag0720 720
19 5965035 5966981 + Conep19aG0074200.1 Cone19ag0721 721
1 10352324 10355736 + Cp4.1LG01g16560.1 Cpe01g01663 1663
1 15929956 15932081 + Cp4.1LG01g18610.1 Cpe01g01860 1860
1 15941270 15943374 + Cp4.1LG01g18620.1 Cpe01g01861 1861
1 15955308 15959953 + Cp4.1LG01g18600.1 Cpe01g01863 1863
13 4648777 4651825 + Cp4.1LG13g06580.1 Cpe13g00431 431
13 4648777 4654741 - Cp4.1LG13g06530.1 Cpe13g00432 432
13 4666398 4669256 + Cp4.1LG13g06490.1 Cpe13g00433 433
13 4675925 4682634 + Cp4.1LG13g06480.1 Cpe13g00434 434
5 38977335 38981680 - CrPI670011_05g028330.1 Cre05g2833 2833
9 36924769 36928995 - CrPI670011_09g018500.1 Cre09g1850 1850
9 36953431 36960993 - CrPI670011_09g018510.1 Cre09g1851 1851
9 36995005 36999872 + CrPI670011_09g018530.1 Cre09g1853 1853
9 37007080 37009430 - CrPI670011_09g018550.1 Cre09g1855 1855
5 9266676 9276320 - CsaV3_5G012990.1 Csa05g00993 993
5 13669911 13674160 + CsaV3_5G017110.1 Csa05g01288 1288
5 13695645 13699528 + CsaV3_5G017120.1 Csa05g01289 1289
5 22950743 22955052 + CsaV3_5G027770.1 Csa05g01958 1958
5 22967887 22971060 - CsaV3_5G027790.1 Csa05g01960 1960
2 72992837 72998343 - Hsped.02g25910.1 Hepe02g2591 2591
2 73108950 73111516 - Hsped.02g25960.1 Hepe02g2596 2596
10 40219213 40224761 - Maker00039807 Lcy10g1585 1585
10 40242471 40248179 - Maker00039574 Lcy10g1586 1586
10 40269853 40274890 + Maker00039620 Lcy10g1587 1587
10 40293615 40296116 - Maker00039737 Lcy10g1590 1590
9 8138699 8141600 + Lsi09G007120.1 Lsi09g00712 712
9 8150841 8153419 - Lsi09G007140.1 Lsi09g00714 714
9 8186455 8194357 + Lsi09G007150.1 Lsi09g00715 715
9 8222946 8228092 + Lsi09G007160.1 Lsi09g00716 716
1 6044216 6047143 + Vvi1g541 Vvi1g541 541
1 6048755 6061508 - Vvi1g542 Vvi1g542 542
1 6068409 6076242 + Vvi1g543 Vvi1g543 543
1 6076527 6083280 + Vvi1g544 Vvi1g544 544
1 6083421 6086124 - Vvi1g545 Vvi1g545 545
1 6088272 6096479 - Vvi1g546 Vvi1g546 546
1 6107793 6110562 + Vvi1g547 Vvi1g547 547
1 6115016 6118768 + Vvi1g548 Vvi1g548 548
1 6118790 6121849 + Vvi1g549 Vvi1g549 549
1 6129833 6135868 + Vvi1g550 Vvi1g550 550
       

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