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
Vvi19g154 . . . . . . Bma10g00486 . Cmo16g00446 Cmo04g00597 . Cma09g00834 . Car09g00749 . Cpe06g00665 . Bhi09g03477 Tan01g0842 . . . Mch11g1034 . Cla11g01729 Cam11g1799 Cec11g1820 Cco11g1826 Clacu11g1958 Cmu11g1768 Cre11g2176 Cone6ag0178 Cone9ag0203 Cone14ag1042 Cone15ag1031 Lsi04g02037 Csa04g02309 Chy07g00045 . Blo07g00959 . Bda05g00779 . . Bpe03g00847 . . . . Cmo09g00829 Cma04g00560 Cma16g00414 Car04g00531 Car16g00379 Cpe14g00348 Cpe01g00505 . . . . . . . Cla07g00940 Cam07g1015 Cec07g1086 Cco07g1064 Clacu07g0985 Cmu07g0981 Cre07g1355 . . Chy07g00954 Cme07g01321
Vvi19g155 . . . . . . . . . . . Cma09g00835 . Car09g00750 . Cpe06g00666 . Bhi09g03475 . . . . Mch11g1035 . Cla11g01730 . . . . . . Cone6ag0176 Cone9ag0201 . . Lsi04g02039 . . Cme07g00559 . . . . Bpe11g00451 . . . . . Cmo09g00830 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g156 . . . . . . Bma10g00487 . Cmo16g00444 Cmo04g00594 . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1043 Cone15ag1032 . . . . Blo07g00958 . Bda05g00778 . . Bpe03g00846 . . . . . . Cma16g00412 Car04g00529 Car16g00376 Cpe14g00346 Cpe01g00502 . . . . . . . Cla05g00991 Cam05g1082 Cec05g1090 Cco05g1084 Clacu05g1076 Cmu05g1026 Cre05g1100 . . Chy06g01173 .
Vvi19g157 . . . . . Bpe08g01000 . . Cmo16g00443 Cmo04g00593 . . . Car09g00555 . Cpe06g00484 . . . . . . . . . . . . . . . Cone6ag0175 Cone9ag0200 Cone14ag1044 Cone15ag1033 . . . . . . . . . . Bma07g01164 . . . Cmo09g00611 Cma04g00558 Cma16g00411 Car04g00528 Car16g00375 Cpe14g00345 Cpe01g00501 . . . . . . . Cla05g00992 Cam05g1083 Cec05g1091 Cco05g1085 Clacu05g1077 Cmu05g1027 Cre05g1101 . . Chy06g01172 .
Vvi19g158 . . . . . . . . Cmo16g00442 . . . . . . . . . . . . . . . . . . . . . . Cone6ag0174 Cone9ag0199 . . . . . . . . . . . . Bma07g01163 . . . . . Cma16g00410 . Car16g00374 Cpe14g00344 . . . . . . . . Cla05g00993 Cam05g1084 Cec05g1092 Cco05g1086 Clacu05g1078 Cmu05g1028 Cre05g1102 . . Chy06g01171 .
Vvi19g159 . . . . . Bpe02g01848 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g160 . . . Bda09g00533 . . . . Cmo16g00440 Cmo04g00591 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda05g00777 . . Bpe01g00452 Bma07g01161 . . . . Cma04g00557 Cma16g00408 Car04g00527 . . Cpe01g00500 . . . . . . . Cla05g00994 Cam05g1085 Cec05g1093 Cco05g1087 Clacu05g1079 Cmu05g1029 Cre05g1103 . . Chy06g01170 .
Vvi19g161 . . . . . . Bma10g00489 . . Cmo04g00590 . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1046 Cone15ag1034 . . . . Blo07g00956 . Bda05g00776 . . Bpe03g00844 . . . . . Cma04g00556 . Car04g00526 . . Cpe01g00499 . . . . . . . Cla05g00995 Cam05g1086 Cec05g1094 Cco05g1088 Clacu05g1080 Cmu05g1030 Cre05g1104 . . Chy06g01169 .
Vvi19g162 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car16g00373 Cpe14g00343 . . . . . . . . Cla05g00996 Cam05g1087 Cec05g1095 Cco05g1089 Clacu05g1081 Cmu05g1031 Cre05g1105 . . Chy06g01168 .
