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
Vvi5g809 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g810 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g811 . . . . . Bpe14g01291 . . . . Cma06g01282 . Car06g01101 . . Cpe08g00366 . Bhi01g00034 . . . . . . . . . . . . . . . . Cone4ag0376 Lsi05g01786 . . Cme06g00435 . . . Bda13g00031 . . Bma02g00742 . . . . . . . . . . . . . . . . . Cla05g00393 Cam05g0428 Cec05g0433 Cco05g0432 Clacu05g0423 Cmu05g0405 Cre05g0467 . Csa03g01150 Chy06g00415 .
Vvi5g812 Blo01g00310 . . Bda08g00015 . . . . . . Cma06g01281 Cma14g01858 Car06g01100 Car14g01664 . Cpe08g00368 Cpe03g01556 Bhi01g00033 . . . . . . . . . . . . . . Cone15ag0211 . . Lsi05g01787 . . Cme06g00434 . . . . Bpe05g01121 . . . . Cmo06g01287 Cmo14g01903 . . . . . . . . . . . . . Cla05g00392 Cam05g0426 Cec05g0431 Cco05g0431 Clacu05g0422 Cmu05g0404 Cre05g0466 . Csa03g01149 Chy06g00414 .
Vvi5g813 . . Bda03g01105 . Bpe04g00973 . Bma04g01031 . . . . Cma14g01860 . Car14g01665 . . Cpe03g01557 Bhi01g00032 . . . . . . . . . . . . . Cone14ag0198 . . . Lsi05g01788 . . Cme06g00433 . . . . . . . . . . Cmo14g01904 . . . . . . . . . . . . . Cla05g00391 Cam05g0425 Cec05g0430 Cco05g0430 Clacu05g0421 Cmu05g0403 Cre05g0465 . Csa03g01148 Chy06g00413 .
Vvi5g814 . . . . Bpe04g01051 . Bma04g01032 . Cmo08g01019 Cmo17g00127 . . . . . . . . . . . . . . . . . . . . . Cone14ag0199 Cone15ag0212 . . . Csa02g01012 Chy05g00276 . . . . . . . . . Sed09g0207 . . Cma08g01048 Cma17g00125 Car08g00923 Car17g00111 Cpe12g00109 . Bhi12g01537 Tan06g2351 Cmetu05g1285 . . . Lcy13g0426 . . . . . . . Lsi09g01178 . . .
Vvi5g815 . . . . . . . . . . Cma06g01278 . . . Sed02g1457 . . Bhi01g00088 Tan10g0596 Cmetu06g2009 . Hepe05g1844 . Lcy11g1727 . . . . . . . . . . . Lsi05g01791 . . Cme06g00432 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g01147 Chy06g00411 .
Vvi5g816 Blo01g00311 . . Bda08g00016 . . . Bma05g01266 . . . Cma14g01861 . . . Cpe08g00369 Cpe03g01558 Bhi01g00030 . . . . . . . . . . . . . . . . . Lsi05g01792 . . Cme06g00431 . . . . . . . . . Cmo06g01286 Cmo14g01905 . . . . . . . . . . . . . . . . . . . . . Csa03g01146 Chy06g00410 .
