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
Vvi5g649 . . . . . Bpe14g01242 . . . . . . Car06g01148 . . Cpe08g00323 Cpe03g01507 . . . . . . . . . . . . . . . . . . . . . Cme06g00511 Blo02g00729 . . Bda13g00075 . . Bma02g00795 . . . . . . . . . . . . . . . . . Cla05g00459 Cam05g0500 Cec05g0514 Cco05g0514 Clacu05g0501 Cmu05g0477 Cre05g0541 . Csa03g01232 Chy06g00485 .
Vvi5g650 . . . . . . . . Cmo08g01069 Cmo17g00170 . Cma14g01800 Car06g01147 Car14g01617 . . Cpe03g01508 . . . . . . . Cla06g00649 Cam06g0694 Cec06g0698 Cco06g0704 Clacu06g0681 Cmu06g0672 Cre06g1441 . . Cone7ag0312 Cone4ag0315 Lsi05g01704 Csa02g01078 Chy05g00338 . . . Bda11g00623 Bda13g00073 . . Bma02g00794 Bma06g01594 Sed09g0698 . Cmo14g01838 Cma08g01093 Cma17g00173 Car08g00968 Car17g00153 Cpe12g00149 Cpe17g00186 Bhi12g01639 Tan06g2429 Cmetu05g0143 . . . Lcy13g0355 . . . . . . . Lsi09g01248 . . Cme05g00547
Vvi5g651 . . . . . Bpe14g01243 . . Cmo08g01068 Cmo17g00169 Cma06g01337 . . . . Cpe08g00324 . . . . . . . . Cla06g00650 Cam06g0695 Cec06g0699 Cco06g0705 Clacu06g0682 Cmu06g0673 Cre06g1442 . . . . . Csa02g01077 Chy05g00337 Cme06g00510 Blo02g00732 Blo07g00253 . . . Bpe13g00565 . . Sed07g0437 Cmo06g01342 . Cma08g01092 Cma17g00172 Car08g00967 Car17g00152 Cpe12g00148 . Bhi12g01638 Tan06g0995 Cmetu01g1325 . . . . . . . . . . . Lsi09g01247 . . Cme05g00549
Vvi5g652 . . . . . . . . . . . Cma14g01801 . Car14g01618 . . . . . . . . . . . . . . . . . . . Cone7ag0313 . Lsi05g01707 . . . . . Bda11g00624 . . . . Bma06g01595 . . Cmo14g01839 . . . . . Cpe17g00187 Bhi12g01637 . . Lac12g2192 Hepe03g0269 . Lcy13g0358 . . . . . . . . Csa03g01230 . .
Vvi5g653 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g654 . . . . . . . . . . . . . . . Cpe08g00326 . . . . . . . . Cla06g00651 Cam06g0697 Cec06g0700 Cco06g0709 Clacu06g0683 Cmu06g0674 Cre06g1443 . . . . . . . . . Blo07g00254 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g01229 . Cme05g00550
Vvi5g655 . . . . . . . . . . . Cma14g01803 . Car14g01619 . . . . . . . . . . . . . . . . . . . . . Lsi05g01708 . . . . . . . . . . . . . Cmo14g01840 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g656 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g657 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g658 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g01228 . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 6266620 6268212 - Bda005367.1 Bda11g00623 623
11 6268875 6270491 + Bda005368.1 Bda11g00624 624
13 964598 966373 - Bda000919.1 Bda13g00073 73
13 980608 987485 + Bda000922.1 Bda13g00075 75
12 52926930 52930592 - XM_039019399.1 Bhi12g01637 1637
12 53033502 53035353 - XM_039050867.1 Bhi12g01638 1638
12 53057821 53060534 + XM_039050735.1 Bhi12g01639 1639
2 23310660 23322188 - BLOR10459 Blo02g00729 729
2 23404125 23407458 - BLOR10462 Blo02g00732 732
7 3108188 3109686 - BLOR18185 Blo07g00253 253
7 3111961 3113952 + BLOR18186 Blo07g00254 254
2 42712538 42714398 + Bma015526.1 Bma02g00794 794
