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
Vvi18g1190 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1191 Blo01g01319 . Bda01g00687 . Bpe02g00619 . . Bma01g02105 . . . Cma09g01066 . . . Cpe06g00869 . Bhi04g02153 . . . . . . . . . . . . . . . Cone6ag1275 . . . . . . . . . . . . . . . Cmo09g01074 . . . Car09g00968 . Cpe02g00867 . . . . . . . . . . . . . . Lsi08g00271 . Chy03g00838 .
Vvi18g1192 Blo01g01321 . Bda01g00688 . Bpe02g00618 . . Bma01g02106 . Cmo15g00642 . . . . Sed01g0954 . . Bhi04g01831 Tan11g1205 Cmetu03g0089 . Hepe02g2751 . Lcy10g1303 . . . . . . . . . . Cone20ag0408 . . . Cme03g00426 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi08g00269 . Chy03g00573 .
Vvi18g1193 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1194 Blo01g01322 . . . Bpe02g00617 Bpe04g00017 Bma04g00025 Bma01g02108 Cmo04g02532 Cmo15g00641 . Cma09g01074 . . Sed14g0960 Cpe06g00875 Cpe13g00658 Bhi04g01830 Tan11g1204 Cmetu05g0148 . . . . Cla08g00653 Cam08g1083 Cec08g0669 Cco08g0777 Clacu08g0787 . Cre08g0592 Cone4ag1448 . . . . . . Cme03g00424 . . . . . . . . . . Cmo09g01081 . . Car05g00777 Car15g00582 Cpe01g02093 . . . . . . . . . . . . . . . Lsi08g00513 . Chy03g00879 .
Vvi18g1195 Blo01g01323 . Bda01g00689 Bda03g00027 Bpe02g00616 . . Bma01g02109 . . Cma01g01007 . Car01g00889 . . . . . . . . . . . . . . . . . . Cone4ag1449 Cone7ag1483 . . . . . . Blo17g00226 . . . Bpe02g01597 . Bma01g00877 . . Cmo01g01045 . . . . . . Cpe02g00884 Bhi09g01482 . . . . . . Cla09g00909 Cam09g0961 Cec09g0966 Cco09g0972 . . Cre09g0930 . . . .
Vvi18g1196 . Blo12g01111 . . . . Bma04g00026 . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1450 Cone7ag1482 . . . . . . . . . . . . . . . . . . . . Car09g00971 . . . . . . . . . . . . . . . . . . . .
Vvi18g1197 . Blo12g01110 . Bda03g00028 . Bpe04g00018 Bma04g00027 . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1451 Cone7ag1481 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1198 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1199 Blo01g01324 Blo12g01109 . Bda03g00029 . Bpe04g00019 . . Cmo04g02534 Cmo15g00640 . . . . Sed11g1319 . Cpe13g00660 Bhi04g01828 Tan11g1203 Cmetu01g1872 . Hepe02g2753 . Lcy10g1305 Cla08g00654 Cam08g1084 Cec08g0670 Cco08g0779 Clacu08g0788 . Cre08g0593 . . Cone17ag0803 Cone20ag0407 . . . Cme03g00422 . . . . . . . . . . . . . Car04g02331 Car15g00581 Cpe01g02094 . . . . . . . . . . . . . . . Lsi08g00514 . Chy03g00578 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 34021124 34022137 - Bda002723.1 Bda01g00687 687
1 34031524 34032017 - Bda002724.1 Bda01g00688 688
1 34048835 34050574 + Bda002725.1 Bda01g00689 689
3 453384 454990 + Bda015960.2 Bda03g00027 27
3 461405 463761 + Bda015961.1 Bda03g00028 28
3 464819 465139 + Bda015962.1 Bda03g00029 29
4 45113496 45114402 - XM_039028310.1 Bhi04g01828 1828
4 45175712 45177440 + XM_039030665.1 Bhi04g01830 1830
4 45187337 45189089 + XM_039029748.1 Bhi04g01831 1831
4 58394681 58395508 + XM_039030032.1 Bhi04g02153 2153
9 38396938 38400288 + XM_039042492.1 Bhi09g01482 1482
