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
Vvi19g24 Blo03g00710 . . . . . . . . . . . . Car09g00599 Sed04g2498 Cpe06g00529 . Bhi09g03571 Tan01g4249 Cmetu07g0378 . Hepe01g1469 . . Cla11g01681 . Cec11g1772 Cco11g1773 Clacu11g1906 Cmu11g1717 Cre11g2130 . . . . Lsi04g01976 . . . . . . . Bpe11g00437 . . . . . Cmo09g00660 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g25 . . . . . . . . . . Cma01g01271 . Car01g01087 Car09g00598 Sed04g2497 Cpe06g00528 Cpe02g00652 Bhi09g03569 Tan01g4251 Cmetu07g2211 . Hepe01g1468 Mch11g0980 . . . . . . . . . . Cone14ag1017 . Lsi04g01977 Csa04g02255 . . . . . . . . . . . Cmo01g01326 Cmo09g00659 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g26 . . . . Bpe09g00271 Bpe08g00995 Bma10g00464 Bma13g00919 . Cmo04g00704 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo10g00719 . Bda12g00810 . . Bma07g01155 . . . . Cma04g00655 . . . . Cpe01g00592 . . . . . . . . . . . . . . . . . .
Vvi19g27 . . . . . Bpe08g00994 . . . . Cma01g01269 . Car01g01086 . Sed04g2496 . Cpe02g00653 Bhi09g03568 Tan01g4254 Cmetu07g2039 . Hepe01g1467 . . Cla11g01682 Cam11g1750 Cec11g1774 Cco11g1775 Clacu11g1908 Cmu11g1719 Cre11g2131 Cone6ag0210 Cone9ag0238 . . Lsi04g01978 Csa04g02256 . Cme07g00497 . . . . . . Bma07g01154 . . Cmo01g01325 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g28 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g29 . . . . . . . . . . . . . Car09g00597 . Cpe06g00527 . . . . . . . . Cla11g01688 Cam11g1752 Cec11g1776 Cco11g1777 Clacu11g1912 . Cre11g2133 . . . . Lsi04g01979 . . . . . . . . . . . . . Cmo09g00658 . . . . . . . . . . . . . . . . . . . . . . Chy07g00984 Cme07g01359
Vvi19g30 . . . . . . Bma10g00463 . . Cmo04g00705 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda05g00813 . . . . . . . . Cma04g00656 . . . . Cpe01g00593 . . . . . . . . . . . . . . . . . .
Vvi19g31 . . . . . . Bma10g00462 . . Cmo04g00706 . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1022 . . . . . . . . . . . . . . . . Cma04g00657 . . . . Cpe01g00594 . . . . . . . . . . . . . . . . . .
Vvi19g32 . . . . Bpe09g00270 . Bma10g00461 Bma13g00920 Cmo16g00458 Cmo04g00707 . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1023 . . . . . . Blo10g00720 . . . . . . . . . Cma04g00659 Cma16g00426 . . Cpe14g00359 Cpe01g00595 . . . . . . . . . . . . . . . . . .
