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
Vvi5g69 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g70 . . . . . . . . . . Cma06g01562 . Car06g01327 . Sed02g1137 Cpe08g00151 . Bhi01g01088 Tan10g1075 Cmetu06g0442 . Hepe05g1383 . Lcy11g1338 . . . . . . . . . Cone7ag0100 . Lsi05g01595 . . Cme06g00788 . Blo07g00145 Bda11g00502 . . Bpe13g00695 . . . Cmo06g01559 . . . . . . . . . . . . . . Cla05g00705 Cam05g0772 Cec05g0780 Cco05g0773 Clacu05g0762 Cmu05g0728 Cre05g0802 . Csa03g01517 Chy06g00754 .
Vvi5g71 . . . . . . . . . . . . . Car14g01401 Sed12g0774 . Cpe03g01329 Bhi01g01087 Tan10g1074 Cmetu06g1614 . Hepe05g1384 . Lcy11g1339 . . . . . . . . . . . Lsi05g01594 . . Cme06g00787 . Blo07g00146 . . . Bpe13g00694 . Bma06g01468 . . Cmo14g01621 . . . . . . . . . . . . . Cla05g00704 Cam05g0770 Cec05g0779 Cco05g0772 Clacu05g0760 Cmu05g0726 Cre05g0800 . Csa03g01516 Chy06g00753 .
Vvi5g72 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g73 . . Bda03g01178 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g74 . . . . . . . . . . Cma06g01561 . Car06g01326 . Sed02g1138 Cpe08g00152 . Bhi01g01086 Tan10g1073 Cmetu06g0331 . Hepe05g1386 . Lcy11g1341 . . . . . . . . . . . Lsi05g01590 . . Cme06g00786 . Blo07g00148 Bda11g00503 . . . . Bma06g01469 . Cmo06g01558 . . . . . . . . . . . . . . Cla05g00703 Cam05g0769 Cec05g0778 Cco05g0771 Clacu05g0759 Cmu05g0725 Cre05g0799 . Csa03g01515 Chy06g00752 .
Vvi5g75 . Blo12g00082 Bda03g01176 . Bpe04g01114 . Bma04g01129 . Cmo08g01242 Cmo17g00356 . . . . . . . . . . . . . . Cla06g00431 Cam06g0457 Cec06g0463 Cco06g0462 Clacu06g0444 Cmu06g0445 Cre06g1221 Cone14ag0722 Cone15ag0731 . . . Csa06g01741 Chy11g01565 . . . . . . . . . Sed04g3106 . . Cma08g01274 Cma17g00366 Car08g01144 Car17g00339 Cpe12g00317 Cpe17g00066 Bhi12g01925 Tan06g2751 Cmetu11g1721 Lac11g0932 Hepe03g0048 . Lcy12g0802 . . . . . . . . . . Cme11g02077
Vvi5g76 . Blo12g00084 Bda03g01174 . Bpe04g01113 Bpe14g01101 . . . . . Cma14g01591 Car06g01325 Car14g01405 Sed12g0777 Cpe08g00153 Cpe03g01331 Bhi01g01084 Tan10g1071 Cmetu06g1226 . Hepe05g1388 . Lcy11g1343 . . . . . . . Cone14ag0723 Cone15ag0732 . . Lsi05g01588 . . Cme06g00783 Blo02g00478 Blo07g00150 Bda11g00504 Bda13g00215 . Bpe13g00693 . Bma06g01471 . . Cmo14g01623 . . . . . . . . . . . . . Cla05g00701 Cam05g0767 Cec05g0776 Cco05g0769 Clacu05g0757 Cmu05g0723 Cre05g0797 . Csa03g01513 Chy06g00750 .
