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
Vvi18g980 Blo01g01575 Blo12g00902 . . . . . . . . Cma01g01923 . . . . . . . . . . . . . . . . . . . . . . . . Lsi04g01693 Csa03g04233 . . . . . . . . . . . Cmo01g01986 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g981 . Blo12g00901 . Bda03g00269 . . Bma04g00217 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy04g00482 . . . . . . . . . . . . . . . . . . . . . . . . . Cla05g01919 Cam05g2056 Cec05g2068 Cco05g2120 Clacu05g2050 Cmu05g1927 Cre05g2050 . . . Cme04g00536
Vvi18g982 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g983 . . Bda01g00519 . Bpe02g00376 . . Bma01g02336 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo01g01988 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g984 . Blo12g00900 . . . Bpe04g00223 Bma04g00218 . Cmo05g00265 Cmo12g00399 Cma01g01925 . Car01g01503 Car12g00425 . . Cpe07g00403 Bhi04g00194 . . . . . Lcy13g1961 Cla08g01467 Cam08g1955 Cec08g1530 Cco08g1668 Clacu08g1645 . Cre08g1430 Cone4ag1927 Cone7ag1839 Cone17ag1355 . Lsi04g01694 Csa03g04234 Chy04g00481 Cme03g01933 . Blo18g00806 . Bda01g01503 Bpe02g01701 . Bma01g00753 . . Cmo01g01990 . Cma12g00449 Cma05g00260 Car05g00217 Car09g00128 Cpe11g00215 Cpe02g00111 . . . . . . . Cla05g01918 Cam05g2055 Cec05g2066 Cco05g2119 Clacu05g2049 Cmu05g1926 Cre05g2049 Lsi08g01377 Csa02g02074 Chy03g01438 Cme04g00534
Vvi18g985 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g986 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g987 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone20ag0127 . . . . . . . Bda01g01504 Bpe02g01702 . Bma01g00752 . . . . . . . . . . . . . . . . . Cla11g00400 Cam11g0445 Cec11g0441 Cco11g0432 Clacu11g0569 Cmu11g0425 Cre11g0909 . . . .
Vvi18g988 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1930 . Cone17ag1356 Cone20ag0126 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla11g00398 Cam11g0444 Cec11g0439 Cco11g0431 Clacu11g0567 Cmu11g0423 Cre11g0908 . . . .
Vvi18g989 Blo01g01576 . Bda01g00517 . Bpe02g00374 . . Bma01g02338 . . Cma01g01929 Cma09g00139 Car01g01506 . . Cpe06g00097 . . . . . . . . . . . . . . . . . . Cone20ag0125 Lsi04g01696 Csa03g04237 Chy04g00478 . . . . . . . . . . Cmo01g01992 Cmo09g00135 . . . Car09g00124 . Cpe02g00108 . . . . . . . Cla05g01915 Cam05g2052 Cec05g2063 Cco05g2116 . Cmu05g1923 Cre05g2046 . . . Cme04g00530
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 32134328 32137101 + Bda002523.1 Bda01g00517 517
1 32153947 32155688 + Bda002526.1 Bda01g00519 519
1 50895615 50898990 + Bda003760.1 Bda01g01503 1503
1 50900548 50901235 - Bda003761.1 Bda01g01504 1504
3 2361007 2363247 - Bda016225.1 Bda03g00269 269
4 4722007 4727408 + XM_039029689.1 Bhi04g00194 194
1 55503233 55507927 - BLOR01575 Blo01g01575 1575
1 55552504 55565409 - BLOR01576 Blo01g01576 1576
12 27199024 27205644 - BLOR04919 Blo12g00900 900
12 27214861 27216650 + BLOR04920 Blo12g00901 901
12 27226650 27227908 + BLOR04921 Blo12g00902 902
18 23774497 23786810 - BLOR09294 Blo18g00806 806
