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
Vvi17g96 . . . . . . . . Cmo13g00844 Cmo18g00225 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma13g00814 Cma18g00311 . Car18g00236 . . . . . . . . . . . . . . . . . . . .
Vvi17g97 . . . Bda15g00631 . . . . . . . . . . . Cpe20g00300 . Bhi02g00671 Tan09g2020 . . . . . . . . . . . . . . . . Lsi02g00513 . Chy12g01157 . . . . . . . . . . . . . . Car13g00660 . Cpe09g00953 . . . . . . . . . . . . . . . . . . .
Vvi17g98 . . . . . Bpe13g00197 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g01591 . . . . . . . . . . . . . . Bhi08g01510 Tan05g2983 . Lac10g0595 Hepe07g2120 . . . . . . . . . . . . .
Vvi17g99 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g100 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone2ag0489 Cone16ag0516 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g101 . Blo16g00272 Bda06g00725 . Bpe12g00479 Bpe13g00200 Bma06g00261 Bma12g01083 Cmo13g00841 Cmo18g00222 . . . . . Cpe20g00303 . Bhi02g00520 . . . . . . . . . . . . . Cone2ag0981 Cone16ag0015 Cone13ag0226 Cone19ag0211 Lsi02g00510 Csa01g00972 Chy12g01161 Cme12g01585 . Blo15g00206 Bda11g01596 Bda14g01358 Bpe07g00892 Bpe15g00222 Bma03g01251 . Sed08g2430 . . Cma13g00811 Cma18g00314 Car13g00657 Car18g00233 Cpe09g00957 . Bhi08g01503 Tan05g2975 Cmetu12g2007 Lac10g0589 Hepe07g2115 . . Cla03g00359 Cam03g0379 Cec03g0365 . Clacu03g0378 Cmu03g0983 Cre03g0675 Lsi06g01644 Csa01g00053 . .
Vvi17g102 . Blo16g00269 . . . Bpe13g00201 Bma06g00260 . . . Cma10g00060 Cma11g00031 . . . . Cpe04g01617 Bhi02g00519 . . . Hepe09g0046 . . Cla06g01743 Cam06g1933 Cec06g1983 Cco06g1988 Clacu06g1889 Cmu06g1831 Cre06g2646 . . Cone13ag0223 . . . . . . . Bda11g01597 . . . . . . Cmo10g00054 Cmo11g00033 . . . . . Cpe18g00907 . . . . . . . . . . . . . . Lsi06g01643 . Chy02g02664 Cme02g02067
Vvi17g103 . Blo16g00268 . . . . Bma06g00259 . . Cmo18g00221 . . . . . . . . . . . . . . . . . . . . . Cone2ag0980 Cone16ag0016 . Cone19ag0209 Lsi02g00509 Csa01g00970 Chy12g01163 Cme12g01586 . . Bda11g01598 . . . . . Sed08g2431 . . . Cma18g00315 . Car18g00232 Cpe09g00958 . Bhi08g01500 Tan05g2974 Cmetu12g0384 Lac10g0588 Hepe07g1935 . . Cla03g00358 Cam03g0378 Cec03g0364 Cco03g0380 Clacu03g0377 Cmu03g0982 Cre03g0674 . . . .
