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
Vvi2g402 Blo02g01095 Blo03g00192 . Bda08g00533 Bpe05g00627 . . . . . Cma02g01486 Cma15g01197 Car02g01244 Car15g01085 . . Cpe05g00306 . . . . . . . . . . . . . . . . Cone6ag0746 Cone9ag0749 . Csa05g00325 Chy09g01184 . . . Bda07g00496 . . Bpe11g00686 . . . Cmo02g01524 Cmo15g01261 . . . . . Cpe13g00177 Bhi12g00202 . . . . . Lcy12g1704 Cla01g00302 Cam01g0314 Cec01g0305 Cco01g0321 Clacu01g0314 Cmu01g0299 Cre09g2209 Lsi09g00310 . . Cme09g01717
Vvi2g403 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g404 . . . . . . . Bma14g00581 . . Cma02g01487 Cma15g01196 Car02g01245 Car15g01084 . . Cpe05g00304 . . . . . . . . . . . . . . Cone8ag0331 Cone12ag0328 . . . Csa05g00326 Chy09g01183 . Blo03g00374 . Bda07g00498 . . Bpe11g00687 . . . Cmo02g01525 Cmo15g01260 . . . . . Cpe13g00178 Bhi12g00201 . . . . . Lcy12g1705 Cla01g00303 Cam01g0315 . Cco01g0322 Clacu01g0315 Cmu01g0300 Cre09g2208 Lsi09g00311 . . Cme09g01716
Vvi2g405 . . . . . . . Bma14g00580 Cmo06g01139 . . Cma15g01195 . Car15g01083 . . . . . . . . . . . . . . . . . Cone8ag0332 Cone12ag0329 . . . Csa05g00327 Chy09g01182 . . . Bda07g00499 . . Bpe11g00688 . . . . Cmo15g01259 Cma06g01112 . Car06g00949 . Cpe08g00505 Cpe13g00179 Bhi12g00199 . . . . . Lcy12g1706 . . . . . . . Lsi09g00313 . . Cme09g01715
Vvi2g406 Blo02g01094 . . Bda08g00534 Bpe05g00626 . . . . . . Cma15g01194 . Car15g01082 . . . . . . . . . . . . . . . . . Cone8ag0333 Cone12ag0330 . . . Csa05g00328 Chy09g01181 . . . . . . . Bma05g00803 . . . Cmo15g01258 . . . . . Cpe13g00180 Bhi12g00197 . . . . . . Cla01g00305 Cam01g0317 Cec01g0307 Cco01g0324 Clacu01g0318 Cmu01g0303 Cre09g2206 Lsi09g00314 . . Cme09g01714
Vvi2g407 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g408 . . . . . . . . . . Cma02g01488 Cma15g01193 Car02g01246 Car15g01081 . . Cpe05g00303 . . . . . . . . . . . . . . . . . . . Csa05g00329 Chy09g01180 Cme07g01606 . . . . . . . . . Cmo02g01526 Cmo15g01256 . . . . . Cpe13g00181 Bhi12g00195 . . . . . Lcy12g1707 Cla01g00306 . . . . . . Lsi09g00315 Csa04g00620 . Cme09g01713
Vvi2g409 . . Bda06g00069 . . Bpe07g00129 . . Cmo06g00731 . . . . . . . . . . . . . . . Cla10g00343 Cam10g0357 Cec10g0371 Cco10g0365 Clacu10g0358 Cmu10g1195 Cre10g0608 . . Cone6ag0744 Cone9ag0748 Lsi07g01394 . . Cme06g02680 . . . . . . . Bma12g00105 . . . . . Car06g00635 . Cpe08g00802 . . . . . . . . . . . . . . . . Csa03g00363 Chy06g01960 .
