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
Vvi2g212 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g213 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g214 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g215 . . . . . Bpe07g00254 . . Cmo06g00596 Cmo16g01269 . . . . . Cpe14g01012 . . . . . . . . Cla10g00090 Cam10g0090 Cec10g0094 Cco10g0096 Clacu10g0091 Cmu10g0938 Cre10g0352 . . . . Lsi07g01119 . . Cme06g02399 . . . . . . . . . . . . Cma16g01225 Car06g00525 Car16g01153 Cpe08g00910 . . . . . . . . . . . . . . . . . . .
Vvi2g216 . . . . . . Bma07g00952 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo03g00817 . . Bda09g00703 Bpe08g00852 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g217 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g218 . . . . . . Bma07g00995 . . . Cma02g00934 Cma15g01308 Car02g00683 Car15g01178 . . Cpe05g00779 . . . . . . . . . . . . . . . Cone12ag0544 . . . Csa05g00177 Chy09g01319 . Blo03g00816 . . Bda09g00683 Bpe08g00875 . . . . Cmo02g00943 Cmo15g01375 . . . . . . Bhi12g00100 . . Lac11g1941 Hepe06g1448 . Lcy12g1536 Cla01g00157 Cam01g0162 Cec01g0159 Cco01g0164 Clacu01g0158 Cmu01g0157 Cre09g2349 Lsi09g00149 . . Cme09g01868
Vvi2g219 . . . . . . . . . . Cma02g00935 Cma15g01310 Car02g00684 Car15g01179 . . . . . . . . . . . . . . . . . . . . . . Csa05g00176 Chy09g01320 . . . . . . . . . . Cmo02g00946 Cmo15g01376 . . . . . . Bhi12g00099 . . Lac11g1940 Hepe06g1447 . . Cla01g00156 Cam01g0161 Cec01g0157 Cco01g0163 Clacu01g0156 Cmu01g0156 Cre09g2350 Lsi09g00148 . . Cme09g01869
Vvi2g220 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g00033 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g221 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
9 10701892 10704693 - Bda031340.1 Bda09g00683 683
9 11184928 11188633 - Bda031368.1 Bda09g00703 703
12 3194727 3198315 - XM_039018886.1 Bhi12g00099 99
12 3237393 3243610 - XM_039019418.1 Bhi12g00100 100
3 33566925 33570357 - BLOR11997 Blo03g00816 816
3 33573018 33575684 - BLOR11998 Blo03g00817 817
7 36050585 36054613 - Bma026087.1 Bma07g00952 952
7 38885990 38888790 + Bma026156.1 Bma07g00995 995
7 1827860 1830681 - Bpe021066.1 Bpe07g00254 254
8 10853145 10856132 + Bpe022974.1 Bpe08g00852 852
8 11134949 11137762 + Bpe022997.1 Bpe08g00875 875
1 1968351 1971150 - CaPI482276_01g001610.1 Cam01g0161 161
1 1973722 1982171 - CaPI482276_01g001620.1 Cam01g0162 162
10 2467926 2472546 - CaPI482276_10g000900.1 Cam10g0090 90
2 5083310 5089014 + Carg08540-RA Car02g00683 683
2 5090692 5093702 + Carg08539-RA Car02g00684 684
6 2952452 2957337 - Carg16277-RA Car06g00525 525
15 9200509 9206906 + Carg21302-RA Car15g01178 1178
15 9208157 9212816 + Carg21303-RA Car15g01179 1179
16 9830359 9835592 + Carg19488-RA Car16g01153 1153
1 1536923 1539730 - CcPI632755_01g001630.1 Cco01g0163 163
1 1542278 1551205 - CcPI632755_01g001640.1 Cco01g0164 164
10 873340 877946 - CcPI632755_10g000960.1 Cco10g0096 96
1 1539942 1542749 - CePI673135_01g001570.1 Cec01g0157 157
