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
Vvi5g1279 . . . . . . . . Cmo08g00196 . . . . . . . . . . . . . . . Cla06g00091 Cam06g0127 Cec06g0103 Cco06g0098 Clacu06g0102 Cmu06g0099 Cre06g0870 . . . . . . . . . . . . . . . . Sed09g0403 . . . . . . . Cpe17g01085 Bhi12g02498 Tan06g1556 Cmetu11g0956 . . . . . . . . . . . . . . Cme11g02452
Vvi5g1280 . . . . . Bpe14g01069 . . . . Cma06g01701 Cma14g01419 . Car14g01252 Sed02g0966 . Cpe03g01194 Bhi01g03703 Tan10g1398 Cmetu07g0313 . Hepe05g1115 . Lcy11g1016 . . . . . . . . . . Cone11ag0645 . . . Cme07g01966 Blo02g00452 Blo07g00121 Bda11g00482 Bda13g00247 . . Bma02g00962 Bma06g01446 . . Cmo14g01455 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1281 . Blo12g00265 Bda03g00973 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo07g00135 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1282 . . . . . Bpe14g01071 . . . . Cma06g01699 Cma14g01422 . Car14g01253 Sed02g0971 . . Bhi01g03700 Tan10g1402 Cmetu07g1098 . . . . . . . . . . . . . . . . . . Cme07g01963 Blo02g00454 . . Bda13g00245 . . Bma02g00960 . . . Cmo14g01457 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1283 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1284 Blo01g00188 . . Bda08g00162 . . . Bma05g01162 . . . . . . . . . . . . . . . . . . . . . . . . . Cone18ag0860 Cone11ag0646 . . . . . . . . Bpe05g00969 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1285 . . . . . . . . . . . Cma14g01425 . Car14g01255 . . Cpe03g01198 . . . . . . . . . . . . . . Cone14ag0625 Cone15ag0635 Cone18ag0862 Cone11ag0647 . . . Cme07g01957 . . . . . . . . . . Cmo14g01461 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1286 . . . . . . . . . . . Cma14g01426 . Car14g01256 . . . . . . . . . . . . . . . . . . . Cone18ag0863 . . . . Cme07g01955 . . . . . . . . . . Cmo14g01462 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1287 . . Bda03g00972 . Bpe04g00898 . . . . . . Cma14g01427 . Car14g01257 Sed12g0549 . Cpe03g01199 Bhi01g03696 Tan10g1419 Cmetu07g0756 . . . . . . . . . . . . . . Cone11ag0649 . . . Cme07g01953 . . . . . . . . . . Cmo14g01463 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1288 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 8779486 8781679 + Bda016982.1 Bda03g00972 972
3 8787227 8789146 + Bda016983.1 Bda03g00973 973
8 1513139 1515104 + Bda024571.1 Bda08g00162 162
11 5105560 5110444 + Bda005219.1 Bda11g00482 482
13 3097236 3100563 + Bda001127.1 Bda13g00245 245
13 3105543 3111401 - Bda001128.3 Bda13g00247 247
1 94715484 94721132 - XM_039019195.1 Bhi01g03696 3696
1 94801094 94806880 + XM_039046185.1 Bhi01g03700 3700
1 94842602 94852280 - XM_039018939.1 Bhi01g03703 3703
12 78430266 78433247 + XM_039050740.1 Bhi12g02498 2498
1 2568618 2570524 - BLOR00188 Blo01g00188 188
2 6333666 6339322 + BLOR10182 Blo02g00452 452
2 6385050 6388795 - BLOR10184 Blo02g00454 454
7 1660249 1669490 + BLOR18053 Blo07g00121 121
7 1829977 1836647 + BLOR18067 Blo07g00135 135
12 16064812 16093910 - BLOR04284 Blo12g00265 265
2 49636560 49639852 + Bma015758.1 Bma02g00960 960
2 49645563 49651138 - Bma015759.2 Bma02g00962 962
5 50680447 50681831 - Bma022352.1 Bma05g01162 1162
6 51167442 51169501 + Bma024561.1 Bma06g01446 1446
4 6018654 6020802 + Bpe015561.2 Bpe04g00898 898
5 22553270 22555264 - Bpe018381.1 Bpe05g00969 969
14 8022055 8027595 + Bpe014443.1 Bpe14g01069 1069
14 8032910 8036109 - Bpe014445.1 Bpe14g01071 1071
6 3230620 3241077 + CaPI482276_06g001270.1 Cam06g0127 127
14 10795346 10805374 + Carg06573-RA Car14g01252 1252
14 10806090 10814199 - Carg06574-RA Car14g01253 1253
