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
Vvi3g466 Blo02g00817 . . . . . . . . . Cma02g00439 . Car02g00297 . . . . . . . . . . . . . . . . . . . . . . Lsi10g00311 . Chy11g00438 . . . . . . . . . . Cmo02g00444 . . . . . . Cpe05g01223 Bhi10g02076 . . . . . . Cla09g01713 . . . . . . . Csa02g01200 . Cme11g00509
Vvi3g467 . . . . . Bpe12g00064 . . . . Cma02g00438 . Car02g00296 . . . . . . . . . . . . . . . . . . Cone12ag1111 Cone8ag1153 . . Lsi10g00312 . Chy11g00436 . . Blo13g00567 Bda15g00027 . . . . . Sed01g0334 Cmo02g00443 . . . . . . Cpe05g01224 Bhi10g02075 Tan05g1392 Cmetu11g0139 . . . . Cla09g01715 Cam09g1809 Cec09g1871 Cco09g1964 . . Cre01g0696 . Csa02g01201 . Cme11g00508
Vvi3g468 . Blo15g00726 Bda06g01033 Bda08g00828 Bpe07g00396 Bpe12g00065 . Bma12g00476 Cmo19g00641 Cmo11g01344 . Cma20g00887 . Car20g00764 Sed10g2052 Cpe04g00264 Cpe15g00505 Bhi05g01152 Tan02g0881 Cmetu01g1216 . Hepe02g0566 . . Cla02g00577 Cam02g0608 Cec02g0608 Cco02g0623 Clacu02g0604 Cmu02g0602 Cre02g0932 Cone12ag1112 Cone8ag1154 Cone3ag1117 Cone10ag1128 Lsi10g00313 Csa07g00784 Chy11g00433 Cme01g00026 . Blo13g00566 . Bda14g00523 . . Bma03g00524 . Sed01g0333 . Cmo20g00894 Cma11g01767 Cma19g00623 Car11g01081 Car19g00475 . . Bhi10g02074 Tan05g1390 Cmetu11g1909 . Hepe08g1062 . . Cla09g01716 Cam09g1810 Cec09g1872 Cco09g1965 . . Cre01g0695 Lsi11g01029 Csa02g01203 Chy01g00032 Cme11g00507
Vvi3g469 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo02g00615 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g470 . . . . . . . . . Cmo11g01342 Cma02g00437 . Car02g00291 . . Cpe04g00263 . Bhi05g01154 . . . . . . Cla02g00576 . . . . . . Cone12ag1115 Cone8ag1156 Cone3ag0926 . Lsi10g00574 Csa07g00785 Chy11g00432 Cme01g00025 Blo04g00493 . . Bda14g00524 Bpe15g00890 . Bma03g00525 . . Cmo02g00439 . Cma11g01769 . Car11g01080 . . Cpe05g01226 Bhi10g02071 . . . . . . . . . . . . . Lsi11g01030 Csa02g01204 Chy01g00031 Cme11g00299
Vvi3g471 . . . . . . . . . Cmo11g01339 . . . . Sed05g2583 Cpe04g00261 Cpe15g00507 Bhi05g01156 Tan02g0877 Cmetu01g1190 . Hepe02g0563 . . Cla02g00574 Cam02g0605 Cec02g0605 Cco02g0620 Clacu02g0601 Cmu02g0599 Cre02g0929 Cone12ag1116 Cone8ag1157 . . . Csa07g00787 . Cme01g00023 . . . Bda14g00525 Bpe15g00888 . Bma03g00527 . . . . Cma11g01771 . Car11g01078 . . . . . . . . . . . . . . . . . Lsi11g01032 . Chy01g00029 .
Vvi3g472 . . . . . . . . . . Cma02g00436 . Car02g00290 . . . . . . . . . . . . . . . . . . . . Cone3ag1119 . Lsi10g00316 . Chy11g00431 . . . . . . . . . . Cmo02g00438 . . . . . . Cpe05g01227 Bhi10g02069 . . . Hepe08g1060 . . Cla09g01722 Cam09g1816 Cec09g1878 Cco09g1970 . . Cre01g0689 . Csa02g01205 . Cme11g00503
Vvi3g473 . . . . . . . . . . Cma02g00434 . Car02g00289 . . . . . . . . . . . . . . . . . . Cone12ag1117 . . . Lsi10g00317 . Chy11g00430 . Blo04g00495 . . Bda14g00526 Bpe15g00887 . Bma03g00528 . . Cmo02g00437 . . . . . . Cpe05g01228 Bhi10g02067 . . . . . . Cla09g01723 Cam09g1818 Cec09g1879 Cco09g1971 . . Cre01g0688 . Csa02g01206 . Cme11g00502
Vvi3g474 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi11g01034 . . .
