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
Vvi17g426 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g427 . . . . . . . . . . . Cma11g00226 . Car11g00202 Sed08g0297 . Cpe04g01445 Bhi02g00060 Tan09g2007 Cmetu02g0001 . . . . Cla06g01524 Cam06g1681 Cec06g1743 Cco06g1741 Clacu06g1648 Cmu06g1595 Cre06g2406 . . Cone13ag0024 . . . . . . Blo15g00344 . . . . . . . . Cmo11g00229 . . . . . . . . . . . . . . . . . . . . Lsi06g01393 Csa01g00335 Chy02g02407 Cme02g01807
Vvi17g428 . . . Bda15g00633 Bpe12g00515 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma08g00251 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g429 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g430 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g01788 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g431 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g432 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g433 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g434 Blo04g00801 . . Bda15g00632 Bpe12g00516 . . . . . Cma10g00285 Cma11g00225 Car10g00267 Car11g00201 Sed08g0293 . Cpe04g01446 Bhi02g00071 Tan09g2011 Cmetu02g0626 . Hepe09g0290 . . Cla06g01525 Cam06g1682 Cec06g1744 Cco06g1742 Clacu06g1649 Cmu06g1596 Cre06g2407 Cone2ag0791 . Cone13ag0025 Cone19ag0034 . . . . . . . Bda14g00893 . Bpe15g00565 . . . Cmo10g00302 Cmo11g00228 . . . . . Cpe18g00717 . . . . . . . . . . . . . . Lsi06g01394 Csa01g00336 Chy02g02406 Cme02g01808
Vvi17g435 . Blo16g00162 . . . . . . . . . . . . . Cpe20g00091 . . . . . . . . . . . . . . . . Cone16ag0225 . . Lsi02g00140 Csa01g00624 Chy12g01477 Cme12g01918 . . Bda11g01769 . . . . . Sed08g2136 . . . . . . . . Bhi08g01056 Tan05g2332 Cmetu12g0390 Lac10g0186 Hepe07g2442 . . Cla04g01138 . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 52517434 52525223 - Bda008689.1 Bda11g01769 1769
11 52778079 52779059 - Bda008712.1 Bda11g01788 1788
14 6928356 6930604 + Bda027672.1 Bda14g00893 893
15 9462692 9466114 + Bda012476.1 Bda15g00632 632
15 9467042 9468787 - Bda012477.1 Bda15g00633 633
2 1175541 1202325 + XM_039022380.1 Bhi02g00060 60
2 1203810 1208522 - XM_039023617.1 Bhi02g00071 71
8 34527826 34530155 + XM_039037637.1 Bhi08g01056 1056
4 8231455 8235981 + BLOR13713 Blo04g00801 801
15 4269935 4286276 + BLOR06738 Blo15g00344 344
16 3689663 3691571 - BLOR07410 Blo16g00162 162
8 3158084 3159755 - Bma027267.1 Bma08g00251 251
12 11005053 11006791 + Bpe005778.2 Bpe12g00515 515
12 11007728 11011181 - Bpe005779.1 Bpe12g00516 516
15 16659038 16661274 - Bpe001499.1 Bpe15g00565 565
6 28186982 28198698 + CaPI482276_06g016810.1 Cam06g1681 1681
6 28201201 28204958 - CaPI482276_06g016820.1 Cam06g1682 1682
10 1268892 1273663 - Carg17876-RA Car10g00267 267
11 1158373 1162469 + Carg09188-RA Car11g00201 201
11 1162625 1174754 - Carg09187-RA Car11g00202 202
6 27893560 27903456 + CcPI632755_06g017410.1 Cco06g1741 1741
6 27906445 27910818 - CcPI632755_06g017420.1 Cco06g1742 1742
6 30938308 30954206 + CePI673135_06g017430.1 Cec06g1743 1743
6 30957596 30961965 - CePI673135_06g017440.1 Cec06g1744 1744
2 27805545 27810413 + Chy2G046730.1 Chy02g02406 2406
