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
Vvi2g752 . . Bda06g01242 . . Bpe07g00239 . . Cmo06g00625 Cmo16g01243 . . . . . Cpe14g00990 . . . . . . . . Cla10g00122 Cam10g0120 Cec10g0129 Cco10g0129 Clacu10g0126 Cmu10g0973 Cre10g0383 Cone8ag0500 Cone12ag0501 . . Lsi07g01155 . . Cme06g02435 . . . . . . . Bma12g00240 . . . Cma06g00618 Cma16g01196 Car06g00551 Car16g01126 . . . . . . . . . . . . . . . . . Csa03g00126 Chy06g02179 .
Vvi2g753 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g754 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g755 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g756 Blo02g00972 . Bda06g01241 Bda08g00645 Bpe05g00514 . . . Cmo06g00624 . . . . . . . . . . . . . . . Cla10g00121 Cam10g0119 Cec10g0128 Cco10g0128 Clacu10g0125 Cmu10g0972 Cre10g0382 . . . . Lsi07g01154 . . Cme06g02433 . . . . . . Bma05g00700 . . . . Cma06g00617 . Car06g00550 . . . . . . . . . . . . . . . . . . Csa03g00125 Chy06g02180 .
Vvi2g757 . . . . . Bpe07g00240 . . . Cmo16g01244 . . . . . Cpe14g00991 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma12g00241 . . . . Cma16g01197 . Car16g01127 . . . . . . . . . . . . . . . . . . . .
Vvi2g758 Blo02g00971 . . Bda08g00646 Bpe05g00513 . . . Cmo06g00623 Cmo16g01245 . . . . . Cpe14g00992 . . . . . . . . Cla10g00120 Cam10g0118 Cec10g0127 Cco10g0127 Clacu10g0124 Cmu10g0971 Cre10g0381 . . . . Lsi07g01153 . . Cme06g02432 Blo03g00890 . Bda07g00070 . . Bpe11g00309 Bma05g00699 . . . . Cma06g00616 Cma16g01198 Car06g00549 Car16g01128 . . . . . . . . . . . . . . . . . Csa03g00124 Chy06g02181 .
Vvi2g759 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g760 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g761 . . Bda06g01239 . . Bpe07g00241 . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0503 Cone12ag0504 . . . . Chy04g00135 . . . . . . . . Bma12g00242 Sed05g0248 . . . . . . . Cpe15g00183 Bhi05g00427 Tan07g2035 Cmetu04g1723 Lac11g2458 Hepe06g1809 . Lcy12g1982 Cla09g01078 Cam09g1135 Cec09g1140 Cco09g1160 . . Cre09g1097 . Csa03g04569 . Cme04g00156
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 42494257 42513889 - Bda023071.2 Bda06g01239 1239
6 42535558 42562884 - Bda023073.2 Bda06g01241 1241
6 42564758 42567142 - Bda023074.1 Bda06g01242 1242
7 925667 926254 + Bda025128.1 Bda07g00070 70
8 6607839 6611502 + Bda029105.1 Bda08g00645 645
8 6612786 6618431 - Bda029106.2 Bda08g00646 646
5 9028421 9037306 - XM_039033048.1 Bhi05g00427 427
2 37686663 37689035 + BLOR10701 Blo02g00971 971
2 37699352 37703827 - BLOR10702 Blo02g00972 972
3 34828192 34838935 - BLOR12071 Blo03g00890 890
5 40887242 40888778 + Bma021770.1 Bma05g00699 699
5 40889894 40893498 - Bma021771.1 Bma05g00700 700
12 3083173 3088383 + Bma007131.1 Bma12g00240 240
12 3107746 3117822 + Bma007132.1 Bma12g00241 241
12 3120549 3128614 + Bma007133.2 Bma12g00242 242
5 19348510 19350097 + Bpe017931.1 Bpe05g00513 513
5 19351402 19354983 - Bpe017932.1 Bpe05g00514 514
7 1694809 1700052 + Bpe021050.1 Bpe07g00239 239
7 1701039 1709873 + Bpe021051.1 Bpe07g00240 240
7 1712002 1719894 + Bpe021052.1 Bpe07g00241 241
11 2250076 2250675 + Bpe003683.1 Bpe11g00309 309
9 11806838 11814957 - CaPI482276_09g011350.1 Cam09g1135 1135
10 2768068 2770132 + CaPI482276_10g001180.1 Cam10g0118 118
10 2773531 2777283 + CaPI482276_10g001190.1 Cam10g0119 119
10 2777938 2783623 - CaPI482276_10g001200.1 Cam10g0120 120
6 3121859 3124335 + Carg23414-RA Car06g00549 549
6 3125863 3130216 + Carg23413-RA Car06g00550 550
6 3129811 3134345 - Carg23412-RA Car06g00551 551
16 9660387 9666055 + Carg23583-RA Car16g01126 1126
16 9665611 9669782 - Carg23582-RA Car16g01127 1127
16 9670641 9672948 - Carg23581-RA Car16g01128 1128
9 11176985 11190492 - CcPI632755_09g011600.1 Cco09g1160 1160
10 1175857 1177927 + CcPI632755_10g001270.1 Cco10g0127 127
10 1181334 1185089 + CcPI632755_10g001280.1 Cco10g0128 128
