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
Vvi5g289 . Blo12g00370 Bda03g00839 . Bpe04g00794 . Bma04g00737 . . . . Cma14g01546 Car06g01357 Car14g01364 Sed02g1091 Cpe08g00124 Cpe03g01292 Bhi01g01152 Tan10g1143 Cmetu06g2510 . Hepe05g1329 . Lcy11g1289 . . . . . . . Cone14ag0672 Cone15ag0682 . . Lsi05g01372 . . Cme06g00847 . . . . . . . . . Cmo06g01591 Cmo14g01582 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g290 . . Bda03g00840 . Bpe04g00795 . Bma04g00738 . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0671 Cone15ag0680 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g291 . Blo12g00017 . . Bpe04g01135 . . . . Cmo17g00320 . . . . . . . . . . . . . . Cla06g00475 . . Cco06g0513 . Cmu06g0495 . . . Cone7ag0144 . . . Chy11g01515 . . . . . . . . . Sed12g1134 . . . Cma17g00330 . Car17g00304 . . Bhi12g02048 Tan06g2683 Cmetu04g0061 Lac11g0844 Hepe03g0098 . Lcy12g0737 . . . . . . . Lsi09g01434 . . Cme11g02016
Vvi5g292 . . . Bda08g00292 . Bpe14g01126 . Bma05g01034 . . Cma06g01504 . Car06g01295 Car14g01440 Sed02g1177 Cpe08g00180 Cpe03g01358 Bhi01g01023 Tan10g1015 Cmetu02g1668 . Hepe05g1441 . Lcy11g1410 . . . . . . . Cone14ag0760 Cone15ag0769 . . Lsi05g01545 . . Cme06g00738 Blo02g00503 Blo07g00170 Bda11g00522 Bda13g00189 Bpe05g00835 Bpe13g00668 . Bma06g01497 . Cmo06g01502 Cmo14g01654 . . . . . . . . . . . . . Cla05g00658 Cam05g0720 Cec05g0730 Cco05g0729 Clacu05g0714 Cmu05g0679 Cre05g0753 . Csa03g01473 Chy06g00710 .
Vvi5g293 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g294 . . . . . Bpe14g01127 . . . . Cma06g01503 . Car06g01294 . . Cpe08g00181 . Bhi01g01022 Tan10g1014 Cmetu06g1461 . Hepe05g1442 . . . . . . . . . . . . . . . . Cme06g00737 Blo02g00504 . . . . . . Bma06g01498 . Cmo06g01501 . . . . . . . . . . . . . . Cla05g00657 Cam05g0719 Cec05g0729 Cco05g0728 Clacu05g0713 Cmu05g0678 Cre05g0752 . Csa03g01472 Chy06g00709 .
Vvi5g295 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g296 . . . Bda08g00291 . . . . Cmo08g01203 Cmo17g00316 . . . . . . . . . . . . . . Cla06g00478 Cam06g0512 Cec06g0513 Cco06g0516 Clacu06g0496 Cmu06g0498 Cre06g1269 Cone14ag0761 Cone15ag0770 . . . . Chy11g01510 . . . . . Bpe05g00836 . . . Sed02g1073 . . Cma08g01228 Cma17g00327 Car08g01104 Car17g00301 Cpe12g00278 Cpe17g00027 Bhi12g02054 Tan06g2680 Cmetu07g0697 . . . . . . . . . . . Lsi09g01431 . . Cme11g02012
Vvi5g297 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g298 . . . Bda08g00290 . . . Bma05g01035 Cmo08g01202 Cmo17g00315 . . . . . . . . . . . . . . . . . . . . . Cone14ag0762 Cone15ag0771 . . . . Chy11g01509 . . . . . Bpe05g00837 . . . Sed09g0246 . . Cma08g01227 Cma17g00326 Car08g01103 Car17g00300 Cpe12g00277 . Bhi12g02057 Tan06g2678 Cmetu11g0237 . Hepe03g0102 . . . . . . . . . Lsi09g01430 . . Cme11g02011
