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
Vvi18g220 . Blo12g01120 . Bda03g00019 . . Bma04g00018 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone20ag0426 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g221 . . . . . . . . . Cmo15g00663 . . . . Sed14g0950 . . Bhi04g01871 Tan11g1243 Cmetu09g0635 . Hepe02g2215 . . Cla08g00621 Cam08g1035 Cec08g0624 Cco08g0736 Clacu08g0745 . Cre08g0553 . . . Cone20ag0427 . . . . . . . Bda13g01470 . Bpe14g00395 . Bma02g00206 . . . . . . Car15g00602 . . . . . . . . . . . . . . . . Lsi08g00461 . Chy03g00757 .
Vvi18g222 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1426 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g223 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g224 Blo01g01553 . . . . Bpe04g00208 . . Cmo04g02503 Cmo15g00664 . . . . Sed01g3080 . . Bhi04g01874 Tan11g1245 Cmetu03g1597 . Hepe02g2217 . Lcy10g1250 Cla08g00620 Cam08g1034 Cec08g0623 Cco08g0735 Clacu08g0744 . Cre08g0552 . . Cone17ag0822 . . . . Cme03g00497 . . . Bda13g01471 . Bpe14g00394 . Bma02g00207 . . . . . Car04g02309 Car15g00604 Cpe01g02071 . . . . . . . . . . . . . . . Lsi08g00460 . Chy03g00758 .
Vvi18g225 . Blo12g00885 . Bda03g00290 . . Bma04g00246 . . . Cma01g01969 Cma09g00108 Car01g01540 . . Cpe06g00072 . . . . . . . . . . . . . . . . . . . Lsi04g01739 . Chy04g00422 . . . Bda08g01222 . . Bpe05g00138 . . . Cmo01g02027 Cmo09g00104 . . . Car09g00098 . . . . . . . . . . . . . . . . . . . .
Vvi18g226 Blo01g01304 Blo12g01121 . Bda03g00018 Bpe02g00633 Bpe04g00012 . Bma01g02080 Cmo04g02502 Cmo15g00665 Cma01g01047 Cma09g00774 Car01g00920 . Sed14g0108 Cpe06g00610 . Bhi04g01875 Tan11g1246 Cmetu03g1325 . Hepe02g2218 . Lcy10g1248 Cla08g00619 Cam08g1033 Cec08g0622 Cco08g0734 Clacu08g0743 . Cre08g0551 Cone6ag1243 Cone9ag1216 . . Lsi04g02413 . . Cme03g00500 . Blo18g00175 . Bda13g01472 Bpe02g01654 Bpe14g00393 Bma01g00800 Bma02g00208 . Cmo01g01086 Cmo09g00767 . . Car04g02308 Car09g00684 Cpe01g02070 Cpe02g00848 Bhi09g01840 Tan01g3248 . . . . . Cla11g01552 Cam11g1617 Cec11g1644 Cco11g1645 Clacu11g1774 Cmu11g1590 Cre11g2008 Lsi08g00459 . Chy07g00619 .
Vvi18g227 . . . . . . . . Cmo04g02501 Cmo15g00666 . . . . Sed01g3097 . . Bhi04g01876 Tan11g1248 Cmetu03g2013 . Hepe02g2219 . Lcy10g1247 Cla08g00618 Cam08g1032 Cec08g0621 Cco08g0733 Clacu08g0742 . Cre08g0550 . . . Cone20ag0430 . . . . . . . Bda01g01456 Bpe02g01653 . Bma01g00801 . . . . . . Car04g02307 Car15g00606 Cpe01g02069 . . . . . . . . . . . . . . . Lsi08g00458 . Chy03g00760 .
