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
Vvi5g29 . . . . . Bpe14g01086 . . . . . Cma14g01577 . Car14g01389 Sed02g1125 . Cpe03g01317 Bhi01g01103 Tan10g1091 Cmetu06g2133 . Hepe05g1362 . Lcy11g1325 . . . . . . . . . Cone7ag0090 Cone4ag0096 Lsi05g01408 . . Cme06g00802 Blo02g00469 . . . . . Bma02g00939 . . . Cmo14g01610 . . . . . . . . . . . . . Cla05g00719 Cam05g0788 Cec05g0793 Cco05g0791 Clacu05g0778 Cmu05g0742 Cre05g0818 . Csa03g01532 Chy06g00769 .
Vvi5g30 Blo01g00042 . . Bda08g00321 . . . Bma05g01009 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe05g00807 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g31 . . . . . . . . . Cmo17g00375 . . . . . . . . . . . . . . Cla06g00410 Cam06g0432 Cec06g0439 Cco06g0437 Clacu06g0418 Cmu06g0418 Cre06g1197 . . . . . Csa06g01850 Chy11g01589 . . . . . . . . . Sed09g0618 . . . Cma17g00386 . Car17g00356 Cpe12g00337 . Bhi12g01954 Tan06g2786 Cmetu11g2362 . . . Lcy12g0872 . . . . . . . Lsi09g01510 . . Cme11g02098
Vvi5g32 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone7ag0091 Cone4ag0097 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g33 . . . . . Bpe14g01087 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g34 Blo01g00041 . . Bda08g00322 . . . Bma05g01008 Cmo08g01259 Cmo17g00374 . . . . . . . . . . . . . . Cla06g00411 Cam06g0434 Cec06g0440 Cco06g0439 Clacu06g0420 Cmu06g0420 Cre06g1199 . . . . . Csa06g01853 Chy11g01588 . . . . . Bpe05g00806 . . . Sed04g3077 . . Cma08g01294 Cma17g00385 Car08g01159 Car17g00355 Cpe12g00336 Cpe17g00081 Bhi12g01953 Tan06g2785 Cmetu11g0566 . . . Lcy12g0870 . . . . . . . . . . Cme11g02097
Vvi5g35 . . Bda03g01193 . . . Bma04g01115 . . Cmo17g00373 . . . . . . . . . . . . . . Cla06g00412 . Cec06g0441 Cco06g0440 Clacu06g0422 Cmu06g0421 . . Cone15ag0715 . . . Csa06g01854 Chy11g01587 . . . . . . . . . Sed05g1232 . . . Cma17g00384 . . Cpe12g00335 . Bhi12g01952 Tan06g2784 Cmetu11g0368 . . . Lcy12g0869 . . . . . . . Lsi09g01509 . . Cme11g02096
Vvi5g36 . . . Bda08g00324 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa06g01856 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g37 Blo01g00040 . . Bda08g00323 . Bpe14g01088 . . . Cmo17g00372 Cma06g01574 . Car06g01337 . . Cpe08g00142 . . . . . . . . Cla06g00414 Cam06g0436 Cec06g0442 Cco06g0441 Clacu06g0423 Cmu06g0422 Cre06g1201 . Cone15ag0717 . . . . Chy11g01586 . Blo02g00470 . . Bda13g00227 . . Bma02g00938 . . Cmo06g01568 . . Cma17g00383 . Car17g00354 Cpe12g00334 . Bhi12g01951 . . Lac11g0985 Hepe03g0033 . . . . . . . . . Lsi09g01508 . . Cme11g02095
Vvi5g38 . . Bda03g01192 . Bpe04g01124 . Bma04g01116 . Cmo08g01256 Cmo17g00370 . . . . . . . . . . . . . . . . . . . . . . Cone5ag1607 Cone6ag0907 Cone9ag0913 . Csa06g01858 . . . . . . . . . . Sed09g0580 . . Cma08g01291 Cma17g00381 Car08g01157 Car17g00352 . Cpe17g00079 Bhi12g01944 Tan06g2781 Cmetu04g2722 Lac11g0982 Hepe03g0034 . Lcy12g0867 . . . . . . . . . . Cme11g02093