Vvi5g817 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g818 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 11111985 11117864 - Bda017150.1 Bda03g01105 1105
8 147248 148924 + Bda024405.1 Bda08g00015 15
8 151173 151914 + Bda024406.2 Bda08g00016 16
13 504384 520743 - Bda000873.2 Bda13g00031 31
1 366375 367636 - XM_039023646.1 Bhi01g00030 30
1 415145 422418 + XM_039039931.1 Bhi01g00032 32
1 423036 426551 - XM_039039936.1 Bhi01g00033 33
1 519537 546584 - XM_039046079.1 Bhi01g00034 34
1 1630727 1633095 - XM_039041378.1 Bhi01g00088 88
12 50037159 50051446 + XM_039050938.1 Bhi12g01537 1537
1 3791178 3792830 + BLOR00310 Blo01g00310 310
1 3795092 3798553 + BLOR00311 Blo01g00311 311
2 38379705 38392070 - Bma015443.2 Bma02g00742 742
4 18051969 18058323 - Bma019648.1 Bma04g01031 1031
4 18154176 18162606 - Bma019651.1 Bma04g01032 1032
5 52026871 52027614 + Bma022458.7 Bma05g01266 1266
4 6718488 6725281 + Bpe015639.1 Bpe04g00973 973
4 7694451 7702960 - Bpe015720.1 Bpe04g01051 1051
5 23550448 23552070 + Bpe018538.1 Bpe05g01121 1121
14 9824096 9835724 + Bpe014648.1 Bpe14g01291 1291
5 3853177 3861948 + CaPI482276_05g004250.1 Cam05g0425 425
5 3862659 3864446 - CaPI482276_05g004260.1 Cam05g0426 426
5 3877070 3903212 - CaPI482276_05g004280.1 Cam05g0428 428
6 8249215 8250902 - Carg06258-RA Car06g01100 1100
6 8259248 8281653 - Carg06257-RA Car06g01101 1101
8 6192735 6201929 - Carg11001-RA Car08g00923 923
14 13269854 13271533 + Carg16523-RA Car14g01664 1664
14 13272522 13274860 - Carg16522-RA Car14g01665 1665
17 691853 701732 - Carg10121-RA Car17g00111 111
5 3507706 3516917 + CcPI632755_05g004300.1 Cco05g0430 430
5 3517468 3519252 - CcPI632755_05g004310.1 Cco05g0431 431
5 3531561 3559328 - CcPI632755_05g004320.1 Cco05g0432 432
5 3502970 3511668 + CePI673135_05g004300.1 Cec05g0430 430
5 3512387 3514174 - CePI673135_05g004310.1 Cec05g0431 431
5 3526608 3533966 - CePI673135_05g004330.1 Cec05g0433 433
5 2579834 2596540 - Chy5G093220.1 Chy05g00276 276
6 2764519 2765276 + Chy6G109380.1 Chy06g00410 410
6 2765740 2768028 + Chy6G109390.1 Chy06g00411 411
6 2784795 2793268 + Chy6G109410.1 Chy06g00413 413
6 2795258 2796971 - Chy6G109420.1 Chy06g00414 414
6 2806607 2824811 - Chy6G109430.1 Chy06g00415 415
5 3565867 3574533 + ClG42_05g0042100.10 Clacu05g0421 421
5 3575259 3577046 - ClG42_05g0042200.10 Clacu05g0422 422
5 3588151 3609599 - ClG42_05g0042300.10 Clacu05g0423 423
5 3527346 3536985 + ClCG05G003790.2 Cla05g00391 391
5 3538043 3541038 - ClCG05G003800.1 Cla05g00392 392
5 3553666 3580118 - ClCG05G003810.2 Cla05g00393 393
6 8501349 8502406 + CmaCh06G012780.1 Cma06g01278 1278
6 8507093 8508778 - CmaCh06G012810.1 Cma06g01281 1281
6 8516480 8540422 - CmaCh06G012820.1 Cma06g01282 1282
8 6553033 6563329 - CmaCh08G010480.1 Cma08g01048 1048
14 13202500 13204181 + CmaCh14G018580.1 Cma14g01858 1858
14 13206417 13212782 - CmaCh14G018600.1 Cma14g01860 1860
14 13213235 13214322 - CmaCh14G018610.1 Cma14g01861 1861
17 636424 646839 - CmaCh17G001250.1 Cma17g00125 125
6 2726324 2728342 + MELO3C006355.2.1 Cme06g00431 431
6 2728935 2730024 + MELO3C006357.2.1 Cme06g00432 432
6 2731189 2737147 + MELO3C006358.2.1 Cme06g00433 433