1 50488068 50489081 - BLOR01319 Blo01g01319 1319
1 50505382 50505878 - BLOR01321 Blo01g01321 1321
1 50509119 50516986 - BLOR01322 Blo01g01322 1322
1 50578727 50580466 + BLOR01323 Blo01g01323 1323
1 50581288 50581985 + BLOR01324 Blo01g01324 1324
12 28769175 28769805 - BLOR05128 Blo12g01109 1109
12 28770429 28772945 - BLOR05129 Blo12g01110 1110
12 28773262 28778824 + BLOR05130 Blo12g01111 1111
17 2326381 2327451 - BLOR16047 Blo17g00226 226
1 8245315 8246961 - Bma001099.1 Bma01g00877 877
1 77202446 77203459 - Bma002930.1 Bma01g02105 2105
1 77206610 77207117 - Bma002931.1 Bma01g02106 2106
1 77211878 77212740 - Bma002933.1 Bma01g02108 2108
1 77250880 77252619 + Bma002935.1 Bma01g02109 2109
4 308389 309383 - Bma018476.1 Bma04g00025 25
4 314405 320563 - Bma018477.2 Bma04g00026 26
4 320865 323183 + Bma018478.2 Bma04g00027 27
2 4014832 4016571 - Bpe008456.1 Bpe02g00616 616
2 4023730 4024751 + Bpe008457.1 Bpe02g00617 617
2 4027419 4027922 + Bpe008458.1 Bpe02g00618 618
2 4028860 4030005 + Bpe008459.1 Bpe02g00619 619
2 18877768 18879414 + Bpe009443.1 Bpe02g01597 1597
4 175826 176821 - Bpe014744.1 Bpe04g00017 17
4 196893 198939 + Bpe025563 Bpe04g00018 18
4 199867 200175 + Bpe014746.1 Bpe04g00019 19
8 17172930 17174379 - CaPI482276_08g010830.1 Cam08g1083 1083
8 17209299 17209940 + CaPI482276_08g010840.1 Cam08g1084 1084
9 9939946 9941658 + CaPI482276_09g009610.1 Cam09g0961 961
1 8233682 8236560 + Carg27665-RA Car01g00889 889
4 18777941 18778814 + Carg15765-RA Car04g02331 2331
5 6074248 6074905 - Carg25811-RA Car05g00777 777
9 6074022 6077567 + Carg26645-RA Car09g00968 968
9 6099569 6106675 + Carg26648-RA Car09g00971 971
15 3215042 3216334 - Carg01574-RA Car15g00581 581
15 3219340 3220564 + Carg01573-RA Car15g00582 582
8 19564343 19565840 - CcPI632755_08g007770.1 Cco08g0777 777
8 19599041 19599682 + CcPI632755_08g007790.1 Cco08g0779 779
9 9199729 9201441 + CcPI632755_09g009720.1 Cco09g0972 972
8 18394889 18396407 - CePI673135_08g006690.1 Cec08g0669 669
8 18416844 18417485 + CePI673135_08g006700.1 Cec08g0670 670
9 9239198 9240910 + CePI673135_09g009660.1 Cec09g0966 966
3 8182882 8184611 - Chy3G055530.1 Chy03g00573 573
3 8280834 8281465 + Chy3G055580.1 Chy03g00578 578
3 11598633 11599619 + Chy3G058180.1 Chy03g00838 838
3 12215072 12217010 + Chy3G058590.1 Chy03g00879 879
8 17891983 17893453 - ClG42_08g0078700.10 Clacu08g0787 787
8 17932034 17932675 + ClG42_08g0078800.10 Clacu08g0788 788
8 18748759 18750229 - ClCG08G006350.1 Cla08g00653 653
8 18791332 18791973 + ClCG08G006360.1 Cla08g00654 654
9 9478221 9481382 + ClCG09G009720.1 Cla09g00909 909
1 7294187 7295917 + CmaCh01G010070.1 Cma01g01007 1007
9 5600678 5601694 + CmaCh09G010660.1 Cma09g01066 1066
9 5652819 5653607 - CmaCh09G010740.1 Cma09g01074 1074
3 5831664 5833077 - MELO3C008421.2.1 Cme03g00422 422
3 5900061 5901924 + MELO3C008423.2.1 Cme03g00424 424
3 5933557 5935512 + MELO3C008424.2.1 Cme03g00426 426
1 516376 518968 - PI0016310.1 Cmetu01g1872 1872
3 10344420 10347936 + PI0026493.1 Cmetu03g0089 89