Vvi19g163 . . . . . . . . . . . . . Car09g00528 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 56241566 56243578 + Bda021929.1 Bda05g00776 776
5 56247794 56248255 - Bda021930.1 Bda05g00777 777
5 56252241 56253311 - Bda021931.1 Bda05g00778 778
5 56260308 56262632 + Bda021932.1 Bda05g00779 779
9 7044046 7045986 + Bda031136.1 Bda09g00533 533
9 87833066 87837456 + XM_039041194.1 Bhi09g03475 3475
9 87838637 87842665 + XM_039041625.1 Bhi09g03477 3477
7 28935086 28936901 + BLOR18888 Blo07g00956 956
7 28952653 28953833 - BLOR18890 Blo07g00958 958
7 28958432 28960713 + BLOR18891 Blo07g00959 959
7 45888406 45890211 - Bma026394.1 Bma07g01161 1161
7 45947807 45961067 - Bma026396.1 Bma07g01163 1163
7 46069972 46080402 - Bma026399.1 Bma07g01164 1164
10 5721691 5723282 - Bma004173.1 Bma10g00486 486
10 5738185 5739303 + Bma004175.1 Bma10g00487 487
10 5746177 5747960 - Bma004177.1 Bma10g00489 489
1 2757679 2758515 - Bpe000437.1 Bpe01g00452 452
2 20604651 20617683 - Bpe009679.1 Bpe02g01848 1848
3 28284504 28286348 + Bpe012752.1 Bpe03g00844 844
3 28292912 28293998 - Bpe012754.1 Bpe03g00846 846
3 28300935 28303212 + Bpe012755.1 Bpe03g00847 847
8 12336901 12346120 - Bpe023125.1 Bpe08g01000 1000
11 3517824 3519856 - Bpe003823.1 Bpe11g00451 451
5 9879102 9881464 + CaPI482276_05g010820.1 Cam05g1082 1082
5 9884249 9890146 + CaPI482276_05g010830.1 Cam05g1083 1083
5 9893265 9898765 + CaPI482276_05g010840.1 Cam05g1084 1084
5 9910689 9913699 + CaPI482276_05g010850.1 Cam05g1085 1085
5 9917715 9921358 - CaPI482276_05g010860.1 Cam05g1086 1086
5 9924910 9926916 - CaPI482276_05g010870.1 Cam05g1087 1087
7 24439885 24448276 + CaPI482276_07g010150.1 Cam07g1015 1015
11 30515423 30519510 - CaPI482276_11g017990.1 Cam11g1799 1799
4 2947877 2950665 + Carg13181-RA Car04g00526 526
4 2952176 2954542 - Carg13180-RA Car04g00527 527
4 2961521 2967324 - Carg13179-RA Car04g00528 528
4 2969429 2971644 - Carg13178-RA Car04g00529 529
4 2980786 2985390 + Carg13176-RA Car04g00531 531
9 2978409 2979794 - Carg03010-RA Car09g00528 528
9 3138596 3144056 + Carg03037-RA Car09g00555 555
9 4448565 4452554 - Carg17071-RA Car09g00749 749
9 4453142 4457317 - Carg17072-RA Car09g00750 750
16 2309559 2312084 - Carg11340-RA Car16g00373 373
16 2314024 2318403 - Carg11341-RA Car16g00374 374
16 2319768 2323675 - Carg11342-RA Car16g00375 375
16 2325167 2327387 - Carg11343-RA Car16g00376 376
16 2336891 2339849 + Carg11346-RA Car16g00379 379
5 9644183 9646418 + CcPI632755_05g010840.1 Cco05g1084 1084
5 9649481 9656017 + CcPI632755_05g010850.1 Cco05g1085 1085
5 9658365 9663865 + CcPI632755_05g010860.1 Cco05g1086 1086
5 9676663 9678969 + CcPI632755_05g010870.1 Cco05g1087 1087
5 9682702 9686372 - CcPI632755_05g010880.1 Cco05g1088 1088
5 9691871 9693879 - CcPI632755_05g010890.1 Cco05g1089 1089
7 24136064 24142663 + CcPI632755_07g010640.1 Cco07g1064 1064
11 30928834 30931173 - CcPI632755_11g018260.1 Cco11g1826 1826
5 9626325 9627404 + CePI673135_05g010900.1 Cec05g1090 1090
5 9630222 9636754 + CePI673135_05g010910.1 Cec05g1091 1091
5 9639231 9644705 + CePI673135_05g010920.1 Cec05g1092 1092
5 9657465 9659768 + CePI673135_05g010930.1 Cec05g1093 1093
5 9663381 9666951 - CePI673135_05g010940.1 Cec05g1094 1094