6 2738894 2741376 - MELO3C006359.2.1 Cme06g00434 434
6 2750439 2769870 - MELO3C006360.2.1 Cme06g00435 435
5 17592463 17604958 - PI0007471.1 Cmetu05g1285 1285
6 2936446 2937329 + PI0029020.1 Cmetu06g2009 2009
6 9691547 9692638 + CmoCh06G012860.1 Cmo06g01286 1286
6 9697409 9699090 - CmoCh06G012870.1 Cmo06g01287 1287
8 6618622 6628838 - CmoCh08G010190.1 Cmo08g01019 1019
14 14188505 14190183 + CmoCh14G019030.1 Cmo14g01903 1903
14 14191868 14199387 - CmoCh14G019040.1 Cmo14g01904 1904
14 14199702 14201044 - CmoCh14G019050.1 Cmo14g01905 1905
17 727296 742231 - CmoCh17G001270.1 Cmo17g00127 127
5 3403044 3411707 + CmPI595203_05g004030.1 Cmu05g0403 403
5 3412445 3414232 - CmPI595203_05g004040.1 Cmu05g0404 404
5 3425302 3452358 - CmPI595203_05g004050.1 Cmu05g0405 405
4 1705561 1718346 + Conep04aG0038900.1 Cone4ag0376 376
14 895431 900889 - Conep14aG0020200.1 Cone14ag0198 198
14 901139 908857 - Conep14aG0020300.1 Cone14ag0199 199
15 993713 995320 + Conep15aG0021500.1 Cone15ag0211 211
15 998800 1003547 - Conep15aG0021600.1 Cone15ag0212 212
3 12082656 12084337 + Cp4.1LG03g18370.1 Cpe03g01556 1556
3 12086200 12093008 - Cp4.1LG03g18150.1 Cpe03g01557 1557
3 12093760 12095344 - Cp4.1LG03g18250.1 Cpe03g01558 1558
8 2271354 2294586 + Cp4.1LG08g03240.1 Cpe08g00366 366
8 2300204 2301872 + Cp4.1LG08g03080.1 Cpe08g00368 368
8 2306686 2307716 - Cp4.1LG08g02950.1 Cpe08g00369 369
12 690708 701020 - Cp4.1LG12g01200.1 Cpe12g00109 109
5 4190671 4199248 + CrPI670011_05g004650.1 Cre05g0465 465
5 4199993 4201779 - CrPI670011_05g004660.1 Cre05g0466 466
5 4215094 4239865 - CrPI670011_05g004670.1 Cre05g0467 467
2 9802088 9820726 - CsaV3_2G012280.1 Csa02g01012 1012
3 8982297 8983619 + CsaV3_3G011460.1 Csa03g01146 1146
3 8987537 8989787 + CsaV3_3G011470.1 Csa03g01147 1147
3 8991586 8998563 + CsaV3_3G011480.1 Csa03g01148 1148
3 8999806 9002526 - CsaV3_3G011490.1 Csa03g01149 1149
3 9010824 9028523 - CsaV3_3G011500.1 Csa03g01150 1150
5 68767235 68769909 + Hsped.05g18440.1 Hepe05g1844 1844
11 41123457 41125398 - Maker00031438 Lcy11g1727 1727
13 4898078 4900644 + Maker00023397 Lcy13g0426 426
5 25176357 25207932 + Lsi05G017860.1 Lsi05g01786 1786
5 25220588 25222634 + Lsi05G017870.1 Lsi05g01787 1787
5 25224320 25244461 - Lsi05G017880.1 Lsi05g01788 1788
5 25249803 25251340 - Lsi05G017910.1 Lsi05g01791 1791
5 25252352 25259553 - Lsi05G017920.1 Lsi05g01792 1792
9 19031445 19044185 - Lsi09G011780.1 Lsi09g01178 1178
2 50627632 50629636 + Sed0018788.1 Sed02g1457 1457
9 1642890 1656855 - Sed0008500.3 Sed09g0207 207
6 75584263 75601454 - Tan0005385.1 Tan06g2351 2351
10 4852895 4855602 + Tan0019264.1 Tan10g0596 596
5 10139343 10141541 + Vvi5g809 Vvi5g809 809
5 10143146 10149603 + Vvi5g810 Vvi5g810 810
5 10177413 10289083 + Vvi5g811 Vvi5g811 811
5 10295156 10296788 + Vvi5g812 Vvi5g812 812
5 10300035 10315809 - Vvi5g813 Vvi5g813 813
5 10470706 10502773 - Vvi5g814 Vvi5g814 814
5 10533651 10534725 + Vvi5g815 Vvi5g815 815
5 10543147 10544181 - Vvi5g816 Vvi5g816 816
5 10572518 10577689 - Vvi5g817 Vvi5g817 817
5 10611366 10626517 - Vvi5g818 Vvi5g818 818
       

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