Vvi5g77 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g78 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 13530086 13531073 - Bda017244.1 Bda03g01174 1174
3 13552500 13558604 + Bda017247.1 Bda03g01176 1176
3 13699470 13713927 - Bda017249.1 Bda03g01178 1178
11 5335023 5338258 + Bda005237.1 Bda11g00502 502
11 5346503 5348062 + Bda005238.1 Bda11g00503 503
11 5350741 5352207 + Bda005239.1 Bda11g00504 504
13 2755516 2756628 - Bda001091.1 Bda13g00215 215
1 20412708 20415337 - XM_039033445.1 Bhi01g01084 1084
1 20436115 20444756 - XM_039024532.1 Bhi01g01086 1086
1 20506330 20509461 + XM_039022025.1 Bhi01g01087 1087
1 20592938 20600715 - XM_039038644.1 Bhi01g01088 1088
12 61305691 61317620 - XM_039019919.1 Bhi12g01925 1925
2 6988987 6990126 + BLOR10208 Blo02g00478 478
7 1924701 1927946 + BLOR18077 Blo07g00145 145
7 1928277 1939372 - BLOR18078 Blo07g00146 146
7 1947717 1953915 + BLOR18080 Blo07g00148 148
7 1965308 1970234 + BLOR18082 Blo07g00150 150
12 5523264 5529672 - BLOR04101 Blo12g00082 82
12 5636560 5638625 + BLOR04103 Blo12g00084 84
4 28035143 28041106 - Bma019840.1 Bma04g01129 1129
6 51333492 51335492 - Bma024583.1 Bma06g01468 1468
6 51338861 51343860 + Bma031332 Bma06g01469 1469
6 51351121 51352154 + Bma024585.1 Bma06g01471 1471
4 9009885 9010880 - Bpe015790.1 Bpe04g01113 1113
4 9024778 9030879 + Bpe015791.1 Bpe04g01114 1114
13 13572972 13582426 - Bpe010394.1 Bpe13g00693 693
13 13584984 13586964 + Bpe010395.1 Bpe13g00694 694
13 13587294 13590444 - Bpe010396.1 Bpe13g00695 695
14 8209770 8210891 + Bpe014475.1 Bpe14g01101 1101
5 6684293 6686672 - CaPI482276_05g007670.1 Cam05g0767 767
5 6697960 6711560 - CaPI482276_05g007690.1 Cam05g0769 769
5 6722742 6725568 + CaPI482276_05g007700.1 Cam05g0770 770
5 6728696 6736257 - CaPI482276_05g007720.1 Cam05g0772 772
6 6693669 6702285 + CaPI482276_06g004570.1 Cam06g0457 457
6 9472089 9474125 - Carg23737-RA Car06g01325 1325
6 9475674 9483350 - Carg23736-RA Car06g01326 1326
6 9483786 9488597 - Carg23735-RA Car06g01327 1327
8 7703369 7708586 - Carg18886-RA Car08g01144 1144
14 11816919 11819225 - Carg19622-RA Car14g01401 1401
14 11834297 11835255 + Carg19626-RA Car14g01405 1405
17 2119106 2127692 - Carg05545-RA Car17g00339 339
5 6392106 6394512 - CcPI632755_05g007690.1 Cco05g0769 769
5 6406290 6420421 - CcPI632755_05g007710.1 Cco05g0771 771
5 6430282 6434436 + CcPI632755_05g007720.1 Cco05g0772 772
5 6437532 6444861 - CcPI632755_05g007730.1 Cco05g0773 773
6 5080864 5089479 + CcPI632755_06g004620.1 Cco06g0462 462
5 6417675 6419986 - CePI673135_05g007760.1 Cec05g0776 776
5 6429329 6445730 - CePI673135_05g007780.1 Cec05g0778 778
5 6456710 6459531 + CePI673135_05g007790.1 Cec05g0779 779
