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
Vvi16g974 . . Bda05g00141 Bda07g01957 . . Bma10g01318 Bma14g02028 Cmo16g00026 Cmo18g01373 . . . . . . Cpe14g00018 . . . . . . . . . . . . . . . . . . . . . . Blo07g00318 Blo09g00003 . . . . . . . . . Cma16g00021 Cma18g01339 Car16g00021 . Cpe09g00011 . . . . . . . . . . . . . . . . . . .
Vvi16g975 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone5ag0724 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g976 . . . . . . . . . . . Cma15g00997 . Car15g00933 . . . . . . . . . . Cla01g00012 Cam01g0012 Cec01g0011 Cco01g0013 Clacu01g0013 Cmu01g0013 Cre09g2492 . . . . . Csa05g00004 Chy09g01476 . . . . . . . . . . . Cmo15g01062 . . . . . Cpe13g00336 Bhi12g00695 . . . Hepe06g0826 . . . . . . . . . . . . Cme09g02023
Vvi16g977 . . . Bda07g01956 Bpe03g00205 . . Bma14g02027 . . . . . . . . . . . . . . . . . . . . . . . . Cone5ag0723 . . . . . . . Blo09g00004 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g978 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone1ag1015 Cone5ag0722 . . . . . . . . . . . . Bma08g00399 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g979 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g980 . . . . . . . . . . . Cma15g00999 . Car15g00934 . . . . . . . . . . Cla01g00013 . . . Clacu01g0014 . . . . . . . Csa05g00003 . . . . . . . . . . . . Cmo15g01063 . . . . . . . . . . . . . . . . . . . . . . . Cme09g02025
Vvi16g981 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g982 Blo06g01050 Blo15g00076 . . . Bpe07g01028 . . . . Cma02g01147 Cma15g01000 Car02g00948 Car15g00935 . Cpe05g00579 . . . . . . . . Cla01g00014 . . Cco01g0015 Clacu01g0015 Cmu01g0015 . Cone1ag1013 Cone5ag0720 . . . Csa05g00002 Chy09g01478 . . . Bda06g00796 Bda15g00797 . . Bma08g00399 Bma12g01223 . Cmo02g01178 Cmo15g01064 . . . . . Cpe13g00335 Bhi12g00691 . . . Hepe06g0825 . . . . . . . . . . . . Cme09g02026
Vvi16g983 . . . . . . . . . . Cma02g01145 Cma15g01002 Car02g00947 Car15g00937 . Cpe05g00580 . . . . . . . . Cla01g00016 Cam01g0015 Cec01g0013 Cco01g0016 Clacu01g0016 Cmu01g0016 Cre09g2491 . . . . . Csa05g00017 Chy09g01464 . . . . . . . . . . Cmo02g01176 Cmo15g01065 . . . . . Cpe13g00334 Bhi12g00689 . . . Hepe06g0824 . . . . . . . . . . . . Cme09g02015
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 6216503 6219671 - Bda020767.2 Bda05g00141 141
6 11015652 11020919 + Bda024119.2 Bda06g00796 796
7 36949833 36951102 - Bda028935.1 Bda07g01956 1956
7 36952438 36955557 - Bda028936.1 Bda07g01957 1957
15 11845755 11852080 + Bda012657.2 Bda15g00797 797
12 20270112 20273738 - XM_039019328.1 Bhi12g00689 689
12 20286917 20294650 + XM_039018379.1 Bhi12g00691 691
12 20342756 20343999 + XM_039020054.1 Bhi12g00695 695
6 33878403 33886861 - BLOR17633 Blo06g01050 1050
7 4005500 4008276 + BLOR18250 Blo07g00318 318
9 44630 47043 + BLOR20918 Blo09g00003 3
9 48272 49926 + BLOR20919 Blo09g00004 4
15 652956 666731 - BLOR06470 Blo15g00076 76
8 9728208 9735498 + Bma027474.1 Bma08g00399 399
10 46822952 46826248 - Bma005434.1 Bma10g01318 1318
12 45105706 45110921 + Bma008585.2 Bma12g01223 1223
14 43594429 43596079 - Bma012835.1 Bma14g02027 2027
14 43597061 43600099 - Bma012836.1 Bma14g02028 2028
3 2449734 2451058 + Bpe012052.1 Bpe03g00205 205
7 15829615 15835713 + Bpe021872.1 Bpe07g01028 1028
1 575691 576470 - CaPI482276_01g000120.1 Cam01g0012 12
1 601878 606292 + CaPI482276_01g000150.1 Cam01g0015 15
2 6682316 6688030 - Carg13994-RA Car02g00947 947
2 6689241 6696135 + Carg13993-RA Car02g00948 948
15 6671606 6672372 - Carg26785-RA Car15g00933 933
15 6673212 6677098 - Carg26784-RA Car15g00934 934
15 6677727 6685190 - Carg26783-RA Car15g00935 935
15 6693723 6697316 + Carg26781-RA Car15g00937 937
16 220404 224928 + Carg15040-RA Car16g00021 21
1 87263 88042 - CcPI632755_01g000130.1 Cco01g0013 13
