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
Vvi1g1271 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1272 . . . Bda11g00385 Bpe13g00816 . . . . . . . . . . . . . . . . . . . Cla06g00195 Cam06g0014 Cec06g0216 Cco06g0210 Clacu06g0213 Cmu06g0206 Cre06g0979 . . . . . . Chy11g01793 Cme11g02324 Blo02g00195 . . Bda11g00385 Bpe14g00797 . . Bma06g01341 . . . . . . . Cpe17g01070 . Bhi12g02451 . . . . . . . . . . . . . Lsi09g01728 . . .
Vvi1g1273 . . . . . . . . . . . . . . . . . . . . . . . . Cla06g00193 Cam06g0016 Cec06g0214 Cco06g0208 Clacu06g0211 Cmu06g0204 Cre06g0977 . . . . . . Chy11g01795 Cme11g02326 . . . . . . . . Sed08g1495 . . . . . . Cpe17g01068 . Bhi12g02448 Tan06g1510 Cmetu11g0895 . Hepe03g1119 . . . . . . . . . Lsi09g01730 . . .
Vvi1g1274 . . . . . . . . . . . . . . . . . . . . . . . . Cla06g00192 Cam06g0018 Cec06g0212 Cco06g0207 Clacu06g0210 Cmu06g0203 Cre06g0976 . . . . . . Chy11g01797 Cme11g02328 Blo02g00196 . . . Bpe14g00798 . . . Sed07g0096 . . . . . . Cpe17g01066 . Bhi12g02442 Tan06g1508 . . Hepe03g1123 . . . . . . . . . Lsi09g01732 . . .
Vvi1g1275 . . Bda01g02132 . Bpe13g00817 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00303 . . . . . . . . . Bma06g01340 . . . . . . . . Cpe03g01223 . . . . . . . . . . . . . . . . Chy07g01479 Cme07g01915
Vvi1g1276 . . . . . . . . . . . . . . . . . . . . . . . . Cla06g00190 Cam06g0020 Cec06g0209 Cco06g0204 Clacu06g0207 Cmu06g0200 Cre06g0974 . . . . . . Chy11g01799 Cme11g02330 . . . . . . . . . . . . . . . Cpe17g01064 . Bhi12g02438 Tan06g1502 . . . . . . . . . . . . Lsi09g01734 . . .
Vvi1g1277 . . . . . . . . . . . . . . . . . . . . . . . . Cla06g00189 Cam06g0021 Cec06g0208 Cco06g0203 Clacu06g0206 Cmu06g0199 Cre06g0973 . . . . . Csa04g00302 Chy11g01800 Cme11g02331 . Blo12g00280 . . Bpe14g00800 . . . Sed02g1006 . . . . . . Cpe17g01063 . Bhi12g02436 Tan06g1499 Cmetu06g2578 . Hepe03g1130 . . . . . . . . . Lsi09g01735 . . Cme07g01916
Vvi1g1278 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1279 . . . . . . . . . . . . . . . . . . . . . . . . Cla06g00186 Cam06g0025 Cec06g0205 Cco06g0199 Clacu06g0203 Cmu06g0196 Cre06g0969 . . . . . . Chy11g01804 Cme11g02336 . Blo12g00282 . . . . . . Sed01g3569 . . . . . . . . Bhi12g02427 Tan06g1495 Cmetu11g1648 . Hepe03g1137 . . . . . . . . . Lsi09g01739 . . .