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 7186052 7188202 + Bda016825.1 Bda03g00839 839
3 7189169 7195899 + Bda016826.1 Bda03g00840 840
8 3045180 3049130 + Bda024724.1 Bda08g00290 290
8 3049796 3056251 - Bda024725.1 Bda08g00291 291
8 3060767 3061702 - Bda033799 Bda08g00292 292
11 5535396 5536774 + Bda033043 Bda11g00522 522
13 2387216 2388163 - Bda032839 Bda13g00189 189
1 18595981 18598207 + XM_039048756.1 Bhi01g01022 1022
1 18598618 18600478 - XM_039022293.1 Bhi01g01023 1023
1 22574339 22577843 + XM_039029434.1 Bhi01g01152 1152
12 63817185 63830896 + XM_039018662.1 Bhi12g02048 2048
12 63890822 63897482 + XM_039018931.1 Bhi12g02054 2054
12 63898781 63905622 - XM_039018935.1 Bhi12g02057 2057
2 7943455 7947558 + BLOR10233 Blo02g00503 503
2 7970199 7972905 - BLOR10234 Blo02g00504 504
7 2178892 2179996 + BLOR18102 Blo07g00170 170
12 1171113 1177070 - BLOR04036 Blo12g00017 17
12 20092662 20093529 - BLOR04389 Blo12g00370 370
4 7728231 7730147 + Bma019246.1 Bma04g00737 737
4 7730755 7734272 + Bma019247.1 Bma04g00738 738
5 48889861 48891170 + Bma022192.1 Bma05g01034 1034
5 48902506 48906671 - Bma022193.1 Bma05g01035 1035
6 51470683 51472003 + Bma024609.1 Bma06g01497 1497
6 51472595 51474443 - Bma024610.1 Bma06g01498 1498
4 5187095 5189240 + Bpe025664 Bpe04g00794 794
4 5190426 5193818 + Bpe015456.3 Bpe04g00795 795
4 9958483 9966760 + Bpe015816.1 Bpe04g01135 1135
5 21589971 21590904 + Bpe018248.1 Bpe05g00835 835
5 21596772 21603221 + Bpe018249.1 Bpe05g00836 836
5 21603959 21608148 - Bpe018250.1 Bpe05g00837 837
13 13442649 13443936 - Bpe010369.1 Bpe13g00668 668
14 8390149 8390855 + Bpe014501.1 Bpe14g01126 1126
14 8391162 8392341 - Bpe014502.1 Bpe14g01127 1127
5 6272008 6273796 + CaPI482276_05g007190.1 Cam05g0719 719
5 6274831 6276367 - CaPI482276_05g007200.1 Cam05g0720 720
6 7208112 7214284 + CaPI482276_06g005120.1 Cam06g0512 512
6 9266333 9268795 + Carg17339-RA Car06g01294 1294
6 9269345 9270514 - Carg17338-RA Car06g01295 1295
6 9764857 9766395 + Carg15519-RA Car06g01357 1357
8 7492261 7496937 + Carg18844-RA Car08g01103 1103
8 7495550 7502882 - Carg18845-RA Car08g01104 1104
14 11543615 11546918 - Carg19585-RA Car14g01364 1364
14 12087083 12088792 + Carg20104-RA Car14g01440 1440
17 1863823 1866493 + Carg05506-RA Car17g00300 300
17 1867341 1873962 - Carg05507-RA Car17g00301 301
17 1885582 1892570 - Carg05510-RA Car17g00304 304
5 5978354 5980443 + CcPI632755_05g007280.1 Cco05g0728 728
5 5981470 5987673 - CcPI632755_05g007290.1 Cco05g0729 729
6 5598777 5612869 + CcPI632755_06g005130.1 Cco06g0513 513
6 5633128 5639277 + CcPI632755_06g005160.1 Cco06g0516 516
5 6003201 6005311 + CePI673135_05g007290.1 Cec05g0729 729
5 6006264 6008006 - CePI673135_05g007300.1 Cec05g0730 730
6 5740130 5746310 + CePI673135_06g005130.1 Cec06g0513 513
6 4827008 4828977 + Chy6G112370.1 Chy06g00709 709
