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
Vvi19g474 . . . . Bpe09g00184 . Bma10g00542 . Cmo16g00904 . . . . . . . . . . . . . . . Cla10g00520 Cam10g0514 Cec10g0531 Cco10g0520 Clacu10g0536 Cmu10g1362 Cre10g0765 Cone6ag0076 . . . . Csa03g00528 . Cme06g02268 Blo07g00912 Blo10g00817 Bda05g00728 Bda12g00899 . Bpe03g00798 . . Sed07g1919 . . . . . Car16g00849 . . Bhi11g00638 Tan01g1688 Cmetu06g2671 . Hepe07g1192 Mch10g1243 . . . . . . . . Lsi05g00614 . Chy06g01803 .
Vvi19g475 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g476 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g477 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g478 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g479 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g480 Blo03g00570 Blo03g01445 Bda07g00351 Bda09g00392 . Bpe08g01131 . . . . Cma01g01137 Cma09g00942 . Car09g00856 . Cpe06g00759 Cpe02g00763 . . . . . . . . . . . . . . . . . . Lsi04g01217 . Chy04g00971 . . . . . Bpe11g00536 . Bma07g01305 Bma14g00345 . Cmo01g01188 Cmo09g00940 . . . Car16g00548 . . . . . . . . . Cla05g01500 Cam05g1618 Cec05g1622 Cco05g1647 Clacu05g1603 Cmu05g1502 . . . . Cme04g00856
Vvi19g481 . . . . Bpe09g00183 . Bma10g00543 . Cmo16g00903 . . . Car01g01000 . . . . Bhi09g01625 . . . . . . Cla10g00517 . . . . . . . . Cone14ag1133 Cone15ag1154 . Csa03g00526 . Cme06g02265 Blo07g00911 Blo10g00819 . . . Bpe03g00797 . . . . . Cma04g00953 Cma16g00856 . Car16g00846 . . Bhi11g00636 . . . . . . . . . . . . . Lsi05g00612 . Chy06g01805 .
Vvi19g482 . . Bda07g00352 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0073 . Cone14ag1134 . Lsi04g01216 . Chy04g00970 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme04g00858
Vvi19g483 . . . . Bpe09g00182 . . Bma13g01050 . . . . . . . . . . . . . . . . Cla10g00516 Cam10g0511 Cec10g0528 Cco10g0515 Clacu10g0532 Cmu10g1358 Cre10g0762 . . . . . Csa03g00524 . Cme06g02264 . Blo10g00820 . Bda12g00901 . . . . Sed07g1921 . . Cma04g00952 . . . . . Bhi11g00632 Tan01g1693 Cmetu06g0543 . Hepe07g1201 Mch10g1254 . . . . . . . . Lsi05g00609 . Chy06g01806 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 55639496 55640775 - Bda033653 Bda05g00728 728
7 4534130 4538870 + Bda033835 Bda07g00351 351
7 4539944 4541770 + Bda025438.1 Bda07g00352 352
9 4976018 4980322 + Bda034090 Bda09g00392 392
12 39724091 39725223 + Bda009434.1 Bda12g00899 899
12 39755328 39756780 + Bda009436.1 Bda12g00901 901
9 43843095 43848272 - XM_039043560.1 Bhi09g01625 1625
11 14689893 14692739 - XM_039047231.1 Bhi11g00632 632
11 14867694 14871202 + XM_039050103.1 Bhi11g00636 636
11 14931536 14933988 + XM_039047485.1 Bhi11g00638 638
3 22477106 22481949 - BLOR11751 Blo03g00570 570
3 41024080 41032672 + BLOR12626 Blo03g01445 1445
7 28059265 28063101 + BLOR18843 Blo07g00911 911
7 28066575 28067708 - BLOR18844 Blo07g00912 912
10 25910551 25911749 + BLOR02607 Blo10g00817 817
10 25932028 25935902 - BLOR02609 Blo10g00819 819
10 25935932 25937383 + BLOR02610 Blo10g00820 820
7 48616837 48621497 - Bma026580.1 Bma07g01305 1305
10 6595462 6596569 + Bma030358 Bma10g00542 542
10 6598170 6600378 - Bma004242.1 Bma10g00543 543
13 43202327 43203789 + Bma030619 Bma13g01050 1050
14 4277645 4282342 - Bma010766.1 Bma14g00345 345
3 27918991 27921190 + Bpe012709.1 Bpe03g00797 797
3 27922597 27923749 - Bpe012710.1 Bpe03g00798 798
8 13217011 13221681 - Bpe023257.1 Bpe08g01131 1131
9 1265411 1268866 - Bpe026210 Bpe09g00182 182
9 1270733 1283699 + Bpe023852.1 Bpe09g00183 183
9 1284288 1285257 - Bpe026211 Bpe09g00184 184
11 4131421 4136139 + Bpe003903.1 Bpe11g00536 536
5 22973995 22979438 - CaPI482276_05g016180.1 Cam05g1618 1618
10 7587497 7589979 - CaPI482276_10g005110.1 Cam10g0511 511
10 7632409 7634225 + CaPI482276_10g005140.1 Cam10g0514 514
1 9474578 9480690 - Carg27980-RA Car01g01000 1000
9 5236526 5242890 + Carg12810-RA Car09g00856 856
16 3473079 3478488 - Carg05633-RA Car16g00548 548
16 6187289 6190918 + Carg24812-RA Car16g00846 846
