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
Vvi17g326 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0286 Cone19ag0280 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g327 . . . . . . . . . . Cma10g00235 Cma11g00267 Car10g00222 Car11g00244 . . Cpe04g01407 . . . . . . . Cla06g01470 Cam06g1623 Cec06g1686 Cco06g1678 Clacu06g1588 Cmu06g1539 Cre06g2350 . . . . . . . . . . . . . . . . . Cmo10g00250 Cmo11g00273 . . . . . Cpe18g00757 . . . . . . . . . . . . . . Lsi06g01333 Csa01g00381 Chy02g02365 Cme02g01743
Vvi17g328 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g329 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g330 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g331 . . . . Bpe12g00689 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe18g00755 . . . . . . . . . . . . . . . Csa01g00379 . Cme02g01745
Vvi17g332 . . . Bda15g00518 . . . . . . Cma10g00237 . Car10g00224 . . . . . . . . . . . Cla06g01472 Cam06g1625 Cec06g1688 Cco06g1681 Clacu06g1590 Cmu06g1541 Cre06g2353 . . . Cone19ag0278 . . . . . . . . . . . Bma08g00064 . Cmo10g00252 . . . . . . . . . . . . . . . . . . . . . Lsi06g01335 . Chy02g02367 .
Vvi17g333 . . Bda06g00801 . . . . Bma12g01227 . . Cma10g00240 . Car10g00226 . . . . . . . . . . . Cla06g01475 Cam06g1629 Cec06g1691 Cco06g1685 Clacu06g1594 Cmu06g1544 Cre06g2356 . . Cone13ag0289 Cone19ag0274 . . . . . Blo15g00075 . . Bpe07g01031 . . . . Cmo10g00254 . . . . . . Cpe18g00753 . . . . . . . . . . . . . . Lsi06g01338 Csa01g00375 Chy02g02369 Cme02g01753
Vvi17g334 . . . . . . . . . . Cma10g00241 . Car10g00227 . . . . . . . . . . . Cla06g01476 Cam06g1630 Cec06g1692 Cco06g1686 Clacu06g1595 Cmu06g1545 Cre06g2357 . . Cone13ag0290 . . . . . . . . . . . . . . Cmo10g00255 . . . . . . Cpe18g00752 . . . . . . . . . . . . . . Lsi06g01339 . Chy02g02370 .
Vvi17g335 . . . . . . . . Cmo13g01070 . . . . . . Cpe20g00115 . . . . . . . . . . . . . . . . . . . Lsi02g00174 Csa01g00656 . . . . . . . . . . Sed01g1714 . . Cma13g01030 . Car13g00864 . . . Bhi08g01223 Tan05g2278 Cmetu12g1605 Lac10g0225 . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 11150458 11151289 + Bda024126.1 Bda06g00801 801
15 8256725 8263425 + Bda012348.1 Bda15g00518 518
8 37855852 37857204 - XM_039039099.1 Bhi08g01223 1223
15 646604 648373 - BLOR06469 Blo15g00075 75
8 784419 792191 + Bma027061.1 Bma08g00064 64
12 45204142 45204887 + Bma008590.1 Bma12g01227 1227
7 15852144 15852976 + Bpe021875.1 Bpe07g01031 1031
12 12480641 12487391 - Bpe005949.1 Bpe12g00689 689
6 27689349 27691509 + CaPI482276_06g016230.1 Cam06g1623 1623
6 27704501 27711652 + CaPI482276_06g016250.1 Cam06g1625 1625
6 27736000 27737022 + CaPI482276_06g016290.1 Cam06g1629 1629
6 27737484 27738340 - CaPI482276_06g016300.1 Cam06g1630 1630
10 1062938 1063778 + Carg17921-RA Car10g00222 222
10 1067047 1073988 + Carg17919-RA Car10g00224 224
10 1079661 1080882 + Carg17917-RA Car10g00226 226
10 1081114 1081943 - Carg17916-RA Car10g00227 227
11 1370866 1371660 - Carg09145-RA Car11g00244 244
13 9174252 9175639 + Carg04808-RA Car13g00864 864
6 27368673 27369516 + CcPI632755_06g016780.1 Cco06g1678 1678
6 27384155 27391058 + CcPI632755_06g016810.1 Cco06g1681 1681
6 27418342 27419361 + CcPI632755_06g016850.1 Cco06g1685 1685
6 27419816 27420672 - CcPI632755_06g016860.1 Cco06g1686 1686
6 30440467 30441310 + CePI673135_06g016860.1 Cec06g1686 1686
6 30454510 30461466 + CePI673135_06g016880.1 Cec06g1688 1688
6 30484760 30488251 + CePI673135_06g016910.1 Cec06g1691 1691
6 30488710 30489566 - CePI673135_06g016920.1 Cec06g1692 1692
2 27514042 27514866 + Chy2G046320.1 Chy02g02365 2365
2 27522644 27529452 + Chy2G046340.1 Chy02g02367 2367
2 27545219 27546125 + Chy2G046360.1 Chy02g02369 2369