2 42736415 42743414 + Bma015527.1 Bma02g00795 795
6 52155701 52157267 - Bma024710.1 Bma06g01594 1594
6 52157962 52159504 + Bma024711.1 Bma06g01595 1595
13 12835136 12836735 + Bpe010268.1 Bpe13g00565 565
14 9350181 9367859 - Bpe014603.1 Bpe14g01242 1242
14 9369540 9371362 + Bpe025548 Bpe14g01243 1243
5 4457053 4472636 + CaPI482276_05g005000.1 Cam05g0500 500
6 9290910 9292919 - CaPI482276_06g006940.1 Cam06g0694 694
6 9307403 9310184 + CaPI482276_06g006950.1 Cam06g0695 695
6 9339405 9342386 + CaPI482276_06g006970.1 Cam06g0697 697
6 8501365 8503667 + Carg06210-RA Car06g01147 1147
6 8504897 8514629 + Carg06209-RA Car06g01148 1148
8 6446925 6448218 - Carg10955-RA Car08g00967 967
8 6451960 6453473 + Carg10954-RA Car08g00968 968
14 13029700 13032806 - Carg16570-RA Car14g01617 1617
14 13032718 13034030 + Carg16569-RA Car14g01618 1618
14 13034122 13036369 + Carg16568-RA Car14g01619 1619
17 946983 948779 - Carg10079-RA Car17g00152 152
17 951718 954933 + Carg10078-RA Car17g00153 153
5 4114971 4130439 + CcPI632755_05g005140.1 Cco05g0514 514
6 7877030 7879045 - CcPI632755_06g007040.1 Cco06g0704 704
6 7893279 7894686 + CcPI632755_06g007050.1 Cco06g0705 705
6 7935239 7938347 + CcPI632755_06g007090.1 Cco06g0709 709
5 4107244 4122854 + CePI673135_05g005140.1 Cec05g0514 514
6 7900340 7902367 - CePI673135_06g006980.1 Cec06g0698 698
6 7920300 7921702 + CePI673135_06g006990.1 Cec06g0699 699
6 7963767 7966980 + CePI673135_06g007000.1 Cec06g0700 700
5 3483756 3485193 - Chy5G093830.1 Chy05g00337 337
5 3496019 3498040 + Chy5G093840.1 Chy05g00338 338
6 3285417 3291733 + Chy6G110130.1 Chy06g00485 485
5 4166148 4181818 + ClG42_05g0050100.10 Clacu05g0501 501
6 7845587 7847612 - ClG42_06g0068100.10 Clacu06g0681 681
6 7861198 7863952 + ClG42_06g0068200.10 Clacu06g0682 682
6 7892977 7895852 + ClG42_06g0068300.10 Clacu06g0683 683
5 4164072 4178300 + ClCG05G004420.1 Cla05g00459 459
6 8022016 8024527 - ClCG06G006850.2 Cla06g00649 649
6 8038245 8040246 + ClCG06G006860.2 Cla06g00650 650
6 8071804 8074860 + ClCG06G006870.1 Cla06g00651 651
6 8777013 8793263 + CmaCh06G013370.1 Cma06g01337 1337
8 6806527 6808179 - CmaCh08G010920.1 Cma08g01092 1092
8 6810693 6813992 + CmaCh08G010930.1 Cma08g01093 1093
14 12956414 12958475 - CmaCh14G018000.1 Cma14g01800 1800
14 12959031 12960657 + CmaCh14G018010.1 Cma14g01801 1801
14 12961404 12962897 + CmaCh14G018030.1 Cma14g01803 1803
17 890602 892517 - CmaCh17G001720.1 Cma17g00172 172
17 895209 897863 + CmaCh17G001730.1 Cma17g00173 173
5 5320308 5323327 - MELO3C022976.2.1 Cme05g00547 547
5 5341435 5343428 + MELO3C022977.2.1 Cme05g00549 549
5 5362169 5364957 + MELO3C022978.2.1 Cme05g00550 550
6 3216781 3219261 + MELO3C006440.2.1 Cme06g00510 510
6 3220034 3232916 + MELO3C006441.2.1 Cme06g00511 511
1 23573545 23577723 - PI0005813.1 Cmetu01g1325 1325
5 18537191 18539321 - PI0028509.1 Cmetu05g0143 143
6 9957267 9971503 + CmoCh06G013420.1 Cmo06g01342 1342
8 6891343 6892836 - CmoCh08G010680.1 Cmo08g01068 1068