5 6461831 6470214 - CePI673135_05g007800.1 Cec05g0780 780
6 5217173 5225754 + CePI673135_06g004630.1 Cec06g0463 463
6 5155926 5157692 - Chy6G112780.1 Chy06g00750 750
6 5164847 5173187 - Chy6G112800.1 Chy06g00752 752
6 5190736 5193607 + Chy6G112810.1 Chy06g00753 753
6 5195050 5201292 - Chy6G112820.1 Chy06g00754 754
11 22174285 22181876 - Chy11G201450.1 Chy11g01565 1565
5 6403632 6406013 - ClG42_05g0075700.10 Clacu05g0757 757
5 6416291 6431227 - ClG42_05g0075900.10 Clacu05g0759 759
5 6436864 6439681 + ClG42_05g0076000.10 Clacu05g0760 760
5 6442808 6450347 - ClG42_05g0076200.10 Clacu05g0762 762
6 5229152 5237777 + ClG42_06g0044400.10 Clacu06g0444 444
5 6530872 6533493 - ClCG05G006520.2 Cla05g00701 701
5 6545532 6560479 - ClCG05G006530.2 Cla05g00703 703
5 6571594 6574459 + ClCG05G006540.1 Cla05g00704 704
5 6576749 6585111 - ClCG05G006550.2 Cla05g00705 705
6 5264023 5272967 + ClCG06G004610.1 Cla06g00431 431
6 9772657 9784384 - CmaCh06G015610.1 Cma06g01561 1561
6 9785377 9790681 - CmaCh06G015620.1 Cma06g01562 1562
8 7737287 7747448 - CmaCh08G012740.1 Cma08g01274 1274
14 11950117 11961254 + CmaCh14G015910.1 Cma14g01591 1591
17 2030351 2038996 - CmaCh17G003660.1 Cma17g00366 366
6 5190260 5192942 - MELO3C006711.2.1 Cme06g00783 783
6 5200483 5208781 - MELO3C006713.2.1 Cme06g00786 786
6 5218607 5221541 + MELO3C006714.2.1 Cme06g00787 787
6 5222561 5229534 - MELO3C006715.2.1 Cme06g00788 788
11 28446761 28454845 - MELO3C021272.2.1 Cme11g02077 2077
6 5406639 5419389 - PI0016255.1 Cmetu06g0331 331
6 5436327 5442355 - PI0020489.1 Cmetu06g0442 442
6 5400268 5402849 - PI0003877.1 Cmetu06g1226 1226
6 5431596 5434928 + PI0003535.1 Cmetu06g1614 1614
11 3775056 3783483 + PI0020156.1 Cmetu11g1721 1721
6 10968856 10980404 - CmoCh06G015580.1 Cmo06g01558 1558
6 10980938 10985593 - CmoCh06G015590.1 Cmo06g01559 1559
8 7855275 7860704 - CmoCh08G012420.1 Cmo08g01242 1242
14 12877158 12878141 - CmoCh14G016210.1 Cmo14g01621 1621
14 12893415 12898227 + CmoCh14G016230.1 Cmo14g01623 1623
17 2168133 2177392 - CmoCh17G003560.1 Cmo17g00356 356
5 6246816 6249202 - CmPI595203_05g007230.1 Cmu05g0723 723
5 6265373 6280320 - CmPI595203_05g007250.1 Cmu05g0725 725
5 6291257 6294057 + CmPI595203_05g007260.1 Cmu05g0726 726
5 6297184 6304723 - CmPI595203_05g007280.1 Cmu05g0728 728
6 5032240 5040864 + CmPI595203_06g004450.1 Cmu06g0445 445
7 435555 438515 + Conep07aG0010100.1 Cone7ag0100 100
14 3991627 3998299 - Conep14aG0073800.1 Cone14ag0722 722
14 3999473 4001148 + Conep14aG0073900.1 Cone14ag0723 723
15 4201522 4207836 - Conep15aG0074600.1 Cone15ag0731 731
15 4208780 4210650 + Conep15aG0074700.1 Cone15ag0732 732
3 10797687 10800762 - Cp4.1LG03g11730.1 Cpe03g01329 1329
