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
Vvi5g359 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g360 . . . . . . Bma04g01093 Bma05g01062 . Cmo17g00299 . . . . . . . . . . . . . . Cla06g00501 Cam06g0538 Cec06g0539 Cco06g0542 Clacu06g0523 Cmu06g0525 Cre06g1295 Cone14ag0783 . . . . . . . . . . . Bpe05g00853 . . . Sed09g0638 . . . . . . Cpe12g00261 . Bhi12g02095 Tan06g2633 Cmetu11g1979 Lac12g2382 Hepe03g0124 . Lcy13g0198 . . . . . . . Lsi09g01402 . . .
Vvi5g361 . . . . . Bpe14g01150 . . . . Cma06g01464 Cma14g01644 Car06g01263 Car14g01474 . Cpe08g00215 Cpe03g01388 Bhi01g00949 . . . . . . . . . . . . . . . Cone7ag0178 Cone4ag0174 Lsi05g01501 . . Cme06g00688 Blo02g00578 Blo07g00189 . . . Bpe13g00648 . . . Cmo06g01464 Cmo14g01688 . . . . . . . . . . . . . Cla05g00613 Cam05g0674 Cec05g0684 Cco05g0679 Clacu05g0668 Cmu05g0636 Cre05g0708 . Csa03g01412 Chy06g00655 .
Vvi5g362 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g363 . . Bda03g01210 . Bpe04g01143 . . Bma05g00956 Cmo08g01179 Cmo17g00297 . . . . . . . . . . . . . . Cla06g00504 Cam06g0543 Cec06g0544 Cco06g0551 Clacu06g0529 Cmu06g0528 Cre06g1298 Cone14ag0785 Cone15ag0787 . . . . Chy11g01470 . . . . . Bpe05g00764 . . . . . . Cma08g01205 Cma17g00307 Car08g01081 Car17g00283 Cpe12g00259 Cpe17g00003 Bhi12g01741 . . . . . . . . . . . . . Lsi09g01398 . . Cme11g01978
Vvi5g364 . . . Bda08g00279 . . . . Cmo08g01177 Cmo17g00296 Cma06g01463 Cma14g01645 Car06g01262 Car14g01476 Sed02g1224 . Cpe03g01389 Bhi01g00948 Tan10g0947 Cmetu07g1074 Lac12g2379 Hepe05g1485 . Lcy11g1455 Cla06g00505 Cam06g0544 Cec06g0545 Cco06g0552 Clacu06g0531 Cmu06g0529 Cre06g1299 Cone14ag0786 . Cone7ag0180 Cone4ag0175 Lsi05g01499 . Chy11g01469 Cme06g00687 . . . . . . . . . . Cmo14g01689 Cma08g01203 Cma17g00306 Car08g01080 . Cpe12g00258 Cpe17g00002 Bhi12g01742 . . . . . . Cla05g00612 Cam05g0673 Cec05g0683 Cco05g0677 Clacu05g0667 Cmu05g0635 Cre05g0707 Lsi09g01396 Csa03g01411 Chy06g00654 Cme11g01977
Vvi5g365 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g366 . . . . . . . . . . Cma06g01462 Cma14g01646 . Car14g01479 Sed12g0869 Cpe08g00217 Cpe03g01390 Bhi01g00933 Tan10g0945 Cmetu06g0148 . . . . . . . . . . . Cone14ag0787 Cone15ag0788 . . Lsi05g01498 . . . . . . . . . . . . Cmo06g01462 Cmo14g01690 . . . . . . . . . . . . . Cla05g00611 Cam05g0671 Cec05g0681 Cco05g0675 Clacu05g0666 Cmu05g0634 Cre05g0704 . Csa03g01410 Chy06g00653 .