8 6895329 6898329 + CmoCh08G010690.1 Cmo08g01069 1069
14 13939830 13941928 - CmoCh14G018380.1 Cmo14g01838 1838
14 13942531 13944021 + CmoCh14G018390.1 Cmo14g01839 1839
14 13944744 13946372 + CmoCh14G018400.1 Cmo14g01840 1840
17 993516 995286 - CmoCh17G001690.1 Cmo17g00169 169
17 998210 1000864 + CmoCh17G001700.1 Cmo17g00170 170
5 4002296 4017958 + CmPI595203_05g004770.1 Cmu05g0477 477
6 7657102 7659127 - CmPI595203_06g006720.1 Cmu06g0672 672
6 7672680 7675432 + CmPI595203_06g006730.1 Cmu06g0673 673
6 7704598 7707496 + CmPI595203_06g006740.1 Cmu06g0674 674
4 1429932 1432001 - Conep04aG0032700.1 Cone4ag0315 315
7 1349623 1354482 - Conep07aG0032000.1 Cone7ag0312 312
7 1362057 1363477 + Conep07aG0032100.1 Cone7ag0313 313
3 11839122 11841182 - Cp4.1LG03g10010.1 Cpe03g01507 1507
3 11841944 11844258 - Cp4.1LG03g09960.1 Cpe03g01508 1508
8 2026365 2036546 - Cp4.1LG08g03510.1 Cpe08g00323 323
8 2037624 2040490 - Cp4.1LG08g03470.1 Cpe08g00324 324
8 2050349 2052181 - Cp4.1LG08g03500.1 Cpe08g00326 326
12 950233 952154 - Cp4.1LG12g01530.1 Cpe12g00148 148
12 955013 957667 + Cp4.1LG12g01400.1 Cpe12g00149 149
17 1194570 1195971 - Cp4.1LG17g01890.1 Cpe17g00186 186
17 1200966 1206636 + Cp4.1LG17g01790.1 Cpe17g00187 187
5 4797898 4813545 + CrPI670011_05g005410.1 Cre05g0541 541
6 8746565 8748609 - CrPI670011_06g014410.1 Cre06g1441 1441
6 8757796 8765141 + CrPI670011_06g014420.1 Cre06g1442 1442
6 8796632 8799831 + CrPI670011_06g014430.1 Cre06g1443 1443
2 10500493 10502963 - CsaV3_2G012930.1 Csa02g01077 1077
2 10513414 10516289 + CsaV3_2G012940.1 Csa02g01078 1078
3 9443532 9445399 - CsaV3_3G012280.1 Csa03g01228 1228
3 9446247 9448079 - CsaV3_3G012290.1 Csa03g01229 1229
3 9449805 9451809 - CsaV3_3G012300.1 Csa03g01230 1230
3 9456287 9473219 + CsaV3_3G012320.1 Csa03g01232 1232
3 3512098 3515678 + Hsped.03g02690.1 Hepe03g0269 269
12 39044169 39045053 - Lag0016564.1 Lac12g2192 2192
13 3969783 3972621 - Maker00024046 Lcy13g0355 355
13 4000446 4001321 + Maker00023307 Lcy13g0358 358
5 24566769 24584296 - Lsi05G017050.1 Lsi05g01704 1704
5 24591007 24592286 + Lsi05G017070.1 Lsi05g01707 1707
5 24598140 24599746 + Lsi05G017080.1 Lsi05g01708 1708
9 20134469 20136460 - Lsi09G012470.1 Lsi09g01247 1247
9 20150945 20153999 + Lsi09G012480.1 Lsi09g01248 1248
7 3267458 3272013 - Sed0027428.1 Sed07g0437 437
9 10321891 10325111 - Sed0025643.1 Sed09g0698 698
6 8833998 8839700 - Tan0012246.1 Tan06g0995 995
6 76765192 76767462 - Tan0018862.1 Tan06g2429 2429
5 7238276 7299021 - Vvi5g649 Vvi5g649 649
5 7300431 7305169 - Vvi5g650 Vvi5g650 650
5 7315630 7319091 + Vvi5g651 Vvi5g651 651
5 7321487 7322977 + Vvi5g652 Vvi5g652 652
5 7335913 7341237 + Vvi5g653 Vvi5g653 653
5 7341803 7344678 + Vvi5g654 Vvi5g654 654
5 7355479 7357179 - Vvi5g655 Vvi5g655 655
5 7357236 7358330 - Vvi5g656 Vvi5g656 656
5 7358339 7360713 - Vvi5g657 Vvi5g657 657
5 7361103 7362625 + Vvi5g658 Vvi5g658 658
       

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