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
Vvi1g391 . . . . . . Bma14g01960 . Cmo04g01545 Cmo18g00991 . Cma18g00983 Car04g01532 Car18g00905 Sed06g1922 Cpe09g00333 Cpe01g01315 Bhi07g01248 Tan04g0787 Cmetu10g0609 Lac13g0553 Hepe01g1146 . . Cla05g02260 Cam05g2429 Cec05g2446 Cco05g2492 Clacu05g2418 Cmu05g2285 Cre05g2403 Cone13ag0788 . . . Lsi04g00204 Csa05g02663 Chy10g01194 Cme10g00208 . . Bda07g01760 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g392 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g393 Blo01g00742 Blo16g00725 . Bda11g00157 Bpe13g01041 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0415 Cone9ag0438 . Csa05g02045 . . . . . Bda11g00157 . . Bma01g00446 Bma06g01101 . . Cmo15g00979 . Cma15g00940 . Car15g00882 Cpe13g00383 . Bhi12g00868 . . . . . Lcy10g1452 Cla01g00590 Cam01g0617 Cec01g0607 Cco01g0633 Clacu01g0609 Cmu01g0582 Cre09g1923 Lsi09g00639 . Chy09g00875 Cme09g01408
Vvi1g394 . . . . . . . . Cmo04g01542 . . . Car04g01530 . Sed06g1921 . Cpe01g01313 Bhi07g01245 Tan04g0785 Cmetu10g0428 . Hepe01g1144 . . Cla05g02259 Cam05g2428 Cec05g2445 Cco05g2489 Clacu05g2417 Cmu05g2284 Cre05g2402 . . . . Lsi04g00202 Csa05g02665 Chy10g01196 Cme10g00206 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g395 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g396 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0786 Cone19ag0790 . . . . . . . . . . . . . . . . Cmo15g00994 . Cma15g00954 . Car15g00899 . . . . . . . . . . . . . . . . . . . .
Vvi1g397 . . . . . Bpe10g00871 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo15g00993 . Cma15g00953 . Car15g00897 . . . . . . . . . . . . . . . . . . . .
Vvi1g398 . . . . . . . . Cmo04g01541 Cmo18g00987 . Cma18g00980 Car04g01528 Car18g00902 . Cpe09g00336 Cpe01g01311 . . . . . . . Cla05g02257 Cam05g2424 Cec05g2441 Cco05g2486 Clacu05g2413 Cmu05g2280 Cre05g2398 Cone13ag0784 Cone19ag0787 . . Lsi04g00200 Csa05g02669 Chy10g01198 Cme10g00203 Blo06g00991 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g399 . . . . . . . . . . . . . . Sed06g1918 . . Bhi07g01242 Tan04g0779 Cmetu10g0205 Lac13g0556 Hepe01g1142 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g400 . . . . . . . Bma15g00062 Cmo04g01539 Cmo18g00985 . Cma18g00979 Car04g01526 Car18g00899 Sed06g1916 Cpe09g00338 Cpe01g01310 Bhi07g01238 Tan04g0768 Cmetu10g1517 Lac13g0559 Hepe01g1139 . . Cla05g02255 Cam05g2422 Cec05g2439 Cco05g2484 Clacu05g2411 Cmu05g2278 Cre05g2396 Cone13ag0782 Cone19ag0785 . . Lsi04g00198 Csa05g02671 Chy10g01200 Cme10g00201 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 33189948 33222447 + Bda028685.1 Bda07g01760 1760
11 2054641 2061202 + Bda033011 Bda11g00157 157
7 38954993 38959674 + XM_039037191.1 Bhi07g01238 1238
7 38979500 38984296 + XM_039037506.1 Bhi07g01242 1242
7 39052963 39059891 + XM_039035441.1 Bhi07g01245 1245
7 39064249 39068260 - XM_039036084.1 Bhi07g01248 1248
12 26296991 26310074 + XM_039051188.1 Bhi12g00868 868
1 9726592 9739936 - BLOR00742 Blo01g00742 742
6 33178491 33184902 - BLOR17574 Blo06g00991 991
16 28153652 28168989 + BLOR21512 Blo16g00725 725
1 3702185 3709112 - Bma000623.2 Bma01g00446 446
6 47802586 47810868 + Bma031312 Bma06g01101 1101
14 42298479 42300031 - Bma012764.1 Bma14g01960 1960
15 760667 767572 - Bma013035.1 Bma15g00062 62
10 14539854 14542607 - Bpe003175.2 Bpe10g00871 871
13 16079911 16086478 - Bpe010722.2 Bpe13g01041 1041
1 6695285 6705964 + CaPI482276_01g006170.1 Cam01g0617 617