Vvi3g475 . . . . . . . . . . . . . . Sed08g2645 . . Bhi05g01157 Tan02g0874 Cmetu01g0432 . . . . . . . . . . . . Cone8ag1158 . . . Csa07g00789 . . . . . . . . . . . . . Cma11g01774 . . . . . . . . . . . . Cla09g01724 Cam09g1820 Cec09g1880 Cco09g1973 . . . . Csa02g01207 . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 36237930 36239802 + Bda022777.1 Bda06g01033 1033
8 12666453 12668185 - Bda029379.1 Bda08g00828 828
14 3784651 3786597 - Bda027269.1 Bda14g00523 523
14 3788176 3791384 + Bda027270.1 Bda14g00524 524
14 3797621 3799226 - Bda027271.1 Bda14g00525 525
14 3800337 3813102 - Bda027272.2 Bda14g00526 526
15 1680512 1682886 + Bda011781.1 Bda15g00027 27
5 41127863 41130299 - XM_039031522.1 Bhi05g01152 1152
5 41147500 41151157 + XM_039031710.1 Bhi05g01154 1154
5 41158621 41163013 - XM_039033136.1 Bhi05g01156 1156
5 41477507 41483077 - XM_039031525.1 Bhi05g01157 1157
10 51783481 51799562 + XM_039045931.1 Bhi10g02067 2067
10 51839914 51845869 - XM_039045621.1 Bhi10g02069 2069
10 51889325 51895428 - XM_039044701.1 Bhi10g02071 2071
10 52035161 52037845 + XM_039046963.1 Bhi10g02074 2074
10 52068617 52072666 + XM_039044624.1 Bhi10g02075 2075
10 52100735 52103144 + XM_039046169.1 Bhi10g02076 2076
2 28947337 28953763 + BLOR10547 Blo02g00817 817
4 4091514 4094848 + BLOR13405 Blo04g00493 493
4 4104420 4120937 - BLOR13407 Blo04g00495 495
13 27747155 27748990 + BLOR19618 Blo13g00566 566
13 27778070 27780536 + BLOR19619 Blo13g00567 567
15 24071720 24081215 + BLOR07120 Blo15g00726 726
3 4078534 4080493 - Bma016807.1 Bma03g00524 524
3 4082641 4088147 + Bma016808.1 Bma03g00525 525
3 4094288 4095822 - Bma016810.1 Bma03g00527 527
3 4096590 4100688 - Bma016811.1 Bma03g00528 528
12 13473861 13475715 - Bma007508.1 Bma12g00476 476
7 3703964 3705830 - Bpe021215.1 Bpe07g00396 396
12 463534 465871 - Bpe005302.1 Bpe12g00064 64
12 467316 468621 - Bpe005303.1 Bpe12g00065 65
15 18794309 18806937 + Bpe001808.1 Bpe15g00887 887
15 18808070 18809584 + Bpe001809.1 Bpe15g00888 888
15 18815845 18819148 - Bpe024589 Bpe15g00890 890
2 6903749 6907487 + CaPI482276_02g006050.1 Cam02g0605 605
2 6939856 6941729 + CaPI482276_02g006080.1 Cam02g0608 608
9 32460498 32463493 - CaPI482276_09g018090.1 Cam09g1809 1809
9 32497833 32499893 - CaPI482276_09g018100.1 Cam09g1810 1810
9 32609193 32614421 + CaPI482276_09g018160.1 Cam09g1816 1816
9 32623720 32641169 - CaPI482276_09g018180.1 Cam09g1818 1818
9 32660230 32663288 - CaPI482276_09g018200.1 Cam09g1820 1820
2 1948134 1963310 + Carg22974-RA Car02g00289 289
2 1963599 1973628 - Carg22975-RA Car02g00290 290
2 1975970 1978779 - Carg22976-RA Car02g00291 291
2 1991228 1994798 + Carg22981-RA Car02g00296 296
2 1998684 2000740 + Carg22982-RA Car02g00297 297
11 8402115 8405764 + Carg27868-RA Car11g01078 1078
