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
Vvi5g1019 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1020 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1021 . . . . . . . . . . . Cma14g01544 . . . . Cpe03g01290 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe13g00751 . Bma06g01294 . . Cmo14g01579 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1022 . . . . . . . . . . Cma06g01659 . Car06g01402 Car14g01361 . . . . . . . . . . . . . . . . . . . Cone18ag0915 Cone11ag0592 . . . . . Blo07g00063 . . . . . Bma06g01395 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1023 . Blo12g00156 Bda03g01072 . Bpe04g01003 . Bma04g00986 . . . Cma06g01650 . Car06g01401 . . . . . . . . . . . . . . . . . . Cone14ag0549 . Cone18ag0910 Cone11ag0595 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1024 . . . . . . . . Cmo08g00949 . Cma06g01605 . Car06g01364 . Sed02g1076 Cpe08g00118 . Bhi01g01171 Tan10g1175 Cmetu06g0798 . Hepe05g1311 . Lcy11g1275 . . . . . . . Cone14ag0547 Cone15ag0568 Cone18ag0909 Cone11ag0596 . . . Cme06g00863 . Blo07g00065 . Bda13g00305 . . . . . . . Cma08g00981 . Car08g00861 . . . . . . . . . . . . . . . . . . . . .
Vvi5g1025 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1026 . . Bda03g01073 . Bpe04g01002 . Bma04g00987 . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0546 Cone15ag0567 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1027 . . . . . . . . . . Cma06g01604 Cma14g01529 Car06g01363 Car14g01355 Sed02g1077 . Cpe03g01286 Bhi01g01170 Tan10g1172 Cmetu07g1670 . Hepe05g1312 . Lcy11g1276 . . . . . . . . . Cone18ag0908 Cone11ag0597 . . . Cme06g00862 . . . . . . Bma02g01012 . . . Cmo14g01563 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1028 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 10784622 10786991 + Bda017116.1 Bda03g01072 1072
3 10788671 10794814 + Bda017117.1 Bda03g01073 1073
13 3880998 3886930 + Bda001195.1 Bda13g00305 305
1 22934877 22940091 + XM_039037837.1 Bhi01g01170 1170
1 22941625 22952828 - XM_039025784.1 Bhi01g01171 1171
7 895935 898963 + BLOR17995 Blo07g00063 63
7 922927 930862 - BLOR17997 Blo07g00065 65
12 10523233 10525759 - BLOR04175 Blo12g00156 156
2 51242473 51245921 + Bma015829.1 Bma02g01012 1012
4 15897976 15900828 + Bma019591.1 Bma04g00986 986
4 15911280 15917451 + Bma019592.1 Bma04g00987 987
6 49994661 49996695 - Bma024402.1 Bma06g01294 1294
6 50703826 50706014 + Bma024510.1 Bma06g01395 1395
4 6986098 6992272 - Bpe015668.1 Bpe04g01002 1002
4 6998227 7000239 - Bpe015669.1 Bpe04g01003 1003
13 14036027 14040062 - Bpe010444.1 Bpe13g00751 751
6 9801432 9806994 + Carg15513-RA Car06g01363 1363
6 9806950 9815052 - Carg15512-RA Car06g01364 1364
6 10058155 10059885 - Carg15475-RA Car06g01401 1401
6 10062529 10066357 - Carg15474-RA Car06g01402 1402
8 5750368 5762087 - Carg11063-RA Car08g00861 861
14 11424895 11429590 - Carg24784-RA Car14g01355 1355
14 11532404 11536628 - Carg19582-RA Car14g01361 1361
6 9988207 9993470 + CmaCh06G016040.1 Cma06g01604 1604
6 9993673 10002853 - CmaCh06G016050.1 Cma06g01605 1605
6 10230904 10235902 - CmaCh06G016500.1 Cma06g01650 1650
6 10259874 10263715 - CmaCh06G016590.1 Cma06g01659 1659
8 6134535 6145749 - CmaCh08G009810.1 Cma08g00981 981
14 11572060 11577166 - CmaCh14G015290.1 Cma14g01529 1529
14 11651397 11655959 - CmaCh14G015440.1 Cma14g01544 1544
6 5888964 5893836 + MELO3C006781.2.1 Cme06g00862 862
6 5894928 5907962 - MELO3C006782.2.1 Cme06g00863 863
6 5958565 5970759 - PI0009509.1 Cmetu06g0798 798
7 21687790 21688737 - PI0007318.1 Cmetu07g1670 1670
8 6175065 6187338 - CmoCh08G009490.1 Cmo08g00949 949
14 12483942 12488903 - CmoCh14G015630.1 Cmo14g01563 1563
14 12575311 12580036 - CmoCh14G015790.1 Cmo14g01579 1579
11 3569048 3571390 + Conep11aG0060800.1 Cone11ag0592 592
11 3647444 3649988 + Conep11aG0061100.1 Cone11ag0595 595
11 3650720 3655740 + Conep11aG0061200.1 Cone11ag0596 596
11 3657541 3661793 - Conep11aG0061300.1 Cone11ag0597 597
14 2713471 2716273 - Conep14aG0055800.1 Cone14ag0546 546
14 2716876 2728615 - Conep14aG0055900.1 Cone14ag0547 547
14 2733193 2734442 + Conep14aG0056100.1 Cone14ag0549 549
15 2845897 2851101 - Conep15aG0057900.1 Cone15ag0567 567
15 2851889 2859060 - Conep15aG0058000.1 Cone15ag0568 568
18 6458072 6462262 + Conep18aG0093400.1 Cone18ag0908 908
18 6462875 6468528 - Conep18aG0093600.1 Cone18ag0909 909
18 6469491 6472264 - Conep18aG0093700.1 Cone18ag0910 910
18 6537423 6540670 - Conep18aG0094200.1 Cone18ag0915 915
3 10426750 10432034 - Cp4.1LG03g12220.1 Cpe03g01286 1286
3 10507193 10512063 - Cp4.1LG03g12060.1 Cpe03g01290 1290
8 763634 771870 + Cp4.1LG08g05660.1 Cpe08g00118 118
5 61261283 61273792 + Hsped.05g13110.1 Hepe05g1311 1311
5 61274637 61280283 - Hsped.05g13120.1 Hepe05g1312 1312
11 36041684 36053385 + Maker00005184 Lcy11g1275 1275
11 36054540 36060199 - Maker00005256 Lcy11g1276 1276
2 48101067 48109044 + Sed0014371.1 Sed02g1076 1076
2 48110182 48115316 - Sed0018641.1 Sed02g1077 1077
10 11804170 11809981 + Tan0018456.2 Tan10g1172 1172
10 11810763 11828323 - Tan0013284.1 Tan10g1175 1175
5 17992484 17997525 - Vvi5g1019 Vvi5g1019 1019
5 18164475 18165829 + Vvi5g1020 Vvi5g1020 1020
5 18212946 18213720 - Vvi5g1021 Vvi5g1021 1021
5 18213732 18216635 - Vvi5g1022 Vvi5g1022 1022
5 18253020 18257945 + Vvi5g1023 Vvi5g1023 1023
5 18260679 18285830 + Vvi5g1024 Vvi5g1024 1024
5 18285915 18286302 + Vvi5g1025 Vvi5g1025 1025
5 18289489 18297376 + Vvi5g1026 Vvi5g1026 1026
5 18299497 18311174 - Vvi5g1027 Vvi5g1027 1027
5 18363003 18370088 - Vvi5g1028 Vvi5g1028 1028
       

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