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
Vvi17g256 . . . . . . . . . . . Cma11g00296 . . . . Cpe04g01386 Bhi02g00113 . . . . . . . . . . . . . . . . . . . . . . Blo15g00062 . . . . . . . Cmo10g00339 Cmo11g00301 . . . . . . . . . . . . . . . . . . . . . Csa01g00418 Chy02g02328 .
Vvi17g257 Blo04g00836 . . . . . . . Cmo13g01040 . . . . . . . . . . . . . . . . . . . . . . Cone2ag0745 . . Cone19ag0320 Lsi02g00218 . . . . . . . . Bpe15g00535 Bma03g00903 . Sed01g1752 . . Cma13g01004 . Car13g00839 . . . Bhi08g01270 Tan05g2217 Cmetu08g1322 Lac10g0272 Hepe07g2367 . . Cla04g01063 Cam04g1106 Cec01g1620 Cco01g1667 Clacu04g1131 Cmu04g1115 Cre01g1416 . . . .
Vvi17g258 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g259 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g260 . . . Bda15g00503 Bpe12g00704 . . . . . Cma10g00315 . Car10g00298 . Sed02g0995 . . Bhi02g00111 Tan09g2059 Cmetu09g0221 . Hepe09g0369 . . . . . . . . . . . . . . . . . Blo13g00181 . . . . . . Bma08g00006 . Cmo10g00338 . . . . . . . . . . . . . . . . . . . . . Lsi06g01305 Csa01g00410 Chy02g02334 Cme02g01706
Vvi17g261 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g262 Blo04g00835 Blo16g00127 . . . Bpe13g00366 Bma06g00054 . Cmo13g01041 . . . . . . Cpe20g00139 . . . . . . . . . . . . . . . . . . . Lsi02g00217 Csa01g00699 Chy12g01413 Cme12g01847 . . Bda11g01779 . . Bpe15g00534 . . Sed02g0902 . . . Cma18g00056 . . Cpe09g01125 . Bhi08g01269 Tan05g2218 Cmetu05g1284 Lac10g0271 Hepe07g2368 . . Cla04g01064 Cam04g1107 Cec01g1621 Cco01g1668 Clacu04g1132 Cmu04g1116 Cre01g1417 . . . .
Vvi17g263 . . . . . . . . . . . Cma11g00295 . Car11g00270 Sed08g0381 . Cpe04g01387 Bhi02g00110 Tan09g1858 Cmetu05g0415 . Hepe09g0368 . . Cla06g01441 Cam06g1595 Cec06g1656 Cco06g1649 Clacu06g1558 Cmu06g1512 Cre06g2320 . . . . . . . . . . . . . . . . . . Cmo11g00300 . . . . . . . . . . . . . . . . . . . . Lsi06g01306 Csa01g00409 Chy02g02335 Cme02g01709
Vvi17g264 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g265 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 52651398 52652999 - Bda008701.1 Bda11g01779 1779
15 8119905 8132325 + Bda012333.1 Bda15g00503 503
2 2026440 2029257 + XM_039024340.1 Bhi02g00110 110
2 2047601 2056433 + XM_039023279.1 Bhi02g00111 111
2 2073321 2077557 + XM_039023384.1 Bhi02g00113 113
8 38977415 38979441 - XM_039038730.1 Bhi08g01269 1269
8 39000544 39001837 - XM_039039792.1 Bhi08g01270 1270
4 8967233 8968834 - BLOR13747 Blo04g00835 835
4 8982244 8983796 - BLOR13748 Blo04g00836 836
13 6977101 6995097 - BLOR05462 Blo13g00181 181
15 496856 500526 + BLOR06456 Blo15g00062 62
16 2888286 2889887 + BLOR07375 Blo16g00127 127
3 8965982 8966575 - Bma017228.1 Bma03g00903 903
6 881019 882620 - Bma022665.1 Bma06g00054 54
8 118875 130312 + Bma026996.1 Bma08g00006 6
12 12591111 12609667 - Bpe005964.2 Bpe12g00704 704
13 11423975 11425429 - Bpe006492.1 Bpe13g00366 366
15 16493274 16494170 - Bpe001469.1 Bpe15g00534 534
15 16496196 16497308 - Bpe001470.1 Bpe15g00535 535
4 25216869 25219576 + CaPI482276_04g011060.1 Cam04g1106 1106
4 25220802 25222403 + CaPI482276_04g011070.1 Cam04g1107 1107
6 27421547 27442944 + CaPI482276_06g015950.1 Cam06g1595 1595
10 1440769 1449011 + Carg15165-RA Car10g00298 298
11 1484703 1487130 + Carg09119-RA Car11g00270 270
13 9044196 9045647 + Carg04833-RA Car13g00839 839
1 29431402 29434098 + CcPI632755_01g016670.1 Cco01g1667 1667
1 29437352 29438953 + CcPI632755_01g016680.1 Cco01g1668 1668
6 27089218 27091380 + CcPI632755_06g016490.1 Cco06g1649 1649
1 30868393 30871095 + CePI673135_01g016200.1 Cec01g1620 1620
1 30874495 30876096 + CePI673135_01g016210.1 Cec01g1621 1621
6 30162880 30165033 + CePI673135_06g016560.1 Cec06g1656 1656
2 27261532 27265048 + Chy2G045950.1 Chy02g02328 2328
2 27293222 27300467 - Chy2G046010.1 Chy02g02334 2334