6 4830509 4832350 - Chy6G112380.1 Chy06g00710 710
11 21740250 21744978 + Chy11G200890.1 Chy11g01509 1509
11 21746748 21752702 - Chy11G200900.1 Chy11g01510 1510
11 21786428 21794608 - Chy11G200950.1 Chy11g01515 1515
5 6008156 6009964 + ClG42_05g0071300.10 Clacu05g0713 713
5 6010984 6012546 - ClG42_05g0071400.10 Clacu05g0714 714
6 5749209 5755252 + ClG42_06g0049600.10 Clacu06g0496 496
5 6111472 6114221 + ClCG05G006150.1 Cla05g00657 657
5 6115264 6117168 - ClCG05G006160.1 Cla05g00658 658
6 5764538 5778065 + ClCG06G005070.1 Cla06g00475 475
6 5800073 5808490 + ClCG06G005100.1 Cla06g00478 478
6 9546573 9548880 + CmaCh06G015030.1 Cma06g01503 1503
6 9549000 9551026 - CmaCh06G015040.1 Cma06g01504 1504
8 7521101 7530602 + CmaCh08G012270.1 Cma08g01227 1227
8 7530734 7537518 - CmaCh08G012280.1 Cma08g01228 1228
14 11664185 11668326 - CmaCh14G015460.1 Cma14g01546 1546
17 1767417 1777584 + CmaCh17G003260.1 Cma17g00326 326
17 1778518 1785451 - CmaCh17G003270.1 Cma17g00327 327
17 1798634 1805866 - CmaCh17G003300.1 Cma17g00330 330
6 4871343 4873719 + MELO3C006669.2.1 Cme06g00737 737
6 4874787 4876039 - MELO3C006670.2.1 Cme06g00738 738
6 5790852 5794508 + MELO3C006766.2.1 Cme06g00847 847
11 27997438 28003989 + MELO3C021328.2.1 Cme11g02011 2011
11 28005201 28011954 - MELO3C021327.2.1 Cme11g02012 2012
11 28034031 28036360 - MELO3C035190.2.1 Cme11g02016 2016
2 715243 717064 - PI0014901.1 Cmetu02g1668 1668
4 7724993 7733051 - PI0011501.1 Cmetu04g0061 61
6 5061905 5064313 + PI0003440.2 Cmetu06g1461 1461
6 5873073 5876700 + PI0027177.1 Cmetu06g2510 2510
7 880127 886611 - PI0026929.1 Cmetu07g0697 697
11 4198753 4204513 - PI0017036.1 Cmetu11g0237 237
6 10756179 10758600 + CmoCh06G015010.1 Cmo06g01501 1501
6 10758877 10761073 - CmoCh06G015020.1 Cmo06g01502 1502
6 11154841 11157437 + CmoCh06G015910.1 Cmo06g01591 1591
8 7630633 7635664 + CmoCh08G012020.1 Cmo08g01202 1202
8 7636026 7642779 - CmoCh08G012030.1 Cmo08g01203 1203
14 12587118 12590472 - CmoCh14G015820.1 Cmo14g01582 1582
14 13076454 13078147 + CmoCh14G016540.1 Cmo14g01654 1654
17 1903800 1908270 + CmoCh17G003150.1 Cmo17g00315 315
17 1908525 1915480 - CmoCh17G003160.1 Cmo17g00316 316
17 1926965 1934216 - CmoCh17G003200.1 Cmo17g00320 320
5 5851386 5853194 + CmPI595203_05g006780.1 Cmu05g0678 678
5 5854214 5855776 - CmPI595203_05g006790.1 Cmu05g0679 679
6 5516760 5528113 + CmPI595203_06g004950.1 Cmu06g0495 495
6 5551088 5557119 + CmPI595203_06g004980.1 Cmu06g0498 498
7 595210 600089 - Conep07aG0014500.1 Cone7ag0144 144
14 3458926 3461479 - Conep14aG0068600.1 Cone14ag0671 671
14 3462725 3464417 + Conep14aG0068700.1 Cone14ag0672 672
14 4305566 4307856 + Conep14aG0077700.1 Cone14ag0760 760
14 4309719 4316114 + Conep14aG0077800.1 Cone14ag0761 761
14 4316729 4320894 - Conep14aG0077900.1 Cone14ag0762 762
