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
Vvi1g851 Blo01g00416 . Bda01g02252 . Bpe13g00466 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0980 . . . . . . . . . . . . . Bma01g00081 . . . . . . . . . Cpe07g00606 . . . . . . . . . . . . . . . . . .
Vvi1g852 Blo01g00417 Blo16g01133 Bda01g02253 . Bpe13g00465 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone19ag0972 . . . . . . . . . . . . Bma01g00082 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g853 . Blo16g01132 . Bda11g01234 Bpe13g01431 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0610 . . . . . . . . Bda11g01234 . . . Bma06g00659 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g854 . . . . . Bpe10g00856 . Bma15g00169 Cmo04g01711 Cmo18g01197 . Cma18g01172 . Car18g01081 . Cpe09g00155 Cpe01g01445 Bhi07g01602 Tan04g1116 . . . . . Cla05g02469 Cam05g2654 Cec05g2689 Cco05g2723 Clacu05g2658 Cmu05g2510 Cre05g2626 Cone13ag0979 Cone19ag0971 . . . Csa05g02421 Chy10g00977 Cme10g00444 Blo06g00896 . . . . . . . . . . Cma04g01633 . Car04g01673 . . . . . . . . . . . . . . . . . . . . .
Vvi1g855 . Blo16g01131 Bda01g02254 Bda11g01233 Bpe13g00464 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g01233 . . Bma01g00083 . . . . . . . . . Cpe07g00605 . . . . . . . . . . . . . . . . . .
Vvi1g856 Blo01g00418 . . . Bpe13g01430 . . . Cmo04g01712 . . . . . Sed08g1352 . . Bhi07g01600 Tan04g1114 Cmetu04g1272 Lac13g0288 . . . Cla05g02468 Cam05g2653 Cec05g2688 Cco05g2722 Clacu05g2657 Cmu05g2509 Cre05g2625 . . . . Lsi04g00455 Csa05g02422 Chy10g00978 Cme10g00443 . . . . . . . Bma06g00660 . . . Cma04g01634 . Car04g01674 . . . . . . . . . . . . . . . . . . . . .
Vvi1g857 . . Bda01g02255 . Bpe13g00463 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g858 . Blo16g01130 . Bda11g01232 Bpe13g01429 . . . Cmo04g01713 Cmo18g01196 . Cma18g01171 . Car18g01080 . Cpe09g00156 Cpe01g01446 . . . . . . . . . . . . . . Cone13ag0977 Cone19ag0969 . . . . . . . . . Bda11g01232 . . . Bma06g00661 . . . Cma04g01635 . Car04g01676 . . . . . . . . . . . . . . . . . . . . .
Vvi1g859 Blo01g00419 . Bda01g02170 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0976 Cone19ag0968 . . . . . . . . . . . Bpe02g02356 Bma01g00085 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g860 . . . Bda11g01231 Bpe13g01428 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0609 Cone9ag0613 . . . . . . . Bda11g01231 . . . Bma06g00662 . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 57615529 57618926 + Bda004509.1 Bda01g02170 2170
1 58291084 58292734 - Bda032998 Bda01g02252 2252
1 58295805 58297270 + Bda004597.1 Bda01g02253 2253
1 58299206 58301033 + Bda004598.1 Bda01g02254 2254
1 58302655 58304715 + Bda004599.1 Bda01g02255 2255
11 12838065 12840618 - Bda007740.1 Bda11g01231 1231
11 12841346 12847020 + Bda007741.1 Bda11g01232 1232
11 12847615 12849534 - Bda033145 Bda11g01233 1233
11 12850646 12853346 + Bda007742.1 Bda11g01234 1234
7 45519784 45523822 - XM_039036811.1 Bhi07g01600 1600
7 45525094 45532777 - XM_039036033.1 Bhi07g01602 1602
1 4706408 4724240 - BLOR00416 Blo01g00416 416
1 4710709 4712032 + BLOR00417 Blo01g00417 417
1 4714030 4718457 + BLOR00418 Blo01g00418 418
1 4724619 4740354 - BLOR00419 Blo01g00419 419
6 32172699 32185664 + BLOR17479 Blo06g00896 896
16 39830802 39834952 + BLOR21917 Blo16g01130 1130
16 39837804 39840287 - BLOR21918 Blo16g01131 1131
16 39842286 39845142 + BLOR21919 Blo16g01132 1132
16 39845973 39847225 - BLOR21920 Blo16g01133 1133
1 806099 807719 - Bma030168 Bma01g00081 81
1 810786 812251 + Bma000247.1 Bma01g00082 82
1 818412 820208 + Bma030169 Bma01g00083 83
1 967531 968519 - Bma000251.1 Bma01g00085 85
6 35583396 35586083 - Bma023622.1 Bma06g00659 659
6 35657954 35659820 + Bma023623.1 Bma06g00660 660
6 35662649 35666632 - Bma023624.1 Bma06g00661 661
6 35667034 35669699 + Bma023625.1 Bma06g00662 662
15 1804369 1810320 - Bma013150.1 Bma15g00169 169
2 24028699 24030250 - Bpe010174.1 Bpe02g02356 2356
10 14448712 14455653 + Bpe003160.1 Bpe10g00856 856
13 12161863 12163889 - Bpe010175.1 Bpe13g00463 463