5 32207701 32211740 + CaPI482276_05g024220.1 Cam05g2422 2422
5 32216110 32220603 - CaPI482276_05g024240.1 Cam05g2424 2424
5 32250649 32251521 + CaPI482276_05g024280.1 Cam05g2428 2428
5 32252512 32255813 - CaPI482276_05g024290.1 Cam05g2429 2429
4 8866395 8870361 + Carg01874-RA Car04g01526 1526
4 8871491 8876972 - Carg01872-RA Car04g01528 1528
4 8883610 8890026 + Carg01870-RA Car04g01530 1530
4 8893106 8896431 - Carg01868-RA Car04g01532 1532
15 5245246 5254748 + Carg24912-RA Car15g00882 882
15 5456797 5458452 + Carg26347-RA Car15g00897 897
15 5460898 5461434 - Carg26345-RA Car15g00899 899
18 9845929 9851375 + Carg19025-RA Car18g00899 899
18 9854221 9860103 - Carg19028-RA Car18g00902 902
18 9868302 9873300 - Carg19031-RA Car18g00905 905
1 6426818 6437489 + CcPI632755_01g006330.1 Cco01g0633 633
5 33263465 33267545 + CcPI632755_05g024840.1 Cco05g2484 2484
5 33272213 33276695 - CcPI632755_05g024860.1 Cco05g2486 2486
5 33295391 33303910 + CcPI632755_05g024890.1 Cco05g2489 2489
5 33308621 33312345 - CcPI632755_05g024920.1 Cco05g2492 2492
1 6486158 6496726 + CePI673135_01g006070.1 Cec01g0607 607
5 35615528 35619605 + CePI673135_05g024390.1 Cec05g2439 2439
5 35623838 35628338 - CePI673135_05g024410.1 Cec05g2441 2441
5 35658140 35659012 + CePI673135_05g024450.1 Cec05g2445 2445
5 35660006 35663322 - CePI673135_05g024460.1 Cec05g2446 2446
9 11496807 11507427 - Chy9G165910.1 Chy09g00875 875
10 16692588 16697096 + Chy10G183880.1 Chy10g01194 1194
10 16701800 16711887 - Chy10G183900.1 Chy10g01196 1196
10 16723761 16729659 + Chy10G183920.1 Chy10g01198 1198
10 16733303 16737075 - Chy10G183940.1 Chy10g01200 1200
1 6338154 6348810 + ClG42_01g0060900.10 Clacu01g0609 609
5 32421258 32425281 + ClG42_05g0241100.10 Clacu05g2411 2411
5 32429557 32434054 - ClG42_05g0241300.10 Clacu05g2413 2413
5 32463963 32464835 + ClG42_05g0241700.10 Clacu05g2417 2417
5 32465401 32469119 - ClG42_05g0241800.10 Clacu05g2418 2418
1 6688116 6699163 + ClCG01G006040.1 Cla01g00590 590
5 34210855 34215115 + ClCG05G022220.1 Cla05g02255 2255
5 34219370 34223867 - ClCG05G022250.2 Cla05g02257 2257
5 34237038 34254980 + ClCG05G022270.2 Cla05g02259 2259
5 34255972 34259264 - ClCG05G022300.2 Cla05g02260 2260
15 4984302 4994699 + CmaCh15G009400.1 Cma15g00940 940
15 5118284 5120920 + CmaCh15G009530.1 Cma15g00953 953
15 5122421 5122942 - CmaCh15G009540.1 Cma15g00954 954
18 8279848 8286929 + CmaCh18G009790.1 Cma18g00979 979
18 8289034 8295210 - CmaCh18G009800.1 Cma18g00980 980
18 8303481 8307106 - CmaCh18G009830.1 Cma18g00983 983
9 19265259 19276010 - MELO3C005328.2.1 Cme09g01408 1408
10 1357174 1361876 + MELO3C012300.2.1 Cme10g00201 201
10 1364723 1371447 - MELO3C012298.2.1 Cme10g00203 203
10 1384801 1391569 + MELO3C012295.2.1 Cme10g00206 206
10 1395894 1399555 - MELO3C012293.2.1 Cme10g00208 208
10 20754949 20759338 - PI0016010.1 Cmetu10g0205 205
10 20735504 20738114 - PI0025308.3 Cmetu10g0428 428
10 20731227 20735372 + PI0011402.2 Cmetu10g0609 609
10 20771249 20775636 - PI0007649.1 Cmetu10g1517 1517
4 7875109 7878961 + CmoCh04G015390.1 Cmo04g01539 1539
4 7880390 7885499 - CmoCh04G015410.1 Cmo04g01541 1541
4 7888985 7899676 + CmoCh04G015420.1 Cmo04g01542 1542
4 7903088 7906451 - CmoCh04G015450.1 Cmo04g01545 1545
15 5164107 5170740 + CmoCh15G009790.1 Cmo15g00979 979
15 5334547 5336443 + CmoCh15G009930.1 Cmo15g00993 993
15 5338480 5339016 - CmoCh15G009940.1 Cmo15g00994 994
18 10817767 10823407 + CmoCh18G009850.1 Cmo18g00985 985
18 10825903 10831863 - CmoCh18G009870.1 Cmo18g00987 987