3 10816823 10820082 + Cp4.1LG03g11740.1 Cpe03g01331 1331
8 984673 989389 + Cp4.1LG08g05370.1 Cpe08g00151 151
8 990198 997892 + Cp4.1LG08g05180.1 Cpe08g00152 152
8 998890 1001263 + Cp4.1LG08g05200.1 Cpe08g00153 153
12 2101994 2110553 - Cp4.1LG12g03290.1 Cpe12g00317 317
17 391085 396354 - Cp4.1LG17g00220.1 Cpe17g00066 66
5 7041507 7043845 - CrPI670011_05g007970.1 Cre05g0797 797
5 7055593 7069708 - CrPI670011_05g007990.1 Cre05g0799 799
5 7080867 7083714 + CrPI670011_05g008000.1 Cre05g0800 800
5 7086856 7094426 - CrPI670011_05g008020.1 Cre05g0802 802
6 6087745 6096344 + CrPI670011_06g012210.1 Cre06g1221 1221
3 11237408 11239834 - CsaV3_3G015130.1 Csa03g01513 1513
3 11245961 11254456 - CsaV3_3G015150.1 Csa03g01515 1515
3 11265033 11267518 + CsaV3_3G015160.1 Csa03g01516 1516
3 11268488 11278469 - CsaV3_3G015170.1 Csa03g01517 1517
6 15307392 15314978 + CsaV3_6G022360.1 Csa06g01741 1741
3 596891 604822 + Hsped.03g00480.1 Hepe03g0048 48
5 62586414 62595562 + Hsped.05g13830.1 Hepe05g1383 1383
5 62595626 62602560 - Hsped.05g13840.1 Hepe05g1384 1384
5 62616976 62628085 + Hsped.05g13860.1 Hepe05g1386 1386
5 62639720 62643144 + Hsped.05g13880.1 Hepe05g1388 1388
11 10144511 10158297 - Lag0031570.1 Lac11g0932 932
11 37049960 37062749 + Maker00031778 Lcy11g1338 1338
11 37061619 37063812 - Maker00031451 Lcy11g1339 1339
11 37079805 37085960 + Maker00031826 Lcy11g1341 1341
11 37097647 37099853 + Maker00031339 Lcy11g1343 1343
12 10447106 10455969 - Maker00024925 Lcy12g0802 802
5 23656849 23660910 - Lsi05G015880.1 Lsi05g01588 1588
5 23666410 23677834 - Lsi05G015900.1 Lsi05g01590 1590
5 23693641 23695371 + Lsi05G015940.1 Lsi05g01594 1594
5 23697349 23706072 - Lsi05G015950.1 Lsi05g01595 1595
2 48576897 48585581 + Sed0008833.1 Sed02g1137 1137
2 48585590 48591770 + Sed0004607.1 Sed02g1138 1138
4 41960692 41970190 + Sed0015207.2 Sed04g3106 3106
12 4707946 4711597 - Sed0016592.1 Sed12g0774 774
12 4735840 4739597 + Sed0009654.1 Sed12g0777 777
6 79794649 79800939 - Tan0002365.2 Tan06g2751 2751
10 9916012 9921897 - Tan0015658.1 Tan10g1071 1071
10 9935506 9944369 - Tan0020038.1 Tan10g1073 1073
10 9970516 9975306 + Tan0002161.1 Tan10g1074 1074
10 9975606 9983218 - Tan0012616.1 Tan10g1075 1075
5 771997 782548 + Vvi5g69 Vvi5g69 69
5 783314 788171 + Vvi5g70 Vvi5g70 70
5 788237 792303 - Vvi5g71 Vvi5g71 71
5 795481 796805 - Vvi5g72 Vvi5g72 72
5 803250 807772 + Vvi5g73 Vvi5g73 73
5 808813 816916 + Vvi5g74 Vvi5g74 74
5 817347 826514 - Vvi5g75 Vvi5g75 75
5 832977 835192 + Vvi5g76 Vvi5g76 76
5 835194 842179 + Vvi5g77 Vvi5g77 77
5 842261 847720 + Vvi5g78 Vvi5g78 78
       

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