Vvi17g104 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g105 . . . . . . . . Cmo13g00838 . . . . . . Cpe20g00304 . . . . . . . . . . . . . . . Cone2ag0978 . . . Lsi02g00506 Csa01g00967 Chy12g01166 Cme12g01587 . . . Bda14g01360 . Bpe15g00221 Bma03g01252 . Sed08g2433 . . Cma13g00806 . Car13g00654 . . . Bhi08g01491 Tan05g2967 Cmetu12g0011 Lac10g0586 Hepe07g2112 . . Cla03g00356 Cam03g0375 Cec03g0362 Cco03g0378 Clacu03g0374 Cmu03g0980 Cre03g0672 . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 9932712 9933007 + Bda024027.1 Bda06g00725 725
11 49472101 49474802 - Bda008469.1 Bda11g01591 1591
11 49575652 49575985 + Bda008477.1 Bda11g01596 1596
11 49581262 49583280 + Bda008478.1 Bda11g01597 1597
11 49584332 49585186 - Bda008479.1 Bda11g01598 1598
14 15857333 15857668 + Bda011056.1 Bda14g01358 1358
14 15904310 15907386 - Bda011058.2 Bda14g01360 1360
15 9445757 9453096 - Bda012475.2 Bda15g00631 631
2 9961329 9963772 - XM_039022999.1 Bhi02g00519 519
2 10017996 10021828 - XM_039023150.1 Bhi02g00520 520
2 12991699 12995165 + XM_039023447.1 Bhi02g00671 671
8 43329028 43336373 + XM_039038367.1 Bhi08g01491 1491
8 43336711 43339166 + XM_039039233.1 Bhi08g01500 1500
8 43347087 43349150 - XM_039037902.1 Bhi08g01503 1503
8 43545430 43548917 + XM_039037761.1 Bhi08g01510 1510
15 2127047 2127381 + BLOR06600 Blo15g00206 206
16 6316563 6317707 + BLOR07516 Blo16g00268 268
16 6318948 6320951 - BLOR07517 Blo16g00269 269
16 6393400 6393726 - BLOR07520 Blo16g00272 272
3 20829954 20833455 + Bma017713.1 Bma03g01251 1251
3 20873077 20875502 - Bma017714.4 Bma03g01252 1252
6 3586699 3587661 + Bma022890.1 Bma06g00259 259
6 3588715 3590730 - Bma022891.1 Bma06g00260 260
6 3602433 3602766 - Bma022892.1 Bma06g00261 261
12 43126557 43126888 - Bma030535 Bma12g01083 1083
7 14974056 14974390 - Bpe021733.1 Bpe07g00892 892
12 10559664 10559996 + Bpe005741.1 Bpe12g00479 479
13 9959621 9962382 - Bpe006318.2 Bpe13g00197 197
13 9976332 9985638 + Bpe006321.1 Bpe13g00200 200
13 9993632 9995647 + Bpe006322.1 Bpe13g00201 201
15 13339704 13342131 - Bpe001157.1 Bpe15g00221 221
15 13346986 13350323 - Bpe001158.1 Bpe15g00222 222
3 4878869 4882809 + CaPI482276_03g003750.1 Cam03g0375 375
3 4887467 4888599 + CaPI482276_03g003780.1 Cam03g0378 378
3 4892599 4892916 - CaPI482276_03g003790.1 Cam03g0379 379
6 30291061 30293049 - CaPI482276_06g019330.1 Cam06g1933 1933
13 8089316 8092038 + Carg07604-RA Car13g00654 654
13 8094860 8097872 - Carg07607-RA Car13g00657 657
13 8113900 8115975 - Carg07610-RA Car13g00660 660
18 1332859 1333966 + Carg06799-RA Car18g00232 232
18 1334513 1337627 - Carg06800-RA Car18g00233 233
18 1347851 1351778 - Carg06803-RA Car18g00236 236
3 4103969 4107930 + CcPI632755_03g003780.1 Cco03g0378 378
3 4109605 4113632 + CcPI632755_03g003800.1 Cco03g0380 380
6 30033378 30035366 - CcPI632755_06g019880.1 Cco06g1988 1988