Vvi5g367 . . . Bda08g00277 . . . Bma05g01064 Cmo08g01176 . . . . . . . . . . . . . . . Cla06g00506 Cam06g0546 Cec06g0546 Cco06g0554 Clacu06g0532 Cmu06g0531 Cre06g1300 . . Cone7ag0181 Cone4ag0176 . . Chy11g01468 . . . . . Bpe05g00855 . . . . . . Cma08g01201 . Car08g01079 . . Cpe17g00001 Bhi12g01743 . . . . . . . . . . . . . Lsi09g01394 . . Cme11g01975
Vvi5g368 . . . . . . . . . . Cma06g01460 Cma14g01647 Car06g01260 Car14g01480 . Cpe08g00218 Cpe03g01391 Bhi01g00928 Tan10g0943 . . . . . . . . . . . . . . . . Lsi05g01497 . . Cme06g00685 . . Bda11g00542 . . Bpe13g00647 . Bma06g01519 Sed01g4000 Cmo06g01461 Cmo14g01691 . . . . . . Bhi12g02125 Tan06g1925 Cmetu09g0227 Lac12g1461 Hepe03g0639 . Lcy13g0912 . . . . . . . . Csa03g01409 Chy06g00652 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 14939428 14940708 - Bda017300.1 Bda03g01210 1210
8 2892266 2895776 + Bda024709.1 Bda08g00277 277
8 2908572 2911354 + Bda024712.1 Bda08g00279 279
11 5660932 5663769 - Bda005277.1 Bda11g00542 542
1 17370317 17375565 + XM_039046507.1 Bhi01g00928 928
1 17384970 17390768 + XM_039044815.1 Bhi01g00933 933
1 17406519 17410332 + XM_039028441.1 Bhi01g00948 948
1 17412968 17417986 - XM_039028432.1 Bhi01g00949 949
12 56460419 56463579 + XM_039018685.1 Bhi12g01741 1741
12 56464738 56468735 - XM_039018793.1 Bhi12g01742 1742
12 56620894 56628207 + XM_039019487.1 Bhi12g01743 1743
12 64744345 64748507 + XM_039019958.1 Bhi12g02095 2095
12 66277665 66284048 + XM_039018868.1 Bhi12g02125 2125
2 10643580 10647457 - BLOR10308 Blo02g00578 578
7 2361335 2364435 + BLOR18121 Blo07g00189 189
4 24756921 24759290 - Bma019774.1 Bma04g01093 1093
5 47754489 47772366 - Bma022100.2 Bma05g00956 956
5 49324318 49326768 + Bma031225 Bma05g01062 1062
5 49333712 49337421 - Bma031226 Bma05g01064 1064
6 51619115 51621974 - Bma024632.1 Bma06g01519 1519
4 10506852 10509362 - Bpe015827.1 Bpe04g01143 1143
5 21000444 21010794 - Bpe025828 Bpe05g00764 764
5 21729319 21731552 + Bpe018266.1 Bpe05g00853 853
5 21739042 21742699 - Bpe018268.1 Bpe05g00855 855
13 13316476 13318583 + Bpe010347.1 Bpe13g00647 647
13 13319298 13322164 - Bpe010348.1 Bpe13g00648 648
14 8570446 8574147 + Bpe014525.1 Bpe14g01150 1150
5 5858454 5863531 + CaPI482276_05g006710.1 Cam05g0671 671
5 5886305 5889144 + CaPI482276_05g006730.1 Cam05g0673 673
5 5892244 5896074 - CaPI482276_05g006740.1 Cam05g0674 674
6 7463079 7467396 + CaPI482276_06g005380.1 Cam06g0538 538
6 7506869 7509529 + CaPI482276_06g005430.1 Cam06g0543 543
6 7510890 7514616 - CaPI482276_06g005440.1 Cam06g0544 544
6 7536890 7543225 + CaPI482276_06g005460.1 Cam06g0546 546
6 9057336 9062085 + Carg17375-RA Car06g01260 1260
6 9073124 9077015 + Carg17371-RA Car06g01262 1262
6 9077875 9081137 - Carg17370-RA Car06g01263 1263
8 7346810 7352606 - Carg15958-RA Car08g01079 1079
8 7360312 7363073 + Carg15959-RA Car08g01080 1080