Vvi2g410 . Blo03g00191 Bda06g00068 . . Bpe07g00130 . . . . Cma02g01489 . Car02g01247 Car15g01080 . . . . . . . . . . . . . . . . . . . Cone6ag0743 Cone9ag0747 . Csa05g00330 Chy09g01179 . Blo03g00375 Blo19g00307 Bda07g00500 Bda09g00060 Bpe08g01473 Bpe11g00689 . Bma12g00106 . Cmo02g01528 . . . . . . Cpe13g00182 Bhi12g00191 . . . . . . Cla01g00307 Cam01g0319 Cec01g0310 Cco01g0327 Clacu01g0320 Cmu01g0305 Cre09g2204 Lsi09g00316 . . Cme09g01712
Vvi2g411 . . . . . . Bma07g01630 . . . . Cma15g01191 . Car15g01079 . . . . . . . . . . . . . . . . . Cone8ag0334 . . . . Csa05g00331 Chy09g01178 . . . . Bda09g00061 Bpe08g01472 . . . . . Cmo15g01255 . . . . . Cpe13g00183 Bhi12g00189 . . . . . Lcy12g1709 Cla01g00308 Cam01g0320 Cec01g0311 Cco01g0328 Clacu01g0321 Cmu01g0306 Cre09g2203 . . . Cme09g01711
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 685497 688335 - Bda023238.1 Bda06g00068 68
6 690247 698331 - Bda023239.1 Bda06g00069 69
7 6224391 6225044 + Bda025602.1 Bda07g00496 496
7 6251723 6254357 + Bda025607.1 Bda07g00498 498
7 6260887 6263290 + Bda033846 Bda07g00499 499
7 6270499 6274662 + Bda033847 Bda07g00500 500
8 5329583 5330233 + Bda024989.1 Bda08g00533 533
8 5343563 5346415 + Bda024990.2 Bda08g00534 534
9 1227855 1235516 + Bda030584.1 Bda09g00060 60
9 1236548 1240266 + Bda030585.1 Bda09g00061 61
12 5640484 5646401 - XM_039051251.1 Bhi12g00189 189
12 5648559 5657006 - XM_039051247.1 Bhi12g00191 191
12 5769021 5772872 + XM_039019407.1 Bhi12g00195 195
12 5774718 5780535 - XM_039019921.1 Bhi12g00197 197
12 5781999 5785042 - XM_039020380.1 Bhi12g00199 199
12 5801754 5806201 - XM_039050531.1 Bhi12g00201 201
12 5831949 5832906 - XM_039050533.1 Bhi12g00202 202
2 41816836 41819678 - BLOR10824 Blo02g01094 1094
2 41857139 41874849 - BLOR10825 Blo02g01095 1095
3 4547755 4551000 - BLOR11372 Blo03g00191 191
3 4603081 4603833 - BLOR11373 Blo03g00192 192
3 8597094 8605678 + BLOR11555 Blo03g00374 374
3 8611522 8623560 + BLOR11556 Blo03g00375 375
19 19628296 19655508 - BLOR09650 Blo19g00307 307
5 45355252 45358801 - Bma021906.1 Bma05g00803 803
7 51902343 51905779 - Bma026927.2 Bma07g01630 1630
12 1687320 1703922 + Bma006977.1 Bma12g00105 105
12 1705495 1708524 + Bma006978.1 Bma12g00106 106
14 6255682 6258039 - Bma011015.1 Bma14g00580 580
14 6284514 6287720 - Bma011016.1 Bma14g00581 581
5 20178140 20181675 - Bpe018042.1 Bpe05g00626 626
5 20182305 20182955 - Bpe018043.1 Bpe05g00627 627
7 914834 923132 + Bpe020941.1 Bpe07g00129 129
7 924966 927875 + Bpe020942.1 Bpe07g00130 130
8 15435862 15438790 - Bpe023584.1 Bpe08g01472 1472
8 15440813 15453018 - Bpe023585.1 Bpe08g01473 1473
11 5285809 5286447 + Bpe004042.1 Bpe11g00686 686
11 5294504 5297680 + Bpe004043.1 Bpe11g00687 687
11 5304867 5307279 + Bpe004044.1 Bpe11g00688 688
