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
Vvi16g994 Blo06g01054 Blo15g00077 . Bda07g01950 . Bpe07g01027 . Bma14g02021 Cmo16g00035 Cmo18g01364 Cma02g01138 Cma15g01011 Car02g00942 Car15g00945 . Cpe05g00585 Cpe14g00023 Bhi01g01520 . . . . Mch10g0036 . Cla01g00024 . . . . . . . . . . . . . Cme06g01170 . Blo09g00009 . Bda15g00794 . Bpe12g00340 . Bma12g01222 . Cmo02g01169 Cmo15g01074 Cma16g00030 Cma18g01333 Car16g00027 Car18g01248 Cpe09g00014 Cpe13g00326 Bhi12g00680 . . Lac11g0112 Hepe06g0815 . Lcy12g0093 Cla05g00988 Cam05g1079 Cec05g1087 Cco05g1081 Clacu05g1073 Cmu05g1023 Cre05g1097 Lsi09g00005 Csa03g01964 Chy06g01176 .
Vvi16g995 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g996 . . Bda05g00134 Bda07g01949 . . Bma10g01311 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo07g00324 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g997 . Blo15g00078 . . . Bpe07g01026 . . Cmo16g00036 . . . . . Sed07g0876 . Cpe14g00024 Bhi01g01519 Tan01g0061 Cmetu06g0246 . Hepe07g0039 Mch10g0037 . . . . . . . . . . . Cone15ag0001 . . . Cme06g01169 . . Bda06g00795 . . . . Bma12g01221 . . . Cma16g00031 . Car16g00029 . . . . . . . . . . Cla05g00987 Cam05g1078 Cec05g1086 Cco05g1080 Clacu05g1072 Cmu05g1022 Cre05g1096 . Csa03g01965 . .
Vvi16g998 Blo06g01055 Blo15g00079 . Bda07g01948 . Bpe07g01025 . Bma14g02020 . . . Cma15g01012 Car02g00941 Car15g00946 . Cpe05g00586 . . . . . . . . Cla01g00026 Cam01g0025 Cec01g0023 Cco01g0026 Clacu01g0026 Cmu01g0025 Cre09g2482 Cone1ag1005 Cone5ag0713 Cone14ag0001 Cone15ag0002 . . . . . Blo09g00012 Bda06g00794 Bda15g00793 . Bpe12g00341 . Bma12g01220 . Cmo02g01168 . . . . . . Cpe13g00324 Bhi12g00679 . . . Hepe06g0814 . . . . . . . . . Lsi09g00006 . . .
Vvi16g999 . . . Bda07g01947 Bpe03g00202 . . . Cmo16g00037 . . . . . Sed07g0875 . . Bhi01g01518 Tan01g0062 Cmetu06g0118 . Hepe07g0040 Mch10g0038 . . . . . . . . . . . . . . . Cme06g01168 . . . . . . . . . . . Cma16g00032 . Car16g00030 . . . . . . . . . . . . . . . . . . Csa03g01966 Chy06g01177 .
Vvi16g1000 . . Bda05g00133 . . . Bma10g01310 . . . . . . . . . . . . . . . . . . . . . . . . Cone1ag1004 Cone5ag0712 . . . . . . Blo07g00325 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1002 . . Bda05g00132 Bda07g01946 Bpe03g00227 . Bma10g01309 Bma14g02019 . . . . . . . . . . . . . . . . . . . . . . . Cone1ag1003 Cone5ag0711 . . . . . . . Blo09g00013 . . . . . . . . . . . . . Cpe09g00026 . . . . . . . . . . . . . . . . . . .
