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
Vvi19g14 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g15 . . . . . . . . . . . . . Car09g00602 . Cpe06g00532 . Bhi09g03579 . . . Hepe01g1475 . . Cla11g01675 Cam11g1742 Cec11g1767 Cco11g1768 Clacu11g1900 Cmu11g1711 Cre11g2125 . Cone9ag0242 . . Lsi04g01969 Csa04g02248 . . . . . . . . . . . . Cmo09g00664 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g16 . . . . Bpe09g00272 . . Bma13g00918 . Cmo04g00703 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo10g00718 . . . . . . . . . . . . . . . . . . . . . . Cla07g00986 Cam07g1059 Cec07g1130 Cco07g1107 Clacu07g1031 Cmu07g1024 Cre07g1401 . . . .
Vvi19g17 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g18 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda12g00807 . . . . . . . Cma04g00641 . Car04g00597 . . . . . . . . . . . . . . . . . . . . .
Vvi19g19 . . . . . . Bma10g00465 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1014 . . . . . . . . . . . . . . . . Cma04g00653 . . . . Cpe01g00590 . . . . . . . . . . . . . . . . . .
Vvi19g20 Blo03g00713 . . . . . . . . . Cma01g01275 . Car01g01090 . Sed04g2504 Cpe06g00531 Cpe02g00649 Bhi09g03574 Tan01g4246 Cmetu07g2173 . Hepe01g1472 Mch11g0976 . Cla11g01678 Cam11g1745 Cec11g1769 Cco11g1770 Clacu11g1902 Cmu11g1713 Cre11g2127 Cone6ag0213 Cone9ag0241 . . Lsi04g01972 Csa04g02251 . Cme07g00488 . . . . Bpe11g00434 . . . . Cmo01g01329 Cmo09g00663 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g21 Blo03g00712 . . . . . . . . . Cma01g01274 . Car01g01089 . Sed04g2503 . . Bhi09g03573 Tan01g4247 Cmetu07g0239 . Hepe01g1471 Mch11g0977 . . . . . . . . . . . . . . . . . . . . . . . . . Cmo01g01328 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g22 . . . . . . . . . . . . . . . . . . . . . . . . Cla11g01679 Cam11g1746 Cec11g1771 Cco11g1771 Clacu11g1903 Cmu11g1714 Cre11g2128 . Cone9ag0240 . . Lsi04g01973 Csa04g02252 . Cme07g00489 . . . . Bpe11g00435 . . Bma14g00275 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g23 Blo03g00711 . . . . . . . . . Cma01g01272 . Car01g01088 Car09g00600 Sed11g1611 Cpe06g00530 Cpe02g00651 Bhi09g03572 Tan01g4248 Cmetu07g1260 . Hepe01g1470 . . . . . . . . . . . Cone14ag1015 . Lsi04g01975 Csa04g02253 . Cme07g00491 . . . . . . . . . Cmo01g01327 Cmo09g00661 . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
12 37186722 37191730 - Bda009313.1 Bda12g00807 807
9 89605209 89611362 + XM_039042076.1 Bhi09g03572 3572
9 89633445 89636130 + XM_039042075.1 Bhi09g03573 3573
9 89649725 89652218 + XM_039041399.1 Bhi09g03574 3574
9 89668826 89670259 + XM_039042388.1 Bhi09g03579 3579
3 30108946 30110789 + BLOR11892 Blo03g00711 711
3 30118917 30121404 + BLOR11893 Blo03g00712 712
3 30126542 30131002 + BLOR11894 Blo03g00713 713