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 14367409 14369769 + Bda017272.1 Bda03g01192 1192
3 14368319 14372270 - Bda033521 Bda03g01193 1193
8 3336324 3339148 - Bda024760.1 Bda08g00321 321
8 3346604 3350708 + Bda024761.1 Bda08g00322 322
8 3351926 3353035 + Bda024762.1 Bda08g00323 323
8 3353737 3355476 - Bda024763.1 Bda08g00324 324
13 2860372 2862257 - Bda001105.1 Bda13g00227 227
1 21191603 21194563 - XM_039019100.1 Bhi01g01103 1103
12 61958150 61963712 + XM_039019954.1 Bhi12g01944 1944
12 61968136 61969754 - XM_039019539.1 Bhi12g01951 1951
12 61986493 61989299 - XM_039050599.1 Bhi12g01952 1952
12 61990072 62000430 - XM_039050597.1 Bhi12g01953 1953
12 62085352 62090080 - XM_039050518.1 Bhi12g01954 1954
1 542376 543477 - BLOR00040 Blo01g00040 40
1 544245 550612 - BLOR00041 Blo01g00041 41
1 575082 578097 + BLOR00042 Blo01g00042 42
2 6675439 6678397 + BLOR10199 Blo02g00469 469
2 6697912 6700288 + BLOR10200 Blo02g00470 470
2 49252054 49253472 - Bma015730.1 Bma02g00938 938
2 49256999 49259299 - Bma015731.1 Bma02g00939 939
4 26299511 26304460 + Bma031128 Bma04g01115 1115
4 26303110 26305801 - Bma019817.2 Bma04g01116 1116
5 48544645 48549268 - Bma022162.1 Bma05g01008 1008
5 48555968 48558717 + Bma022163.1 Bma05g01009 1009
4 9683836 9686831 + Bpe015804.1 Bpe04g01124 1124
5 21374465 21379087 - Bpe018219.1 Bpe05g00806 806
5 21384628 21387368 + Bpe018220.1 Bpe05g00807 807
14 8131720 8134562 + Bpe014460.2 Bpe14g01086 1086
14 8135299 8136378 + Bpe014461.1 Bpe14g01087 1087
14 8138126 8139549 + Bpe014462.1 Bpe14g01088 1088
5 6894327 6896940 - CaPI482276_05g007880.1 Cam05g0788 788
6 6458355 6463584 + CaPI482276_06g004320.1 Cam06g0432 432
6 6470150 6475703 + CaPI482276_06g004340.1 Cam06g0434 434
6 6489918 6491239 + CaPI482276_06g004360.1 Cam06g0436 436
6 9592791 9594886 - Carg25646-RA Car06g01337 1337
8 7763888 7767478 + Carg18899-RA Car08g01157 1157
8 7773012 7779019 - Carg18901-RA Car08g01159 1159
14 11738617 11742035 + Carg19610-RA Car14g01389 1389
17 2231061 2235701 + Carg05558-RA Car17g00352 352
17 2241737 2246063 - Carg05560-RA Car17g00354 354
17 2246865 2252652 - Carg05562-RA Car17g00355 355
17 2255894 2263161 - Carg05563-RA Car17g00356 356
5 6607423 6610046 - CcPI632755_05g007910.1 Cco05g0791 791
6 4834008 4839234 + CcPI632755_06g004370.1 Cco06g0437 437
6 4846448 4852049 + CcPI632755_06g004390.1 Cco06g0439 439
6 4853076 4855486 + CcPI632755_06g004400.1 Cco06g0440 440
6 4866124 4867472 + CcPI632755_06g004410.1 Cco06g0441 441
5 6627670 6630278 - CePI673135_05g007930.1 Cec05g0793 793
6 4971079 4982711 + CePI673135_06g004390.1 Cec06g0439 439
6 4982763 4988359 + CePI673135_06g004400.1 Cec06g0440 440
6 4989379 4992208 + CePI673135_06g004410.1 Cec06g0441 441
6 5004150 5005497 + CePI673135_06g004420.1 Cec06g0442 442
6 5314954 5317643 - Chy6G112970.1 Chy06g00769 769
11 22422922 22424260 - Chy11G201660.1 Chy11g01586 1586