10 1185737 1191372 - CcPI632755_10g001290.1 Cco10g0129 129
9 11225904 11234295 - CePI673135_09g011400.1 Cec09g1140 1140
10 1190338 1192076 + CePI673135_10g001270.1 Cec10g0127 127
10 1195773 1199517 + CePI673135_10g001280.1 Cec10g0128 128
10 1200171 1205862 - CePI673135_10g001290.1 Cec10g0129 129
4 1210354 1223747 + Chy4G068530.1 Chy04g00135 135
6 26057685 26062925 + Chy6G127070.1 Chy06g02179 2179
6 26063556 26067377 - Chy6G127080.1 Chy06g02180 2180
6 26070524 26072265 - Chy6G127090.1 Chy06g02181 2181
10 1491344 1493074 + ClG42_10g0012400.10 Clacu10g0124 124
10 1496770 1500515 + ClG42_10g0012500.10 Clacu10g0125 125
10 1501171 1506910 - ClG42_10g0012600.10 Clacu10g0126 126
9 11436895 11445237 - ClCG09G011510.2 Cla09g01078 1078
10 1223470 1226473 + ClCG10G001200.1 Cla10g00120 120
10 1229450 1233786 + ClCG10G001210.2 Cla10g00121 121
10 1232447 1240635 - ClCG10G001220.1 Cla10g00122 122
6 3005709 3007587 + CmaCh06G006160.1 Cma06g00616 616
6 3009478 3013830 + CmaCh06G006170.1 Cma06g00617 617
6 3013035 3018651 - CmaCh06G006180.1 Cma06g00618 618
16 9109705 9116390 + CmaCh16G011960.1 Cma16g01196 1196
16 9115028 9119018 - CmaCh16G011970.1 Cma16g01197 1197
16 9119166 9122212 - CmaCh16G011980.1 Cma16g01198 1198
4 1202465 1211125 + MELO3C030376.2.1 Cme04g00156 156
6 31392585 31395072 + MELO3C013813.2.1 Cme06g02432 2432
6 31399210 31404122 + MELO3C013814.2.1 Cme06g02433 2433
6 31403596 31409994 - MELO3C013815.2.1 Cme06g02435 2435
4 32213802 32216244 - PI0018931.1 Cmetu04g1723 1723
6 3098690 3101472 + CmoCh06G006230.1 Cmo06g00623 623
6 3102576 3105939 + CmoCh06G006240.1 Cmo06g00624 624
6 3106169 3111740 - CmoCh06G006250.1 Cmo06g00625 625
16 8889767 8895161 + CmoCh16G012430.1 Cmo16g01243 1243
16 8895175 8898848 - CmoCh16G012440.1 Cmo16g01244 1244
16 8899382 8901407 - CmoCh16G012450.1 Cmo16g01245 1245
10 1642612 1644342 + CmPI595203_10g009710.1 Cmu10g0971 971
10 1648028 1651775 + CmPI595203_10g009720.1 Cmu10g0972 972
10 1652432 1658163 - CmPI595203_10g009730.1 Cmu10g0973 973
8 3559470 3565959 + Conep08aG0052100.1 Cone8ag0500 500
8 3582218 3588506 + Conep08aG0052400.1 Cone8ag0503 503
12 3391111 3397896 + Conep12aG0052200.1 Cone12ag0501 501
12 3416282 3423338 + Conep12aG0052500.1 Cone12ag0504 504
14 8357647 8364338 + Cp4.1LG14g09880.1 Cpe14g00990 990
14 8363067 8367392 - Cp4.1LG14g09970.1 Cpe14g00991 991
14 8368361 8370994 - Cp4.1LG14g09950.1 Cpe14g00992 992
15 1493939 1501760 - Cp4.1LG15g01880.1 Cpe15g00183 183
9 11369445 11379479 - CrPI670011_09g010970.1 Cre09g1097 1097
10 2602966 2604698 + CrPI670011_10g003810.1 Cre10g0381 381
10 2608442 2612174 + CrPI670011_10g003820.1 Cre10g0382 382
10 2612831 2618507 - CrPI670011_10g003830.1 Cre10g0383 383
3 972890 974927 + CsaV3_3G001240.1 Csa03g00124 124
3 977608 981606 + CsaV3_3G001250.1 Csa03g00125 125
3 980855 988413 - CsaV3_3G001260.1 Csa03g00126 126
3 39769207 39777806 - CsaV3_3G048750.1 Csa03g04569 4569
6 69181488 69188264 + Hsped.06g18090.1 Hepe06g1809 1809
11 40763732 40776160 + Lag0033096.1 Lac11g2458 2458
12 41203821 41211997 + Maker00037886 Lcy12g1982 1982
7 16994144 16997344 + Lsi07G011530.1 Lsi07g01153 1153
7 17007445 17011762 + Lsi07G011540.1 Lsi07g01154 1154
7 17011473 17019005 - Lsi07G011550.1 Lsi07g01155 1155
5 1466968 1475434 - Sed0012782.1 Sed05g0248 248
7 71911369 71919455 + Tan0015945.5 Tan07g2035 2035
2 10191222 10201433 + Vvi2g752 Vvi2g752 752
2 10221813 10224480 - Vvi2g753 Vvi2g753 753
2 10234830 10235846 - Vvi2g754 Vvi2g754 754
2 10267238 10267661 + Vvi2g755 Vvi2g755 755
2 10269856 10276842 - Vvi2g756 Vvi2g756 756
2 10278099 10293984 - Vvi2g757 Vvi2g757 757
2 10370626 10374009 - Vvi2g758 Vvi2g758 758
2 10418027 10430565 + Vvi2g759 Vvi2g759 759
2 10443999 10444299 + Vvi2g760 Vvi2g760 760
2 10491213 10506570 + Vvi2g761 Vvi2g761 761
       

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