8 7363506 7365965 - Carg15960-RA Car08g01081 1081
14 12256152 12259735 + Carg20138-RA Car14g01474 1474
14 12260396 12264675 - Carg20140-RA Car14g01476 1476
14 12274154 12276762 - Carg20143-RA Car14g01479 1479
14 12277835 12281585 - Carg20144-RA Car14g01480 1480
17 1742759 1745693 - Carg05489-RA Car17g00283 283
5 5555907 5561074 + CcPI632755_05g006750.1 Cco05g0675 675
5 5583842 5586726 + CcPI632755_05g006770.1 Cco05g0677 677
5 5590154 5593978 - CcPI632755_05g006790.1 Cco05g0679 679
6 5886486 5890821 + CcPI632755_06g005420.1 Cco06g0542 542
6 5944073 5946714 + CcPI632755_06g005510.1 Cco06g0551 551
6 5948576 5951713 - CcPI632755_06g005520.1 Cco06g0552 552
6 5972658 5978977 + CcPI632755_06g005540.1 Cco06g0554 554
5 5573599 5578827 + CePI673135_05g006810.1 Cec05g0681 681
5 5601650 5604571 + CePI673135_05g006830.1 Cec05g0683 683
5 5607655 5611491 - CePI673135_05g006840.1 Cec05g0684 684
6 6000351 6004668 + CePI673135_06g005390.1 Cec06g0539 539
6 6047217 6049871 + CePI673135_06g005440.1 Cec06g0544 544
6 6051805 6054955 - CePI673135_06g005450.1 Cec06g0545 545
6 6074491 6080756 + CePI673135_06g005460.1 Cec06g0546 546
6 4464624 4468290 + Chy6G111800.1 Chy06g00652 652
6 4473169 4478574 + Chy6G111810.1 Chy06g00653 653
6 4489235 4492307 + Chy6G111820.1 Chy06g00654 654
6 4494701 4498308 - Chy6G111830.1 Chy06g00655 655
11 21423386 21430617 - Chy11G200480.1 Chy11g01468 1468
11 21443334 21445753 + Chy11G200490.1 Chy11g01469 1469
11 21448425 21450675 - Chy11G200500.1 Chy11g01470 1470
5 5587707 5607157 + ClG42_05g0066600.10 Clacu05g0666 666
5 5615677 5618535 + ClG42_05g0066700.10 Clacu05g0667 667
5 5621629 5625442 - ClG42_05g0066800.10 Clacu05g0668 668
6 6004634 6008956 + ClG42_06g0052300.10 Clacu06g0523 523
6 6048579 6051235 + ClG42_06g0052900.10 Clacu06g0529 529
6 6053206 6056336 - ClG42_06g0053100.10 Clacu06g0531 531
6 6078624 6084937 + ClG42_06g0053200.10 Clacu06g0532 532
5 5652798 5670848 + ClCG05G005770.1 Cla05g00611 611
5 5680576 5683632 + ClCG05G005780.2 Cla05g00612 612
5 5686445 5690930 - ClCG05G005790.1 Cla05g00613 613
6 6067132 6071877 + ClCG06G005360.1 Cla06g00501 501
6 6111892 6115107 + ClCG06G005390.1 Cla06g00504 504
6 6119251 6123110 - ClCG06G005400.1 Cla06g00505 505
6 6145109 6151763 + ClCG06G005410.1 Cla06g00506 506
6 9330290 9335104 + CmaCh06G014600.1 Cma06g01460 1460
6 9337577 9344839 + CmaCh06G014620.1 Cma06g01462 1462
6 9347211 9350624 + CmaCh06G014630.1 Cma06g01463 1463
6 9351664 9355173 - CmaCh06G014640.1 Cma06g01464 1464
8 7385483 7391030 - CmaCh08G012010.1 Cma08g01201 1201
8 7397977 7399911 + CmaCh08G012030.1 Cma08g01203 1203
8 7401471 7404107 - CmaCh08G012050.1 Cma08g01205 1205
14 12296897 12300335 + CmaCh14G016440.1 Cma14g01644 1644
14 12300711 12304810 - CmaCh14G016450.1 Cma14g01645 1645
14 12309583 12315890 - CmaCh14G016460.1 Cma14g01646 1646
