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
Vvi5g379 . . . . . . . . Cmo08g01170 . . . . . . . . . . . . . . . Cla06g00516 . . . . . . . . Cone7ag0184 . . . Chy11g01459 . . . . . . . . . . . . Cma08g01197 . Car08g01073 . . . . . . . . . . . . . . . . . Lsi09g01386 . . Cme11g01964
Vvi5g380 . . . . Bpe04g01179 . . . . . . . . . . . . . . . . . . . Cla06g00517 . . . . . . Cone14ag0796 Cone15ag0797 . . . . . . . . . . . . . . . . . . . . . . Cpe17g00102 Bhi12g01751 . . . . . . . . . . . . . . . . .
Vvi5g381 . . . . . Bpe14g01154 . . Cmo08g01169 Cmo17g00285 . . . . . . . . . . . . . . Cla06g00518 Cam06g0557 Cec06g0557 Cco06g0564 Clacu06g0545 Cmu06g0542 Cre06g1310 . . Cone7ag0185 Cone4ag0181 . . Chy11g01457 . Blo02g00573 . . . . . . . . . . Cma08g01196 Cma17g00297 Car08g01072 Car17g00273 Cpe12g00249 Cpe17g00103 Bhi12g01753 . . . . . . . . . . . . . Lsi09g01384 . . Cme11g01961
Vvi5g382 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g383 . . . . . Bpe14g01156 . . Cmo08g01168 Cmo17g00283 . . . . . . . . . . . . . . . . . . . . . Cone14ag0797 Cone15ag0799 . . . . . . Blo02g00572 Blo07g00192 Bda11g00545 . . Bpe13g00644 . Bma06g01522 . . . Cma08g01195 Cma17g00295 Car08g01071 Car17g00271 Cpe12g00247 Cpe17g00104 Bhi12g01754 . . . . . . . . . . . . . . . . .
Vvi5g384 . . . . . Bpe14g01158 . . . . Cma06g01455 Cma14g01651 Car06g01257 Car14g01485 . Cpe08g00222 Cpe03g01395 . . . . . . . . . . . . . . . . Cone7ag0187 Cone4ag0183 Lsi05g01490 . . Cme06g00679 Blo02g00570 Blo07g00193 Bda11g00547 . . Bpe13g00642 . Bma06g01524 . Cmo06g01456 Cmo14g01695 . . . . . . Bhi12g02132 . . . . . Lcy13g0944 Cla05g00605 Cam05g0666 Cec05g0675 Cco05g0670 Clacu05g0660 Cmu05g0629 Cre05g0698 . Csa03g01404 Chy06g00647 .
Vvi5g385 . . . . . . . . . Cmo17g00282 . Cma14g01652 . . . . Cpe03g01396 . . . . . . . Cla06g00520 Cam06g0559 Cec06g0559 Cco06g0566 Clacu06g0547 Cmu06g0543 Cre06g1312 . . . . Lsi05g01489 . Chy11g01455 Cme06g00678 . . . . . . . . . . Cmo14g01696 . . . Car17g00270 Cpe12g00246 . Bhi12g01756 . . . . . . Cla05g00604 Cam05g0665 Cec05g0674 Cco05g0669 Clacu05g0659 Cmu05g0628 Cre05g0697 Lsi09g01383 Csa03g01403 Chy06g00646 Cme11g01960
Vvi5g386 . . Bda03g01239 . . . . . Cmo08g01166 Cmo17g00281 . . . . . . . . . . . . . . Cla06g00521 Cam06g0560 Cec06g0560 Cco06g0567 Clacu06g0548 Cmu06g0544 Cre06g1313 . . . . . . Chy11g01454 . . . . . . . . . . . . Cma08g01192 Cma17g00294 Car08g01070 . Cpe12g00245 Cpe17g00105 Bhi12g01758 . . . . . . . . . . . . . Lsi09g01382 . . Cme11g01959
Vvi5g387 . . . . . . . . . . . Cma14g01653 . Car14g01487 . . Cpe03g01397 . . . . . . . . . . . . . . . . Cone7ag0188 . Lsi05g01487 . . Cme06g00677 . Blo07g00194 . . . Bpe13g00641 . Bma06g01525 . . Cmo14g01697 . . . . . . . . . . . . . Cla05g00603 Cam05g0664 Cec05g0673 Cco05g0668 Clacu05g0658 Cmu05g0627 Cre05g0696 . Csa03g01402 Chy06g00645 .