11 5315293 5319461 + Bpe004045.1 Bpe11g00689 689
1 3497656 3498345 + CaPI482276_01g003140.1 Cam01g0314 314
1 3509596 3512795 + CaPI482276_01g003150.1 Cam01g0315 315
1 3523644 3529737 + CaPI482276_01g003170.1 Cam01g0317 317
1 3563646 3570069 + CaPI482276_01g003190.1 Cam01g0319 319
1 3572927 3580184 + CaPI482276_01g003200.1 Cam01g0320 320
10 5748854 5765856 - CaPI482276_10g003570.1 Cam10g0357 357
2 8412622 8413311 + Carg02504-RA Car02g01244 1244
2 8415151 8417761 + Carg02503-RA Car02g01245 1245
2 8417976 8421462 - Carg02502-RA Car02g01246 1246
2 8425776 8433619 + Carg02501-RA Car02g01247 1247
6 3720946 3733810 + Carg21647-RA Car06g00635 635
6 7317109 7320627 + Carg23884-RA Car06g00949 949
15 8474683 8478358 - Carg16663-RA Car15g01079 1079
15 8479980 8488157 - Carg16662-RA Car15g01080 1080
15 8494918 8498742 + Carg16661-RA Car15g01081 1081
15 8499285 8504749 - Carg16660-RA Car15g01082 1082
15 8505185 8507346 - Carg16659-RA Car15g01083 1083
15 8511199 8513738 - Carg16658-RA Car15g01084 1084
15 8516066 8523263 - Carg16657-RA Car15g01085 1085
1 3140559 3141248 + CcPI632755_01g003210.1 Cco01g0321 321
1 3152528 3159720 + CcPI632755_01g003220.1 Cco01g0322 322
1 3166434 3172430 + CcPI632755_01g003240.1 Cco01g0324 324
1 3206285 3212782 + CcPI632755_01g003270.1 Cco01g0327 327
1 3215631 3222941 + CcPI632755_01g003280.1 Cco01g0328 328
10 4248851 4264221 - CcPI632755_10g003650.1 Cco10g0365 365
1 3114058 3114747 + CePI673135_01g003050.1 Cec01g0305 305
1 3139598 3145582 + CePI673135_01g003070.1 Cec01g0307 307
1 3176206 3183274 + CePI673135_01g003100.1 Cec01g0310 310
1 3186142 3193367 + CePI673135_01g003110.1 Cec01g0311 311
10 4433181 4449305 - CePI673135_10g003710.1 Cec10g0371 371
6 23589927 23603673 + Chy6G124880.1 Chy06g01960 1960
9 13974778 13978624 - Chy9G168940.1 Chy09g01178 1178
9 13979421 13987323 - Chy9G168950.1 Chy09g01179 1179
9 14010073 14012628 + Chy9G168960.1 Chy09g01180 1180
9 14013680 14018418 - Chy9G168970.1 Chy09g01181 1181
9 14019743 14022132 - Chy9G168980.1 Chy09g01182 1182
9 14028236 14031102 - Chy9G168990.1 Chy09g01183 1183
9 14035460 14036134 - Chy9G169000.1 Chy09g01184 1184
1 3113053 3113742 + ClG42_01g0031400.10 Clacu01g0314 314
1 3124902 3128037 + ClG42_01g0031500.10 Clacu01g0315 315
1 3138889 3144938 + ClG42_01g0031800.10 Clacu01g0318 318
1 3175708 3182176 + ClG42_01g0032000.10 Clacu01g0320 320
1 3184890 3192141 + ClG42_01g0032100.10 Clacu01g0321 321
10 4523720 4541186 - ClG42_10g0035800.10 Clacu10g0358 358
1 3196725 3197414 + ClCG01G003120.1 Cla01g00302 302
1 3208586 3211909 + ClCG01G003130.2 Cla01g00303 303
1 3218734 3231532 + ClCG01G003150.2 Cla01g00305 305
1 3233053 3237027 - ClCG01G003180.2 Cla01g00306 306
1 3263294 3272655 + ClCG01G003190.1 Cla01g00307 307
1 3274732 3280555 + ClCG01G003200.2 Cla01g00308 308