15 3667298 3668538 - Conep15aG0069400.1 Cone15ag0680 680
15 3670041 3671817 + Conep15aG0069600.1 Cone15ag0682 682
15 4587560 4589917 + Conep15aG0078400.1 Cone15ag0769 769
15 4593962 4600106 + Conep15aG0078500.1 Cone15ag0770 770
15 4600575 4604826 - Conep15aG0078600.1 Cone15ag0771 771
3 10519517 10523937 - Cp4.1LG03g12100.1 Cpe03g01292 1292
3 10997206 10998910 + Cp4.1LG03g11490.1 Cpe03g01358 1358
8 813246 822108 - Cp4.1LG08g05470.1 Cpe08g00124 124
8 1236718 1238912 + Cp4.1LG08g04970.1 Cpe08g00180 180
8 1239183 1242254 - Cp4.1LG08g04910.1 Cpe08g00181 181
12 1844271 1849236 + Cp4.1LG12g02700.1 Cpe12g00277 277
12 1849832 1857978 - Cp4.1LG12g02780.1 Cpe12g00278 278
17 177397 183916 - Cp4.1LG17g00590.1 Cpe17g00027 27
5 6651505 6653540 + CrPI670011_05g007520.1 Cre05g0752 752
5 6654564 6656337 - CrPI670011_05g007530.1 Cre05g0753 753
6 6611855 6618011 + CrPI670011_06g012690.1 Cre06g1269 1269
3 10937990 10939928 + CsaV3_3G014720.1 Csa03g01472 1472
3 10941198 10943545 - CsaV3_3G014730.1 Csa03g01473 1473
3 1192549 1200872 + Hsped.03g00980.1 Hepe03g0098 98
3 1251972 1259210 - Hsped.03g01020.1 Hepe03g0102 102
5 61652923 61658424 - Hsped.05g13290.1 Hepe05g1329 1329
5 63701569 63703809 + Hsped.05g14410.1 Hepe05g1441 1441
5 63704727 63707370 - Hsped.05g14420.1 Hepe05g1442 1442
11 9035010 9041926 - Lag0031482.1 Lac11g0844 844
11 36335372 36339518 - Maker00032018 Lcy11g1289 1289
11 37893310 37895631 + Maker00032076 Lcy11g1410 1410
12 9350059 9357439 - Maker00025116 Lcy12g0737 737
5 21588602 21592642 - Lsi05G013720.1 Lsi05g01372 1372
5 23226285 23232955 - Lsi05G015450.1 Lsi05g01545 1545
9 22308160 22314910 + Lsi09G014300.1 Lsi09g01430 1430
9 22315197 22323063 - Lsi09G014310.1 Lsi09g01431 1431
9 22344595 22349380 - Lsi09G014340.1 Lsi09g01434 1434
2 48077683 48085403 - Sed0005082.2 Sed02g1073 1073
2 48280567 48285440 - Sed0019465.1 Sed02g1091 1091
2 48816020 48818495 + Sed0013337.1 Sed02g1177 1177
9 1929014 1934191 + Sed0005683.1 Sed09g0246 246
12 7518641 7528227 + Sed0020412.1 Sed12g1134 1134
6 79240804 79247598 + Tan0007782.1 Tan06g2678 2678
6 79248281 79255401 - Tan0007093.2 Tan06g2680 2680
6 79277770 79287940 - Tan0016232.1 Tan06g2683 2683
10 8957094 8959018 + Tan0018741.1 Tan10g1014 1014
10 8970827 8973581 - Tan0004198.1 Tan10g1015 1015
10 11198930 11202855 + Tan0002504.1 Tan10g1143 1143
5 2897129 2900064 + Vvi5g289 Vvi5g289 289
5 2902756 2906309 + Vvi5g290 Vvi5g290 290
5 2906779 2913701 - Vvi5g291 Vvi5g291 291
5 2941405 2943466 + Vvi5g292 Vvi5g292 292
5 2943703 2952400 - Vvi5g293 Vvi5g293 293
5 2953485 2954622 - Vvi5g294 Vvi5g294 294
5 2955065 2962398 + Vvi5g295 Vvi5g295 295
5 2962422 2970890 + Vvi5g296 Vvi5g296 296
5 2970889 2971437 + Vvi5g297 Vvi5g297 297
5 2972086 2979785 - Vvi5g298 Vvi5g298 298
       

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