Vvi5g388 . . . . . Bpe14g01159 . . Cmo08g01164 Cmo17g00280 Cma06g01452 . Car06g01254 Car14g01488 . Cpe08g00223 Cpe03g01398 . . . . . . . Cla06g00522 Cam06g0561 Cec06g0561 Cco06g0568 Clacu06g0549 Cmu06g0545 Cre06g1314 Cone14ag0800 . . . . . Chy11g01453 Cme06g00676 Blo02g00569 . Bda11g00549 . . Bpe13g00640 . Bma06g01526 . Cmo06g01453 Cmo14g01698 . Cma17g00292 Car08g01069 Car17g00269 Cpe12g00244 Cpe17g00106 Bhi12g01760 . . . . . . Cla05g00602 Cam05g0663 Cec05g0672 Cco05g0667 Clacu05g0657 Cmu05g0626 Cre05g0695 Lsi09g01381 Csa03g01401 Chy06g00644 Cme11g01958
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 17293422 17293789 - Bda017358.1 Bda03g01239 1239
11 5673382 5675027 + Bda005280.1 Bda11g00545 545
11 5683288 5689564 + Bda005282.2 Bda11g00547 547
11 5716642 5718191 - Bda005285.1 Bda11g00549 549
12 56828600 56831067 + XM_039020023.1 Bhi12g01751 1751
12 56833245 56837448 - XM_039018773.1 Bhi12g01753 1753
12 56879503 56885761 + XM_039050877.1 Bhi12g01754 1754
12 56887272 56894294 + XM_039050942.1 Bhi12g01756 1756
12 56940830 56941524 + XM_039019337.1 Bhi12g01758 1758
12 56944004 56946575 - XM_039019335.1 Bhi12g01760 1760
12 66812565 66816600 + XM_039050827.1 Bhi12g02132 2132
2 10500644 10501861 + BLOR10299 Blo02g00569 569
2 10502934 10508475 - BLOR10300 Blo02g00570 570
2 10558286 10559977 - BLOR10302 Blo02g00572 572
2 10568613 10571562 + BLOR10303 Blo02g00573 573
7 2388120 2390021 + BLOR18124 Blo07g00192 192
7 2401303 2407047 + BLOR18125 Blo07g00193 193
7 2417426 2421844 + BLOR18126 Blo07g00194 194
6 51629973 51631169 + Bma024635.1 Bma06g01522 1522
6 51642502 51648640 + Bma024637.1 Bma06g01524 1524
6 51652203 51656563 + Bma024638.1 Bma06g01525 1525
6 51657028 51658439 - Bma024639.1 Bma06g01526 1526
4 13438196 13439724 - Bpe015874.1 Bpe04g01179 1179
13 13274008 13275548 + Bpe010340.1 Bpe13g00640 640
13 13276002 13280488 - Bpe010341.1 Bpe13g00641 641
13 13284927 13296866 - Bpe010342.1 Bpe13g00642 642
13 13305254 13306810 - Bpe010344.1 Bpe13g00644 644
14 8607708 8611252 - Bpe014529.1 Bpe14g01154 1154
14 8616507 8617980 + Bpe025532 Bpe14g01156 1156
14 8630194 8635770 + Bpe014531.1 Bpe14g01158 1158
14 8636692 8637849 - Bpe014532.1 Bpe14g01159 1159
5 5720792 5731326 + CaPI482276_05g006630.1 Cam05g0663 663
5 5731893 5738070 - CaPI482276_05g006640.1 Cam05g0664 664
5 5745355 5756676 - CaPI482276_05g006650.1 Cam05g0665 665
5 5761178 5769009 - CaPI482276_05g006660.1 Cam05g0666 666
6 7652286 7656122 - CaPI482276_06g005570.1 Cam06g0557 557
6 7673745 7679639 + CaPI482276_06g005590.1 Cam06g0559 559
6 7681939 7682796 + CaPI482276_06g005600.1 Cam06g0560 560
6 7684878 7687350 - CaPI482276_06g005610.1 Cam06g0561 561
6 9018981 9021080 + Carg17381-RA Car06g01254 1254
6 9023511 9028739 - Carg17378-RA Car06g01257 1257
8 7292726 7295211 + Carg15948-RA Car08g01069 1069
8 7297338 7297923 - Carg15949-RA Car08g01070 1070