Vvi18g228 . . . . . . . . . Cmo15g00667 . . . . Sed03g0428 . . Bhi04g01877 Tan11g1249 Cmetu03g0593 . Hepe02g2220 . Lcy10g1246 Cla08g00617 Cam08g1031 Cec08g0620 Cco08g0732 Clacu08g0741 . Cre08g0549 . . Cone17ag0825 . . . . . . Blo18g00176 . Bda01g01455 Bpe02g01652 . Bma01g00803 . . . . . . . Car15g00607 . . . . . . . . . . . . . . . . Lsi08g00457 . Chy03g00761 .
Vvi18g229 . . . . . . . Bma01g02702 . . . . . . . . . Bhi04g01878 . . . Hepe02g2221 . Lcy10g1245 Cla08g01172 Cam08g1636 Cec08g1210 . Clacu08g1332 . . Cone4ag1423 Cone7ag1514 Cone17ag0869 . . . . Cme03g00509 . . . . . Bpe14g00392 . Bma02g00209 . . . . . . . . . . . . . . . . . . . . . . . Lsi08g01033 . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 50458284 50460383 - Bda003701.2 Bda01g01455 1455
1 50468406 50470770 + Bda003702.1 Bda01g01456 1456
3 383594 385526 + Bda015950.1 Bda03g00018 18
3 387166 390059 + Bda015951.1 Bda03g00019 19
3 2522305 2523980 + Bda016247.1 Bda03g00290 290
8 50076592 50078282 - Bda030208.1 Bda08g01222 1222
13 37610303 37611070 - Bda000313.1 Bda13g01470 1470
13 37613089 37617545 + Bda000314.1 Bda13g01471 1471
13 37619910 37621508 - Bda000315.1 Bda13g01472 1472
4 47092213 47096022 - XM_039029290.1 Bhi04g01871 1871
4 47157071 47163192 + XM_039029365.1 Bhi04g01874 1874
4 47181494 47187956 - XM_039029710.1 Bhi04g01875 1875
4 47233582 47236389 - XM_039029540.1 Bhi04g01876 1876
4 47292686 47295025 + XM_039028683.1 Bhi04g01877 1877
4 47295005 47298692 - XM_039028685.1 Bhi04g01878 1878
9 50308795 50318194 + XM_039040825.1 Bhi09g01840 1840
1 50122158 50124101 + BLOR01304 Blo01g01304 1304
1 55291080 55296929 - BLOR01553 Blo01g01553 1553
12 27044154 27046378 - BLOR04904 Blo12g00885 885
12 28838408 28851900 - BLOR05139 Blo12g01120 1120
12 28853618 28855528 - BLOR05140 Blo12g01121 1121
18 1692526 1694454 - BLOR08663 Blo18g00175 175
18 1703251 1705344 + BLOR08664 Blo18g00176 176
1 7511626 7513482 - Bma001018.1 Bma01g00800 800
1 7517715 7520076 - Bma001019.1 Bma01g00801 801
1 7531907 7533973 + Bma001021.1 Bma01g00803 803
1 76330499 76332441 + Bma002895.1 Bma01g02080 2080
1 84443833 84445726 - Bma003584.2 Bma01g02702 2702
2 2240165 2241547 - Bma030859 Bma02g00206 206
2 2243404 2247643 + Bma014664.1 Bma02g00207 207
2 2248767 2250372 - Bma014665.1 Bma02g00208 208
2 2255994 2259084 - Bma014666.1 Bma02g00209 209
4 226013 239366 + Bma018466.3 Bma04g00018 18
4 2103621 2105374 + Bma018698.1 Bma04g00246 246
2 4133603 4135510 - Bpe025090 Bpe02g00633 633
2 19242759 19244825 - Bpe009494.1 Bpe02g01652 1652
2 19250938 19253279 + Bpe009495.1 Bpe02g01653 1653
2 19256784 19259502 + Bpe009496.1 Bpe02g01654 1654
4 123374 125464 + Bpe014738.1 Bpe04g00012 12