5 9670846 9672854 - CePI673135_05g010950.1 Cec05g1095 1095
7 25999651 26006481 + CePI673135_07g010860.1 Cec07g1086 1086
11 32381968 32385126 - CePI673135_11g018200.1 Cec11g1820 1820
6 10373563 10375527 + Chy6G116960.1 Chy06g01168 1168
6 10377985 10381842 + Chy6G116970.1 Chy06g01169 1169
6 10388064 10390262 - Chy6G116980.1 Chy06g01170 1170
6 10398115 10402437 - Chy6G116990.1 Chy06g01171 1171
6 10404667 10410021 - Chy6G117000.1 Chy06g01172 1172
6 10412102 10413481 - Chy6G117010.1 Chy06g01173 1173
7 418139 421255 - Chy7G128750.1 Chy07g00045 45
7 14136914 14140887 + Chy7G137840.1 Chy07g00954 954
5 9615371 9617681 + ClG42_05g0107600.10 Clacu05g1076 1076
5 9620517 9626413 + ClG42_05g0107700.10 Clacu05g1077 1077
5 9629497 9635006 + ClG42_05g0107800.10 Clacu05g1078 1078
5 9647091 9649403 + ClG42_05g0107900.10 Clacu05g1079 1079
5 9653573 9657312 - ClG42_05g0108000.10 Clacu05g1080 1080
5 9660590 9662590 - ClG42_05g0108100.10 Clacu05g1081 1081
7 24251843 24258552 + ClG42_07g0098500.10 Clacu07g0985 985
11 30551675 30554404 - ClG42_11g0195800.10 Clacu11g1958 1958
5 9969580 9978969 + ClCG05G009180.2 Cla05g00991 991
5 9981509 9987996 + ClCG05G009190.1 Cla05g00992 992
5 9990611 9996779 + ClCG05G009200.2 Cla05g00993 993
5 10009126 10011835 + ClCG05G009205.1 Cla05g00994 994
5 10016919 10021154 - ClCG05G009210.2 Cla05g00995 995
5 10024074 10026255 - ClCG05G009220.2 Cla05g00996 996
7 25554230 25561319 + ClCG07G009880.1 Cla07g00940 940
11 30910691 30914280 - ClCG11G017720.1 Cla11g01729 1729
11 30915363 30919680 - ClCG11G017730.1 Cla11g01730 1730
4 2816316 2819943 + CmaCh04G005560.1 Cma04g00556 556
4 2820509 2822845 - CmaCh04G005570.1 Cma04g00557 557
4 2828915 2840105 - CmaCh04G005580.1 Cma04g00558 558
4 2847238 2851830 + CmaCh04G005600.1 Cma04g00560 560
9 4100613 4103711 - CmaCh09G008340.1 Cma09g00834 834
9 4115291 4119363 - CmaCh09G008350.1 Cma09g00835 835
16 2031318 2033525 + CmaCh16G004080.1 Cma16g00408 408
16 2037720 2046262 - CmaCh16G004100.1 Cma16g00410 410
16 2047668 2053880 - CmaCh16G004110.1 Cma16g00411 411
16 2055178 2057384 - CmaCh16G004120.1 Cma16g00412 412
16 2064349 2070451 + CmaCh16G004140.1 Cma16g00414 414
7 4693259 4696644 - MELO3C025620.2.1 Cme07g00559 559
7 18655884 18663508 + MELO3C016085.2.1 Cme07g01321 1321
4 2942342 2944764 + CmoCh04G005900.1 Cmo04g00590 590
4 2946400 2948715 - CmoCh04G005910.1 Cmo04g00591 591
4 2955833 2960854 - CmoCh04G005930.1 Cmo04g00593 593
4 2962686 2966319 - CmoCh04G005940.1 Cmo04g00594 594
4 2977153 2980242 + CmoCh04G005970.1 Cmo04g00597 597
9 3034324 3040934 + CmoCh09G006110.1 Cmo09g00611 611
9 4262496 4266144 - CmoCh09G008290.1 Cmo09g00829 829
9 4266851 4271426 - CmoCh09G008300.1 Cmo09g00830 830
16 2102562 2104772 + CmoCh16G004400.1 Cmo16g00440 440
16 2110401 2119952 - CmoCh16G004420.1 Cmo16g00442 442
16 2121098 2125558 - CmoCh16G004430.1 Cmo16g00443 443
16 2127292 2130025 - CmoCh16G004440.1 Cmo16g00444 444
16 2135931 2142272 + CmoCh16G004460.1 Cmo16g00446 446
5 9453663 9457799 + CmPI595203_05g010260.1 Cmu05g1026 1026
5 9460635 9466531 + CmPI595203_05g010270.1 Cmu05g1027 1027
5 9469608 9475117 + CmPI595203_05g010280.1 Cmu05g1028 1028
5 9487157 9489484 + CmPI595203_05g010290.1 Cmu05g1029 1029
