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
Vvi1g1021 . Blo16g01070 . . Bpe13g01357 Bpe10g00923 Bma14g01627 Bma15g00100 Cmo04g01636 Cmo18g01096 Cma04g00989 Cma18g01074 Car04g01617 Car18g00997 Sed06g1827 Cpe09g00249 Cpe01g01390 Bhi07g01419 Tan04g0937 Cmetu09g1500 Lac13g0423 Hepe10g1837 . . Cla05g02362 Cam05g2533 Cec05g2562 Cco05g2601 Clacu05g2528 Cmu05g2388 Cre05g2504 . . . . Lsi04g00324 Csa05g02545 Chy10g01085 Cme10g00324 Blo06g00950 Blo11g00811 Bda07g01496 . Bpe11g01623 . . Bma06g00750 . . Cmo15g00873 . . . Car15g00216 Cpe13g00999 . . . . . . . . . . . . . . . . . Chy09g00171 .
Vvi1g1022 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1023 Blo01g00471 . Bda01g02109 . . . . . . . . . . . . . Cpe01g01905 . . . . . . . . . . . . . . . . . . . Csa05g02552 Chy10g01092 . . . . . . Bpe02g02297 Bma01g00142 Bma06g00787 . Cmo04g02295 Cmo15g00868 Cma04g02195 Cma15g00838 Car04g02122 Car15g00787 . . Bhi12g01050 . . . Hepe02g2533 . Lcy10g1523 Cla01g00726 Cam01g0754 Cec01g0753 Cco01g0779 Clacu01g0746 Cmu01g0715 Cre09g1790 Lsi09g00788 . . Cme09g01199
Vvi1g1024 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1025 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1026 Blo01g00391 . . . . . . . Cmo04g01633 . . . . . . Cpe09g00254 . . . . . . . . . . . . . . . . . . . Lsi04g00318 . . . . . . . . . . . . Cmo04g02293 . Cma04g02193 . Car04g02119 Car15g00214 Cpe13g01002 . Bhi12g01049 . . . . . . Cla01g00725 . . . . . . Lsi09g00786 Csa05g01367 Chy09g00415 Cme09g01202
Vvi1g1027 . . . . . . . . Cmo04g01632 . . Cma18g01071 Car04g01613 . . . Cpe01g01386 . . . . . . . Cla05g02358 Cam05g2527 Cec05g2554 Cco05g2595 Clacu05g2522 Cmu05g2384 Cre05g2499 . . . Cone9ag0506 . . . . . Blo11g00816 Bda07g01512 . Bpe11g01675 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1028 . . . . . . . . . Cmo18g01091 . . . Car18g00992 Sed06g1833 . . Bhi07g01411 Tan04g0933 Cmetu10g0062 Lac13g0428 Hepe10g1843 . . . . . . . . . . . . . . . . Cme10g00320 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1029 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1030 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 57157787 57161389 - Bda004440.1 Bda01g02109 2109
7 27728115 27728711 - Bda028335.1 Bda07g01496 1496
7 28110936 28112375 + Bda028362.1 Bda07g01512 1512
7 42173862 42176092 - XM_039036789.1 Bhi07g01411 1411
7 42289768 42291846 + XM_039036079.1 Bhi07g01419 1419
12 31948895 31952431 - XM_039018561.1 Bhi12g01049 1049
12 32070628 32080764 + XM_039019352.1 Bhi12g01050 1050
1 4427087 4430465 - BLOR00391 Blo01g00391 391
1 5195262 5212363 + BLOR00471 Blo01g00471 471
6 32717700 32718296 - BLOR17533 Blo06g00950 950
11 13286754 13289061 + BLOR03687 Blo11g00811 811
11 13400014 13405945 + BLOR03692 Blo11g00816 816