1 100633 113231 - CcPI632755_01g000150.1 Cco01g0015 15
1 113275 116417 + CcPI632755_01g000160.1 Cco01g0016 16
1 107857 108636 - CePI673135_01g000110.1 Cec01g0011 11
1 131054 135649 + CePI673135_01g000130.1 Cec01g0013 13
9 16100768 16103680 - Chy9G171800.1 Chy09g01464 1464
9 16167689 16170408 - Chy9G171920.1 Chy09g01476 1476
9 16180916 16195059 - Chy9G171940.1 Chy09g01478 1478
1 177660 178439 - ClG42_01g0001300.10 Clacu01g0013 13
1 179666 186360 - ClG42_01g0001400.10 Clacu01g0014 14
1 191279 201157 - ClG42_01g0001500.10 Clacu01g0015 15
1 205983 210399 + ClG42_01g0001600.10 Clacu01g0016 16
1 94076 94855 - ClCG01G000120.1 Cla01g00012 12
1 95685 106352 - ClCG01G000130.1 Cla01g00013 13
1 110232 120555 - ClCG01G000140.2 Cla01g00014 14
1 125783 130959 + ClCG01G000150.2 Cla01g00016 16
2 6753807 6757858 - CmaCh02G011450.1 Cma02g01145 1145
2 6760695 6781485 + CmaCh02G011470.1 Cma02g01147 1147
15 6038566 6040388 - CmaCh15G009970.1 Cma15g00997 997
15 6041245 6046223 - CmaCh15G009990.1 Cma15g00999 999
15 6046970 6054199 - CmaCh15G010000.1 Cma15g01000 1000
15 6063913 6067613 + CmaCh15G010020.1 Cma15g01002 1002
16 112728 116108 + CmaCh16G000210.1 Cma16g00021 21
18 10199527 10203149 - CmaCh18G013390.1 Cma18g01339 1339
9 23849039 23852156 - MELO3C005914.2.1 Cme09g02015 2015
9 23915732 23918658 - MELO3C005923.2.1 Cme09g02023 2023
9 23919463 23926175 - MELO3C005924.2.1 Cme09g02025 2025
9 23929108 23936670 - MELO3C005925.2.1 Cme09g02026 2026
2 7063788 7068060 - CmoCh02G011760.1 Cmo02g01176 1176
2 7070555 7075770 + CmoCh02G011780.1 Cmo02g01178 1178
15 6921213 6922114 - CmoCh15G010620.1 Cmo15g01062 1062
15 6922463 6926761 - CmoCh15G010630.1 Cmo15g01063 1063
15 6927265 6934300 - CmoCh15G010640.1 Cmo15g01064 1064
15 6942757 6946281 + CmoCh15G010650.1 Cmo15g01065 1065
16 129037 132609 + CmoCh16G000260.1 Cmo16g00026 26
18 12834456 12838954 - CmoCh18G013730.1 Cmo18g01373 1373
1 122598 123377 - CmPI595203_01g000130.1 Cmu01g0013 13
1 135716 146101 - CmPI595203_01g000150.1 Cmu01g0015 15
1 150932 155348 + CmPI595203_01g000160.1 Cmu01g0016 16
1 55085588 55090830 + Conep01aG0106100.1 Cone1ag1013 1013
1 55095021 55096322 + Conep01aG0106300.1 Cone1ag1015 1015
5 3100684 3106078 + Conep05aG0074500.1 Cone5ag0720 720
5 3113204 3114948 + Conep05aG0074700.1 Cone5ag0722 722
5 3115307 3116977 - Conep05aG0074800.1 Cone5ag0723 723
5 3118506 3119516 + Conep05aG0074900.1 Cone5ag0724 724
5 3508536 3515550 - Cp4.1LG05g05760.1 Cpe05g00579 579
5 3516773 3520938 + Cp4.1LG05g05720.1 Cpe05g00580 580
9 50087 56425 + Cp4.1LG09g00050.1 Cpe09g00011 11
13 2970401 2975269 - Cp4.1LG13g03340.1 Cpe13g00334 334
13 2997805 3005296 + Cp4.1LG13g03290.1 Cpe13g00335 335
13 3006097 3012322 + Cp4.1LG13g03280.1 Cpe13g00336 336
14 110863 114761 + Cp4.1LG14g07120.1 Cpe14g00018 18
9 44169819 44174260 - CrPI670011_09g024910.1 Cre09g2491 2491
9 44198349 44199128 + CrPI670011_09g024920.1 Cre09g2492 2492
5 18479 29620 + CsaV3_5G000020.1 Csa05g00002 2
5 31873 35517 + CsaV3_5G000030.1 Csa05g00003 3
5 35597 38762 + CsaV3_5G000040.1 Csa05g00004 4
5 91393 94287 + CsaV3_5G000170.1 Csa05g00017 17
6 55029735 55034705 - Hsped.06g08240.1 Hepe06g0824 824
6 55044414 55053147 + Hsped.06g08250.1 Hepe06g0825 825
6 55066615 55067952 + Hsped.06g08260.1 Hepe06g0826 826
16 21322700 21327801 + Vvi16g974 Vvi16g974 974
16 21329146 21331591 - Vvi16g975 Vvi16g975 975
16 21339141 21340093 - Vvi16g976 Vvi16g976 976
16 21341511 21343257 + Vvi16g977 Vvi16g977 977
16 21346553 21349482 - Vvi16g978 Vvi16g978 978
16 21357595 21361368 + Vvi16g979 Vvi16g979 979
16 21361626 21365096 - Vvi16g980 Vvi16g980 980
16 21365296 21369283 + Vvi16g981 Vvi16g981 981
16 21369300 21380824 - Vvi16g982 Vvi16g982 982
16 21384983 21390817 + Vvi16g983 Vvi16g983 983
       

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