5 13885914 13890727 - PI0025502.1 Cmetu05g0148 148
1 8241594 8243324 + CmoCh01G010450.1 Cmo01g01045 1045
4 18604743 18606095 - CmoCh04G025320.1 Cmo04g02532 2532
4 18609825 18610848 + CmoCh04G025340.1 Cmo04g02534 2534
9 5819490 5820506 + CmoCh09G010740.1 Cmo09g01074 1074
9 5877887 5878844 - CmoCh09G010810.1 Cmo09g01081 1081
15 3103449 3104334 - CmoCh15G006400.1 Cmo15g00640 640
15 3115111 3116263 + CmoCh15G006410.1 Cmo15g00641 641
15 3117999 3120777 + CmoCh15G006420.1 Cmo15g00642 642
4 11487057 11488313 - Conep04aG0150000.1 Cone4ag1448 1448
4 11499843 11502947 + Conep04aG0150100.1 Cone4ag1449 1449
4 11503041 11507498 - Conep04aG0150200.1 Cone4ag1450 1450
4 11509372 11511686 + Conep04aG0150300.1 Cone4ag1451 1451
6 10185469 10186533 + Conep06aG0132300.1 Cone6ag1275 1275
7 10397910 10400258 - Conep07aG0152300.1 Cone7ag1481 1481
7 10400406 10404752 + Conep07aG0152400.1 Cone7ag1482 1482
7 10404947 10406483 - Conep07aG0152500.1 Cone7ag1483 1483
17 6354776 6356144 - Conep17aG0082100.1 Cone17ag0803 803
20 1980626 1980847 + Conep20aG0042100.1 Cone20ag0407 407
20 1984118 1985231 + Conep20aG0042200.1 Cone20ag0408 408
1 17728078 17729253 - Cp4.1LG01g20980.1 Cpe01g02093 2093
1 17732502 17735332 + Cp4.1LG01g20890.1 Cpe01g02094 2094
2 5822288 5823172 - Cp4.1LG02g00090.1 Cpe02g00867 867
2 6289824 6291554 - Cp4.1LG02g08950.1 Cpe02g00884 884
6 5667255 5679493 + Cp4.1LG06g07910.1 Cpe06g00869 869
6 5735571 5736407 - Cp4.1LG06g07790.1 Cpe06g00875 875
13 6219010 6220166 - Cp4.1LG13g04250.1 Cpe13g00658 658
13 6223255 6226050 + Cp4.1LG13g04310.1 Cpe13g00660 660
8 18836778 18838277 - CrPI670011_08g005920.1 Cre08g0592 592
8 18868883 18869524 + CrPI670011_08g005930.1 Cre08g0593 593
9 9445925 9447637 + CrPI670011_09g009300.1 Cre09g0930 930
2 76034083 76035241 - Hsped.02g27510.1 Hepe02g2751 2751
2 76061269 76062409 + Hsped.02g27530.1 Hepe02g2753 2753
10 35916295 35919063 - Maker00008475 Lcy10g1303 1303
10 35940847 35942399 + Maker00008441 Lcy10g1305 1305
8 6510731 6513705 + Lsi08G002690.1 Lsi08g00269 269
8 6619255 6650134 + Lsi08G002710.1 Lsi08g00271 271
8 13050742 13052387 - Lsi08G005130.1 Lsi08g00513 513
8 13066182 13067163 + Lsi08G005140.1 Lsi08g00514 514
1 7062571 7065409 - Sed0011445.1 Sed01g0954 954
11 28954127 28955796 + Sed0012698.1 Sed11g1319 1319
14 18736855 18738219 - Sed0005366.1 Sed14g0960 960
11 9963568 9964615 - Tan0021086.1 Tan11g1203 1203
11 9979444 9981067 + Tan0005199.1 Tan11g1204 1204
11 9986976 9988850 + Tan0018473.1 Tan11g1205 1205
18 13306082 13306887 - Vvi18g1190 Vvi18g1190 1190
18 13311779 13316460 + Vvi18g1191 Vvi18g1191 1191
18 13365473 13366663 - Vvi18g1192 Vvi18g1192 1192
18 13388959 13391077 + Vvi18g1193 Vvi18g1193 1193
18 13397961 13399162 - Vvi18g1194 Vvi18g1194 1194
18 13408108 13413196 + Vvi18g1195 Vvi18g1195 1195
18 13418281 13429828 - Vvi18g1196 Vvi18g1196 1196
18 13430849 13443079 + Vvi18g1197 Vvi18g1197 1197
18 13444138 13444288 + Vvi18g1198 Vvi18g1198 1198
18 13444643 13445959 + Vvi18g1199 Vvi18g1199 1199
       

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