11 8411765 8415006 - Carg27866-RA Car11g01080 1080
11 8420723 8422801 + Carg27865-RA Car11g01081 1081
19 6399948 6402676 - Carg22049-RA Car19g00475 475
20 4504460 4506560 + Carg23619-RA Car20g00764 764
2 6082531 6086438 + CcPI632755_02g006200.1 Cco02g0620 620
2 6118225 6120093 + CcPI632755_02g006230.1 Cco02g0623 623
9 33675351 33678347 - CcPI632755_09g019640.1 Cco09g1964 1964
9 33708172 33710226 - CcPI632755_09g019650.1 Cco09g1965 1965
9 33839363 33844603 + CcPI632755_09g019700.1 Cco09g1970 1970
9 33854281 33870821 - CcPI632755_09g019710.1 Cco09g1971 1971
9 33894496 33897601 - CcPI632755_09g019730.1 Cco09g1973 1973
2 5962619 5966370 + CePI673135_02g006050.1 Cec02g0605 605
2 6002401 6004272 + CePI673135_02g006080.1 Cec02g0608 608
9 35353570 35356570 - CePI673135_09g018710.1 Cec09g1871 1871
9 35402635 35404692 - CePI673135_09g018720.1 Cec09g1872 1872
9 35540213 35545462 + CePI673135_09g018780.1 Cec09g1878 1878
9 35551200 35571912 - CePI673135_09g018790.1 Cec09g1879 1879
9 35585292 35588352 - CePI673135_09g018800.1 Cec09g1880 1880
1 202709 205840 + Chy1G000290.1 Chy01g00029 29
1 213279 215989 - Chy1G000310.1 Chy01g00031 31
1 223102 224194 + Chy1G000320.1 Chy01g00032 32
11 4151148 4166969 + Chy11G190100.1 Chy11g00430 430
11 4167798 4171378 - Chy11G190110.1 Chy11g00431 431
11 4178486 4184187 - Chy11G190120.1 Chy11g00432 432
11 4223862 4225862 + Chy11G190130.1 Chy11g00433 433
11 4255695 4258410 + Chy11G190160.1 Chy11g00436 436
11 4275532 4277785 + Chy11G190180.1 Chy11g00438 438
2 5892742 5896496 + ClG42_02g0060100.10 Clacu02g0601 601
2 5928528 5930401 + ClG42_02g0060400.10 Clacu02g0604 604
2 6168830 6173691 + ClCG02G005650.2 Cla02g00574 574
2 6183228 6186198 - ClCG02G005670.1 Cla02g00576 576
2 6205058 6207337 + ClCG02G005680.1 Cla02g00577 577
9 34292212 34294645 - ClCG09G017510.1 Cla09g01713 1713
9 34310612 34314665 - ClCG09G017530.2 Cla09g01715 1715
9 34370889 34373545 - ClCG09G017540.2 Cla09g01716 1716
9 34490303 34496002 + ClCG09G017590.1 Cla09g01722 1722
9 34504977 34519830 - ClCG09G017600.2 Cla09g01723 1723
9 34552886 34555879 - ClCG09G017610.1 Cla09g01724 1724
2 2193889 2209501 + CmaCh02G004340.1 Cma02g00434 434
2 2209178 2220804 - CmaCh02G004360.1 Cma02g00436 436
2 2223355 2226147 - CmaCh02G004370.1 Cma02g00437 437
2 2230180 2233648 + CmaCh02G004380.1 Cma02g00438 438
2 2235723 2237328 + CmaCh02G004390.1 Cma02g00439 439
11 11829593 11831986 - CmaCh11G017670.1 Cma11g01767 1767
11 11836336 11839752 + CmaCh11G017690.1 Cma11g01769 1769
11 11845780 11849181 - CmaCh11G017710.1 Cma11g01771 1771
11 11857451 11859430 - CmaCh11G017740.1 Cma11g01774 1774
19 6734560 6737275 - CmaCh19G006230.1 Cma19g00623 623
20 4264375 4268262 + CmaCh20G008870.1 Cma20g00887 887
1 195932 199350 + MELO3C018427.2.1 Cme01g00023 23
1 207086 210610 - MELO3C018429.2.1 Cme01g00025 25