4 1423371 1427178 - Bpe014926.1 Bpe04g00208 208
5 3254886 3256528 + Bpe017522.1 Bpe05g00138 138
14 3677387 3681903 + Bpe007045.1 Bpe14g00392 392
14 3686847 3688774 + Bpe007046.1 Bpe14g00393 393
14 3690560 3694961 - Bpe007047.2 Bpe14g00394 394
14 3696294 3697739 + Bpe007048.1 Bpe14g00395 395
8 16544978 16547185 - CaPI482276_08g010310.1 Cam08g1031 1031
8 16552227 16555040 + CaPI482276_08g010320.1 Cam08g1032 1032
8 16579039 16581164 + CaPI482276_08g010330.1 Cam08g1033 1033
8 16591330 16597052 - CaPI482276_08g010340.1 Cam08g1034 1034
8 16610073 16617839 + CaPI482276_08g010350.1 Cam08g1035 1035
8 22569366 22570325 - CaPI482276_08g016360.1 Cam08g1636 1636
11 28924562 28927839 - CaPI482276_11g016170.1 Cam11g1617 1617
1 8911742 8918270 - Carg23362-RA Car01g00920 920
1 12929108 12931082 + Carg17195-RA Car01g01540 1540
4 18579592 18582916 + Carg15741-RA Car04g02307 2307
4 18587641 18589535 + Carg15742-RA Car04g02308 2308
4 18592960 18599038 - Carg15743-RA Car04g02309 2309
9 476995 478820 - Carg08682-RA Car09g00098 98
9 4018478 4021282 + Carg20091-RA Car09g00684 684
15 3339582 3341024 - Carg01553-RA Car15g00602 602
15 3344331 3347995 + Carg01551-RA Car15g00604 604
15 3359784 3362904 - Carg01549-RA Car15g00606 606
15 3362725 3364836 + Carg01548-RA Car15g00607 607
8 18904390 18906597 - CcPI632755_08g007320.1 Cco08g0732 732
8 18912018 18914845 + CcPI632755_08g007330.1 Cco08g0733 733
8 18936840 18942062 + CcPI632755_08g007340.1 Cco08g0734 734
8 18953585 18959263 - CcPI632755_08g007350.1 Cco08g0735 735
8 18972332 18982419 + CcPI632755_08g007360.1 Cco08g0736 736
11 29290117 29293371 - CcPI632755_11g016450.1 Cco11g1645 1645
8 17742090 17744294 - CePI673135_08g006200.1 Cec08g0620 620
8 17749484 17752306 + CePI673135_08g006210.1 Cec08g0621 621
8 17774171 17778973 + CePI673135_08g006220.1 Cec08g0622 622
8 17789640 17795349 - CePI673135_08g006230.1 Cec08g0623 623
8 17800657 17802096 + CePI673135_08g006240.1 Cec08g0624 624
8 24036758 24037717 - CePI673135_08g012100.1 Cec08g1210 1210
11 30748485 30751735 - CePI673135_11g016440.1 Cec11g1644 1644
3 10148916 10153398 - Chy3G057370.1 Chy03g00757 757
3 10156227 10166750 + Chy3G057380.1 Chy03g00758 758
3 10242100 10244541 - Chy3G057400.1 Chy03g00760 760
3 10261049 10263160 + Chy3G057410.1 Chy03g00761 761
4 3738463 3740547 - Chy4G071400.1 Chy04g00422 422
7 5730615 5733593 + Chy7G134490.1 Chy07g00619 619
8 17283449 17285656 - ClG42_08g0074100.10 Clacu08g0741 741
8 17290891 17293704 + ClG42_08g0074200.10 Clacu08g0742 742
8 17315541 17320769 + ClG42_08g0074300.10 Clacu08g0743 743
8 17330819 17336544 - ClG42_08g0074400.10 Clacu08g0744 744
8 17351505 17352944 + ClG42_08g0074500.10 Clacu08g0745 745