14 10820203 10824923 + Carg06576-RA Car14g01255 1255
14 10825555 10827208 - Carg06577-RA Car14g01256 1256
14 10827702 10831950 - Carg06578-RA Car14g01257 1257
6 917563 919299 - CcPI632755_06g000980.1 Cco06g0098 98
6 948974 950747 - CePI673135_06g001030.1 Cec06g0103 103
6 1106004 1115767 - ClG42_06g0010200.10 Clacu06g0102 102
6 936358 946787 - ClCG06G000980.2 Cla06g00091 91
6 10443832 10448190 + CmaCh06G016990.1 Cma06g01699 1699
6 10452238 10464666 - CmaCh06G017010.1 Cma06g01701 1701
14 10918230 10924329 + CmaCh14G014190.1 Cma14g01419 1419
14 10930193 10933987 - CmaCh14G014220.1 Cma14g01422 1422
14 10942629 10948323 + CmaCh14G014250.1 Cma14g01425 1425
14 10948718 10949952 - CmaCh14G014260.1 Cma14g01426 1426
14 10950509 10960239 - CmaCh14G014270.1 Cma14g01427 1427
7 24674362 24678020 + MELO3C017776.2.1 Cme07g01953 1953
7 24679188 24681686 + MELO3C017777.2.1 Cme07g01955 1955
7 24682228 24689879 - MELO3C017779.2.1 Cme07g01957 1957
7 24732236 24737930 + MELO3C017786.2.1 Cme07g01963 1963
7 24744567 24755225 - MELO3C017790.2.1 Cme07g01966 1966
11 31244868 31250862 + MELO3C022441.2.1 Cme11g02452 2452
7 2138112 2146192 + PI0000424.1 Cmetu07g0313 313
7 2209442 2214008 - PI0009602.1 Cmetu07g0756 756
7 2154407 2159914 - PI0016985.1 Cmetu07g1098 1098
11 748330 750527 - PI0018290.1 Cmetu11g0956 956
8 1144106 1147195 + CmoCh08G001960.1 Cmo08g00196 196
14 11819350 11825256 + CmoCh14G014550.1 Cmo14g01455 1455
14 11831157 11836219 - CmoCh14G014570.1 Cmo14g01457 1457
14 11845226 11850958 + CmoCh14G014610.1 Cmo14g01461 1461
14 11851445 11853175 - CmoCh14G014620.1 Cmo14g01462 1462
14 11853499 11857298 - CmoCh14G014630.1 Cmo14g01463 1463
6 894953 905342 - CmPI595203_06g000990.1 Cmu06g0099 99
11 4281071 4286828 + Conep11aG0066200.1 Cone11ag0645 645
11 4291733 4295792 + Conep11aG0066300.1 Cone11ag0646 646
11 4297679 4305619 + Conep11aG0066400.1 Cone11ag0647 647
11 4313548 4317256 - Conep11aG0066600.1 Cone11ag0649 649
14 3133014 3136075 + Conep14aG0063900.1 Cone14ag0625 625
15 3320285 3329199 + Conep15aG0064800.1 Cone15ag0635 635
18 5909299 5914223 - Conep18aG0088600.1 Cone18ag0860 860
18 5937977 5948390 + Conep18aG0088800.1 Cone18ag0862 862
18 5949001 5951938 - Conep18aG0088900.1 Cone18ag0863 863
3 9777035 9783003 + Cp4.1LG03g13250.1 Cpe03g01194 1194
3 9802024 9807683 + Cp4.1LG03g13060.1 Cpe03g01198 1198
3 9808013 9813881 - Cp4.1LG03g13020.1 Cpe03g01199 1199
17 8227991 8229815 + Cp4.1LG17g10780.1 Cpe17g01085 1085
6 1998054 2004508 - CrPI670011_06g008700.1 Cre06g0870 870
5 55120279 55127480 + Hsped.05g11150.1 Hepe05g1115 1115
11 31045403 31054798 + Maker00037568 Lcy11g1016 1016
2 47190067 47197837 + Sed0012019.2 Sed02g0966 966
2 47204183 47210042 - Sed0021507.1 Sed02g0971 971
9 3858360 3861591 + Sed0001553.2 Sed09g0403 403
12 3353036 3357461 - Sed0015623.1 Sed12g0549 549
6 24082355 24084671 + Tan0008654.1 Tan06g1556 1556
10 18721499 18729120 + Tan0014398.2 Tan10g1398 1398
10 18858739 18864266 - Tan0008285.1 Tan10g1402 1402
10 19050615 19055265 - Tan0007599.1 Tan10g1419 1419
5 23364999 23368333 - Vvi5g1279 Vvi5g1279 1279
5 23397412 23403662 + Vvi5g1280 Vvi5g1280 1280
5 23407513 23410306 - Vvi5g1281 Vvi5g1281 1281
5 23448148 23451578 - Vvi5g1282 Vvi5g1282 1282
5 23451589 23454866 - Vvi5g1283 Vvi5g1283 1283
5 23457926 23461484 - Vvi5g1284 Vvi5g1284 1284
5 23463410 23471324 + Vvi5g1285 Vvi5g1285 1285
5 23471447 23475044 - Vvi5g1286 Vvi5g1286 1286
5 23476503 23482193 - Vvi5g1287 Vvi5g1287 1287
5 23484127 23488627 + Vvi5g1288 Vvi5g1288 1288
       

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