3 4045764 4049730 + CePI673135_03g003620.1 Cec03g0362 362
3 4051436 4055459 + CePI673135_03g003640.1 Cec03g0364 364
3 4059448 4059765 - CePI673135_03g003650.1 Cec03g0365 365
6 33110517 33112505 - CePI673135_06g019830.1 Cec06g1983 1983
2 29646094 29648091 - Chy2G049310.1 Chy02g02664 2664
12 16513080 16515110 + Chy12G217570.1 Chy12g01157 1157
12 16535894 16538198 + Chy12G217610.1 Chy12g01161 1161
12 16540289 16541418 - Chy12G217630.1 Chy12g01163 1163
12 16545681 16549816 - Chy12G217660.1 Chy12g01166 1166
3 4194183 4198072 + ClG42_03g0037400.10 Clacu03g0374 374
3 4202718 4203850 + ClG42_03g0037700.10 Clacu03g0377 377
3 4207825 4208142 - ClG42_03g0037800.10 Clacu03g0378 378
6 29341834 29343822 - ClG42_06g0188900.10 Clacu06g1889 1889
3 4138441 4143167 + ClCG03G003790.2 Cla03g00356 356
3 4143933 4148475 + ClCG03G003810.2 Cla03g00358 358
3 4150464 4153977 - ClCG03G003820.2 Cla03g00359 359
6 30990920 30992908 - ClCG06G017910.1 Cla06g01743 1743
10 221001 222989 + CmaCh10G000600.1 Cma10g00060 60
11 144613 146598 + CmaCh11G000310.1 Cma11g00031 31
13 6846682 6850216 + CmaCh13G008060.1 Cma13g00806 806
13 6855220 6858290 - CmaCh13G008110.1 Cma13g00811 811
13 6867175 6869854 - CmaCh13G008140.1 Cma13g00814 814
18 1659344 1662912 + CmaCh18G003110.1 Cma18g00311 311
18 1672229 1674970 + CmaCh18G003140.1 Cma18g00314 314
18 1675694 1677354 - CmaCh18G003150.1 Cma18g00315 315
2 26640693 26643089 - MELO3C026205.2.1 Cme02g02067 2067
12 23171973 23174453 + MELO3C002366.2.1 Cme12g01585 1585
12 23176197 23178142 - MELO3C002365.2.1 Cme12g01586 1586
12 23179015 23185684 - MELO3C002363.2.1 Cme12g01587 1587
12 3159787 3163795 + PI0027823.1 Cmetu12g0011 11
12 3167670 3169482 + PI0011697.1 Cmetu12g0384 384
12 3171551 3174061 - PI0014341.1 Cmetu12g2007 2007
10 252232 254229 + CmoCh10G000540.1 Cmo10g00054 54
11 139635 141629 + CmoCh11G000330.1 Cmo11g00033 33
13 7777008 7783102 + CmoCh13G008380.1 Cmo13g00838 838
13 7785405 7788197 - CmoCh13G008410.1 Cmo13g00841 841
13 7798999 7802021 - CmoCh13G008440.1 Cmo13g00844 844
18 1451099 1452419 + CmoCh18G002210.1 Cmo18g00221 221
18 1453066 1455822 - CmoCh18G002220.1 Cmo18g00222 222
18 1465808 1469611 - CmoCh18G002250.1 Cmo18g00225 225
3 4408212 4412101 + CmPI595203_03g009800.1 Cmu03g0980 980
3 4416749 4417881 + CmPI595203_03g009820.1 Cmu03g0982 982
3 4421687 4422171 - CmPI595203_03g009830.1 Cmu03g0983 983
6 29244776 29246764 - CmPI595203_06g018310.1 Cmu06g1831 1831
2 2653343 2654988 - Conep02aG0050200.1 Cone2ag0489 489
2 35256651 35259254 + Conep02aG0201200.1 Cone2ag0978 978
2 35263456 35264819 + Conep02aG0201400.1 Cone2ag0980 980
2 35266871 35267190 - Conep02aG0201500.1 Cone2ag0981 981
13 1456599 1464385 - Conep13aG0022900.1 Cone13ag0223 223
13 1474393 1476589 - Conep13aG0023200.1 Cone13ag0226 226