1 6947574 6948055 + Bma000969.1 Bma01g00752 752
1 6949717 6953115 - Bma000970.1 Bma01g00753 753
1 80956756 80958814 - Bma003200.1 Bma01g02336 2336
1 81000478 81003280 - Bma003205.1 Bma01g02338 2338
4 1857829 1859234 - Bma018667.1 Bma04g00217 217
4 1869537 1873612 + Bma018669.2 Bma04g00218 218
2 2460164 2462911 + Bpe008215.1 Bpe02g00374 374
2 2475844 2477807 + Bpe008217.1 Bpe02g00376 376
2 19514721 19518247 + Bpe009535.1 Bpe02g01701 1701
2 19519788 19520450 - Bpe009536.1 Bpe02g01702 1702
4 1500383 1504510 + Bpe014939.2 Bpe04g00223 223
5 29197649 29208375 + CaPI482276_05g020520.1 Cam05g2052 2052
5 29214424 29219795 - CaPI482276_05g020550.1 Cam05g2055 2055
5 29243884 29249216 + CaPI482276_05g020560.1 Cam05g2056 2056
8 25464442 25470455 - CaPI482276_08g019550.1 Cam08g1955 1955
11 5886138 5890219 - CaPI482276_11g004440.1 Cam11g0444 444
11 5895869 5911427 + CaPI482276_11g004450.1 Cam11g0445 445
1 12748608 12753324 + Carg17158-RA Car01g01503 1503
1 12760400 12763854 - Carg17161-RA Car01g01506 1506
5 1122150 1128091 + Carg11784-RA Car05g00217 217
9 600962 604302 + Carg08708-RA Car09g00124 124
9 611547 615787 - Carg08712-RA Car09g00128 128
12 2729617 2730986 - Carg04033-RA Car12g00425 425
5 30134667 30147359 + CcPI632755_05g021160.1 Cco05g2116 2116
5 30154110 30158882 - CcPI632755_05g021190.1 Cco05g2119 2119
5 30182717 30184573 + CcPI632755_05g021200.1 Cco05g2120 2120
8 28145086 28151446 - CcPI632755_08g016680.1 Cco08g1668 1668
11 4521758 4525874 - CcPI632755_11g004310.1 Cco11g0431 431
11 4531692 4547313 + CcPI632755_11g004320.1 Cco11g0432 432
5 32519304 32525021 + CePI673135_05g020630.1 Cec05g2063 2063
5 32532525 32541635 - CePI673135_05g020660.1 Cec05g2066 2066
5 32567338 32570579 + CePI673135_05g020680.1 Cec05g2068 2068
8 27008679 27015320 - CePI673135_08g015300.1 Cec08g1530 1530
11 4637376 4641489 - CePI673135_11g004390.1 Cec11g0439 439
11 4656445 4663141 + CePI673135_11g004410.1 Cec11g0441 441
3 17039001 17043476 - Chy3G064180.1 Chy03g01438 1438
4 4538044 4541353 + Chy4G071960.1 Chy04g00478 478
4 4563190 4568192 - Chy4G071990.1 Chy04g00481 481
4 4605813 4607465 + Chy4G072000.1 Chy04g00482 482
5 29414219 29418991 - ClG42_05g0204900.10 Clacu05g2049 2049
5 29442728 29444579 + ClG42_05g0205000.10 Clacu05g2050 2050
8 26209063 26215049 - ClG42_08g0164500.10 Clacu08g1645 1645
11 5373150 5377227 - ClG42_11g0056700.10 Clacu11g0567 567
11 5391238 5398560 + ClG42_11g0056900.10 Clacu11g0569 569
5 31004146 31008066 + ClCG05G018745.1 Cla05g01915 1915
5 31014272 31018978 - ClCG05G018770.1 Cla05g01918 1918
5 31042590 31044688 + ClCG05G018780.1 Cla05g01919 1919
8 27586818 27592817 - ClCG08G014810.1 Cla08g01467 1467
11 4490255 4494332 - ClCG11G004210.2 Cla11g00398 398
11 4513644 4518895 + ClCG11G004230.2 Cla11g00400 400
1 12515046 12517701 - CmaCh01G019230.1 Cma01g01923 1923
1 12523901 12528407 + CmaCh01G019250.1 Cma01g01925 1925
1 12535565 12537055 - CmaCh01G019290.1 Cma01g01929 1929
5 1096330 1102099 + CmaCh05G002600.1 Cma05g00260 260
9 599994 602704 + CmaCh09G001390.1 Cma09g00139 139
12 2368845 2376265 - CmaCh12G004490.1 Cma12g00449 449