2 27811665 27822425 - Chy2G046740.1 Chy02g02407 2407
12 18680921 18682894 + Chy12G220770.1 Chy12g01477 1477
6 27244249 27256407 + ClG42_06g0164800.10 Clacu06g1648 1648
6 27258935 27262673 - ClG42_06g0164900.10 Clacu06g1649 1649
4 26568095 26570330 + ClCG04G011580.1 Cla04g01138 1138
6 28785098 28796153 + ClCG06G015450.1 Cla06g01524 1524
6 28802806 28807211 - ClCG06G015460.2 Cla06g01525 1525
10 1261289 1266088 - CmaCh10G002850.1 Cma10g00285 285
11 1126992 1130680 + CmaCh11G002250.1 Cma11g00225 225
11 1132314 1145548 - CmaCh11G002260.1 Cma11g00226 226
2 24841520 24851786 + MELO3C017248.2.1 Cme02g01807 1807
2 24854767 24859072 - MELO3C017247.2.1 Cme02g01808 1808
12 25227726 25230592 + MELO3C002052.2.1 Cme12g01918 1918
2 23184614 23197118 + PI0016024.1 Cmetu02g0001 1
2 23197456 23201967 - PI0015676.1 Cmetu02g0626 626
12 921086 923167 - PI0027221.1 Cmetu12g0390 390
10 1346569 1351671 - CmoCh10G003020.1 Cmo10g00302 302
11 1126340 1130403 + CmoCh11G002280.1 Cmo11g00228 228
11 1130933 1142585 - CmoCh11G002290.1 Cmo11g00229 229
6 27153061 27163845 + CmPI595203_06g015950.1 Cmu06g1595 1595
6 27167733 27171472 - CmPI595203_06g015960.1 Cmu06g1596 1596
2 33889733 33893318 - Conep02aG0181800.1 Cone2ag0791 791
13 155887 161523 + Conep13aG0002600.1 Cone13ag0024 24
13 162819 165506 - Conep13aG0002700.1 Cone13ag0025 25
16 1653918 1658788 - Conep16aG0022900.1 Cone16ag0225 225
19 238320 241222 - Conep19aG0003700.1 Cone19ag0034 34
4 11538298 11549765 + Cp4.1LG04g14390.1 Cpe04g01445 1445
4 11549958 11557882 - Cp4.1LG04g14430.1 Cpe04g01446 1446
18 7057352 7063197 + Cp4.1LG18g07150.1 Cpe18g00717 717
20 483199 485230 - Cp4.1LG20g00850.1 Cpe20g00091 91
6 31950773 31962398 + CrPI670011_06g024060.1 Cre06g2406 2406
6 31964326 31968722 - CrPI670011_06g024070.1 Cre06g2407 2407
1 2079545 2089782 + CsaV3_1G003350.1 Csa01g00335 335
1 2092164 2097151 - CsaV3_1G003360.1 Csa01g00336 336
1 3987222 3989827 - CsaV3_1G006240.1 Csa01g00624 624
7 68767739 68770220 + Hsped.07g24420.1 Hepe07g2442 2442
9 2495224 2499634 + Hsped.09g02900.1 Hepe09g0290 290
10 1433878 1435817 - Lag0024231.1 Lac10g0186 186
2 1159217 1165449 - Lsi02G001400.1 Lsi02g00140 140
6 24492973 24505794 + Lsi06G013930.1 Lsi06g01393 1393
6 24507288 24512080 - Lsi06G013940.1 Lsi06g01394 1394
8 1750760 1755364 + Sed0015454.1 Sed08g0293 293
8 1758809 1775325 - Sed0020336.3 Sed08g0297 297
8 35355427 35359538 - Sed0020260.1 Sed08g2136 2136
5 74759570 74761788 + Tan0007677.1 Tan05g2332 2332
9 70771414 70783806 + Tan0018490.1 Tan09g2007 2007
9 70785622 70789982 - Tan0007536.1 Tan09g2011 2011
17 5278332 5292370 - Vvi17g426 Vvi17g426 426
17 5295199 5310273 + Vvi17g427 Vvi17g427 427
17 5315018 5318138 + Vvi17g428 Vvi17g428 428
17 5354563 5357443 - Vvi17g429 Vvi17g429 429
17 5376017 5377433 - Vvi17g430 Vvi17g430 430
17 5379735 5389939 + Vvi17g431 Vvi17g431 431
17 5393703 5394224 - Vvi17g432 Vvi17g432 432
17 5396605 5397916 + Vvi17g433 Vvi17g433 433
17 5399434 5414482 - Vvi17g434 Vvi17g434 434
17 5419517 5430208 + Vvi17g435 Vvi17g435 435
       

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