5 9493660 9497402 - CmPI595203_05g010300.1 Cmu05g1030 1030
5 9500680 9502680 - CmPI595203_05g010310.1 Cmu05g1031 1031
7 24496729 24505118 + CmPI595203_07g009810.1 Cmu07g0981 981
11 29807067 29811129 - CmPI595203_11g017680.1 Cmu11g1768 1768
6 838841 841681 - Conep06aG0017500.1 Cone6ag0174 174
6 842221 844035 - Conep06aG0017600.1 Cone6ag0175 175
6 844427 847022 - Conep06aG0017700.1 Cone6ag0176 176
6 850605 853502 + Conep06aG0017900.1 Cone6ag0178 178
9 854915 857415 - Conep09aG0020100.1 Cone9ag0199 199
9 857891 860100 - Conep09aG0020200.1 Cone9ag0200 200
9 860341 861776 - Conep09aG0020300.1 Cone9ag0201 201
9 865854 868842 + Conep09aG0020500.1 Cone9ag0203 203
14 8796149 8800951 - Conep14aG0106300.1 Cone14ag1042 1042
14 8804726 8806317 + Conep14aG0106400.1 Cone14ag1043 1043
14 8806738 8809652 + Conep14aG0106500.1 Cone14ag1044 1044
14 8814303 8816596 - Conep14aG0106700.1 Cone14ag1046 1046
15 8566639 8571229 - Conep15aG0105300.1 Cone15ag1031 1031
15 8573816 8575580 + Conep15aG0105400.1 Cone15ag1032 1032
15 8576963 8580786 + Conep15aG0105500.1 Cone15ag1033 1033
15 8582993 8585176 - Conep15aG0105600.1 Cone15ag1034 1034
1 2874334 2877355 + Cp4.1LG01g01740.1 Cpe01g00499 499
1 2878560 2881333 - Cp4.1LG01g01650.1 Cpe01g00500 500
1 2887891 2893113 - Cp4.1LG01g01690.1 Cpe01g00501 501
1 2894966 2898029 - Cp4.1LG01g01450.1 Cpe01g00502 502
1 2906623 2911447 + Cp4.1LG01g01570.1 Cpe01g00505 505
6 2851980 2859299 + Cp4.1LG06g03830.1 Cpe06g00484 484
6 4139958 4144146 - Cp4.1LG06g06680.1 Cpe06g00665 665
6 4144700 4148786 - Cp4.1LG06g06650.1 Cpe06g00666 666
14 2097169 2099728 - Cp4.1LG14g03630.1 Cpe14g00343 343
14 2101605 2106798 - Cp4.1LG14g03680.1 Cpe14g00344 344
14 2107933 2112154 - Cp4.1LG14g03640.1 Cpe14g00345 345
14 2114076 2116227 - Cp4.1LG14g03660.1 Cpe14g00346 346
14 2123259 2129767 + Cp4.1LG14g03770.1 Cpe14g00348 348
5 10327272 10329788 + CrPI670011_05g011000.1 Cre05g1100 1100
5 10332689 10339155 + CrPI670011_05g011010.1 Cre05g1101 1101
5 10341618 10347140 + CrPI670011_05g011020.1 Cre05g1102 1102
5 10359963 10362269 + CrPI670011_05g011030.1 Cre05g1103 1103
5 10366463 10370300 - CrPI670011_05g011040.1 Cre05g1104 1104
5 10375033 10377082 - CrPI670011_05g011050.1 Cre05g1105 1105
7 28424391 28430931 + CrPI670011_07g013550.1 Cre07g1355 1355
11 33471157 33474324 - CrPI670011_11g021760.1 Cre11g2176 2176
4 23623371 23630899 - CsaV3_4G033350.1 Csa04g02309 2309
4 27484335 27486674 - Lsi04G020370.1 Lsi04g02037 2037
4 27490055 27494961 - Lsi04G020390.1 Lsi04g02039 2039
11 7206831 7210929 - MC11g0845 Mch11g1034 1034
11 7211894 7214600 - MC11g0846 Mch11g1035 1035
1 8196894 8203990 + Tan0017086.1 Tan01g0842 842
19 2035402 2044271 - Vvi19g154 Vvi19g154 154
19 2050403 2057179 + Vvi19g155 Vvi19g155 155
19 2061552 2065112 + Vvi19g156 Vvi19g156 156
19 2065686 2074580 + Vvi19g157 Vvi19g157 157
19 2074706 2079553 + Vvi19g158 Vvi19g158 158
19 2082213 2096660 - Vvi19g159 Vvi19g159 159
19 2107496 2113818 + Vvi19g160 Vvi19g160 160
19 2114580 2119163 - Vvi19g161 Vvi19g161 161
19 2124048 2125945 - Vvi19g162 Vvi19g162 162
19 2128358 2130017 + Vvi19g163 Vvi19g163 163
       

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