3 27382610 27386657 - MELO3C010962.2.1 Cme03g01933 1933
4 4585438 4589720 + MELO3C003799.2.1 Cme04g00530 530
4 4613997 4618595 - MELO3C003802.2.1 Cme04g00534 534
4 4657036 4658924 + MELO3C003803.2.1 Cme04g00536 536
1 14043622 14044795 - CmoCh01G019860.1 Cmo01g01986 1986
1 14050821 14052096 - CmoCh01G019880.1 Cmo01g01988 1988
1 14057622 14061925 + CmoCh01G019900.1 Cmo01g01990 1990
1 14069086 14072127 - CmoCh01G019920.1 Cmo01g01992 1992
5 1135369 1140997 + CmoCh05G002650.1 Cmo05g00265 265
9 622988 625668 + CmoCh09G001350.1 Cmo09g00135 135
12 2491991 2497467 - CmoCh12G003990.1 Cmo12g00399 399
5 29127401 29133313 + CmPI595203_05g019230.1 Cmu05g1923 1923
5 29139426 29144772 - CmPI595203_05g019260.1 Cmu05g1926 1926
5 29168473 29170319 + CmPI595203_05g019270.1 Cmu05g1927 1927
11 4684016 4688092 - CmPI595203_11g004230.1 Cmu11g0423 423
11 4702098 4709591 + CmPI595203_11g004250.1 Cmu11g0425 425
4 13651508 13654333 + Conep04aG0198900.1 Cone4ag1927 1927
4 13658176 13661452 - Conep04aG0199200.1 Cone4ag1930 1930
7 11955250 11957552 + Conep07aG0189400.1 Cone7ag1839 1839
17 9473231 9475488 + Conep17aG0138800.1 Cone17ag1355 1355
17 9475939 9486129 - Conep17aG0138900.1 Cone17ag1356 1356
20 557236 560819 + Conep20aG0013200.1 Cone20ag0125 125
20 561561 565810 + Conep20aG0013300.1 Cone20ag0126 126
20 566034 567243 + Conep20aG0013400.1 Cone20ag0127 127
2 543713 547729 + Cp4.1LG02g07570.1 Cpe02g00108 108
2 553156 560012 - Cp4.1LG02g07440.1 Cpe02g00111 111
6 478507 482155 + Cp4.1LG06g00830.1 Cpe06g00097 97
7 2625089 2633182 - Cp4.1LG07g04000.1 Cpe07g00403 403
11 1153310 1160267 + Cp4.1LG11g02060.1 Cpe11g00215 215
5 32459681 32465372 + CrPI670011_05g020460.1 Cre05g2046 2046
5 32472179 32476974 - CrPI670011_05g020490.1 Cre05g2049 2049
5 32501490 32503356 + CrPI670011_05g020500.1 Cre05g2050 2050
8 27275396 27282332 - CrPI670011_08g014300.1 Cre08g1430 1430
11 6312307 6316406 - CrPI670011_11g009080.1 Cre11g0908 908
11 6322224 6338055 + CrPI670011_11g009090.1 Cre11g0909 909
2 18947264 18953638 + CsaV3_2G028930.1 Csa02g02074 2074
3 37062534 37064406 - CsaV3_3G045390.1 Csa03g04233 4233
3 37084253 37090120 + CsaV3_3G045400.1 Csa03g04234 4234
3 37097725 37102400 - CsaV3_3G045430.1 Csa03g04237 4237
13 38664583 38667802 - Maker00033690 Lcy13g1961 1961
4 24317138 24319661 - Lsi04G016930.1 Lsi04g01693 1693
4 24338355 24343123 + Lsi04G016940.1 Lsi04g01694 1694
4 24351506 24355411 - Lsi04G016960.1 Lsi04g01696 1696
8 22060694 22068505 - Lsi08G013770.1 Lsi08g01377 1377
18 10974283 10985490 - Vvi18g980 Vvi18g980 980
18 10990247 10993974 - Vvi18g981 Vvi18g981 981
18 10994504 10997621 - Vvi18g982 Vvi18g982 982
18 10999095 11003121 - Vvi18g983 Vvi18g983 983
18 11011764 11016811 + Vvi18g984 Vvi18g984 984
18 11018627 11019094 - Vvi18g985 Vvi18g985 985
18 11019356 11020304 + Vvi18g986 Vvi18g986 986
18 11025677 11029475 - Vvi18g987 Vvi18g987 987
18 11035475 11042060 - Vvi18g988 Vvi18g988 988
18 11043668 11050016 - Vvi18g989 Vvi18g989 989
       

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