Vvi19g33 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 56623140 56624516 + Bda021970.1 Bda05g00813 813
12 37323613 37325718 + Bda009319.1 Bda12g00810 810
9 89522830 89539040 + XM_039041696.1 Bhi09g03568 3568
9 89562798 89565947 + XM_039043892.1 Bhi09g03569 3569
9 89566197 89568473 - XM_039043894.1 Bhi09g03571 3571
3 30103984 30104559 - BLOR11891 Blo03g00710 710
10 22788782 22790887 + BLOR02509 Blo10g00719 719
10 22822165 22824679 + BLOR02510 Blo10g00720 720
7 45762061 45771562 + Bma026386.1 Bma07g01154 1154
7 45772026 45774248 - Bma026387.1 Bma07g01155 1155
10 5244910 5246506 - Bma004132.1 Bma10g00461 461
10 5250418 5251755 + Bma004133.2 Bma10g00462 462
10 5252464 5255001 - Bma004134.2 Bma10g00463 463
10 5256232 5258328 - Bma004135.1 Bma10g00464 464
13 39612345 39615965 + Bma009996.1 Bma13g00919 919
13 39618056 39620670 + Bma009997.1 Bma13g00920 920
8 12279186 12288745 + Bpe023119.1 Bpe08g00994 994
8 12289233 12291441 - Bpe023120.1 Bpe08g00995 995
9 2009553 2012206 - Bpe026214 Bpe09g00270 270
9 2015695 2017800 - Bpe023941.1 Bpe09g00271 271
11 3315259 3315974 + Bpe003810.1 Bpe11g00437 437
11 30042654 30052627 - CaPI482276_11g017500.1 Cam11g1750 1750
11 30080716 30082817 - CaPI482276_11g017520.1 Cam11g1752 1752
1 10183913 10194895 + Carg14751-RA Car01g01086 1086
1 10196917 10199346 + Carg14752-RA Car01g01087 1087
9 3396686 3400177 + Carg03080-RA Car09g00597 597
9 3402894 3406250 + Carg03081-RA Car09g00598 598
9 3407037 3407495 - Carg03082-RA Car09g00599 599
11 30437692 30438801 + CcPI632755_11g017730.1 Cco11g1773 1773
11 30452428 30467908 - CcPI632755_11g017750.1 Cco11g1775 1775
11 30496221 30497374 - CcPI632755_11g017770.1 Cco11g1777 1777
11 31900769 31901868 + CePI673135_11g017720.1 Cec11g1772 1772
11 31910192 31920119 - CePI673135_11g017740.1 Cec11g1774 1774
11 31950223 31952324 - CePI673135_11g017760.1 Cec11g1776 1776
7 14498817 14502032 - Chy7G138140.1 Chy07g00984 984
11 30061999 30063090 + ClG42_11g0190600.10 Clacu11g1906 1906
11 30064092 30066013 - ClG42_11g0190800.10 Clacu11g1908 1908
11 30117058 30119585 - ClG42_11g0191200.10 Clacu11g1912 1912
11 30398940 30400330 + ClCG11G017140.2 Cla11g01681 1681
11 30400639 30426650 - ClCG11G017150.2 Cla11g01682 1682
11 30454605 30458163 - ClCG11G017200.1 Cla11g01688 1688
1 9157325 9166189 + CmaCh01G012690.1 Cma01g01269 1269
1 9168856 9171628 + CmaCh01G012710.1 Cma01g01271 1271
4 3351372 3354750 + CmaCh04G006550.1 Cma04g00655 655
4 3355501 3360358 + CmaCh04G006560.1 Cma04g00656 656
4 3360989 3362689 - CmaCh04G006570.1 Cma04g00657 657
4 3365505 3367975 + CmaCh04G006590.1 Cma04g00659 659
16 2125173 2128774 - CmaCh16G004260.1 Cma16g00426 426
7 4052377 4069970 - MELO3C025673.2.1 Cme07g00497 497
7 19102907 19106249 - MELO3C016122.2.1 Cme07g01359 1359
7 21121967 21123251 + PI0017897.1 Cmetu07g0378 378
7 21133829 21150995 - PI0016713.1 Cmetu07g2039 2039
7 21124299 21126226 - PI0000557.1 Cmetu07g2211 2211
1 10538104 10542100 + CmoCh01G013250.1 Cmo01g01325 1325