16 39252815 39253321 - BLOR21857 Blo16g01070 1070
1 1367660 1371281 + Bma000308.1 Bma01g00142 142
6 38858855 38859334 + Bma023739.1 Bma06g00750 750
6 40472748 40478068 - Bma023798.1 Bma06g00787 787
14 34310533 34311333 - Bma012334.1 Bma14g01627 1627
15 1091531 1092127 + Bma013075.1 Bma15g00100 100
2 23693877 23697467 - Bpe010114.3 Bpe02g02297 2297
10 14832899 14833495 - Bpe003226.1 Bpe10g00923 923
11 12365775 12366578 - Bpe004937.1 Bpe11g01623 1623
11 12995547 12996986 + Bpe004988.1 Bpe11g01675 1675
13 18821390 18821869 - Bpe011019.1 Bpe13g01357 1357
1 8369529 8377048 + CaPI482276_01g007540.1 Cam01g0754 754
5 33118575 33120104 - CaPI482276_05g025270.1 Cam05g2527 2527
5 33159612 33160214 + CaPI482276_05g025330.1 Cam05g2533 2533
4 9319426 9321014 - Carg01787-RA Car04g01613 1613
4 9338660 9340665 + Carg01783-RA Car04g01617 1617
4 17248356 17249404 - Carg17726-RA Car04g02119 2119
4 17265474 17274890 + Carg17729-RA Car04g02122 2122
15 1181391 1184941 + Carg02195-RA Car15g00214 214
15 1195954 1196418 - Carg02197-RA Car15g00216 216
15 4477535 4482765 - Carg01368-RA Car15g00787 787
18 10400190 10402236 - Carg21537-RA Car18g00992 992
18 10420111 10420737 + Carg21532-RA Car18g00997 997
1 8161861 8169368 + CcPI632755_01g007790.1 Cco01g0779 779
5 34218526 34220039 - CcPI632755_05g025950.1 Cco05g2595 2595
5 34262391 34262993 + CcPI632755_05g026010.1 Cco05g2601 2601
1 8237115 8244590 + CePI673135_01g007530.1 Cec01g0753 753
5 36551737 36553259 - CePI673135_05g025540.1 Cec05g2554 2554
5 36598692 36599294 + CePI673135_05g025620.1 Cec05g2562 2562
9 1447735 1456747 - Chy9G158870.1 Chy09g00171 171
9 3647389 3650304 + Chy9G161310.1 Chy09g00415 415
10 15951534 15953231 - Chy10G182790.1 Chy10g01085 1085
10 15986058 16002498 + Chy10G182860.1 Chy10g01092 1092
1 8038492 8045981 + ClG42_01g0074600.10 Clacu01g0746 746
5 33330895 33332409 - ClG42_05g0252200.10 Clacu05g2522 2522
5 33371639 33372241 + ClG42_05g0252800.10 Clacu05g2528 2528
1 8419245 8436574 - ClCG01G007420.2 Cla01g00725 725
1 8454778 8463376 + ClCG01G007440.1 Cla01g00726 726
5 35163667 35165440 - ClCG05G023330.2 Cla05g02358 2358
5 35204935 35207247 + ClCG05G023370.1 Cla05g02362 2362
4 5095834 5101543 + CmaCh04G009890.1 Cma04g00989 989
4 15292397 15296452 - CmaCh04G021930.1 Cma04g02193 2193
4 15308647 15316974 + CmaCh04G021950.1 Cma04g02195 2195
15 4239916 4247258 - CmaCh15G008380.1 Cma15g00838 838
18 8863158 8867056 - CmaCh18G010710.1 Cma18g01071 1071
18 8883631 8884973 + CmaCh18G010740.1 Cma18g01074 1074
9 16854174 16855823 - MELO3C005163.2.1 Cme09g01199 1199
9 16940827 16944580 + MELO3C005170.2.1 Cme09g01202 1202
10 2100680 2102866 - MELO3C012185.2.1 Cme10g00320 320
10 2130478 2131940 + MELO3C012181.2.1 Cme10g00324 324
9 8669003 8669560 + PI0014910.1 Cmetu09g1500 1500