Vvi1g1280 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo12g00283 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy07g01483 Cme07g01920
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 57313980 57314873 - Bda004463.1 Bda01g02132 2132
11 4218295 4225635 + Bda005124.1 Bda11g00385 385
12 76602782 76605853 + XM_039019751.1 Bhi12g02427 2427
12 76803859 76809844 + XM_039018393.1 Bhi12g02436 2436
12 76833220 76840764 - XM_039019878.1 Bhi12g02438 2438
12 76874371 76883903 + XM_039019600.1 Bhi12g02442 2442
12 76970988 76974371 + XM_039020225.1 Bhi12g02448 2448
12 77158681 77164945 + XM_039051065.1 Bhi12g02451 2451
2 1761044 1767936 - BLOR09925 Blo02g00195 195
2 1775380 1791251 - BLOR09926 Blo02g00196 196
12 16805633 16822874 - BLOR04299 Blo12g00280 280
12 16889745 16891156 - BLOR04301 Blo12g00282 282
12 16907251 16909731 + BLOR04302 Blo12g00283 283
6 50333972 50339230 + Bma024451.1 Bma06g01340 1340
6 50356222 50364662 + Bma024452.1 Bma06g01341 1341
13 14457272 14464148 - Bpe010506.1 Bpe13g00816 816
13 14475450 14476614 - Bpe010507.1 Bpe13g00817 817
14 6020677 6024385 - Bpe014175.1 Bpe14g00797 797
14 6030076 6036177 - Bpe014176.1 Bpe14g00798 798
14 6040373 6042753 - Bpe014178.1 Bpe14g00800 800
6 1946685 1952470 - CaPI482276_06g000140.1 Cam06g0014 14
6 2001007 2002909 - CaPI482276_06g000160.1 Cam06g0016 16
6 2024445 2034224 - CaPI482276_06g000180.1 Cam06g0018 18
6 2043425 2050741 + CaPI482276_06g000200.1 Cam06g0020 20
6 2055075 2057379 - CaPI482276_06g000210.1 Cam06g0021 21
6 2089237 2090641 - CaPI482276_06g000250.1 Cam06g0025 25
6 2090738 2092146 + CcPI632755_06g001990.1 Cco06g0199 199
6 2124952 2127277 + CcPI632755_06g002030.1 Cco06g0203 203
6 2129379 2139849 - CcPI632755_06g002040.1 Cco06g0204 204
6 2166391 2174791 + CcPI632755_06g002070.1 Cco06g0207 207
6 2185093 2186996 + CcPI632755_06g002080.1 Cco06g0208 208
6 2234046 2239806 + CcPI632755_06g002100.1 Cco06g0210 210
6 2120361 2121765 + CePI673135_06g002050.1 Cec06g0205 205
6 2160777 2163249 + CePI673135_06g002080.1 Cec06g0208 208
6 2168465 2175813 - CePI673135_06g002090.1 Cec06g0209 209
6 2201847 2210335 + CePI673135_06g002120.1 Cec06g0212 212
6 2224405 2226190 + CePI673135_06g002140.1 Cec06g0214 214
6 2287040 2292820 + CePI673135_06g002160.1 Cec06g0216 216
7 19127167 19128798 - Chy7G143090.1 Chy07g01479 1479
7 19153284 19158409 - Chy7G143130.1 Chy07g01483 1483
11 24294112 24306051 - Chy11G203730.1 Chy11g01793 1793
11 24330473 24332385 - Chy11G203750.1 Chy11g01795 1795
11 24349473 24358364 - Chy11G203770.1 Chy11g01797 1797
11 24366657 24372982 + Chy11G203790.1 Chy11g01799 1799
11 24376773 24378814 - Chy11G203800.1 Chy11g01800 1800
11 24402269 24403415 - Chy11G203840.1 Chy11g01804 1804
6 2266711 2268115 + ClG42_06g0020300.10 Clacu06g0203 203
6 2300273 2302578 + ClG42_06g0020600.10 Clacu06g0206 206
6 2304689 2315333 - ClG42_06g0020700.10 Clacu06g0207 207
6 2344671 2353127 + ClG42_06g0021000.10 Clacu06g0210 210
6 2363718 2365620 + ClG42_06g0021100.10 Clacu06g0211 211
6 2427328 2433133 + ClG42_06g0021300.10 Clacu06g0213 213
6 2154126 2155530 + ClCG06G002030.1 Cla06g00186 186
6 2191852 2194280 + ClCG06G002060.2 Cla06g00189 189
6 2199208 2207000 - ClCG06G002070.1 Cla06g00190 190
6 2225777 2244794 + ClCG06G002090.2 Cla06g00192 192
6 2256226 2259305 + ClCG06G002110.1 Cla06g00193 193
6 2321007 2328285 + ClCG06G002130.2 Cla06g00195 195