2 27304367 27306606 - Chy2G046020.1 Chy02g02335 2335
12 18226809 18228410 + Chy12G220130.1 Chy12g01413 1413
4 25588570 25591272 + ClG42_04g0113100.10 Clacu04g1131 1131
4 25592446 25594047 + ClG42_04g0113200.10 Clacu04g1132 1132
6 26488665 26490969 + ClG42_06g0155800.10 Clacu06g1558 1558
4 25808576 25816511 + ClCG04G010800.2 Cla04g01063 1063
4 25817685 25819286 + ClCG04G010810.1 Cla04g01064 1064
6 27986719 27988881 + ClCG06G014540.1 Cla06g01441 1441
10 1428868 1436832 + CmaCh10G003150.1 Cma10g00315 315
11 1465378 1468390 + CmaCh11G002950.1 Cma11g00295 295
11 1469380 1472250 + CmaCh11G002960.1 Cma11g00296 296
13 7752516 7753967 + CmaCh13G010040.1 Cma13g01004 1004
18 241922 243523 - CmaCh18G000560.1 Cma18g00056 56
2 24120225 24128364 - MELO3C017336.2.1 Cme02g01706 1706
2 24145488 24148385 - MELO3C017334.2.1 Cme02g01709 1709
12 24799860 24801936 + MELO3C002117.2.1 Cme12g01847 1847
5 4155832 4158211 - PI0015031.1 Cmetu05g0415 415
5 183541 189112 + PI0026354.1 Cmetu05g1284 1284
8 7545336 7548556 + PI0010631.1 Cmetu08g1322 1322
9 21310588 21312611 - PI0014506.1 Cmetu09g0221 221
10 1517532 1526309 + CmoCh10G003380.1 Cmo10g00338 338
10 1527518 1532778 + CmoCh10G003390.1 Cmo10g00339 339
11 1446008 1450897 + CmoCh11G003000.1 Cmo11g00300 300
11 1452068 1455446 + CmoCh11G003010.1 Cmo11g00301 301
13 8744009 8745466 + CmoCh13G010400.1 Cmo13g01040 1040
13 8746037 8749978 + CmoCh13G010410.1 Cmo13g01041 1041
4 25769654 25772375 + CmPI595203_04g011150.1 Cmu04g1115 1115
4 25773549 25775150 + CmPI595203_04g011160.1 Cmu04g1116 1116
6 26391978 26394282 + CmPI595203_06g015120.1 Cmu06g1512 1512
2 33228875 33230190 - Conep02aG0175800.1 Cone2ag0745 745
19 2528600 2529064 + Conep19aG0033100.1 Cone19ag0320 320
4 11213709 11221274 - Cp4.1LG04g13910.1 Cpe04g01386 1386
4 11222436 11225120 - Cp4.1LG04g13900.1 Cpe04g01387 1387
9 9668267 9669868 + Cp4.1LG09g11240.1 Cpe09g01125 1125
20 775578 777179 - Cp4.1LG20g01470.1 Cpe20g00139 139
1 27421613 27424337 + CrPI670011_01g014160.1 Cre01g1416 1416
1 27427756 27429357 + CrPI670011_01g014170.1 Cre01g1417 1417
6 31148932 31161275 + CrPI670011_06g023200.1 Cre06g2320 2320
1 2564011 2566523 + CsaV3_1G004090.1 Csa01g00409 409
1 2569251 2577675 + CsaV3_1G004100.1 Csa01g00410 410
1 2606644 2607971 - CsaV3_1G004180.1 Csa01g00418 418
1 4425616 4428136 - CsaV3_1G006990.1 Csa01g00699 699
7 68050420 68052350 + Hsped.07g23670.1 Hepe07g2367 2367
7 68056198 68058248 + Hsped.07g23680.1 Hepe07g2368 2368
9 3248696 3250901 + Hsped.09g03680.1 Hepe09g0368 368
9 3252942 3261796 + Hsped.09g03690.1 Hepe09g0369 369
10 2058818 2060419 - Lag0024316.1 Lac10g0271 271
10 2061710 2063492 - Lag0024317.1 Lac10g0272 272
2 1790788 1792389 - Lsi02G002170.1 Lsi02g00217 217
2 1794440 1796869 - Lsi02G002180.1 Lsi02g00218 218
6 23612871 23621377 - Lsi06G013050.1 Lsi06g01305 1305
6 23624029 23626696 - Lsi06G013060.1 Lsi06g01306 1306
1 12728615 12730869 - Sed0001976.1 Sed01g1752 1752
2 46496790 46503256 + Sed0013215.1 Sed02g0902 902
2 47350195 47352840 - Sed0002514.1 Sed02g0995 995
8 2303753 2306686 + Sed0026718.1 Sed08g0381 381
5 73167909 73182174 + Tan0020517.1 Tan05g2217 2217
5 73185428 73187532 + Tan0021411.1 Tan05g2218 2218
9 69866110 69868458 - Tan0016339.1 Tan09g1858 1858
9 71072638 71086567 - Tan0005364.1 Tan09g2059 2059
17 2767984 2782669 - Vvi17g256 Vvi17g256 256
17 2798897 2800520 + Vvi17g257 Vvi17g257 257
17 2801894 2818700 - Vvi17g258 Vvi17g258 258
17 2821132 2821522 - Vvi17g259 Vvi17g259 259
17 2821873 2869660 - Vvi17g260 Vvi17g260 260
17 2870159 2871375 - Vvi17g261 Vvi17g261 261
17 2871427 2872600 + Vvi17g262 Vvi17g262 262
17 2877373 2879496 - Vvi17g263 Vvi17g263 263
17 2882629 2888851 - Vvi17g264 Vvi17g264 264
17 2893560 2898013 + Vvi17g265 Vvi17g265 265
       

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