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
Vvi19g684 Blo03g00503 . . . . Bpe08g01089 . . . . Cma01g01070 Cma09g01017 Car01g00945 Car09g00922 Sed04g3648 Cpe06g00825 . Bhi09g01785 Tan01g3201 Cmetu01g0128 . . . . . . . . . . . . . . Cone15ag1276 . Csa07g00852 . . . . . . . . Bma07g01243 . . Cmo01g01111 Cmo09g01020 . . . . . . . . . . . . . . . . . . . . . . Chy01g01134 Cme01g00891
Vvi19g685 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g686 . . Bda07g00415 Bda09g00440 . . Bma10g00595 . . . . Cma09g01018 . . . Cpe06g00826 Cpe02g00829 Bhi09g01787 Tan01g3202 Cmetu01g0091 . . . . . . . . . . . Cone6ag0005 . . . Lsi02g01818 Csa07g01068 . . . . . . Bpe11g00592 . . Bma14g00677 . . Cmo09g01021 . . . . . . . . . . . . . . . . . . . . . . Chy01g01136 Cme01g00888
Vvi19g687 . . . . Bpe09g00119 . . . . Cmo06g00678 . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1256 Cone15ag1278 . Csa03g00417 . . . Blo10g00872 . Bda12g00972 . . . . . . . . . . . Cpe14g00781 . Bhi11g00468 . . . . . . . . . . . . . . . Chy06g01895 .
Vvi19g688 . . . . Bpe09g00118 . . Bma13g01123 . . Cma01g01068 Cma09g01019 Car01g00944 Car09g00923 Sed04g3640 Cpe06g00827 Cpe02g00830 Bhi09g01790 Tan01g3206 Cmetu01g1047 . . Mch11g1291 . . . . . . . . Cone6ag0004 Cone9ag0007 . . . . . . . Blo10g00873 . Bda12g00973 . . . . . Cmo01g01110 Cmo09g01022 . . . . . . . . . . . . . Cla09g02087 Cam09g2174 Cec09g2240 . . . . . . Chy01g01131 Cme01g00886
Vvi19g689 Blo03g00502 . Bda07g00416 . . Bpe08g01088 . . . Cmo06g00677 . . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g00416 . . . . . . Bpe11g00593 . Bma07g01242 Bma14g00676 . . . . . . . Cpe14g00780 . Bhi11g00467 . . . . . . . . . . . . . . . Chy06g01896 .
Vvi19g690 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g691 . . . . Bpe09g00117 . . Bma13g01124 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone15ag1280 . . . . . . . Bda12g00974 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g692 . . . . . . Bma10g00596 . . Cmo06g00676 . . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g00415 . . . . . . . . . . Sed08g2915 . . . . . . . . Bhi11g00465 Tan01g1832 Cmetu06g2791 . . . . . . . . . . . Lsi05g00502 . Chy06g01897 .
Vvi19g693 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 5315017 5318066 - Bda025508.1 Bda07g00415 415
7 5320426 5323192 + Bda025509.1 Bda07g00416 416
9 5819405 5822900 - Bda031029.1 Bda09g00440 440
12 40890000 40892130 + Bda009519.1 Bda12g00972 972
12 40892909 40895492 + Bda033189 Bda12g00973 973
12 40896033 40898348 - Bda009520.2 Bda12g00974 974
9 48408431 48411723 - XM_039041897.1 Bhi09g01785 1785
9 48416967 48428382 - XM_039043662.1 Bhi09g01787 1787
9 48626772 48630037 - XM_039041968.1 Bhi09g01790 1790
11 11078102 11084434 + XM_039047548.1 Bhi11g00465 465
11 11094295 11099819 + XM_039047693.1 Bhi11g00467 467
11 11100143 11103934 - XM_039047692.1 Bhi11g00468 468
3 18692837 18700271 - BLOR11683 Blo03g00502 502
3 18701914 18704966 + BLOR11684 Blo03g00503 503
10 27491576 27494521 + BLOR02662 Blo10g00872 872
10 27494629 27497167 + BLOR02663 Blo10g00873 873
7 47365775 47368538 - Bma026494.1 Bma07g01242 1242
7 47417258 47421058 + Bma026497.1 Bma07g01243 1243
10 7285024 7287983 - Bma004302.1 Bma10g00595 595
10 7299887 7302860 - Bma004303.1 Bma10g00596 596
13 44335992 44341726 + Bma010252.1 Bma13g01123 1123
13 44342261 44344591 - Bma010253.1 Bma13g01124 1124
14 7314967 7317484 - Bma011127.1 Bma14g00676 676
14 7319802 7322870 + Bma011128.2 Bma14g00677 677
8 12982417 12985827 - Bpe023213.1 Bpe08g01088 1088
8 12987676 12991503 + Bpe023214.1 Bpe08g01089 1089
9 795239 797575 + Bpe023793.1 Bpe09g00117 117
9 798105 800865 - Bpe026202 Bpe09g00118 118
9 801662 803919 - Bpe026203 Bpe09g00119 119
11 4498455 4501504 - Bpe003957.1 Bpe11g00592 592
11 4503753 4506450 + Bpe003958.1 Bpe11g00593 593