14 12315919 12322125 - CmaCh14G016470.1 Cma14g01647 1647
17 1640574 1643658 + CmaCh17G003060.1 Cma17g00306 306
17 1645024 1647931 - CmaCh17G003070.1 Cma17g00307 307
6 4457423 4462112 + MELO3C006603.2.1 Cme06g00685 685
6 4481950 4489175 + MELO3C006604.2.1 Cme06g00687 687
6 4487424 4492115 - MELO3C006605.2.1 Cme06g00688 688
11 27727998 27735696 - MELO3C021364.2.1 Cme11g01975 1975
11 27746532 27750497 + MELO3C021363.2.1 Cme11g01977 1977
11 27752131 27754957 - MELO3C021362.2.1 Cme11g01978 1978
6 4711947 4719606 + PI0001443.1 Cmetu06g0148 148
7 7074878 7078978 + PI0026007.1 Cmetu07g1074 1074
9 3159304 3162987 - PI0019762.1 Cmetu09g0227 227
11 4395864 4400153 + PI0014780.1 Cmetu11g1979 1979
6 10534791 10539762 + CmoCh06G014610.1 Cmo06g01461 1461
6 10540710 10547965 + CmoCh06G014620.1 Cmo06g01462 1462
6 10556839 10560626 - CmoCh06G014640.1 Cmo06g01464 1464
8 7482903 7488855 - CmoCh08G011760.1 Cmo08g01176 1176
8 7495224 7497163 + CmoCh08G011770.1 Cmo08g01177 1177
8 7498153 7501526 - CmoCh08G011790.1 Cmo08g01179 1179
14 13249022 13252695 + CmoCh14G016880.1 Cmo14g01688 1688
14 13253699 13257575 - CmoCh14G016890.1 Cmo14g01689 1689
14 13262143 13269461 - CmoCh14G016900.1 Cmo14g01690 1690
14 13270314 13274936 - CmoCh14G016910.1 Cmo14g01691 1691
17 1778045 1781084 + CmoCh17G002960.1 Cmo17g00296 296
17 1782987 1785837 - CmoCh17G002970.1 Cmo17g00297 297
17 1791193 1794838 + CmoCh17G002990.1 Cmo17g00299 299
5 5431152 5454838 + CmPI595203_05g006340.1 Cmu05g0634 634
5 5459149 5462007 + CmPI595203_05g006350.1 Cmu05g0635 635
5 5465101 5468914 - CmPI595203_05g006360.1 Cmu05g0636 636
6 5812012 5816329 + CmPI595203_06g005250.1 Cmu06g0525 525
6 5855938 5858594 + CmPI595203_06g005280.1 Cmu06g0528 528
6 5860565 5863695 - CmPI595203_06g005290.1 Cmu06g0529 529
6 5886007 5892326 + CmPI595203_06g005310.1 Cmu06g0531 531
4 812123 815815 + Conep04aG0018000.1 Cone4ag0174 174
4 819037 822282 - Conep04aG0018300.1 Cone4ag0175 175
4 826177 829410 + Conep04aG0018400.1 Cone4ag0176 176
7 747060 750347 + Conep07aG0018000.1 Cone7ag0178 178
7 753931 756959 - Conep07aG0018400.1 Cone7ag0180 180
7 761678 764862 + Conep07aG0018500.1 Cone7ag0181 181
14 4572348 4575045 - Conep14aG0080000.1 Cone14ag0783 783
14 4590292 4593102 + Conep14aG0080200.1 Cone14ag0785 785
14 4593835 4596597 - Conep14aG0080300.1 Cone14ag0786 786
14 4598324 4606097 - Conep14aG0080400.1 Cone14ag0787 787
15 4783172 4786261 + Conep15aG0080200.1 Cone15ag0787 787
15 4788611 4797558 - Conep15aG0080300.1 Cone15ag0788 788
3 11172333 11176001 + Cp4.1LG03g11320.1 Cpe03g01388 1388
3 11176850 11180875 - Cp4.1LG03g11220.1 Cpe03g01389 1389
3 11186462 11196605 - Cp4.1LG03g11250.1 Cpe03g01390 1390
3 11197366 11201280 - Cp4.1LG03g11110.1 Cpe03g01391 1391
8 1430904 1434475 + Cp4.1LG08g04640.1 Cpe08g00215 215
8 1442456 1449721 - Cp4.1LG08g04580.1 Cpe08g00217 217