1 1548471 1553298 - CePI673135_01g001590.1 Cec01g0159 159
10 899887 904489 - CePI673135_10g000940.1 Cec10g0094 94
9 15111523 15117566 + Chy9G170350.1 Chy09g01319 1319
9 15120045 15122933 + Chy9G170360.1 Chy09g01320 1320
1 1588393 1591187 - ClG42_01g0015600.10 Clacu01g0156 156
1 1597473 1602265 - ClG42_01g0015800.10 Clacu01g0158 158
10 1190135 1194771 - ClG42_10g0009100.10 Clacu10g0091 91
1 1585161 1588581 - ClCG01G001600.1 Cla01g00156 156
1 1594124 1599428 - ClCG01G001610.1 Cla01g00157 157
10 911312 915948 - ClCG10G000870.2 Cla10g00090 90
2 5553181 5559981 + CmaCh02G009340.1 Cma02g00934 934
2 5561683 5565770 + CmaCh02G009350.1 Cma02g00935 935
15 8243397 8249274 + CmaCh15G013080.1 Cma15g01308 1308
15 8251622 8255167 + CmaCh15G013100.1 Cma15g01310 1310
16 9273155 9278059 + CmaCh16G012250.1 Cma16g01225 1225
6 31124400 31129537 - MELO3C013782.2.1 Cme06g02399 2399
9 22855260 22860444 + MELO3C005776.2.1 Cme09g01868 1868
9 22863296 22867101 + MELO3C005777.2.1 Cme09g01869 1869
2 5773750 5775519 + CmoCh02G009430.1 Cmo02g00943 943
2 5781968 5790763 + CmoCh02G009460.1 Cmo02g00946 946
6 2939292 2944712 - CmoCh06G005960.1 Cmo06g00596 596
15 9365759 9371993 + CmoCh15G013750.1 Cmo15g01375 1375
15 9374276 9378361 + CmoCh15G013760.1 Cmo15g01376 1376
16 9054022 9059121 + CmoCh16G012690.1 Cmo16g01269 1269
1 1541727 1544522 - CmPI595203_01g001560.1 Cmu01g0156 156
1 1550804 1555596 - CmPI595203_01g001570.1 Cmu01g0157 157
10 1341694 1346336 - CmPI595203_10g009380.1 Cmu10g0938 938
12 3854410 3858620 - Conep12aG0056500.1 Cone12ag0544 544
5 4827239 4836298 - Cp4.1LG05g07900.1 Cpe05g00779 779
8 7165960 7171476 + Cp4.1LG08g09020.1 Cpe08g00910 910
14 8525085 8539016 + Cp4.1LG14g10060.1 Cpe14g01012 1012
9 42756539 42761313 + CrPI670011_09g023490.1 Cre09g2349 2349
9 42767772 42770571 + CrPI670011_09g023500.1 Cre09g2350 2350
10 2312263 2316885 - CrPI670011_10g003520.1 Cre10g0352 352
5 157878 158468 - CsaV3_5G000330.1 Csa05g00033 33
5 1012906 1016984 - CsaV3_5G001760.1 Csa05g00176 176
5 1018884 1024315 - CsaV3_5G001770.1 Csa05g00177 177
6 65035686 65039587 - Hsped.06g14470.1 Hepe06g1447 1447
6 65046493 65054540 - Hsped.06g14480.1 Hepe06g1448 1448
11 34886319 34889180 - Lag0032578.1 Lac11g1940 1940
11 34905600 34916547 - Lag0032579.1 Lac11g1941 1941
12 35197652 35198970 - Maker00029457 Lcy12g1536 1536
7 16606113 16611701 - Lsi07G011190.1 Lsi07g01119 1119
9 1497210 1500893 - Lsi09G001480.1 Lsi09g00148 148
9 1505767 1512020 - Lsi09G001490.1 Lsi09g00149 149
2 2029174 2029598 + Vvi2g212 Vvi2g212 212
2 2035369 2036535 + Vvi2g213 Vvi2g213 213
2 2040490 2040918 + Vvi2g214 Vvi2g214 214
2 2064380 2070248 + Vvi2g215 Vvi2g215 215
2 2072754 2075212 + Vvi2g216 Vvi2g216 216
2 2075829 2079813 + Vvi2g217 Vvi2g217 217
2 2079817 2091015 + Vvi2g218 Vvi2g218 218
2 2093245 2099598 + Vvi2g219 Vvi2g219 219
2 2100593 2102056 - Vvi2g220 Vvi2g220 220
2 2102062 2102771 - Vvi2g221 Vvi2g221 221
       

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