8 7301309 7302796 - Carg15950-RA Car08g01071 1071
8 7304383 7308042 + Carg15951-RA Car08g01072 1072
8 7309057 7310752 - Carg15952-RA Car08g01073 1073
14 12330882 12332581 + Carg20149-RA Car14g01485 1485
14 12340480 12355930 + Carg20151-RA Car14g01487 1487
14 12355236 12357202 - Carg20152-RA Car14g01488 1488
17 1657585 1661496 + Carg05475-RA Car17g00269 269
17 1663927 1671938 - Carg05476-RA Car17g00270 270
17 1673636 1678160 - Carg05477-RA Car17g00271 271
17 1683591 1689094 + Carg05479-RA Car17g00273 273
5 5416774 5427254 + CcPI632755_05g006670.1 Cco05g0667 667
5 5427401 5433936 - CcPI632755_05g006680.1 Cco05g0668 668
5 5442022 5453326 - CcPI632755_05g006690.1 Cco05g0669 669
5 5457753 5465549 - CcPI632755_05g006700.1 Cco05g0670 670
6 6091955 6095782 - CcPI632755_06g005640.1 Cco06g0564 564
6 6113245 6119347 + CcPI632755_06g005660.1 Cco06g0566 566
6 6121666 6122451 + CcPI632755_06g005670.1 Cco06g0567 567
6 6124605 6126648 - CcPI632755_06g005680.1 Cco06g0568 568
5 5428290 5437776 + CePI673135_05g006720.1 Cec05g0672 672
5 5438343 5444524 - CePI673135_05g006730.1 Cec05g0673 673
5 5452724 5464431 - CePI673135_05g006740.1 Cec05g0674 674
5 5468962 5476749 - CePI673135_05g006750.1 Cec05g0675 675
6 6189212 6193045 - CePI673135_06g005570.1 Cec06g0557 557
6 6210303 6216220 + CePI673135_06g005590.1 Cec06g0559 559
6 6218516 6220348 + CePI673135_06g005600.1 Cec06g0560 560
6 6221455 6223898 - CePI673135_06g005610.1 Cec06g0561 561
6 4363583 4365023 + Chy6G111720.1 Chy06g00644 644
6 4365526 4372032 - Chy6G111730.1 Chy06g00645 645
6 4372516 4383601 - Chy6G111740.1 Chy06g00646 646
6 4387129 4396078 - Chy6G111750.1 Chy06g00647 647
11 21329690 21331419 + Chy11G200330.1 Chy11g01453 1453
11 21334110 21334485 - Chy11G200340.1 Chy11g01454 1454
11 21336032 21341865 - Chy11G200350.1 Chy11g01455 1455
11 21352629 21356363 + Chy11G200370.1 Chy11g01457 1457
11 21358776 21360911 - Chy11G200390.1 Chy11g01459 1459
5 5445983 5456543 + ClG42_05g0065700.10 Clacu05g0657 657
5 5457109 5463275 - ClG42_05g0065800.10 Clacu05g0658 658
5 5471398 5482974 - ClG42_05g0065900.10 Clacu05g0659 659
5 5487472 5495256 - ClG42_05g0066000.10 Clacu05g0660 660
6 6197234 6201089 - ClG42_06g0054500.10 Clacu06g0545 545
6 6221907 6227778 + ClG42_06g0054700.10 Clacu06g0547 547
6 6230113 6230893 + ClG42_06g0054800.10 Clacu06g0548 548
6 6233053 6235526 - ClG42_06g0054900.10 Clacu06g0549 549
5 5502008 5520043 + ClCG05G005640.2 Cla05g00602 602
5 5519631 5526481 - ClCG05G005670.2 Cla05g00603 603
5 5535276 5546852 - ClCG05G005680.2 Cla05g00604 604
5 5550743 5559372 - ClCG05G005690.2 Cla05g00605 605
6 6238791 6241624 + ClCG06G005500.2 Cla06g00516 516
6 6258343 6263813 + ClCG06G005510.2 Cla06g00517 517
6 6264023 6269241 - ClCG06G005530.2 Cla06g00518 518
6 6289583 6295571 + ClCG06G005550.2 Cla06g00520 520
6 6297718 6307667 + ClCG06G005560.2 Cla06g00521 521
6 6300196 6303319 - ClCG06G005570.1 Cla06g00522 522