8 1450922 1456145 - Cp4.1LG08g04570.1 Cpe08g00218 218
12 1722248 1725882 + Cp4.1LG12g02550.1 Cpe12g00258 258
12 1727584 1730459 - Cp4.1LG12g02630.1 Cpe12g00259 259
12 1735719 1740027 + Cp4.1LG12g02570.1 Cpe12g00261 261
17 13054 16580 - Cp4.1LG17g00770.1 Cpe17g00001 1
17 23583 28095 + Cp4.1LG17g00800.1 Cpe17g00002 2
17 26301 30805 - Cp4.1LG17g00720.1 Cpe17g00003 3
5 6224126 6229351 + CrPI670011_05g007040.1 Cre05g0704 704
5 6252309 6255176 + CrPI670011_05g007070.1 Cre05g0707 707
5 6258340 6262175 - CrPI670011_05g007080.1 Cre05g0708 708
6 6863123 6867445 + CrPI670011_06g012950.1 Cre06g1295 1295
6 6906931 6909585 + CrPI670011_06g012980.1 Cre06g1298 1298
6 6911502 6914610 - CrPI670011_06g012990.1 Cre06g1299 1299
6 6936222 6943406 + CrPI670011_06g013000.1 Cre06g1300 1300
3 10580399 10585325 + CsaV3_3G014090.1 Csa03g01409 1409
3 10588879 10599914 + CsaV3_3G014100.1 Csa03g01410 1410
3 10605878 10613554 + CsaV3_3G014110.1 Csa03g01411 1411
3 10610724 10615878 - CsaV3_3G014120.1 Csa03g01412 1412
3 1479429 1483623 + Hsped.03g01240.1 Hepe03g0124 124
3 13210025 13221865 + Hsped.03g06390.1 Hepe03g0639 639
5 64291328 64296671 - Hsped.05g14850.1 Hepe05g1485 1485
12 26519509 26531271 - Lag0015833.1 Lac12g1461 1461
12 40902928 40905205 + Lag0016751.1 Lac12g2379 2379
12 40935642 40939252 - Lag0016754.1 Lac12g2382 2382
11 38444903 38448699 - Maker00031949 Lcy11g1455 1455
13 2061271 2065742 + Maker00023848 Lcy13g0198 198
13 16607827 16619799 + Maker00026352 Lcy13g0912 912
5 22798749 22803438 + Lsi05G014970.1 Lsi05g01497 1497
5 22810994 22820333 + Lsi05G014980.1 Lsi05g01498 1498
5 22828303 22833223 + Lsi05G014990.1 Lsi05g01499 1499
5 22835363 22839712 - Lsi05G015010.1 Lsi05g01501 1501
9 21975581 21981927 - Lsi09G013940.1 Lsi09g01394 1394
9 21999286 22002188 + Lsi09G013960.1 Lsi09g01396 1396
9 22004641 22007830 - Lsi09G013980.1 Lsi09g01398 1398
9 22035642 22041776 - Lsi09G014020.1 Lsi09g01402 1402
1 69055964 69059452 + Sed0004190.2 Sed01g4000 4000
2 49103413 49107782 - Sed0022804.1 Sed02g1224 1224
9 8012407 8019456 - Sed0008062.1 Sed09g0638 638
12 5378985 5386227 - Sed0026345.3 Sed12g0869 869
6 57701137 57713485 - Tan0015512.1 Tan06g1925 1925
6 78921370 78925637 - Tan0001245.3 Tan06g2633 2633
10 8214868 8221470 + Tan0022696.1 Tan10g0943 943
10 8227769 8235978 + Tan0013489.1 Tan10g0945 945
10 8248324 8252394 + Tan0016110.1 Tan10g0947 947
5 3574215 3577147 + Vvi5g359 Vvi5g359 359
5 3584704 3592030 - Vvi5g360 Vvi5g360 360
5 3594892 3606380 + Vvi5g361 Vvi5g361 361
5 3607218 3608355 + Vvi5g362 Vvi5g362 362
5 3615705 3618981 + Vvi5g363 Vvi5g363 363
5 3627457 3630257 - Vvi5g364 Vvi5g364 364
5 3635847 3639351 - Vvi5g365 Vvi5g365 365
5 3639530 3657495 - Vvi5g366 Vvi5g366 366
5 3676949 3684048 + Vvi5g367 Vvi5g367 367
5 3684999 3691063 - Vvi5g368 Vvi5g368 368
       

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