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
Vvi5g1269 . . . . . Bpe14g01060 . . . . Cma06g01613 . Car06g01370 . Sed02g1063 Cpe08g00110 . Bhi01g01190 Tan10g1202 . . . . . . . . . . . . . . Cone18ag0852 Cone11ag0660 . . . . Blo02g00446 Blo07g00113 Bda11g00476 Bda13g00254 . . Bma02g00970 Bma06g01438 . Cmo06g01610 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1270 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1271 Blo01g00192 . . Bda08g00159 . . . . . . . . . . . . . Bhi01g01191 . . . Hepe05g1298 . Lcy11g1257 . . . . . . . . . . . . . . . . . . . Bpe05g00973 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1272 . . . . . . . . . . . . . . Sed02g1061 . . Bhi01g01192 Tan10g1203 Cmetu06g2378 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1273 Blo01g00191 Blo12g00264 . Bda08g00160 . . . . Cmo08g00197 Cmo17g00590 . . . . . . . . . . . . . . Cla06g00090 Cam06g0129 Cec06g0101 Cco06g0096 Clacu06g0101 Cmu06g0098 Cre06g0869 . . . . . . . . . . . . Bpe05g00972 . . . Sed01g0608 . . . . Car08g00176 Car17g00575 . Cpe17g01087 Bhi12g02504 Tan06g1561 Cmetu11g2454 . Hepe03g1070 . . . . . . . . . . . . Cme11g02454
Vvi5g1274 . . . . . . . . . . . . Car06g01373 . Sed12g0690 . . Bhi01g01193 Tan10g1204 Cmetu06g2044 . Hepe05g1297 . Lcy11g1256 . . . . . . . . . . Cone11ag0658 . . . . . Blo07g00114 . . . . . Bma06g01439 . Cmo06g01612 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1275 . . . . . Bpe14g01061 . . . . Cma06g01708 Cma14g01412 . Car14g01242 Sed02g0960 . . Bhi01g03727 Tan10g1384 Cmetu07g1769 . . . Lcy11g1001 . . . . . . . . . . . . . . Cme07g01973 Blo02g00447 Blo07g00115 Bda11g00477 Bda13g00253 . . Bma02g00969 Bma06g01440 . . Cmo14g01447 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1276 . . . . . . . . . . . . . . . . Cpe03g01186 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1277 . . . . . Bpe14g01063 . . . Cmo17g00591 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo02g00449 . Bda11g00478 Bda13g00251 . . Bma02g00967 . . . . . Cma17g00609 Car08g00175 Car17g00576 . Cpe17g01086 . . . . . . . . . . . . . . . . . Cme11g02453
Vvi5g1278 Blo01g00190 . . Bda08g00161 . . . Bma05g01164 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe05g00971 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 1470956 1473054 - Bda024566.1 Bda08g00159 159
8 1476361 1483053 - Bda024567.1 Bda08g00160 160
8 1484096 1486054 - Bda024568.1 Bda08g00161 161
11 4994943 4998142 - Bda005214.1 Bda11g00476 476
11 5011703 5022686 - Bda005215.1 Bda11g00477 477
11 5048458 5050349 - Bda005216.1 Bda11g00478 478
13 3183575 3186874 + Bda001132.1 Bda13g00251 251
13 3211734 3219551 + Bda001134.1 Bda13g00253 253
13 3223467 3227157 + Bda001135.1 Bda13g00254 254
1 23411561 23422206 - XM_039018700.1 Bhi01g01190 1190
1 23454434 23459911 - XM_039042652.1 Bhi01g01191 1191
1 23457213 23459914 - XM_039042663.1 Bhi01g01192 1192
1 23462560 23472661 - XM_039042032.1 Bhi01g01193 1193
1 95735935 95742136 - XM_039050561.1 Bhi01g03727 3727
12 78614070 78628491 - XM_039019889.1 Bhi12g02504 2504
1 2579287 2581571 + BLOR00190 Blo01g00190 190
1 2582938 2588966 + BLOR00191 Blo01g00191 191
1 2592231 2595160 + BLOR00192 Blo01g00192 192
2 6101551 6104045 - BLOR10176 Blo02g00446 446
2 6124000 6131025 - BLOR10177 Blo02g00447 447
2 6154644 6158210 - BLOR10179 Blo02g00449 449
7 1572574 1577719 - BLOR18045 Blo07g00113 113
7 1577956 1584109 - BLOR18046 Blo07g00114 114
7 1588834 1608313 - BLOR18047 Blo07g00115 115
12 16012748 16019587 - BLOR04283 Blo12g00264 264
2 49810460 49813759 + Bma015766.1 Bma02g00967 967
2 49879562 49885597 + Bma015770.1 Bma02g00969 969
2 49888214 49891612 + Bma015771.1 Bma02g00970 970
5 50692475 50695089 + Bma022353.2 Bma05g01164 1164
6 51085516 51090208 - Bma024553.1 Bma06g01438 1438
6 51091846 51098398 - Bma024554.2 Bma06g01439 1439