6 9289823 9293888 + CmaCh06G014520.1 Cma06g01452 1452
6 9296111 9302100 - CmaCh06G014550.1 Cma06g01455 1455
8 7330478 7335682 - CmaCh08G011920.1 Cma08g01192 1192
8 7339389 7341260 - CmaCh08G011950.1 Cma08g01195 1195
8 7343171 7347317 + CmaCh08G011960.1 Cma08g01196 1196
8 7347661 7349705 - CmaCh08G011970.1 Cma08g01197 1197
14 12371437 12377768 + CmaCh14G016510.1 Cma14g01651 1651
14 12380224 12386455 + CmaCh14G016520.1 Cma14g01652 1652
14 12389603 12396176 + CmaCh14G016530.1 Cma14g01653 1653
17 1563551 1566029 + CmaCh17G002920.1 Cma17g00292 292
17 1567896 1569077 - CmaCh17G002940.1 Cma17g00294 294
17 1569873 1583955 - CmaCh17G002950.1 Cma17g00295 295
17 1588176 1593720 + CmaCh17G002970.1 Cma17g00297 297
6 4352113 4354262 + MELO3C006593.2.1 Cme06g00676 676
6 4352452 4360865 - MELO3C006594.2.1 Cme06g00677 677
6 4366519 4372741 - MELO3C006595.2.1 Cme06g00678 678
6 4375358 4386104 - MELO3C006596.2.1 Cme06g00679 679
11 27629704 27632540 + MELO3C021379.2.1 Cme11g01958 1958
11 27634344 27635238 - MELO3C021378.2.1 Cme11g01959 1959
11 27636194 27646445 - MELO3C021377.2.1 Cme11g01960 1960
11 27651454 27655918 + MELO3C021375.2.1 Cme11g01961 1961
11 27658964 27661415 - MELO3C021373.2.1 Cme11g01964 1964
6 10494445 10499111 + CmoCh06G014530.1 Cmo06g01453 1453
6 10498923 10504376 - CmoCh06G014560.1 Cmo06g01456 1456
8 7427242 7429020 + CmoCh08G011640.1 Cmo08g01164 1164
8 7431088 7432381 - CmoCh08G011660.1 Cmo08g01166 1166
8 7435884 7438290 - CmoCh08G011680.1 Cmo08g01168 1168
8 7440291 7444047 + CmoCh08G011690.1 Cmo08g01169 1169
8 7444955 7446655 - CmoCh08G011700.1 Cmo08g01170 1170
14 13325908 13332181 + CmoCh14G016950.1 Cmo14g01695 1695
14 13334339 13340644 + CmoCh14G016960.1 Cmo14g01696 1696
14 13343955 13350256 + CmoCh14G016970.1 Cmo14g01697 1697
14 13350281 13352835 - CmoCh14G016980.1 Cmo14g01698 1698
17 1686402 1689163 + CmoCh17G002800.1 Cmo17g00280 280
17 1690698 1691970 - CmoCh17G002810.1 Cmo17g00281 281
17 1693785 1701922 - CmoCh17G002820.1 Cmo17g00282 282
17 1708862 1709536 - CmoCh17G002830.1 Cmo17g00283 283
17 1714509 1719829 + CmoCh17G002850.1 Cmo17g00285 285
5 5289457 5300009 + CmPI595203_05g006260.1 Cmu05g0626 626
5 5300299 5306741 - CmPI595203_05g006270.1 Cmu05g0627 627
5 5314857 5326430 - CmPI595203_05g006280.1 Cmu05g0628 628
5 5330928 5338712 - CmPI595203_05g006290.1 Cmu05g0629 629
6 6004474 6008328 - CmPI595203_06g005420.1 Cmu06g0542 542
6 6029011 6034998 + CmPI595203_06g005430.1 Cmu06g0543 543
6 6037332 6038112 + CmPI595203_06g005440.1 Cmu06g0544 544
6 6040272 6042339 - CmPI595203_06g005450.1 Cmu06g0545 545
4 843979 846688 - Conep04aG0019000.1 Cone4ag0181 181
4 853187 858113 + Conep04aG0019200.1 Cone4ag0183 183
7 777112 778290 + Conep07aG0018900.1 Cone7ag0184 184
7 778809 782713 - Conep07aG0019000.1 Cone7ag0185 185
7 791801 796679 + Conep07aG0019200.1 Cone7ag0187 187