8 23341959 23342918 - ClG42_08g0133200.10 Clacu08g1332 1332
11 28945722 28948984 - ClG42_11g0177400.10 Clacu11g1774 1774
8 18114177 18116384 - ClCG08G005940.2 Cla08g00617 617
8 18121344 18124645 + ClCG08G005950.1 Cla08g00618 618
8 18149066 18154693 + ClCG08G005960.1 Cla08g00619 619
8 18164315 18170500 - ClCG08G005970.2 Cla08g00620 620
8 18186900 18194781 + ClCG08G005980.1 Cla08g00621 621
8 24600321 24601280 - ClCG08G011760.1 Cla08g01172 1172
11 29237576 29248034 - ClCG11G015930.2 Cla11g01552 1552
1 7737037 7743287 - CmaCh01G010470.1 Cma01g01047 1047
1 12700578 12702761 + CmaCh01G019690.1 Cma01g01969 1969
9 472478 474568 - CmaCh09G001080.1 Cma09g00108 108
9 3743263 3745645 + CmaCh09G007740.1 Cma09g00774 774
3 7428101 7441789 + MELO3C010649.2.1 Cme03g00497 497
3 7503786 7508525 - MELO3C010648.2.1 Cme03g00500 500
3 7597299 7603598 - MELO3C010643.2.1 Cme03g00509 509
3 12077137 12079749 + PI0026155.1 Cmetu03g0593 593
3 12029267 12033962 - PI0013620.1 Cmetu03g1325 1325
3 11985424 11995814 + PI0004747.1 Cmetu03g1597 1597
3 12068310 12071788 - PI0015135.1 Cmetu03g2013 2013
9 5033438 5036298 - PI0023841.1 Cmetu09g0635 635
1 9049475 9055538 - CmoCh01G010860.1 Cmo01g01086 1086
1 14238762 14240666 + CmoCh01G020270.1 Cmo01g02027 2027
4 18399731 18403094 + CmoCh04G025010.1 Cmo04g02501 2501
4 18406782 18409741 + CmoCh04G025020.1 Cmo04g02502 2502
4 18412155 18418786 - CmoCh04G025030.1 Cmo04g02503 2503
9 494843 496899 - CmoCh09G001040.1 Cmo09g00104 104
9 3886453 3889143 + CmoCh09G007670.1 Cmo09g00767 767
15 3240927 3242369 - CmoCh15G006630.1 Cmo15g00663 663
15 3243158 3249135 + CmoCh15G006640.1 Cmo15g00664 664
15 3251174 3253284 - CmoCh15G006650.1 Cmo15g00665 665
15 3260457 3266739 - CmoCh15G006660.1 Cmo15g00666 666
15 3264613 3266724 + CmoCh15G006670.1 Cmo15g00667 667
11 28199175 28202435 - CmPI595203_11g015900.1 Cmu11g1590 1590
4 11351242 11354702 + Conep04aG0147500.1 Cone4ag1423 1423
4 11369690 11371534 + Conep04aG0147800.1 Cone4ag1426 1426
6 9907337 9909366 + Conep06aG0129100.1 Cone6ag1243 1243
7 10540540 10543170 - Conep07aG0155700.1 Cone7ag1514 1514
9 8844679 8846766 + Conep09aG0125000.1 Cone9ag1216 1216
17 6577675 6583008 + Conep17aG0084100.1 Cone17ag0822 822
17 6603698 6606043 + Conep17aG0084400.1 Cone17ag0825 825
17 6892006 6893882 - Conep17aG0088900.1 Cone17ag0869 869
20 2118673 2122322 - Conep20aG0044000.1 Cone20ag0426 426
20 2122854 2125483 - Conep20aG0044200.1 Cone20ag0427 427
20 2139234 2142755 - Conep20aG0044500.1 Cone20ag0430 430
1 17537862 17541238 + Cp4.1LG01g20660.1 Cpe01g02069 2069
1 17545339 17548267 + Cp4.1LG01g20670.1 Cpe01g02070 2070
1 17554515 17560518 - Cp4.1LG01g20700.1 Cpe01g02071 2071