10 22764522 22775424 + BLOR02508 Blo10g00718 718
10 5263625 5265929 - Bma004136.1 Bma10g00465 465
13 39603351 39609126 + Bma009995.1 Bma13g00918 918
14 3288238 3290648 + Bma030651 Bma14g00275 275
9 2021823 2024127 - Bpe023942.1 Bpe09g00272 272
11 3300071 3301102 - Bpe003807.1 Bpe11g00434 434
11 3302511 3304862 - Bpe003808.1 Bpe11g00435 435
7 24941368 24944412 + CaPI482276_07g010590.1 Cam07g1059 1059
11 29998215 29999112 - CaPI482276_11g017420.1 Cam11g1742 1742
11 30007430 30009202 - CaPI482276_11g017450.1 Cam11g1745 1745
11 30011591 30014077 - CaPI482276_11g017460.1 Cam11g1746 1746
1 10200114 10211632 + Carg14753-RA Car01g01088 1088
1 10212126 10215317 + Carg14754-RA Car01g01089 1089
1 10216488 10217614 + Carg14755-RA Car01g01090 1090
4 3409660 3419658 - Carg13108-RA Car04g00597 597
9 3409438 3414213 + Carg03083-RA Car09g00600 600
9 3424579 3426872 + Carg03085-RA Car09g00602 602
7 24633189 24639326 + CcPI632755_07g011070.1 Cco07g1107 1107
11 30402398 30403290 - CcPI632755_11g017680.1 Cco11g1768 1768
11 30411536 30413292 - CcPI632755_11g017700.1 Cco11g1770 1770
11 30415718 30418206 - CcPI632755_11g017710.1 Cco11g1771 1771
7 26537451 26540506 + CePI673135_07g011300.1 Cec07g1130 1130
11 31865175 31866262 - CePI673135_11g017670.1 Cec11g1767 1767
11 31874519 31876284 - CePI673135_11g017690.1 Cec11g1769 1769
11 31889469 31899525 - CePI673135_11g017710.1 Cec11g1771 1771
7 24737701 24740723 + ClG42_07g0103100.10 Clacu07g1031 1031
11 30026190 30027278 - ClG42_11g0190000.10 Clacu11g1900 1900
11 30035611 30037398 - ClG42_11g0190200.10 Clacu11g1902 1902
11 30039768 30042251 - ClG42_11g0190300.10 Clacu11g1903 1903
7 26059501 26062980 + ClCG07G010350.2 Cla07g00986 986
11 30363196 30364252 - ClCG11G017090.2 Cla11g01675 1675
11 30372427 30374444 - ClCG11G017110.2 Cla11g01678 1678
11 30375860 30394954 - ClCG11G017120.2 Cla11g01679 1679
1 9172201 9174993 + CmaCh01G012720.1 Cma01g01272 1272
1 9183703 9186801 + CmaCh01G012740.1 Cma01g01274 1274
1 9187597 9189139 + CmaCh01G012750.1 Cma01g01275 1275
4 3273122 3286431 - CmaCh04G006410.1 Cma04g00641 641
4 3336026 3345509 - CmaCh04G006530.1 Cma04g00653 653
7 4006642 4008420 - MELO3C025676.2.1 Cme07g00488 488
7 4013072 4016594 - MELO3C025675.2.1 Cme07g00489 489
7 4027369 4031678 - MELO3C025674.2.1 Cme07g00491 491
7 21100588 21103598 - PI0029113.1 Cmetu07g0239 239
7 21115606 21118872 - PI0021419.1 Cmetu07g1260 1260
7 21096325 21098187 - PI0024381.1 Cmetu07g2173 2173
1 10547250 10549944 + CmoCh01G013270.1 Cmo01g01327 1327
1 10558007 10561981 + CmoCh01G013280.1 Cmo01g01328 1328
1 10562944 10564493 + CmoCh01G013290.1 Cmo01g01329 1329
4 3490037 3493208 - CmoCh04G007030.1 Cmo04g00703 703
9 3312625 3316931 + CmoCh09G006610.1 Cmo09g00661 661
9 3323131 3328253 + CmoCh09G006630.1 Cmo09g00663 663