11 22427144 22429401 - Chy11G201670.1 Chy11g01587 1587
11 22430770 22436291 - Chy11G201680.1 Chy11g01588 1588
11 22440479 22445217 - Chy11G201690.1 Chy11g01589 1589
5 6602335 6604958 - ClG42_05g0077800.10 Clacu05g0778 778
6 4995431 5000286 + ClG42_06g0041800.10 Clacu06g0418 418
6 5007161 5012752 + ClG42_06g0042000.10 Clacu06g0420 420
6 5024877 5025419 - ClG42_06g0042200.10 Clacu06g0422 422
6 5029287 5030635 + ClG42_06g0042300.10 Clacu06g0423 423
5 6748940 6751810 - ClCG05G006700.2 Cla05g00719 719
6 5025156 5030438 + ClCG06G004390.2 Cla06g00410 410
6 5036915 5043087 + ClCG06G004400.2 Cla06g00411 411
6 5043544 5046748 + ClCG06G004410.2 Cla06g00412 412
6 5059028 5060389 + ClCG06G004430.1 Cla06g00414 414
6 9846779 9851433 - CmaCh06G015740.1 Cma06g01574 1574
8 7806087 7807215 + CmaCh08G012910.1 Cma08g01291 1291
8 7852510 7858709 - CmaCh08G012940.1 Cma08g01294 1294
14 11860433 11863291 + CmaCh14G015770.1 Cma14g01577 1577
17 2126994 2131856 + CmaCh17G003810.1 Cma17g00381 381
17 2136578 2138206 - CmaCh17G003830.1 Cma17g00383 383
17 2139260 2141369 - CmaCh17G003840.1 Cma17g00384 384
17 2142683 2149049 - CmaCh17G003850.1 Cma17g00385 385
17 2149090 2159241 - CmaCh17G003860.1 Cma17g00386 386
6 5343046 5346261 - MELO3C006727.2.1 Cme06g00802 802
11 28585808 28591196 + MELO3C035198.2.1 Cme11g02093 2093
11 28594691 28596062 - MELO3C021256.2.1 Cme11g02095 2095
11 28598554 28601702 - MELO3C021255.2.1 Cme11g02096 2096
11 28602320 28609667 - MELO3C021254.2.1 Cme11g02097 2097
11 28612554 28617334 - MELO3C021253.2.1 Cme11g02098 2098
4 8897312 8901379 + PI0020869.1 Cmetu04g2722 2722
6 5554732 5558077 - PI0004867.1 Cmetu06g2133 2133
11 3603179 3604534 + PI0017515.1 Cmetu11g0368 368
11 3589965 3595582 + PI0003334.1 Cmetu11g0566 566
11 3578432 3583833 + PI0023845.1 Cmetu11g2362 2362
6 11042625 11047194 - CmoCh06G015680.1 Cmo06g01568 1568
8 7919942 7923854 + CmoCh08G012560.1 Cmo08g01256 1256
8 7929457 7936059 - CmoCh08G012590.1 Cmo08g01259 1259
14 12789601 12793170 + CmoCh14G016100.1 Cmo14g01610 1610
17 2272598 2277931 + CmoCh17G003700.1 Cmo17g00370 370
17 2283650 2284933 - CmoCh17G003720.1 Cmo17g00372 372
17 2285975 2287684 - CmoCh17G003730.1 Cmo17g00373 373
17 2288710 2294717 - CmoCh17G003740.1 Cmo17g00374 374
17 2294758 2304939 - CmoCh17G003750.1 Cmo17g00375 375
5 6458384 6461008 - CmPI595203_05g007420.1 Cmu05g0742 742
6 4790745 4795600 + CmPI595203_06g004180.1 Cmu06g0418 418
6 4802479 4808016 + CmPI595203_06g004200.1 Cmu06g0420 420
6 4809054 4814952 + CmPI595203_06g004210.1 Cmu06g0421 421
6 4823434 4824782 + CmPI595203_06g004220.1 Cmu06g0422 422
4 464931 467488 + Conep04aG0009800.1 Cone4ag0096 96
4 468130 469227 + Conep04aG0009900.1 Cone4ag0097 97
5 11283806 11289371 - Conep05aG0165600.1 Cone5ag1607 1607
6 4654071 4659347 - Conep06aG0093500.1 Cone6ag0907 907
7 397378 400648 + Conep07aG0009000.1 Cone7ag0090 90
