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
Vvi5g789 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone7ag0354 Cone4ag0366 . . . . . Blo07g00289 Bda11g00650 . . Bpe13g00536 . Bma06g01618 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g790 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g791 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g792 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone15ag0199 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g793 . . . . . Bpe14g01287 . . . . . . . Car14g01656 . . Cpe03g01548 . . . . . . . . . . . . . . Cone14ag0185 . . . . . . Cme06g00444 Blo02g00683 . . Bda13g00033 . . Bma02g00746 . . . Cmo14g01893 . . . . . . . . . . . . . . . . . . . . . Csa03g01161 Chy06g00424 .
Vvi5g794 . . . . Bpe04g01038 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag0367 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g795 . . . . . . . . . . Cma06g01288 Cma14g01848 Car06g01106 Car14g01657 Sed02g1426 Cpe08g00363 Cpe03g01549 Bhi01g00662 Tan10g0615 Cmetu06g1762 . . . . . . . . . . . Cone14ag0186 . . . Lsi05g01778 . . Cme06g00443 . . Bda11g00651 . . . . Bma06g01619 . Cmo06g01294 Cmo14g01894 . . . . . . . . . . . . . Cla05g00402 Cam05g0438 Cec05g0445 Cco05g0445 Clacu05g0434 Cmu05g0414 Cre05g0476 . Csa03g01160 Chy06g00423 .
Vvi5g796 . . Bda03g01099 . . . Bma04g01024 . Cmo08g01027 Cmo17g00134 . . . . . . . . . . . . . . Cla06g00702 Cam06g0753 Cec06g0759 Cco06g0771 Clacu06g0744 Cmu06g0727 Cre06g1504 . . . . . Csa02g01023 . . . . . . . . . . . . . Cma08g01056 Cma17g00131 Car08g00932 Car17g00117 Cpe12g00115 Cpe17g00220 . . . . . . . . . . . . . . Lsi09g01191 . . .
Vvi5g797 . Blo12g00135 . . Bpe04g00980 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0187 . . . . . Chy05g00285 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme05g00623
Vvi5g798 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 11043507 11046715 - Bda017143.1 Bda03g01099 1099
11 6446080 6451891 - Bda005396.1 Bda11g00650 650
11 6452586 6453244 - Bda005397.1 Bda11g00651 651
13 534128 561948 - Bda032830 Bda13g00033 33
1 12039703 12042046 - XM_039025865.1 Bhi01g00662 662
2 19979097 19981570 - BLOR10413 Blo02g00683 683
7 3365310 3372658 - BLOR18221 Blo07g00289 289
12 9577626 9580841 + BLOR04154 Blo12g00135 135
2 38499335 38529142 - Bma015448.2 Bma02g00746 746
4 17992218 17995412 - Bma019639.1 Bma04g01024 1024
6 52311927 52318583 - Bma024732.1 Bma06g01618 1618
6 52326610 52327271 - Bma024733.1 Bma06g01619 1619
4 6794769 6797975 + Bpe015646.1 Bpe04g00980 980
4 7504062 7506147 - Bpe015708.1 Bpe04g01038 1038
13 12677764 12683595 + Bpe010240.1 Bpe13g00536 536
14 9752738 9783958 + Bpe014644.1 Bpe14g01287 1287
5 3973031 3974734 + CaPI482276_05g004380.1 Cam05g0438 438
6 10133016 10136807 - CaPI482276_06g007530.1 Cam06g0753 753
6 8305404 8306815 + Carg06252-RA Car06g01106 1106
8 6257085 6262478 + Carg10992-RA Car08g00932 932
14 13219765 13229190 + Carg16531-RA Car14g01656 1656
14 13229419 13231169 - Carg16530-RA Car14g01657 1657
17 736448 741834 + Carg10115-RA Car17g00117 117