Vvi16g1003 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 6130183 6133211 + Bda020757.1 Bda05g00132 132
5 6144752 6154875 + Bda020758.1 Bda05g00133 133
5 6157873 6160771 - Bda020759.1 Bda05g00134 134
6 11006190 11008731 - Bda024117.1 Bda06g00794 794
6 11009567 11010348 + Bda024118.1 Bda06g00795 795
7 36902774 36905384 + Bda028925.1 Bda07g01946 1946
7 36919766 36920469 + Bda028927.1 Bda07g01947 1947
7 36920874 36924184 - Bda028928.1 Bda07g01948 1948
7 36924960 36928395 - Bda028929.1 Bda07g01949 1949
7 36929345 36933147 - Bda028930.1 Bda07g01950 1950
15 11810444 11813230 - Bda012653.1 Bda15g00793 793
15 11835017 11836411 - Bda012654.1 Bda15g00794 794
1 30953703 30956394 + XM_039027029.1 Bhi01g01518 1518
1 30956643 30958887 + XM_039027020.1 Bhi01g01519 1519
1 30959013 30963416 - XM_039027008.1 Bhi01g01520 1520
12 20061871 20066114 - XM_039018345.1 Bhi12g00679 679
12 20159751 20162172 - XM_039018399.1 Bhi12g00680 680
6 33923078 33924487 + BLOR17637 Blo06g01054 1054
6 33925511 33930375 + BLOR17638 Blo06g01055 1055
7 4122974 4126639 + BLOR18256 Blo07g00324 324
7 4127591 4140187 - BLOR18257 Blo07g00325 325
9 67563 69313 + BLOR20924 Blo09g00009 9
9 124450 133614 + BLOR20927 Blo09g00012 12
9 137069 139781 - BLOR20928 Blo09g00013 13
15 670165 672063 + BLOR06471 Blo15g00077 77
15 673356 674227 - BLOR06472 Blo15g00078 78
15 678611 681674 + BLOR06473 Blo15g00079 79
10 46538627 46541613 + Bma005419.1 Bma10g01309 1309
10 46577841 46590082 + Bma005421.1 Bma10g01310 1310
10 46592911 46595912 - Bma005422.1 Bma10g01311 1311
12 45096301 45098236 - Bma008582.1 Bma12g01220 1220
12 45099402 45100505 + Bma008583.1 Bma12g01221 1221
12 45101505 45103419 - Bma008584.1 Bma12g01222 1222
14 43547691 43560831 + Bma012828.1 Bma14g02019 2019
14 43561317 43564501 - Bma030757 Bma14g02020 2020
14 43565363 43577894 - Bma012829.1 Bma14g02021 2021
3 2364044 2364748 + Bpe012049.1 Bpe03g00202 202
3 3026411 3029408 - Bpe012082.1 Bpe03g00227 227
7 15821128 15823539 - Bpe021869.1 Bpe07g01025 1025
7 15824111 15825195 + Bpe021870.1 Bpe07g01026 1026
7 15826275 15828180 - Bpe021871.1 Bpe07g01027 1027
12 8506244 8507635 + Bpe005597.2 Bpe12g00340 340
12 8508577 8511227 + Bpe024887 Bpe12g00341 341
1 649212 654859 + CaPI482276_01g000250.1 Cam01g0025 25
5 9833332 9838400 + CaPI482276_05g010780.1 Cam05g1078 1078
5 9839416 9843365 - CaPI482276_05g010790.1 Cam05g1079 1079
2 6651589 6656902 - Carg14000-RA Car02g00941 941
2 6658444 6661762 - Carg13999-RA Car02g00942 942
15 6746642 6748081 + Carg26773-RA Car15g00945 945
15 6750267 6755019 + Carg26772-RA Car15g00946 946
16 245708 249879 + Carg15046-RA Car16g00027 27
16 249990 252097 - Carg15048-RA Car16g00029 29
16 252562 254956 - Carg15049-RA Car16g00030 30
18 11878606 11883424 - Carg20322-RA Car18g01248 1248
1 160780 172157 + CcPI632755_01g000260.1 Cco01g0026 26
5 9598020 9599809 + CcPI632755_05g010800.1 Cco05g1080 1080
5 9600814 9604687 - CcPI632755_05g010810.1 Cco05g1081 1081
1 185092 185748 + CePI673135_01g000230.1 Cec01g0023 23
5 9577326 9579119 + CePI673135_05g010860.1 Cec05g1086 1086
5 9580207 9584180 - CePI673135_05g010870.1 Cec05g1087 1087
6 10436979 10440823 + Chy6G117040.1 Chy06g01176 1176
6 10441553 10454102 - Chy6G117050.1 Chy06g01177 1177
1 253226 261838 + ClG42_01g0002600.10 Clacu01g0026 26
5 9567769 9572812 + ClG42_05g0107200.10 Clacu05g1072 1072
5 9573813 9577740 - ClG42_05g0107300.10 Clacu05g1073 1073
1 161550 167733 + ClCG01G000220.1 Cla01g00024 24
1 173770 183725 + ClCG01G000230.2 Cla01g00026 26
5 9926625 9928412 + ClCG05G009130.2 Cla05g00987 987
5 9929126 9933555 - ClCG05G009140.1 Cla05g00988 988
2 6729206 6732917 - CmaCh02G011380.1 Cma02g01138 1138