10 4511768 4528755 - ClCG10G003630.1 Cla10g00343 343
2 8494391 8495080 + CmaCh02G014860.1 Cma02g01486 1486
2 8496923 8499613 + CmaCh02G014870.1 Cma02g01487 1487
2 8500635 8504084 - CmaCh02G014880.1 Cma02g01488 1488
2 8507571 8516129 + CmaCh02G014890.1 Cma02g01489 1489
6 7502115 7506112 + CmaCh06G011120.1 Cma06g01112 1112
15 7540738 7552434 - CmaCh15G011910.1 Cma15g01191 1191
15 7560840 7564828 + CmaCh15G011930.1 Cma15g01193 1193
15 7565507 7570829 - CmaCh15G011940.1 Cma15g01194 1194
15 7572242 7574517 - CmaCh15G011950.1 Cma15g01195 1195
15 7577284 7580149 - CmaCh15G011960.1 Cma15g01196 1196
15 7581626 7583520 - CmaCh15G011970.1 Cma15g01197 1197
6 33922016 33939609 - MELO3C014034.2.1 Cme06g02680 2680
7 21853197 21857723 + MELO3C016330.2.1 Cme07g01606 1606
9 21747136 21751815 - MELO3C005623.2.1 Cme09g01711 1711
9 21753789 21761906 - MELO3C005624.2.1 Cme09g01712 1712
9 21778869 21782458 + MELO3C005625.2.1 Cme09g01713 1713
9 21783404 21788116 - MELO3C005626.2.1 Cme09g01714 1714
9 21789202 21792323 - MELO3C005627.2.1 Cme09g01715 1715
9 21796091 21799316 - MELO3C005628.2.1 Cme09g01716 1716
9 21805168 21806264 - MELO3C005629.2.1 Cme09g01717 1717
2 8865848 8867506 + CmoCh02G015240.1 Cmo02g01524 1524
2 8869471 8872050 + CmoCh02G015250.1 Cmo02g01525 1525
2 8873069 8876451 - CmoCh02G015260.1 Cmo02g01526 1526
2 8881268 8888607 + CmoCh02G015280.1 Cmo02g01528 1528
6 3749259 3760934 + CmoCh06G007310.1 Cmo06g00731 731
6 8750766 8754899 + CmoCh06G011390.1 Cmo06g01139 1139
15 8613229 8626473 - CmoCh15G012550.1 Cmo15g01255 1255
15 8633290 8636686 + CmoCh15G012560.1 Cmo15g01256 1256
15 8637789 8643253 - CmoCh15G012580.1 Cmo15g01258 1258
15 8643676 8646170 - CmoCh15G012590.1 Cmo15g01259 1259
15 8649652 8652314 - CmoCh15G012600.1 Cmo15g01260 1260
15 8654286 8654975 - CmoCh15G012610.1 Cmo15g01261 1261
1 3069107 3069796 + CmPI595203_01g002990.1 Cmu01g0299 299
1 3080976 3084124 + CmPI595203_01g003000.1 Cmu01g0300 300
1 3094984 3101040 + CmPI595203_01g003030.1 Cmu01g0303 303
1 3131868 3138293 + CmPI595203_01g003050.1 Cmu01g0305 305
1 3141002 3148264 + CmPI595203_01g003060.1 Cmu01g0306 306
10 4663840 4679984 - CmPI595203_10g011950.1 Cmu10g1195 1195
6 3753011 3758425 - Conep06aG0076600.1 Cone6ag0743 743
6 3760052 3767317 - Conep06aG0076700.1 Cone6ag0744 744
6 3787184 3787897 - Conep06aG0076900.1 Cone6ag0746 746
8 1905135 1907673 + Conep08aG0034600.1 Cone8ag0331 331
8 1908055 1910097 + Conep08aG0034700.1 Cone8ag0332 332
8 1910926 1914102 + Conep08aG0034800.1 Cone8ag0333 333
8 1917643 1920827 + Conep08aG0034900.1 Cone8ag0334 334
9 3546827 3552285 - Conep09aG0076400.1 Cone9ag0747 747
9 3553475 3560609 - Conep09aG0076500.1 Cone9ag0748 748
9 3572793 3573793 - Conep09aG0076600.1 Cone9ag0749 749