2 5480733 5488148 + Cp4.1LG02g00240.1 Cpe02g00848 848
6 351484 353672 - Cp4.1LG06g00670.1 Cpe06g00072 72
6 3767606 3770258 + Cp4.1LG06g06020.1 Cpe06g00610 610
8 18190141 18192336 - CrPI670011_08g005490.1 Cre08g0549 549
8 18203315 18206139 + CrPI670011_08g005500.1 Cre08g0550 550
8 18227994 18233250 + CrPI670011_08g005510.1 Cre08g0551 551
8 18243842 18249952 - CrPI670011_08g005520.1 Cre08g0552 552
8 18262872 18264311 + CrPI670011_08g005530.1 Cre08g0553 553
11 31848773 31852075 - CrPI670011_11g020080.1 Cre11g2008 2008
2 62734348 62736717 - Hsped.02g22150.1 Hepe02g2215 2215
2 62797131 62804454 + Hsped.02g22170.1 Hepe02g2217 2217
2 62813086 62815372 - Hsped.02g22180.1 Hepe02g2218 2218
2 62974589 62978103 - Hsped.02g22190.1 Hepe02g2219 2219
2 62979882 62982299 + Hsped.02g22200.1 Hepe02g2220 2220
2 62982401 62986078 - Hsped.02g22210.1 Hepe02g2221 2221
10 35131578 35137912 + Maker00008469 Lcy10g1245 1245
10 35135673 35138187 - Maker00008863 Lcy10g1246 1246
10 35138015 35140849 + Maker00008664 Lcy10g1247 1247
10 35165684 35171449 + Maker00008581 Lcy10g1248 1248
10 35179707 35182790 - Maker00008502 Lcy10g1250 1250
4 24718482 24721552 + Lsi04G017390.1 Lsi04g01739 1739
4 31246667 31250461 - Lsi04G024130.1 Lsi04g02413 2413
8 12232240 12234393 - Lsi08G004570.1 Lsi08g00457 457
8 12240350 12247638 + Lsi08G004580.1 Lsi08g00458 458
8 12276129 12282275 + Lsi08G004590.1 Lsi08g00459 459
8 12296349 12301851 - Lsi08G004600.1 Lsi08g00460 460
8 12307911 12309353 + Lsi08G004610.1 Lsi08g00461 461
8 18926357 18927316 - Lsi08G010330.1 Lsi08g01033 1033
1 41425528 41438804 - Sed0023790.1 Sed01g3080 3080
1 41830130 41833215 - Sed0013651.1 Sed01g3097 3097
3 2541481 2543778 - Sed0002798.1 Sed03g0428 428
14 1142381 1148377 + Sed0022549.2 Sed14g0108 108
14 18627980 18631089 + Sed0020730.1 Sed14g0950 950
1 87304061 87315613 - Tan0022617.1 Tan01g3248 3248
11 10572991 10576461 - Tan0015761.1 Tan11g1243 1243
11 10583632 10590839 + Tan0019100.2 Tan11g1245 1245
11 10599335 10605123 - Tan0014659.1 Tan11g1246 1246
11 10633150 10636779 - Tan0001902.2 Tan11g1248 1248
11 10637757 10639859 + Tan0015182.1 Tan11g1249 1249
18 2406172 2411495 - Vvi18g220 Vvi18g220 220
18 2411696 2414689 + Vvi18g221 Vvi18g221 221
18 2415457 2417215 - Vvi18g222 Vvi18g222 222
18 2418885 2421454 + Vvi18g223 Vvi18g223 223
18 2421814 2426715 + Vvi18g224 Vvi18g224 224
18 2438213 2441650 + Vvi18g225 Vvi18g225 225
18 2450412 2454610 - Vvi18g226 Vvi18g226 226
18 2460773 2467215 - Vvi18g227 Vvi18g227 227
18 2477471 2479865 + Vvi18g228 Vvi18g228 228
18 2479869 2485400 - Vvi18g229 Vvi18g229 229
       

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