10 19951461 19952992 + PI0013219.1 Cmetu10g0062 62
4 8339196 8348721 - CmoCh04G016320.1 Cmo04g01632 1632
4 8339374 8342431 + CmoCh04G016330.1 Cmo04g01633 1633
4 8360757 8364133 + CmoCh04G016360.1 Cmo04g01636 1636
4 17046288 17050416 - CmoCh04G022930.1 Cmo04g02293 2293
4 17064529 17073793 + CmoCh04G022950.1 Cmo04g02295 2295
15 4412577 4418246 - CmoCh15G008680.1 Cmo15g00868 868
15 4433238 4433678 - CmoCh15G008730.1 Cmo15g00873 873
18 11417508 11419004 - CmoCh18G010910.1 Cmo18g01091 1091
18 11438837 11439448 + CmoCh18G010960.1 Cmo18g01096 1096
1 8006161 8013646 + CmPI595203_01g007150.1 Cmu01g0715 715
5 33068895 33070409 - CmPI595203_05g023840.1 Cmu05g2384 2384
5 33109667 33110269 + CmPI595203_05g023880.1 Cmu05g2388 2388
9 2420086 2420872 - Conep09aG0051600.1 Cone9ag0506 506
1 8343439 8347795 - Cp4.1LG01g13300.1 Cpe01g01386 1386
1 8363780 8365810 + Cp4.1LG01g13280.1 Cpe01g01390 1390
1 16248641 16258075 + Cp4.1LG01g19020.1 Cpe01g01905 1905
9 1441424 1443425 - Cp4.1LG09g02550.1 Cpe09g00249 249
9 1462093 1466184 - Cp4.1LG09g02490.1 Cpe09g00254 254
13 8255848 8256387 + Cp4.1LG13g07930.1 Cpe13g00999 999
13 8267740 8274891 - Cp4.1LG13g07860.1 Cpe13g01002 1002
5 36413086 36414597 - CrPI670011_05g024990.1 Cre05g2499 2499
5 36454422 36455024 + CrPI670011_05g025040.1 Cre05g2504 2504
9 36337409 36344968 - CrPI670011_09g017900.1 Cre09g1790 1790
5 14374418 14377747 - CsaV3_5G018890.1 Csa05g01367 1367
5 26886863 26889093 - CsaV3_5G033640.1 Csa05g02545 2545
5 26929064 26934293 + CsaV3_5G033710.1 Csa05g02552 2552
2 72184820 72188743 - Hsped.02g25330.1 Hepe02g2533 2533
10 55111928 55113333 - Hsped.10g18370.1 Hepe10g1837 1837
10 55152380 55154425 + Hsped.10g18430.1 Hepe10g1843 1843
13 2976756 2977358 - Lag0040219.1 Lac13g0423 423
13 3013957 3015455 + Lag0040224.1 Lac13g0428 428
10 39663626 39673786 - Maker00006948 Lcy10g1523 1523
4 3258592 3262288 + Lsi04G003180.1 Lsi04g00318 318
4 3309103 3313301 + Lsi04G003240.1 Lsi04g00324 324
9 8919148 8926865 - Lsi09G007860.1 Lsi09g00786 786
9 8982564 8993426 + Lsi09G007880.1 Lsi09g00788 788
6 42720276 42723538 - Sed0016295.1 Sed06g1827 1827
6 42767469 42768956 + Sed0017649.1 Sed06g1833 1833
4 8207941 8209450 - Tan0003145.1 Tan04g0933 933
4 8259566 8262057 + Tan0011340.1 Tan04g0937 937
1 16444084 16444672 - Vvi1g1021 Vvi1g1021 1021
1 16474189 16475881 + Vvi1g1022 Vvi1g1022 1022
1 16476401 16490940 - Vvi1g1023 Vvi1g1023 1023
1 16513245 16515107 - Vvi1g1024 Vvi1g1024 1024
1 16525844 16535560 + Vvi1g1025 Vvi1g1025 1025
1 16552191 16556024 + Vvi1g1026 Vvi1g1026 1026
1 16556737 16559153 - Vvi1g1027 Vvi1g1027 1027
1 16584263 16590008 - Vvi1g1028 Vvi1g1028 1028
1 16601693 16612318 + Vvi1g1029 Vvi1g1029 1029
1 16618593 16619285 - Vvi1g1030 Vvi1g1030 1030
       

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