6 51099076 51104464 - Bma024555.1 Bma06g01440 1440
5 22567826 22569788 + Bpe018383.1 Bpe05g00971 971
5 22570936 22577011 + Bpe018384.1 Bpe05g00972 972
5 22580205 22582414 + Bpe018385.1 Bpe05g00973 973
14 7929959 7933148 - Bpe014434.1 Bpe14g01060 1060
14 7935044 7943525 - Bpe014435.1 Bpe14g01061 1061
14 7952240 7954719 - Bpe014437.1 Bpe14g01063 1063
6 3260133 3273686 + CaPI482276_06g001290.1 Cam06g0129 129
6 9850774 9854180 - Carg15506-RA Car06g01370 1370
6 9869718 9876581 - Carg15503-RA Car06g01373 1373
8 1071366 1074731 + Carg05020-RA Car08g00175 175
8 1075443 1084321 + Carg05021-RA Car08g00176 176
14 10745212 10750468 + Carg06563-RA Car14g01242 1242
17 5451484 5461568 - Carg18907-RA Car17g00575 575
17 5462702 5465620 - Carg18908-RA Car17g00576 576
6 875593 896117 - CcPI632755_06g000960.1 Cco06g0096 96
6 922543 928440 - CePI673135_06g001010.1 Cec06g0101 101
6 1088444 1093560 - ClG42_06g0010100.10 Clacu06g0101 101
6 903927 925442 - ClCG06G000960.2 Cla06g00090 90
6 10037514 10041213 - CmaCh06G016130.1 Cma06g01613 1613
6 10500110 10506823 - CmaCh06G017080.1 Cma06g01708 1708
14 10865338 10870713 + CmaCh14G014120.1 Cma14g01412 1412
17 5153865 5172649 - CmaCh17G006090.1 Cma17g00609 609
7 24865389 24871548 - MELO3C017798.2.1 Cme07g01973 1973
11 31255903 31262189 + MELO3C022442.2.1 Cme11g02453 2453
11 31263017 31274351 + MELO3C022443.2.1 Cme11g02454 2454
6 6086378 6095531 - PI0022223.1 Cmetu06g2044 2044
6 6079836 6085694 - PI0010571.4 Cmetu06g2378 2378
7 2024253 2029715 + PI0005951.1 Cmetu07g1769 1769
11 720393 733965 - PI0027098.1 Cmetu11g2454 2454
6 11262263 11266363 - CmoCh06G016100.1 Cmo06g01610 1610
6 11267763 11275094 - CmoCh06G016120.1 Cmo06g01612 1612
8 1154353 1171444 + CmoCh08G001970.1 Cmo08g00197 197
14 11764510 11773213 + CmoCh14G014470.1 Cmo14g01447 1447
17 6258442 6271254 - CmoCh17G005900.1 Cmo17g00590 590
17 6272311 6275587 - CmoCh17G005910.1 Cmo17g00591 591
6 877871 883148 - CmPI595203_06g000980.1 Cmu06g0098 98
11 4389331 4396128 + Conep11aG0067500.1 Cone11ag0658 658
11 4403987 4408621 + Conep11aG0067700.1 Cone11ag0660 660
18 5842041 5846348 - Conep18aG0087800.1 Cone18ag0852 852
3 9708696 9714831 + Cp4.1LG03g13270.1 Cpe03g01186 1186
8 710408 714062 + Cp4.1LG08g05820.1 Cpe08g00110 110
17 8235964 8239939 + Cp4.1LG17g10730.1 Cpe17g01086 1086
17 8241363 8252364 + Cp4.1LG17g10910.1 Cpe17g01087 1087
6 1980279 1986163 - CrPI670011_06g008690.1 Cre06g0869 869
3 60556255 60570433 - Hsped.03g10700.1 Hepe03g1070 1070
5 61031980 61044168 + Hsped.05g12970.1 Hepe05g1297 1297
5 61069371 61080561 + Hsped.05g12980.1 Hepe05g1298 1298
11 30441704 30449276 + Maker00030890 Lcy11g1001 1001
11 35749180 35758523 + Maker00005282 Lcy11g1256 1256
11 35761326 35767853 + Maker00005204 Lcy11g1257 1257
1 4343620 4352400 + Sed0006734.2 Sed01g0608 608
2 47129400 47137375 + Sed0019662.1 Sed02g0960 960
2 48034501 48040917 + Sed0013039.1 Sed02g1061 1061
2 48043232 48047305 + Sed0025172.1 Sed02g1063 1063
12 4106472 4121743 + Sed0027421.2 Sed12g0690 690
6 24343289 24356382 + Tan0016343.1 Tan06g1561 1561
10 12104647 12109815 - Tan0002397.1 Tan10g1202 1202
10 12134174 12152558 - Tan0021747.1 Tan10g1203 1203
10 12163887 12171715 - Tan0007896.1 Tan10g1204 1204
10 17809268 17815819 + Tan0008240.1 Tan10g1384 1384
5 23226431 23231766 - Vvi5g1269 Vvi5g1269 1269
5 23240256 23242704 + Vvi5g1270 Vvi5g1270 1270
5 23250770 23262877 - Vvi5g1271 Vvi5g1271 1271
5 23266926 23286035 - Vvi5g1272 Vvi5g1272 1272
5 23297174 23305154 - Vvi5g1273 Vvi5g1273 1273
5 23307089 23315437 - Vvi5g1274 Vvi5g1274 1274
5 23317513 23326057 - Vvi5g1275 Vvi5g1275 1275
5 23330063 23338852 - Vvi5g1276 Vvi5g1276 1276
5 23339212 23345975 - Vvi5g1277 Vvi5g1277 1277
5 23355076 23362508 - Vvi5g1278 Vvi5g1278 1278
       

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