9 3328923 3330837 + CmoCh09G006640.1 Cmo09g00664 664
7 24982299 24992308 + CmPI595203_07g010240.1 Cmu07g1024 1024
11 29279210 29280298 - CmPI595203_11g017110.1 Cmu11g1711 1711
11 29288646 29290423 - CmPI595203_11g017130.1 Cmu11g1713 1713
11 29292790 29295273 - CmPI595203_11g017140.1 Cmu11g1714 1714
6 1004890 1005684 + Conep06aG0021500.1 Cone6ag0213 213
9 1026492 1028708 + Conep09aG0024300.1 Cone9ag0240 240
9 1029375 1030483 + Conep09aG0024400.1 Cone9ag0241 241
9 1032461 1033574 + Conep09aG0024500.1 Cone9ag0242 242
14 8491794 8494288 + Conep14aG0103400.1 Cone14ag1014 1014
14 8494782 8500137 - Conep14aG0103500.1 Cone14ag1015 1015
1 3410930 3415022 - Cp4.1LG01g00610.1 Cpe01g00590 590
2 3995301 4003029 - Cp4.1LG02g02200.1 Cpe02g00649 649
2 4004095 4014704 - Cp4.1LG02g02260.1 Cpe02g00651 651
6 3178726 3187887 + Cp4.1LG06g05250.1 Cpe06g00530 530
6 3188388 3191305 + Cp4.1LG06g05320.1 Cpe06g00531 531
6 3193077 3200634 + Cp4.1LG06g05330.1 Cpe06g00532 532
7 28917261 28920313 + CrPI670011_07g014010.1 Cre07g1401 1401
11 32947369 32948906 - CrPI670011_11g021250.1 Cre11g2125 2125
11 32955888 32957652 - CrPI670011_11g021270.1 Cre11g2127 2127
11 32960141 32962632 - CrPI670011_11g021280.1 Cre11g2128 2128
4 23111804 23116235 - CsaV3_4G032740.1 Csa04g02248 2248
4 23124396 23126447 - CsaV3_4G032770.1 Csa04g02251 2251
4 23131403 23135438 - CsaV3_4G032780.1 Csa04g02252 2252
4 23136610 23149258 - CsaV3_4G032790.1 Csa04g02253 2253
1 80023529 80038400 + Hsped.01g14700.1 Hepe01g1470 1470
1 80040427 80043647 + Hsped.01g14710.1 Hepe01g1471 1471
1 80049013 80051027 + Hsped.01g14720.1 Hepe01g1472 1472
1 80061257 80065475 + Hsped.01g14750.1 Hepe01g1475 1475
4 26742050 26745738 - Lsi04G019700.1 Lsi04g01969 1969
4 26757191 26759490 - Lsi04G019720.1 Lsi04g01972 1972
4 26762621 26765635 - Lsi04G019730.1 Lsi04g01973 1973
4 26779296 26785366 - Lsi04G019750.1 Lsi04g01975 1975
11 6683263 6684231 - MC11g0802 Mch11g0976 976
11 6686054 6705409 - MC11g0803 Mch11g0977 977
4 38036279 38039816 + Sed0007276.1 Sed04g2503 2503
4 38041201 38043282 + Sed0014657.1 Sed04g2504 2504
11 31521956 31528735 + Sed0000394.3 Sed11g1611 1611
1 107247095 107248804 - Tan0006917.1 Tan01g4246 4246
1 107252242 107255071 - Tan0006060.1 Tan01g4247 4247
1 107280578 107284248 - Tan0021120.1 Tan01g4248 4248
19 150326 151494 - Vvi19g14 Vvi19g14 14
19 153173 156479 - Vvi19g15 Vvi19g15 15
19 157110 163022 + Vvi19g16 Vvi19g16 16
19 192852 198053 - Vvi19g17 Vvi19g17 17
19 201969 211104 - Vvi19g18 Vvi19g18 18
19 224298 234190 + Vvi19g19 Vvi19g19 19
19 241616 242370 - Vvi19g20 Vvi19g20 20
19 244858 262438 - Vvi19g21 Vvi19g21 21
19 263272 265338 - Vvi19g22 Vvi19g22 22
19 271505 275207 - Vvi19g23 Vvi19g23 23
       

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