18 10840251 10843608 - CmoCh18G009910.1 Cmo18g00991 991
1 6294841 6305498 + CmPI595203_01g005820.1 Cmu01g0582 582
5 32159143 32163166 + CmPI595203_05g022780.1 Cmu05g2278 2278
5 32167441 32171938 - CmPI595203_05g022800.1 Cmu05g2280 2280
5 32201853 32202725 + CmPI595203_05g022840.1 Cmu05g2284 2284
5 32203717 32207008 - CmPI595203_05g022850.1 Cmu05g2285 2285
6 2001732 2007318 - Conep06aG0042500.1 Cone6ag0415 415
9 2020026 2025701 - Conep09aG0044800.1 Cone9ag0438 438
13 7322464 7326847 + Conep13aG0080700.1 Cone13ag0782 782
13 7332415 7336473 - Conep13aG0080900.1 Cone13ag0784 784
13 7342335 7343072 - Conep13aG0081100.1 Cone13ag0786 786
13 7346447 7348195 - Conep13aG0081300.1 Cone13ag0788 788
19 6379004 6382543 + Conep19aG0080700.1 Cone19ag0785 785
19 6386771 6390931 - Conep19aG0080900.1 Cone19ag0787 787
19 6398104 6399091 - Conep19aG0081200.1 Cone19ag0790 790
1 7881948 7888658 + Cp4.1LG01g14000.1 Cpe01g01310 1310
1 7885090 7892636 - Cp4.1LG01g13970.1 Cpe01g01311 1311
1 7899614 7906067 + Cp4.1LG01g14030.1 Cpe01g01313 1313
1 7907260 7912844 - Cp4.1LG01g13960.1 Cpe01g01315 1315
9 2018589 2026414 + Cp4.1LG09g03310.1 Cpe09g00333 333
9 2031714 2037536 + Cp4.1LG09g03320.1 Cpe09g00336 336
9 2039878 2045388 - Cp4.1LG09g03380.1 Cpe09g00338 338
13 4165992 4176390 - Cp4.1LG13g06870.1 Cpe13g00383 383
5 35485629 35489707 + CrPI670011_05g023960.1 Cre05g2396 2396
5 35493599 35498024 - CrPI670011_05g023980.1 Cre05g2398 2398
5 35528256 35529128 + CrPI670011_05g024020.1 Cre05g2402 2402
5 35529727 35533472 - CrPI670011_05g024030.1 Cre05g2403 2403
9 38009934 38020582 - CrPI670011_09g019230.1 Cre09g1923 1923
5 23767629 23778773 - CsaV3_5G028640.1 Csa05g02045 2045
5 27608644 27612989 + CsaV3_5G034820.1 Csa05g02663 2663
5 27616636 27623741 - CsaV3_5G034840.1 Csa05g02665 2665
5 27638337 27644168 + CsaV3_5G034880.1 Csa05g02669 2669
5 27647503 27652142 - CsaV3_5G034900.1 Csa05g02671 2671
1 76545293 76549681 + Hsped.01g11390.1 Hepe01g1139 1139
1 76564186 76566686 + Hsped.01g11420.1 Hepe01g1142 1142
1 76573565 76583273 + Hsped.01g11440.1 Hepe01g1144 1144
1 76588109 76592346 - Hsped.01g11460.1 Hepe01g1146 1146
13 4070341 4074022 + Lag0040349.1 Lac13g0553 553
13 4107379 4109858 - Lag0040352.1 Lac13g0556 556
13 4124926 4129088 - Lag0040355.1 Lac13g0559 559
10 38310411 38325126 - Maker00006904 Lcy10g1452 1452
4 2109047 2113472 + Lsi04G001980.1 Lsi04g00198 198
4 2122885 2128891 - Lsi04G002000.1 Lsi04g00200 200
4 2140776 2152360 + Lsi04G002020.1 Lsi04g00202 202
4 2156719 2161158 - Lsi04G002040.1 Lsi04g00204 204
9 7061939 7072795 + Lsi09G006390.1 Lsi09g00639 639
6 43498566 43502985 + Sed0012611.2 Sed06g1916 1916
6 43506908 43512327 + Sed0026570.1 Sed06g1918 1918
6 43514979 43518089 + Sed0020048.3 Sed06g1921 1921
6 43518806 43522339 - Sed0017516.1 Sed06g1922 1922
4 6591927 6596506 + Tan0008896.1 Tan04g0768 768
4 6626734 6630547 + Tan0021117.1 Tan04g0779 779
4 6647464 6675298 + Tan0005884.1 Tan04g0785 785
4 6676299 6680589 - Tan0012902.2 Tan04g0787 787
1 4084590 4090555 + Vvi1g391 Vvi1g391 391
1 4091417 4094089 - Vvi1g392 Vvi1g392 392
1 4095416 4103225 + Vvi1g393 Vvi1g393 393
1 4104653 4112761 - Vvi1g394 Vvi1g394 394
1 4113894 4115778 + Vvi1g395 Vvi1g395 395
1 4117217 4124629 + Vvi1g396 Vvi1g396 396
1 4133089 4137759 + Vvi1g397 Vvi1g397 397
1 4138481 4147477 - Vvi1g398 Vvi1g398 398
1 4151718 4154782 + Vvi1g399 Vvi1g399 399
1 4154896 4163111 - Vvi1g400 Vvi1g400 400
       

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