2 27546582 27547397 - Chy2G046370.1 Chy02g02370 2370
6 26746811 26750745 + ClG42_06g0158800.10 Clacu06g1588 1588
6 26759758 26769464 + ClG42_06g0159000.10 Clacu06g1590 1590
6 26792268 26793290 + ClG42_06g0159400.10 Clacu06g1594 1594
6 26793752 26794607 - ClG42_06g0159500.10 Clacu06g1595 1595
6 28260719 28261895 + ClCG06G014820.2 Cla06g01470 1470
6 28273839 28281258 + ClCG06G014860.2 Cla06g01472 1472
6 28306344 28307672 + ClCG06G014890.1 Cla06g01475 1475
6 28307889 28308744 - ClCG06G014900.1 Cla06g01476 1476
10 1053099 1054472 + CmaCh10G002350.1 Cma10g00235 235
10 1057890 1064791 + CmaCh10G002370.1 Cma10g00237 237
10 1070235 1071879 + CmaCh10G002400.1 Cma10g00240 240
10 1071914 1072657 - CmaCh10G002410.1 Cma10g00241 241
11 1358315 1359522 - CmaCh11G002670.1 Cma11g00267 267
13 7881915 7882846 + CmaCh13G010300.1 Cma13g01030 1030
2 24424860 24426670 + MELO3C017305.2.1 Cme02g01743 1743
2 24434098 24441491 + MELO3C017303.2.1 Cme02g01745 1745
2 24467729 24469017 + MELO3C017300.2.1 Cme02g01753 1753
12 1194432 1195190 - PI0020813.1 Cmetu12g1605 1605
10 1112817 1113747 + CmoCh10G002500.1 Cmo10g00250 250
10 1117355 1124257 + CmoCh10G002520.1 Cmo10g00252 252
10 1129938 1131369 + CmoCh10G002540.1 Cmo10g00254 254
10 1131405 1132147 - CmoCh10G002550.1 Cmo10g00255 255
11 1337398 1339846 - CmoCh11G002730.1 Cmo11g00273 273
13 8886419 8887491 + CmoCh13G010700.1 Cmo13g01070 1070
6 26649842 26653815 + CmPI595203_06g015390.1 Cmu06g1539 1539
6 26662633 26669556 + CmPI595203_06g015410.1 Cmu06g1541 1541
6 26695044 26696066 + CmPI595203_06g015440.1 Cmu06g1544 1544
6 26696528 26697383 - CmPI595203_06g015450.1 Cmu06g1545 1545
13 2136062 2137309 + Conep13aG0030400.1 Cone13ag0286 286
13 2171108 2172160 + Conep13aG0030700.1 Cone13ag0289 289
13 2172130 2173010 - Conep13aG0030800.1 Cone13ag0290 290
19 1933003 1934486 + Conep19aG0028400.1 Cone19ag0274 274
19 1986645 1991163 - Conep19aG0028800.1 Cone19ag0278 278
19 2004222 2005429 - Conep19aG0029000.1 Cone19ag0280 280
4 11336629 11338242 + Cp4.1LG04g13950.1 Cpe04g01407 1407
18 7260070 7262427 + Cp4.1LG18g07420.1 Cpe18g00752 752
18 7260200 7262562 - Cp4.1LG18g07520.1 Cpe18g00753 753
18 7268081 7275245 - Cp4.1LG18g07550.1 Cpe18g00755 755
18 7279054 7283178 - Cp4.1LG18g07500.1 Cpe18g00757 757
20 641583 643103 - Cp4.1LG20g01180.1 Cpe20g00115 115
6 31443051 31443894 + CrPI670011_06g023500.1 Cre06g2350 2350
6 31456455 31463460 + CrPI670011_06g023530.1 Cre06g2353 2353
6 31490109 31491130 + CrPI670011_06g023560.1 Cre06g2356 2356
6 31491592 31492448 - CrPI670011_06g023570.1 Cre06g2357 2357
1 2337216 2340976 - CsaV3_1G003750.1 Csa01g00375 375
1 2354015 2361755 - CsaV3_1G003790.1 Csa01g00379 379
1 2368012 2369905 - CsaV3_1G003810.1 Csa01g00381 381
1 4213244 4213892 - CsaV3_1G006560.1 Csa01g00656 656
10 1768983 1771913 - Lag0024270.1 Lac10g0225 225
2 1459392 1461170 - Lsi02G001740.1 Lsi02g00174 174
6 23917405 23918670 + Lsi06G013330.1 Lsi06g01333 1333
6 23930451 23939032 + Lsi06G013350.1 Lsi06g01335 1335
6 23967351 23968910 + Lsi06G013380.1 Lsi06g01338 1338
6 23968978 23969834 - Lsi06G013390.1 Lsi06g01339 1339
1 12470006 12471033 - Sed0021850.1 Sed01g1714 1714
5 74114591 74115321 + Tan0019410.1 Tan05g2278 2278
17 3638193 3654846 - Vvi17g326 Vvi17g326 326
17 3660238 3661508 - Vvi17g327 Vvi17g327 327
17 3670795 3671231 + Vvi17g328 Vvi17g328 328
17 3690416 3693662 - Vvi17g329 Vvi17g329 329
17 3693769 3695087 + Vvi17g330 Vvi17g330 330
17 3695152 3700317 + Vvi17g331 Vvi17g331 331
17 3700339 3715271 + Vvi17g332 Vvi17g332 332
17 3747800 3760737 + Vvi17g333 Vvi17g333 333
17 3761459 3762435 - Vvi17g334 Vvi17g334 334
17 3763194 3764950 + Vvi17g335 Vvi17g335 335
       

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