7 24377154 24378652 - MELO3C017743.2.1 Cme07g01915 1915
7 24392282 24394624 - MELO3C032845.2.1 Cme07g01916 1916
7 24414089 24417037 - MELO3C017746.2.1 Cme07g01920 1920
11 30303986 30310526 - MELO3C022316.2.1 Cme11g02324 2324
11 30336669 30339983 - MELO3C022318.2.1 Cme11g02326 2326
11 30357666 30367298 - MELO3C022320.2.1 Cme11g02328 2328
11 30373907 30380684 + MELO3C022321.2.1 Cme11g02330 2330
11 30384093 30386669 - MELO3C022322.2.1 Cme11g02331 2331
11 30409446 30410934 - MELO3C022327.2.1 Cme11g02336 2336
6 21166663 21169796 - PI0023527.1 Cmetu06g2578 2578
11 1745057 1748424 + PI0008670.1 Cmetu11g0895 895
11 1663266 1665619 + PI0015037.2 Cmetu11g1648 1648
6 2062263 2063666 + CmPI595203_06g001960.1 Cmu06g0196 196
6 2095791 2098096 + CmPI595203_06g001990.1 Cmu06g0199 199
6 2103303 2110851 - CmPI595203_06g002000.1 Cmu06g0200 200
6 2140238 2151670 + CmPI595203_06g002030.1 Cmu06g0203 203
6 2159256 2161158 + CmPI595203_06g002040.1 Cmu06g0204 204
6 2209977 2215761 + CmPI595203_06g002060.1 Cmu06g0206 206
3 9956281 9957935 + Cp4.1LG03g12920.1 Cpe03g01223 1223
17 8046546 8049649 + Cp4.1LG17g10650.1 Cpe17g01063 1063
17 8051954 8059724 - Cp4.1LG17g10710.1 Cpe17g01064 1064
17 8065990 8072181 + Cp4.1LG17g10660.1 Cpe17g01066 1066
17 8083301 8086452 + Cp4.1LG17g10620.1 Cpe17g01068 1068
17 8101437 8105557 + Cp4.1LG17g10640.1 Cpe17g01070 1070
6 3158230 3159628 + CrPI670011_06g009690.1 Cre06g0969 969
6 3191874 3194197 + CrPI670011_06g009730.1 Cre06g0973 973
6 3196426 3215579 - CrPI670011_06g009740.1 Cre06g0974 974
6 3228899 3237415 + CrPI670011_06g009760.1 Cre06g0976 976
6 3247078 3249551 + CrPI670011_06g009770.1 Cre06g0977 977
6 3301801 3307590 + CrPI670011_06g009790.1 Cre06g0979 979
4 1868364 1873985 + CsaV3_4G003020.1 Csa04g00302 302
4 1881152 1882944 + CsaV3_4G003030.1 Csa04g00303 303
3 64225248 64228579 - Hsped.03g11190.1 Hepe03g1119 1119
3 64298812 64309403 - Hsped.03g11230.1 Hepe03g1123 1123
3 64397575 64399599 - Hsped.03g11300.1 Hepe03g1130 1130
3 64511474 64513466 - Hsped.03g11370.1 Hepe03g1137 1137
9 25887574 25894027 - Lsi09G017280.1 Lsi09g01728 1728
9 25940387 25943863 - Lsi09G017300.1 Lsi09g01730 1730
9 25966793 25975824 - Lsi09G017320.1 Lsi09g01732 1732
9 25987111 25994165 + Lsi09G017340.1 Lsi09g01734 1734
9 25998193 26000814 - Lsi09G017350.1 Lsi09g01735 1735
9 26038450 26039483 - Lsi09G017390.1 Lsi09g01739 1739
1 64886959 64889083 + Sed0025495.1 Sed01g3569 3569
2 47446961 47451573 - Sed0009839.2 Sed02g1006 1006
7 953972 961879 - Sed0016155.1 Sed07g0096 96
8 29441337 29443530 - Sed0019106.1 Sed08g1495 1495
6 20516442 20517825 + Tan0004520.1 Tan06g1495 1495
6 20687261 20690083 + Tan0013901.1 Tan06g1499 1499
6 20710645 20718096 - Tan0018924.2 Tan06g1502 1502
6 20773481 20783011 + Tan0011489.4 Tan06g1508 1508
6 20857181 20860392 + Tan0021019.1 Tan06g1510 1510
1 21240515 21262171 - Vvi1g1271 Vvi1g1271 1271
1 21368897 21386389 - Vvi1g1272 Vvi1g1272 1272
1 21412775 21417820 - Vvi1g1273 Vvi1g1273 1273
1 21434899 21451879 - Vvi1g1274 Vvi1g1274 1274
1 21460122 21461397 - Vvi1g1275 Vvi1g1275 1275
1 21477710 21484817 + Vvi1g1276 Vvi1g1276 1276
1 21491274 21495686 - Vvi1g1277 Vvi1g1277 1277
1 21504804 21506303 + Vvi1g1278 Vvi1g1278 1278
1 21510137 21511444 - Vvi1g1279 Vvi1g1279 1279
1 21560277 21561387 + Vvi1g1280 Vvi1g1280 1280
       

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