5 3629189 3630850 + CcPI632755_05g004450.1 Cco05g0445 445
6 8846473 8850266 - CcPI632755_06g007710.1 Cco06g0771 771
5 3626102 3627859 + CePI673135_05g004450.1 Cec05g0445 445
6 8876554 8880273 - CePI673135_06g007590.1 Cec06g0759 759
5 2801839 2810512 + Chy5G093310.1 Chy05g00285 285
6 2873841 2875631 + Chy6G109510.1 Chy06g00423 423
6 2877060 2892200 - Chy6G109520.1 Chy06g00424 424
5 3685146 3686870 + ClG42_05g0043400.10 Clacu05g0434 434
6 8696884 8700681 - ClG42_06g0074400.10 Clacu06g0744 744
5 3651768 3653492 + ClCG05G003930.2 Cla05g00402 402
6 8922234 8926897 - ClCG06G007290.2 Cla06g00702 702
6 8566579 8568269 + CmaCh06G012880.1 Cma06g01288 1288
8 6619527 6624656 + CmaCh08G010560.1 Cma08g01056 1056
14 13162165 13163896 - CmaCh14G018480.1 Cma14g01848 1848
17 681866 688217 + CmaCh17G001310.1 Cma17g00131 131
5 6478891 6481743 - MELO3C023047.2.1 Cme05g00623 623
6 2819268 2821465 + MELO3C006368.2.1 Cme06g00443 443
6 2822398 2838860 - MELO3C006369.2.1 Cme06g00444 444
6 3039219 3041795 + PI0006343.1 Cmetu06g1762 1762
6 9754180 9756537 + CmoCh06G012940.1 Cmo06g01294 1294
8 6687693 6693069 + CmoCh08G010270.1 Cmo08g01027 1027
14 14135941 14146630 + CmoCh14G018930.1 Cmo14g01893 1893
14 14146801 14149122 - CmoCh14G018940.1 Cmo14g01894 1894
17 774075 779289 + CmoCh17G001340.1 Cmo17g00134 134
5 3521798 3522975 + CmPI595203_05g004140.1 Cmu05g0414 414
6 8515136 8518933 - CmPI595203_06g007270.1 Cmu06g0727 727
4 1659016 1663858 - Conep04aG0037800.1 Cone4ag0366 366
4 1664008 1666365 + Conep04aG0037900.1 Cone4ag0367 367
7 1536990 1540688 - Conep07aG0036200.1 Cone7ag0354 354
14 853252 859181 + Conep14aG0018900.1 Cone14ag0185 185
14 859415 860109 - Conep14aG0019000.1 Cone14ag0186 186
14 860309 863216 - Conep14aG0019100.1 Cone14ag0187 187
15 943533 945496 + Conep15aG0020300.1 Cone15ag0199 199
3 12033756 12040847 + Cp4.1LG03g09680.1 Cpe03g01548 1548
3 12041016 12043430 - Cp4.1LG03g09560.1 Cpe03g01549 1549
8 2244887 2253684 - Cp4.1LG08g03110.1 Cpe08g00363 363
12 735904 741371 + Cp4.1LG12g01130.1 Cpe12g00115 115
17 1396548 1405974 - Cp4.1LG17g02260.1 Cpe17g00220 220
5 4311170 4312897 + CrPI670011_05g004760.1 Cre05g0476 476
6 9682360 9686205 - CrPI670011_06g015040.1 Cre06g1504 1504
2 9946289 9949531 + CsaV3_2G012390.1 Csa02g01023 1023
3 9071123 9074866 + CsaV3_3G011600.1 Csa03g01160 1160
3 9074473 9091164 - CsaV3_3G011610.1 Csa03g01161 1161
5 25097068 25099764 - Lsi05G017780.1 Lsi05g01778 1778
9 19150990 19157237 + Lsi09G011910.1 Lsi09g01191 1191
2 50417533 50419145 + Sed0020873.1 Sed02g1426 1426
10 5053603 5056936 + Tan0000591.1 Tan10g0615 615
5 9466481 9475315 - Vvi5g789 Vvi5g789 789
5 9520536 9521514 - Vvi5g790 Vvi5g790 790
5 9596527 9599584 + Vvi5g791 Vvi5g791 791
5 9621837 9626257 + Vvi5g792 Vvi5g792 792
5 9637018 9715468 + Vvi5g793 Vvi5g793 793
5 9748663 9758707 + Vvi5g794 Vvi5g794 794
5 9759207 9759919 - Vvi5g795 Vvi5g795 795
5 9760803 9763204 - Vvi5g796 Vvi5g796 796
5 9763794 9777367 - Vvi5g797 Vvi5g797 797
5 9780150 9799953 + Vvi5g798 Vvi5g798 798
       

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