13 12165144 12166966 - Bpe010176.1 Bpe13g00464 464
13 12170164 12172017 - Bpe010177.1 Bpe13g00465 465
13 12174664 12176305 + Bpe010178.1 Bpe13g00466 466
13 19571690 19574233 - Bpe011092.1 Bpe13g01428 1428
13 19574941 19578878 + Bpe011093.1 Bpe13g01429 1429
13 19581657 19583542 - Bpe011094.1 Bpe13g01430 1430
13 19588848 19591489 + Bpe011095.1 Bpe13g01431 1431
5 34010859 34012417 - CaPI482276_05g026530.1 Cam05g2653 2653
5 34014166 34021969 - CaPI482276_05g026540.1 Cam05g2654 2654
4 9632427 9636148 + Carg01726-RA Car04g01673 1673
4 9637243 9639142 + Carg01725-RA Car04g01674 1674
4 9642090 9644630 - Carg01723-RA Car04g01676 1676
18 10947144 10952431 + Carg17250-RA Car18g01080 1080
18 10952946 10959981 - Carg17249-RA Car18g01081 1081
5 35129545 35131103 - CcPI632755_05g027220.1 Cco05g2722 2722
5 35132915 35140632 - CcPI632755_05g027230.1 Cco05g2723 2723
5 37456422 37457980 - CePI673135_05g026880.1 Cec05g2688 2688
5 37459747 37467512 - CePI673135_05g026890.1 Cec05g2689 2689
10 15252319 15261006 + Chy10G181710.1 Chy10g00977 977
10 15262669 15264208 + Chy10G181720.1 Chy10g00978 978
5 34212655 34214213 - ClG42_05g0265700.10 Clacu05g2657 2657
5 34215964 34223731 - ClG42_05g0265800.10 Clacu05g2658 2658
5 36113391 36114949 - ClCG05G024540.1 Cla05g02468 2468
5 36116190 36125068 - ClCG05G024550.1 Cla05g02469 2469
4 8233692 8244427 + CmaCh04G016330.1 Cma04g01633 1633
4 8245667 8247553 + CmaCh04G016340.1 Cma04g01634 1634
4 8247694 8253125 - CmaCh04G016350.1 Cma04g01635 1635
18 9379613 9384996 + CmaCh18G011710.1 Cma18g01171 1171
18 9385903 9395509 - CmaCh18G011720.1 Cma18g01172 1172
10 2815338 2817428 - MELO3C012072.2.1 Cme10g00443 443
10 2818204 2827155 - MELO3C012071.2.1 Cme10g00444 444
4 8863655 8866021 - PI0016863.1 Cmetu04g1272 1272
4 8674205 8676196 + CmoCh04G017110.1 Cmo04g01711 1711
4 8678089 8680294 + CmoCh04G017120.1 Cmo04g01712 1712
4 8680797 8686594 - CmoCh04G017130.1 Cmo04g01713 1713
18 11974361 11979811 + CmoCh18G011960.1 Cmo18g01196 1196
18 11979638 11987774 - CmoCh18G011970.1 Cmo18g01197 1197
5 33950432 33951990 - CmPI595203_05g025090.1 Cmu05g2509 2509
5 33953741 33961509 - CmPI595203_05g025100.1 Cmu05g2510 2510
6 3011776 3014774 - Conep06aG0062700.1 Cone6ag0609 609
6 3018367 3020802 + Conep06aG0062800.1 Cone6ag0610 610
9 2905174 2907621 - Conep09aG0062700.1 Cone9ag0613 613
13 8309799 8312419 + Conep13aG0100600.1 Cone13ag0976 976
13 8312809 8317018 + Conep13aG0100700.1 Cone13ag0977 977
13 8319659 8324926 - Conep13aG0100900.1 Cone13ag0979 979
13 8326683 8328756 + Conep13aG0101000.1 Cone13ag0980 980
19 7355453 7358060 + Conep19aG0100000.1 Cone19ag0968 968
19 7358384 7362558 + Conep19aG0100100.1 Cone19ag0969 969
19 7365327 7370821 - Conep19aG0100300.1 Cone19ag0971 971
19 7371249 7375005 - Conep19aG0100400.1 Cone19ag0972 972
1 8656007 8662405 + Cp4.1LG01g12680.1 Cpe01g01445 1445
1 8663789 8671681 - Cp4.1LG01g12590.1 Cpe01g01446 1446
7 4119676 4121608 + Cp4.1LG07g05740.1 Cpe07g00605 605
7 4143844 4147148 - Cp4.1LG07g05610.1 Cpe07g00606 606
9 899974 906694 + Cp4.1LG09g01550.1 Cpe09g00155 155
9 907771 913086 - Cp4.1LG09g01630.1 Cpe09g00156 156
5 37313946 37315504 - CrPI670011_05g026250.1 Cre05g2625 2625
5 37317273 37325025 - CrPI670011_05g026260.1 Cre05g2626 2626
5 26223683 26232704 + CsaV3_5G032400.1 Csa05g02421 2421
5 26233901 26236156 + CsaV3_5G032410.1 Csa05g02422 2422
13 2053129 2054781 + Lag0040084.1 Lac13g0288 288
4 4319274 4331729 - Lsi04G004550.1 Lsi04g00455 455
8 28116850 28118251 - Sed0004596.1 Sed08g1352 1352
4 10207175 10208941 - Tan0020466.1 Tan04g1114 1114
4 10211853 10226830 - Tan0009706.2 Tan04g1116 1116
1 10782019 10787013 - Vvi1g851 Vvi1g851 851
1 10805859 10813853 + Vvi1g852 Vvi1g852 852
1 10815151 10819031 - Vvi1g853 Vvi1g853 853
1 10829205 10842136 + Vvi1g854 Vvi1g854 854
1 10843186 10845074 + Vvi1g855 Vvi1g855 855
1 10846296 10848235 + Vvi1g856 Vvi1g856 856
1 10860181 10861942 - Vvi1g857 Vvi1g857 857
1 10863423 10880276 - Vvi1g858 Vvi1g858 858
1 10908567 10915503 - Vvi1g859 Vvi1g859 859
1 10929346 10935415 + Vvi1g860 Vvi1g860 860
       

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