12 1793169 1797250 + Conep12aG0034300.1 Cone12ag0328 328
12 1797638 1800071 + Conep12aG0034400.1 Cone12ag0329 329
12 1800957 1804251 + Conep12aG0034500.1 Cone12ag0330 330
5 1702929 1706164 + Cp4.1LG05g03850.1 Cpe05g00303 303
5 1706930 1709927 - Cp4.1LG05g03630.1 Cpe05g00304 304
5 1715512 1716027 - Cp4.1LG05g03770.1 Cpe05g00306 306
8 3266449 3272671 - Cp4.1LG08g01750.1 Cpe08g00505 505
8 6382545 6395872 - Cp4.1LG08g07990.1 Cpe08g00802 802
13 1392367 1400162 + Cp4.1LG13g01840.1 Cpe13g00177 177
13 1402043 1404828 + Cp4.1LG13g01820.1 Cpe13g00178 178
13 1407799 1410292 + Cp4.1LG13g01810.1 Cpe13g00179 179
13 1410714 1416308 + Cp4.1LG13g01790.1 Cpe13g00180 180
13 1416994 1421309 - Cp4.1LG13g01850.1 Cpe13g00181 181
13 1427796 1435928 + Cp4.1LG13g01800.1 Cpe13g00182 182
13 1437733 1441281 + Cp4.1LG13g01830.1 Cpe13g00183 183
9 41165118 41172194 - CrPI670011_09g022030.1 Cre09g2203 2203
9 41174561 41180990 - CrPI670011_09g022040.1 Cre09g2204 2204
9 41212493 41218590 - CrPI670011_09g022060.1 Cre09g2206 2206
9 41224774 41232117 - CrPI670011_09g022080.1 Cre09g2208 2208
9 41243439 41244128 - CrPI670011_09g022090.1 Cre09g2209 2209
10 5581123 5596625 - CrPI670011_10g006080.1 Cre10g0608 608
3 3030998 3044100 - CsaV3_3G003630.1 Csa03g00363 363
4 4109551 4114326 - CsaV3_4G006200.1 Csa04g00620 620
5 2039646 2041467 + CsaV3_5G003250.1 Csa05g00325 325
5 2045459 2049141 + CsaV3_5G003260.1 Csa05g00326 326
5 2051378 2054656 + CsaV3_5G003270.1 Csa05g00327 327
5 2055334 2060752 + CsaV3_5G003280.1 Csa05g00328 328
5 2061091 2065013 - CsaV3_5G003290.1 Csa05g00329 329
5 2084005 2092264 + CsaV3_5G003300.1 Csa05g00330 330
5 2095089 2098190 + CsaV3_5G003310.1 Csa05g00331 331
12 37543431 37548455 + Maker00003023 Lcy12g1704 1704
12 37550902 37555319 + Maker00003016 Lcy12g1705 1705
12 37564217 37574621 + Maker00003020 Lcy12g1706 1706
12 37575586 37579591 - Maker00003015 Lcy12g1707 1707
12 37611311 37617242 + Maker00003082 Lcy12g1709 1709
7 20273952 20290880 - Lsi07G013940.1 Lsi07g01394 1394
9 3187047 3187736 + Lsi09G003100.1 Lsi09g00310 310
9 3201179 3205180 + Lsi09G003110.1 Lsi09g00311 311
9 3220390 3223189 + Lsi09G003130.1 Lsi09g00313 313
9 3224786 3231494 + Lsi09G003140.1 Lsi09g00314 314
9 3232659 3236748 - Lsi09G003150.1 Lsi09g00315 315
9 3257684 3274702 + Lsi09G003160.1 Lsi09g00316 316
2 3923540 3929358 + Vvi2g402 Vvi2g402 402
2 3929624 3930580 - Vvi2g403 Vvi2g403 403
2 3946576 3947398 + Vvi2g404 Vvi2g404 404
2 3979434 3982809 + Vvi2g405 Vvi2g405 405
2 3982829 4016481 + Vvi2g406 Vvi2g406 406
2 4017701 4020569 + Vvi2g407 Vvi2g407 407
2 4020866 4025226 - Vvi2g408 Vvi2g408 408
2 4035664 4081274 + Vvi2g409 Vvi2g409 409
2 4081775 4093358 + Vvi2g410 Vvi2g410 410
2 4096657 4100463 + Vvi2g411 Vvi2g411 411
       

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