15 6095861 6108506 + CmaCh15G010110.1 Cma15g01011 1011
15 6110598 6118234 + CmaCh15G010120.1 Cma15g01012 1012
16 138093 142618 + CmaCh16G000300.1 Cma16g00030 30
16 142607 144644 - CmaCh16G000310.1 Cma16g00031 31
16 145135 147199 - CmaCh16G000320.1 Cma16g00032 32
18 10170257 10175259 - CmaCh18G013330.1 Cma18g01333 1333
6 9092906 9095330 + MELO3C019381.2.1 Cme06g01168 1168
6 9095916 9098562 + MELO3C019382.2.1 Cme06g01169 1169
6 9097548 9102419 - MELO3C019383.2.1 Cme06g01170 1170
6 8377558 8380193 + PI0028739.1 Cmetu06g0118 118
6 8380770 8382966 + PI0008640.1 Cmetu06g0246 246
2 7031186 7036801 - CmoCh02G011680.1 Cmo02g01168 1168
2 7038582 7041973 - CmoCh02G011690.1 Cmo02g01169 1169
15 6990648 6994904 + CmoCh15G010740.1 Cmo15g01074 1074
16 159861 163980 + CmoCh16G000350.1 Cmo16g00035 35
16 164072 166016 - CmoCh16G000360.1 Cmo16g00036 36
16 166280 168798 - CmoCh16G000370.1 Cmo16g00037 37
18 12809485 12814454 - CmoCh18G013640.1 Cmo18g01364 1364
1 198188 206802 + CmPI595203_01g000250.1 Cmu01g0025 25
5 9400869 9412901 + CmPI595203_05g010220.1 Cmu05g1022 1022
5 9413902 9417830 - CmPI595203_05g010230.1 Cmu05g1023 1023
1 55040931 55044263 + Conep01aG0104900.1 Cone1ag1003 1003
1 55049073 55051204 + Conep01aG0105200.1 Cone1ag1004 1004
1 55052672 55055957 - Conep01aG0105300.1 Cone1ag1005 1005
5 3051433 3054413 + Conep05aG0073500.1 Cone5ag0711 711
5 3055862 3066673 + Conep05aG0073700.1 Cone5ag0712 712
5 3068565 3072016 - Conep05aG0073800.1 Cone5ag0713 713
14 16371 20393 + Conep14aG0000100.1 Cone14ag0001 1
15 18647 20451 - Conep15aG0000100.1 Cone15ag0001 1
15 27113 31637 + Conep15aG0000200.1 Cone15ag0002 2
5 3545490 3548822 + Cp4.1LG05g05870.1 Cpe05g00585 585
5 3550667 3556180 + Cp4.1LG05g05920.1 Cpe05g00586 586
9 80867 85981 + Cp4.1LG09g00090.1 Cpe09g00014 14
9 145111 148395 + Cp4.1LG09g00190.1 Cpe09g00026 26
13 2901806 2906519 - Cp4.1LG13g03250.1 Cpe13g00324 324
13 2911349 2914377 - Cp4.1LG13g03260.1 Cpe13g00326 326
14 137935 144403 + Cp4.1LG14g07050.1 Cpe14g00023 23
14 141424 147265 - Cp4.1LG14g06930.1 Cpe14g00024 24
5 10274792 10286835 + CrPI670011_05g010960.1 Cre05g1096 1096
5 10287855 10291811 - CrPI670011_05g010970.1 Cre05g1097 1097
9 44120581 44126258 - CrPI670011_09g024820.1 Cre09g2482 2482
3 15520035 15526874 + CsaV3_3G019640.1 Csa03g01964 1964
3 15524940 15526565 - CsaV3_3G019650.1 Csa03g01965 1965
3 15527446 15529563 - CsaV3_3G019660.1 Csa03g01966 1966
6 54941487 54946195 - Hsped.06g08140.1 Hepe06g0814 814
6 54955975 54957516 - Hsped.06g08150.1 Hepe06g0815 815
7 448452 451334 - Hsped.07g00390.1 Hepe07g0039 39
7 452278 454154 - Hsped.07g00400.1 Hepe07g0040 40
11 1027551 1027961 - Lag0030750.1 Lac11g0112 112
12 1228241 1229137 - Maker00038639 Lcy12g0093 93
9 38943 40385 + Lsi09G000050.1 Lsi09g00005 5
9 44356 51266 + Lsi09G000060.1 Lsi09g00006 6
10 206506 212634 + MC10g0032 Mch10g0036 36
10 210396 213505 - MC10g0033 Mch10g0037 37
10 214354 217128 - MC10g0034 Mch10g0038 38
7 6332600 6335216 + Sed0010771.1 Sed07g0875 875
7 6336154 6339045 + Sed0004447.1 Sed07g0876 876
1 740861 742605 - Tan0000156.1 Tan01g0061 61
1 743227 746026 - Tan0009177.1 Tan01g0062 62
16 21519346 21527110 + Vvi16g994 Vvi16g994 994
16 21530830 21531934 + Vvi16g995 Vvi16g995 995
16 21532534 21537566 + Vvi16g996 Vvi16g996 996
16 21537642 21539945 - Vvi16g997 Vvi16g997 997
16 21544159 21548340 + Vvi16g998 Vvi16g998 998
16 21549118 21553502 - Vvi16g999 Vvi16g999 999
16 21554277 21569250 - Vvi16g1000 Vvi16g1000 1000
16 21583559 21588492 + Vvi16g1001 Vvi16g1001 1001
16 21599918 21603635 - Vvi16g1002 Vvi16g1002 1002
16 21607167 21608207 - Vvi16g1003 Vvi16g1003 1003
       

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