1 10544081 10546675 + CmoCh01G013260.1 Cmo01g01326 1326
4 3493830 3498109 + CmoCh04G007040.1 Cmo04g00704 704
4 3498140 3502952 + CmoCh04G007050.1 Cmo04g00705 705
4 3503585 3507374 - CmoCh04G007060.1 Cmo04g00706 706
4 3508231 3511214 + CmoCh04G007070.1 Cmo04g00707 707
9 3300980 3303337 + CmoCh09G006580.1 Cmo09g00658 658
9 3306201 3308135 + CmoCh09G006590.1 Cmo09g00659 659
9 3310625 3311083 - CmoCh09G006600.1 Cmo09g00660 660
16 2198493 2202246 - CmoCh16G004580.1 Cmo16g00458 458
11 29315022 29316111 + CmPI595203_11g017170.1 Cmu11g1717 1717
11 29317113 29319028 - CmPI595203_11g017190.1 Cmu11g1719 1719
6 992992 998874 + Conep06aG0021200.1 Cone6ag0210 210
9 1015255 1021008 + Conep09aG0024100.1 Cone9ag0238 238
14 8506376 8509270 - Conep14aG0103700.1 Cone14ag1017 1017
14 8534590 8536577 - Conep14aG0104200.1 Cone14ag1022 1022
14 8542344 8544637 + Conep14aG0104300.1 Cone14ag1023 1023
1 3421344 3423687 + Cp4.1LG01g00730.1 Cpe01g00592 592
1 3424361 3429187 + Cp4.1LG01g00770.1 Cpe01g00593 593
1 3428507 3433653 - Cp4.1LG01g00680.1 Cpe01g00594 594
1 3434320 3438059 + Cp4.1LG01g00700.1 Cpe01g00595 595
2 4015328 4017274 - Cp4.1LG02g02230.1 Cpe02g00652 652
2 4020471 4036865 - Cp4.1LG02g02250.1 Cpe02g00653 653
6 3167730 3170298 + Cp4.1LG06g05260.1 Cpe06g00527 527
6 3172890 3176432 + Cp4.1LG06g05200.1 Cpe06g00528 528
6 3175497 3177148 - Cp4.1LG06g05280.1 Cpe06g00529 529
14 2185559 2189928 - Cp4.1LG14g03500.1 Cpe14g00359 359
11 32982305 32983422 + CrPI670011_11g021300.1 Cre11g2130 2130
11 32983854 33001699 - CrPI670011_11g021310.1 Cre11g2131 2131
11 33030607 33032708 - CrPI670011_11g021330.1 Cre11g2133 2133
4 23152858 23156512 - CsaV3_4G032810.1 Csa04g02255 2255
4 23161353 23170505 - CsaV3_4G032820.1 Csa04g02256 2256
1 79991460 80002061 + Hsped.01g14670.1 Hepe01g1467 1467
1 80012190 80014873 + Hsped.01g14680.1 Hepe01g1468 1468
1 80016603 80017979 - Hsped.01g14690.1 Hepe01g1469 1469
4 26790250 26791727 + Lsi04G019760.1 Lsi04g01976 1976
4 26791356 26794885 - Lsi04G019770.1 Lsi04g01977 1977
4 26807945 26826498 - Lsi04G019780.1 Lsi04g01978 1978
4 26848631 26851000 - Lsi04G019790.1 Lsi04g01979 1979
11 6709302 6710132 - MC11g0805 Mch11g0980 980
4 37982706 38001365 + Sed0019760.4 Sed04g2496 2496
4 38011106 38013429 + Sed0004014.1 Sed04g2497 2497
4 38014749 38015734 - Sed0021060.1 Sed04g2498 2498
1 107297875 107299710 + Tan0020144.1 Tan01g4249 4249
1 107299990 107303233 - Tan0005458.2 Tan01g4251 4251
1 107334470 107352679 - Tan0004977.1 Tan01g4254 4254
19 276077 276974 + Vvi19g24 Vvi19g24 24
19 278702 280954 - Vvi19g25 Vvi19g25 25
19 289914 291185 + Vvi19g26 Vvi19g26 26
19 292202 312996 - Vvi19g27 Vvi19g27 27
19 329776 330095 + Vvi19g28 Vvi19g28 28
19 338322 344985 - Vvi19g29 Vvi19g29 29
19 347975 351626 + Vvi19g30 Vvi19g30 30
19 352672 354668 - Vvi19g31 Vvi19g31 31
19 356888 371743 + Vvi19g32 Vvi19g32 32
19 371901 374095 - Vvi19g33 Vvi19g33 33
       

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