9 36253680 36256471 - CaPI482276_09g021740.1 Cam09g2174 2174
1 9093393 9096882 + Carg22419-RA Car01g00944 944
1 9100304 9103675 + Carg22418-RA Car01g00945 945
9 5677702 5681820 - Carg24752-RA Car09g00922 922
9 5684971 5689764 - Carg24751-RA Car09g00923 923
9 39281193 39283985 - CePI673135_09g022400.1 Cec09g2240 2240
1 13062966 13065716 + Chy1G011310.1 Chy01g01131 1131
1 13137731 13143246 + Chy1G011340.1 Chy01g01134 1134
1 13171891 13173505 + Chy1G011360.1 Chy01g01136 1136
6 22801337 22803442 + Chy6G124230.1 Chy06g01895 1895
6 22804390 22808657 - Chy6G124240.1 Chy06g01896 1896
6 22819584 22829751 - Chy6G124250.1 Chy06g01897 1897
9 38412208 38415190 - ClCG09G021440.2 Cla09g02087 2087
1 7896589 7900242 + CmaCh01G010680.1 Cma01g01068 1068
1 7904883 7908332 + CmaCh01G010700.1 Cma01g01070 1070
9 5208251 5213096 - CmaCh09G010170.1 Cma09g01017 1017
9 5215970 5221847 - CmaCh09G010180.1 Cma09g01018 1018
9 5225075 5229569 - CmaCh09G010190.1 Cma09g01019 1019
1 10179209 10182305 + MELO3C024953.2.1 Cme01g00886 886
1 10227880 10233678 + MELO3C024951.2.1 Cme01g00888 888
1 10253437 10257414 + MELO3C024950.2.1 Cme01g00891 891
1 10080383 10085248 + PI0021257.1 Cmetu01g0091 91
1 13989710 13993571 - PI0019949.1 Cmetu01g0128 128
1 14031226 14034512 - PI0004328.1 Cmetu01g1047 1047
6 27088551 27097788 - PI0028138.1 Cmetu06g2791 2791
1 9214896 9218762 + CmoCh01G011100.1 Cmo01g01110 1110
1 9223270 9226876 + CmoCh01G011110.1 Cmo01g01111 1111
6 3413687 3423769 + CmoCh06G006760.1 Cmo06g00676 676
6 3428238 3432641 + CmoCh06G006770.1 Cmo06g00677 677
6 3432833 3435223 - CmoCh06G006780.1 Cmo06g00678 678
9 5436290 5440512 - CmoCh09G010200.1 Cmo09g01020 1020
9 5443733 5449280 - CmoCh09G010210.1 Cmo09g01021 1021
9 5451935 5456603 - CmoCh09G010220.1 Cmo09g01022 1022
6 39090 40480 + Conep06aG0000400.1 Cone6ag0004 4
6 41332 44537 + Conep06aG0000500.1 Cone6ag0005 5
9 48287 51913 + Conep09aG0000700.1 Cone9ag0007 7
14 10101199 10101637 - Conep14aG0128800.1 Cone14ag1256 1256
15 10029975 10034255 - Conep15aG0130500.1 Cone15ag1276 1276
15 10040779 10043882 - Conep15aG0130700.1 Cone15ag1278 1278
15 10048589 10052167 - Conep15aG0130900.1 Cone15ag1280 1280
2 5300559 5304939 - Cp4.1LG02g00420.1 Cpe02g00829 829
2 5309006 5312711 - Cp4.1LG02g00450.1 Cpe02g00830 830
6 5294023 5297074 - Cp4.1LG06g08350.1 Cpe06g00825 825
6 5301306 5307267 - Cp4.1LG06g08330.1 Cpe06g00826 826
6 5309812 5315239 - Cp4.1LG06g08200.1 Cpe06g00827 827
14 6151270 6158316 + Cp4.1LG14g07780.1 Cpe14g00780 780
14 6156393 6160416 - Cp4.1LG14g07790.1 Cpe14g00781 781
3 3512213 3523388 + CsaV3_3G004150.1 Csa03g00415 415
3 3530220 3534506 + CsaV3_3G004160.1 Csa03g00416 416
3 3535173 3538898 - CsaV3_3G004170.1 Csa03g00417 417
7 6294877 6300393 - CsaV3_7G011490.1 Csa07g00852 852
7 10241751 10247936 + CsaV3_7G021570.1 Csa07g01068 1068
2 24001811 24005029 + Lsi02G018180.1 Lsi02g01818 1818
5 6304099 6312356 + Lsi05G005020.1 Lsi05g00502 502
11 9135744 9140362 - MC11g1070 Mch11g1291 1291
4 45526558 45530927 + Sed0005604.1 Sed04g3640 3640
4 45583951 45588775 + Sed0016012.1 Sed04g3648 3648
8 40091045 40097549 - Sed0017208.2 Sed08g2915 2915
1 19578295 19586512 + Tan0020244.2 Tan01g1832 1832
1 86021181 86025609 - Tan0007209.1 Tan01g3201 3201
1 86021181 86025609 - Tan0007209.2 Tan01g3202 3202
1 86153048 86155873 - Tan0000736.1 Tan01g3206 3206
19 8786717 8790827 - Vvi19g684 Vvi19g684 684
19 8791186 8805475 + Vvi19g685 Vvi19g685 685
19 8806001 8809821 - Vvi19g686 Vvi19g686 686
19 8871321 8877907 + Vvi19g687 Vvi19g687 687
19 8878189 8883497 + Vvi19g688 Vvi19g688 688
19 8884921 8891239 - Vvi19g689 Vvi19g689 689
19 8891255 8891686 - Vvi19g690 Vvi19g690 690
19 8904731 8909949 - Vvi19g691 Vvi19g691 691
19 8915465 8922437 - Vvi19g692 Vvi19g692 692
19 8923327 8925003 + Vvi19g693 Vvi19g693 693
       

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