7 801752 805700 + Conep07aG0019300.1 Cone7ag0188 188
14 4694281 4696555 + Conep14aG0081300.1 Cone14ag0796 796
14 4699718 4702789 + Conep14aG0081400.1 Cone14ag0797 797
14 4720928 4723173 - Conep14aG0081700.1 Cone14ag0800 800
15 4884337 4887044 + Conep15aG0081200.1 Cone15ag0797 797
15 4894136 4897235 + Conep15aG0081400.1 Cone15ag0799 799
3 11249933 11256486 + Cp4.1LG03g11170.1 Cpe03g01395 1395
3 11258636 11264999 + Cp4.1LG03g11180.1 Cpe03g01396 1396
3 11268025 11277872 + Cp4.1LG03g11160.1 Cpe03g01397 1397
3 11274291 11277872 - Cp4.1LG03g11120.1 Cpe03g01398 1398
8 1487386 1493094 + Cp4.1LG08g04480.1 Cpe08g00222 222
8 1495058 1497319 - Cp4.1LG08g04380.1 Cpe08g00223 223
12 1640107 1642689 + Cp4.1LG12g02440.1 Cpe12g00244 244
12 1640170 1645506 - Cp4.1LG12g02490.1 Cpe12g00245 245
12 1645899 1655480 - Cp4.1LG12g02510.1 Cpe12g00246 246
12 1660873 1661574 - Cp4.1LG12g02520.1 Cpe12g00247 247
12 1665891 1671061 + Cp4.1LG12g02400.1 Cpe12g00249 249
17 634253 636065 + Cp4.1LG17g01030.1 Cpe17g00102 102
17 637001 640524 - Cp4.1LG17g01110.1 Cpe17g00103 103
17 642196 644313 + Cp4.1LG17g01000.1 Cpe17g00104 104
17 647591 648447 + Cp4.1LG17g01020.1 Cpe17g00105 105
17 650561 653779 - Cp4.1LG17g01150.1 Cpe17g00106 106
5 6073242 6086950 + CrPI670011_05g006950.1 Cre05g0695 695
5 6087517 6093684 - CrPI670011_05g006960.1 Cre05g0696 696
5 6101612 6113335 - CrPI670011_05g006970.1 Cre05g0697 697
5 6117808 6125616 - CrPI670011_05g006980.1 Cre05g0698 698
6 7053935 7057779 - CrPI670011_06g013100.1 Cre06g1310 1310
6 7075631 7081654 + CrPI670011_06g013120.1 Cre06g1312 1312
6 7083978 7084758 + CrPI670011_06g013130.1 Cre06g1313 1313
6 7086912 7089183 - CrPI670011_06g013140.1 Cre06g1314 1314
3 10478435 10479884 + CsaV3_3G014010.1 Csa03g01401 1401
3 10480062 10486989 - CsaV3_3G014020.1 Csa03g01402 1402
3 10490146 10496822 - CsaV3_3G014030.1 Csa03g01403 1403
3 10499279 10508952 - CsaV3_3G014040.1 Csa03g01404 1404
13 17699911 17704829 + Maker00026396 Lcy13g0944 944
5 22646001 22655695 - Lsi05G014880.1 Lsi05g01487 1487
5 22676416 22685177 - Lsi05G014890.1 Lsi05g01489 1489
5 22688528 22698154 - Lsi05G014900.1 Lsi05g01490 1490
9 21833818 21845953 + Lsi09G013810.1 Lsi09g01381 1381
9 21849114 21849488 - Lsi09G013820.1 Lsi09g01382 1382
9 21855912 21859326 - Lsi09G013830.1 Lsi09g01383 1383
9 21869561 21878373 + Lsi09G013840.1 Lsi09g01384 1384
9 21880522 21883549 - Lsi09G013860.1 Lsi09g01386 1386
5 3842707 3844012 + Vvi5g379 Vvi5g379 379
5 3846130 3847498 + Vvi5g380 Vvi5g380 380
5 3851154 3856278 - Vvi5g381 Vvi5g381 381
5 3864994 3870165 - Vvi5g382 Vvi5g382 382
5 3870661 3884456 + Vvi5g383 Vvi5g383 383
5 3885148 3896071 + Vvi5g384 Vvi5g384 384
5 3900556 3903993 + Vvi5g385 Vvi5g385 385
5 3916716 3917496 + Vvi5g386 Vvi5g386 386
5 3929620 3935511 + Vvi5g387 Vvi5g387 387
5 3943019 3944862 - Vvi5g388 Vvi5g388 388
       

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