16 6209672 6210734 + Carg24815-RA Car16g00849 849
5 22688677 22694142 - CcPI632755_05g016470.1 Cco05g1647 1647
10 6154525 6157011 - CcPI632755_10g005150.1 Cco10g0515 515
10 6199814 6201627 + CcPI632755_10g005200.1 Cco10g0520 520
5 25407944 25413425 - CePI673135_05g016220.1 Cec05g1622 1622
10 6351650 6354116 - CePI673135_10g005280.1 Cec10g0528 528
10 6410661 6412477 + CePI673135_10g005310.1 Cec10g0531 531
4 14208056 14210194 + Chy4G076880.1 Chy04g00970 970
4 14232337 14252114 - Chy4G076890.1 Chy04g00971 971
6 21692812 21694608 - Chy6G123310.1 Chy06g01803 1803
6 21715067 21724737 - Chy6G123330.1 Chy06g01805 1805
6 21737401 21739971 + Chy6G123340.1 Chy06g01806 1806
5 23020230 23025695 - ClG42_05g0160300.10 Clacu05g1603 1603
10 6422088 6424557 - ClG42_10g0053200.10 Clacu10g0532 532
10 6467333 6469149 + ClG42_10g0053600.10 Clacu10g0536 536
5 24303468 24309153 - ClCG05G014420.1 Cla05g01500 1500
10 6826366 6829215 - ClCG10G005510.1 Cla10g00516 516
10 6839670 6847223 + ClCG10G005520.2 Cla10g00517 517
10 6875123 6877129 + ClCG10G005560.1 Cla10g00520 520
1 8325042 8330827 - CmaCh01G011370.1 Cma01g01137 1137
4 4882507 4884625 - CmaCh04G009520.1 Cma04g00952 952
4 4887290 4889699 + CmaCh04G009530.1 Cma04g00953 953
9 4725304 4731813 + CmaCh09G009420.1 Cma09g00942 942
16 5061478 5083047 - CmaCh16G008560.1 Cma16g00856 856
4 10959217 10972122 + MELO3C018075.2.1 Cme04g00856 856
4 10984712 10986853 - MELO3C018073.2.1 Cme04g00858 858
6 29638218 29639261 - MELO3C031911.2.1 Cme06g02264 2264
6 29655336 29658551 + MELO3C025392.2.1 Cme06g02265 2265
6 29714265 29716705 + MELO3C025397.2.1 Cme06g02268 2268
6 26069771 26072570 + PI0022299.1 Cmetu06g0543 543
6 26021532 26023568 - PI0019158.1 Cmetu06g2671 2671
1 9651569 9657202 - CmoCh01G011880.1 Cmo01g01188 1188
9 4931819 4938416 + CmoCh09G009400.1 Cmo09g00940 940
16 5382706 5402053 + CmoCh16G009030.1 Cmo16g00903 903
16 5402643 5403758 + CmoCh16G009040.1 Cmo16g00904 904
5 22731906 22737373 - CmPI595203_05g015020.1 Cmu05g1502 1502
10 6543805 6546273 - CmPI595203_10g013580.1 Cmu10g1358 1358
10 6589075 6590891 + CmPI595203_10g013620.1 Cmu10g1362 1362
6 370140 371894 + Conep06aG0007300.1 Cone6ag0073 73
6 379181 380228 + Conep06aG0007600.1 Cone6ag0076 76
14 9414814 9417130 - Conep14aG0115700.1 Cone14ag1133 1133
14 9426584 9429133 + Conep14aG0115800.1 Cone14ag1134 1134
15 9341508 9344520 - Conep15aG0118200.1 Cone15ag1154 1154
2 4874577 4876523 + Cp4.1LG02g01110.1 Cpe02g00763 763
6 4788558 4797629 + Cp4.1LG06g09100.1 Cpe06g00759 759
10 7421562 7424036 - CrPI670011_10g007620.1 Cre10g0762 762
10 7467207 7469013 + CrPI670011_10g007650.1 Cre10g0765 765
3 4364482 4367602 - CsaV3_3G005240.1 Csa03g00524 524
3 4374615 4378144 + CsaV3_3G005260.1 Csa03g00526 526
3 4401887 4404566 + CsaV3_3G005280.1 Csa03g00528 528
7 28277104 28278625 + Hsped.07g11920.1 Hepe07g1192 1192
7 29124712 29127490 + Hsped.07g12010.1 Hepe07g1201 1201
4 18739045 18741198 + Lsi04G012160.1 Lsi04g01216 1216
4 18742527 18749218 - Lsi04G012170.1 Lsi04g01217 1217
5 7530977 7534341 - Lsi05G006090.1 Lsi05g00609 609
5 7554669 7560612 + Lsi05G006120.1 Lsi05g00612 612
5 7581041 7583401 + Lsi05G006140.1 Lsi05g00614 614
10 10054560 10056792 - MC10g1034 Mch10g1243 1243
10 10136711 10139096 + MC10g1037 Mch10g1254 1254
7 33339098 33341464 - Sed0007548.1 Sed07g1919 1919
7 33394485 33406806 + Sed0021211.1 Sed07g1921 1921
1 17950065 17952406 - Tan0016755.1 Tan01g1688 1688
1 18029927 18032472 + Tan0005265.1 Tan01g1693 1693
19 6182058 6184697 - Vvi19g474 Vvi19g474 474
19 6186162 6186602 + Vvi19g475 Vvi19g475 475
19 6186658 6188485 - Vvi19g476 Vvi19g476 476
19 6198077 6205568 - Vvi19g477 Vvi19g477 477
19 6208063 6214320 - Vvi19g478 Vvi19g478 478
19 6217097 6219801 + Vvi19g479 Vvi19g479 479
19 6224945 6231062 + Vvi19g480 Vvi19g480 480
19 6231409 6232754 - Vvi19g481 Vvi19g481 481
19 6234392 6236285 - Vvi19g482 Vvi19g482 482
19 6242147 6245586 + Vvi19g483 Vvi19g483 483
       

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