16 121582 123119 + Conep16aG0001500.1 Cone16ag0015 15
16 123693 125000 - Conep16aG0001600.1 Cone16ag0016 16
16 7198955 7200601 + Conep16aG0287500.1 Cone16ag0516 516
19 1325399 1326996 + Conep19aG0021500.1 Cone19ag0209 209
19 1336327 1336670 - Conep19aG0021700.1 Cone19ag0211 211
4 12555056 12557050 - Cp4.1LG04g16100.1 Cpe04g01617 1617
9 8542517 8545123 + Cp4.1LG09g09480.1 Cpe09g00953 953
9 8563124 8566128 + Cp4.1LG09g09600.1 Cpe09g00957 957
9 8567044 8568157 - Cp4.1LG09g09660.1 Cpe09g00958 958
18 8119700 8121688 - Cp4.1LG18g09150.1 Cpe18g00907 907
20 1684871 1686762 + Cp4.1LG20g02930.1 Cpe20g00300 300
20 1700975 1705758 + Cp4.1LG20g03020.1 Cpe20g00303 303
20 1705977 1712534 - Cp4.1LG20g03100.1 Cpe20g00304 304
3 5618302 5622281 + CrPI670011_03g006720.1 Cre03g0672 672
3 5623986 5628037 + CrPI670011_03g006740.1 Cre03g0674 674
3 5632067 5632384 - CrPI670011_03g006750.1 Cre03g0675 675
6 34075484 34077472 - CrPI670011_06g026460.1 Cre06g2646 2646
1 302869 303915 + CsaV3_1G000530.1 Csa01g00053 53
1 6001489 6005643 + CsaV3_1G009670.1 Csa01g00967 967
1 6009071 6011547 + CsaV3_1G009700.1 Csa01g00970 970
1 6012907 6016113 - CsaV3_1G009720.1 Csa01g00972 972
7 63131661 63136930 + Hsped.07g19350.1 Hepe07g1935 1935
7 65456636 65463838 + Hsped.07g21120.1 Hepe07g2112 2112
7 65468637 65470807 - Hsped.07g21150.1 Hepe07g2115 2115
7 65531127 65534760 + Hsped.07g21200.1 Hepe07g2120 2120
9 378259 380740 + Hsped.09g00460.1 Hepe09g0046 46
10 4515951 4519669 + Lag0024631.1 Lac10g0586 586
10 4521804 4524807 + Lag0024633.1 Lac10g0588 588
10 4525693 4528534 - Lag0024634.1 Lac10g0589 589
10 4567100 4576342 + Lag0024640.1 Lac10g0595 595
2 4304664 4308925 + Lsi02G005060.1 Lsi02g00506 506
2 4312748 4314638 + Lsi02G005090.1 Lsi02g00509 509
2 4316239 4318699 - Lsi02G005100.1 Lsi02g00510 510
2 4369515 4373839 - Lsi02G005130.1 Lsi02g00513 513
6 26732777 26734777 - Lsi06G016430.1 Lsi06g01643 1643
6 26741318 26749889 - Lsi06G016440.1 Lsi06g01644 1644
8 37365820 37369200 + Sed0006341.1 Sed08g2430 2430
8 37369933 37371094 - Sed0027384.1 Sed08g2431 2431
8 37376378 37379672 - Sed0001636.1 Sed08g2433 2433
5 81733153 81737702 + Tan0017840.1 Tan05g2967 2967
5 81741543 81743335 + Tan0004784.2 Tan05g2974 2974
5 81746040 81748599 - Tan0014096.1 Tan05g2975 2975
5 81810523 81814087 + Tan0016123.1 Tan05g2983 2983
9 70815040 70820875 + Tan0017819.8 Tan09g2020 2020
17 895126 901496 - Vvi17g96 Vvi17g96 96
17 904846 907405 - Vvi17g97 Vvi17g97 97
17 914170 918824 + Vvi17g98 Vvi17g98 98
17 922599 925171 - Vvi17g99 Vvi17g99 99
17 928685 931518 - Vvi17g100 Vvi17g100 100
17 938853 939343 + Vvi17g101 Vvi17g101 101
17 942498 942936 + Vvi17g102 Vvi17g102 102
17 943891 946048 - Vvi17g103 Vvi17g103 103
17 948281 949180 - Vvi17g104 Vvi17g104 104
17 949851 955503 - Vvi17g105 Vvi17g105 105
       

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