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
Vvi1g1261 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1262 Blo01g00178 . . Bda11g00390 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo02g00192 . . Bda11g00390 Bpe14g00793 . . Bma06g01347 . . . . . . . Cpe17g01075 . . . . . . . . . . . . . . . . . . .
Vvi1g1263 . . . . Bpe13g00811 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma06g01346 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1264 . . . . . . . . . . . . . . . . . . . . . . . . Cla06g00204 Cam06g0005 Cec06g0223 Cco06g0219 Clacu06g0219 Cmu06g0214 Cre06g0986 . . . . . . Chy11g01787 Cme11g02319 . Blo12g00277 . . . . . . . . . . . . . Cpe17g01074 . Bhi12g02460 Tan06g1521 . . Hepe03g1107 . . . . . . . . . Lsi09g01720 . . .
Vvi1g1265 . . . . . . . . . . . . . . . . . . . . . . . . Cla06g00203 Cam06g0006 Cec06g0222 Cco06g0218 Clacu06g0218 Cmu06g0213 Cre06g0985 . . . . . Csa04g00305 Chy11g01788 Cme11g02320 . . . . . . . . Sed07g0084 . . . . . . . . Bhi12g02459 Tan06g1520 Cmetu07g2213 . Hepe03g1108 . . . . . . . . . . . Chy07g01477 .
Vvi1g1266 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1267 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1268 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1269 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1270 . . . . . . . . . . . . . . . . . . . . . . . . Cla06g00202 Cam06g0008 Cec06g0221 Cco06g0217 Clacu06g0217 Cmu06g0212 Cre06g0984 . . . . . . Chy11g01789 Cme11g02321 . Blo12g00279 . . . . . . Sed09g0385 . . . . . . Cpe17g01072 . Bhi12g02457 Tan06g1519 Cmetu11g2536 . Hepe03g1109 . . . . . . . . . Lsi09g01722 . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 4246607 4247560 + Bda005130.1 Bda11g00390 390
12 77363557 77403049 + XM_039018643.1 Bhi12g02457 2457
12 77404201 77405628 + XM_039018646.1 Bhi12g02459 2459
12 77407907 77415147 - XM_039019927.1 Bhi12g02460 2460
1 2422784 2425012 + BLOR00178 Blo01g00178 178
2 1744382 1745071 - BLOR09922 Blo02g00192 192
12 16640388 16644820 + BLOR04296 Blo12g00277 277
12 16649107 16668362 - BLOR04298 Blo12g00279 279
6 50384842 50387139 + Bma024459.1 Bma06g01346 1346
6 50389757 50390571 + Bma024460.1 Bma06g01347 1347
13 14438844 14441141 - Bpe010501.1 Bpe13g00811 811
14 6011586 6014434 - Bpe014171.1 Bpe14g00793 793
6 1856743 1863190 + CaPI482276_06g000050.1 Cam06g0005 5
6 1866301 1867261 - CaPI482276_06g000060.1 Cam06g0006 6
6 1880328 1886225 - CaPI482276_06g000080.1 Cam06g0008 8
6 2306524 2325355 + CcPI632755_06g002170.1 Cco06g0217 217
6 2325400 2326344 + CcPI632755_06g002180.1 Cco06g0218 218
6 2329359 2335798 - CcPI632755_06g002190.1 Cco06g0219 219
6 2358294 2377213 + CePI673135_06g002210.1 Cec06g0221 221
6 2377258 2378218 + CePI673135_06g002220.1 Cec06g0222 222
6 2381343 2387777 - CePI673135_06g002230.1 Cec06g0223 223
7 19120884 19122815 + Chy7G143070.1 Chy07g01477 1477
11 24234847 24240032 + Chy11G203670.1 Chy11g01787 1787
11 24242814 24243719 - Chy11G203680.1 Chy11g01788 1788
11 24244590 24255554 - Chy11G203690.1 Chy11g01789 1789
6 2495983 2514377 + ClG42_06g0021700.10 Clacu06g0217 217
6 2514422 2515382 + ClG42_06g0021800.10 Clacu06g0218 218
6 2518324 2524740 - ClG42_06g0021900.10 Clacu06g0219 219
6 2394206 2414122 + ClCG06G002180.2 Cla06g00202 202
6 2413721 2415521 + ClCG06G002190.1 Cla06g00203 203
6 2419644 2426526 - ClCG06G002200.1 Cla06g00204 204
11 30244922 30250747 + MELO3C022310.2.1 Cme11g02319 2319
11 30252461 30254151 - MELO3C022311.2.1 Cme11g02320 2320
11 30254567 30267985 - MELO3C022312.2.1 Cme11g02321 2321
7 2513926 2517246 - PI0011951.1 Cmetu07g2213 2213
11 1829061 1848387 + PI0020919.1 Cmetu11g2536 2536
6 2300076 2317221 + CmPI595203_06g002120.1 Cmu06g0212 212
6 2318537 2319497 + CmPI595203_06g002130.1 Cmu06g0213 213
6 2322448 2328866 - CmPI595203_06g002140.1 Cmu06g0214 214
17 8150984 8159154 + Cp4.1LG17g10770.1 Cpe17g01072 1072
17 8161488 8167077 - Cp4.1LG17g10820.1 Cpe17g01074 1074
17 8170678 8173581 + Cp4.1LG17g10720.1 Cpe17g01075 1075
6 3363884 3386700 + CrPI670011_06g009840.1 Cre06g0984 984
6 3388020 3388956 + CrPI670011_06g009850.1 Cre06g0985 985
6 3392000 3401939 - CrPI670011_06g009860.1 Cre06g0986 986
4 1886380 1888616 - CsaV3_4G003050.1 Csa04g00305 305
3 63614763 63622107 + Hsped.03g11070.1 Hepe03g1107 1107
3 63624591 63625523 - Hsped.03g11080.1 Hepe03g1108 1108
3 63630930 63679889 - Hsped.03g11090.1 Hepe03g1109 1109
9 25778254 25784895 + Lsi09G017200.1 Lsi09g01720 1720
9 25791157 25819289 - Lsi09G017220.1 Lsi09g01722 1722
7 895472 897854 - Sed0011154.2 Sed07g0084 84
9 3518840 3549878 - Sed0008606.1 Sed09g0385 385
6 21691763 21725526 + Tan0010155.1 Tan06g1519 1519
6 21729349 21731514 + Tan0010601.1 Tan06g1520 1520
6 21733151 21741327 - Tan0014319.1 Tan06g1521 1521
1 21096154 21107668 - Vvi1g1261 Vvi1g1261 1261
1 21108239 21119819 - Vvi1g1262 Vvi1g1262 1262
1 21119832 21128587 - Vvi1g1263 Vvi1g1263 1263
1 21155197 21161393 + Vvi1g1264 Vvi1g1264 1264
1 21177721 21180031 - Vvi1g1265 Vvi1g1265 1265
1 21183178 21183481 - Vvi1g1266 Vvi1g1266 1266
1 21183537 21185707 + Vvi1g1267 Vvi1g1267 1267
1 21186171 21192801 - Vvi1g1268 Vvi1g1268 1268
1 21198346 21199218 + Vvi1g1269 Vvi1g1269 1269
1 21202169 21215480 - Vvi1g1270 Vvi1g1270 1270
       

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