7 400815 403474 + Conep07aG0009100.1 Cone7ag0091 91
9 4485337 4491816 - Conep09aG0093600.1 Cone9ag0913 913
15 3972547 3974175 + Conep15aG0072900.1 Cone15ag0715 715
15 3974709 3975805 + Conep15aG0073100.1 Cone15ag0717 717
3 10715609 10718731 + Cp4.1LG03g11940.1 Cpe03g01317 1317
8 923011 928017 + Cp4.1LG08g05390.1 Cpe08g00142 142
12 2215256 2219519 - Cp4.1LG12g03400.1 Cpe12g00334 334
12 2219845 2222704 - Cp4.1LG12g03410.1 Cpe12g00335 335
12 2223314 2230637 - Cp4.1LG12g03370.1 Cpe12g00336 336
12 2231583 2239318 - Cp4.1LG12g03380.1 Cpe12g00337 337
17 451799 456193 + Cp4.1LG17g00110.1 Cpe17g00079 79
17 462260 469618 - Cp4.1LG17g00050.1 Cpe17g00081 81
5 7252708 7255328 - CrPI670011_05g008180.1 Cre05g0818 818
6 5847900 5852872 + CrPI670011_06g011970.1 Cre06g1197 1197
6 5859963 5865552 + CrPI670011_06g011990.1 Cre06g1199 1199
6 5883782 5885127 + CrPI670011_06g012010.1 Cre06g1201 1201
3 11388914 11392281 - CsaV3_3G015320.1 Csa03g01532 1532
6 16732516 16737029 + CsaV3_6G028400.1 Csa06g01850 1850
6 16743643 16745991 + CsaV3_6G028430.1 Csa06g01853 1853
6 16747366 16749344 + CsaV3_6G028440.1 Csa06g01854 1854
6 16754642 16755724 - CsaV3_6G028460.1 Csa06g01856 1856
6 16759000 16763114 - CsaV3_6G028480.1 Csa06g01858 1858
3 364780 367499 + Hsped.03g00330.1 Hepe03g0033 33
3 372309 377526 + Hsped.03g00340.1 Hepe03g0034 34
5 62238233 62241586 + Hsped.05g13620.1 Hepe05g1362 1362
11 10975176 10979053 + Lag0031620.1 Lac11g0982 982
11 10991487 10992598 - Lag0031623.1 Lac11g0985 985
11 36875581 36878884 + Maker00031832 Lcy11g1325 1325
12 12047317 12051620 + Maker00024718 Lcy12g0867 867
12 12057324 12062298 - Maker00024898 Lcy12g0869 869
12 12062607 12071629 - Maker00024847 Lcy12g0870 870
12 12184747 12189791 + Maker00025115 Lcy12g0872 872
5 22007593 22011136 + Lsi05G014080.1 Lsi05g01408 1408
9 23130753 23132521 - Lsi09G015080.1 Lsi09g01508 1508
9 23137452 23143988 - Lsi09G015090.1 Lsi09g01509 1509
9 23144060 23164604 - Lsi09G015100.1 Lsi09g01510 1510
2 48464116 48467610 + Sed0026404.1 Sed02g1125 1125
4 41790104 41797549 + Sed0005370.1 Sed04g3077 3077
5 20215830 20217459 + Sed0021320.2 Sed05g1232 1232
9 6658274 6668066 - Sed0002970.1 Sed09g0580 580
9 7672613 7679906 - Sed0028172.2 Sed09g0618 618
6 80002001 80006157 + Tan0004396.1 Tan06g2781 2781
6 80024752 80031277 - Tan0009087.1 Tan06g2784 2784
6 80032185 80047388 - Tan0010844.1 Tan06g2785 2785
6 80051411 80056407 - Tan0003227.1 Tan06g2786 2786
10 10298816 10301813 - Tan0018735.1 Tan10g1091 1091
5 339327 343662 + Vvi5g29 Vvi5g29 29
5 343989 346779 - Vvi5g30 Vvi5g30 30
5 365485 371314 + Vvi5g31 Vvi5g31 31
5 372794 377697 + Vvi5g32 Vvi5g32 32
5 378954 380758 + Vvi5g33 Vvi5g33 33
5 388111 396826 + Vvi5g34 Vvi5g34 34
5 397743 400384 + Vvi5g35 Vvi5g35 35
5 401102 404183 - Vvi5g36 Vvi5g36 36
5 422188 430622 + Vvi5g37 Vvi5g37 37
5 431247 437819 - Vvi5g38 Vvi5g38 38
       

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