1 218283 220638 + MELO3C018430.2.1 Cme01g00026 26
11 3211241 3216943 - MELO3C020888.2.1 Cme11g00299 299
11 5029012 5045508 + MELO3C021920.2.1 Cme11g00502 502
11 5052183 5057918 - MELO3C021919.2.1 Cme11g00503 503
11 5113944 5116521 + MELO3C021917.2.1 Cme11g00507 507
11 5170489 5174271 + MELO3C021915.2.1 Cme11g00508 508
11 5199458 5201943 + MELO3C021914.2.1 Cme11g00509 509
1 218700 219998 + PI0011621.1 Cmetu01g0432 432
1 235889 239369 + PI0002820.1 Cmetu01g1190 1190
1 257954 260351 + PI0011299.1 Cmetu01g1216 1216
11 26798732 26801731 - PI0006880.1 Cmetu11g0139 139
11 26810430 26813067 - PI0017269.1 Cmetu11g1909 1909
2 2274966 2290591 + CmoCh02G004370.1 Cmo02g00437 437
2 2290319 2301812 - CmoCh02G004380.1 Cmo02g00438 438
2 2304010 2306690 - CmoCh02G004390.1 Cmo02g00439 439
2 2324879 2328449 + CmoCh02G004430.1 Cmo02g00443 443
2 2332209 2334956 + CmoCh02G004440.1 Cmo02g00444 444
2 3814547 3821137 - CmoCh02G006150.1 Cmo02g00615 615
11 9278030 9281558 + CmoCh11G013390.1 Cmo11g01339 1339
11 9288635 9291768 - CmoCh11G013420.1 Cmo11g01342 1342
11 9297895 9300322 + CmoCh11G013440.1 Cmo11g01344 1344
19 6941472 6944114 - CmoCh19G006410.1 Cmo19g00641 641
20 4537018 4539456 + CmoCh20G008940.1 Cmo20g00894 894
2 5799437 5803191 + CmPI595203_02g005990.1 Cmu02g0599 599
2 5835219 5837092 + CmPI595203_02g006020.1 Cmu02g0602 602
3 4748049 4751375 + Conep03aG0095700.1 Cone3ag0926 926
3 29755232 29758029 - Conep03aG0162100.1 Cone3ag1117 1117
3 29775879 29780056 - Conep03aG0162300.1 Cone3ag1119 1119
8 10043296 10046000 - Conep08aG0118500.1 Cone8ag1153 1153
8 10046877 10049356 - Conep08aG0118600.1 Cone8ag1154 1154
8 10056188 10059383 + Conep08aG0118800.1 Cone8ag1156 1156
8 10059534 10061159 - Conep08aG0118900.1 Cone8ag1157 1157
8 10062526 10063982 - Conep08aG0119000.1 Cone8ag1158 1158
10 8117462 8120306 - Conep10aG0116000.1 Cone10ag1128 1128
12 8997215 9000102 - Conep12aG0114700.1 Cone12ag1111 1111
12 9000945 9003466 - Conep12aG0114800.1 Cone12ag1112 1112
12 9013490 9016541 + Conep12aG0115100.1 Cone12ag1115 1115
12 9016675 9018228 - Conep12aG0115200.1 Cone12ag1116 1116
12 9018356 9030736 - Conep12aG0115300.1 Cone12ag1117 1117
4 3251932 3255524 + Cp4.1LG04g08240.1 Cpe04g00261 261
4 3260186 3264986 - Cp4.1LG04g08220.1 Cpe04g00263 263
4 3270980 3273081 + Cp4.1LG04g08210.1 Cpe04g00264 264
5 8570302 8571736 - Cp4.1LG05g12350.1 Cpe05g01223 1223
5 8576019 8579845 - Cp4.1LG05g12300.1 Cpe05g01224 1224
5 8588148 8593542 + Cp4.1LG05g12260.1 Cpe05g01226 1226
5 8595371 8602972 + Cp4.1LG05g12240.1 Cpe05g01227 1227
5 8603147 8618354 - Cp4.1LG05g12290.1 Cpe05g01228 1228
15 5996107 5998797 - Cp4.1LG15g05060.1 Cpe15g00505 505
15 6005483 6009398 - Cp4.1LG15g05130.1 Cpe15g00507 507
1 6417218 6437021 + CrPI670011_01g006880.1 Cre01g0688 688
1 6447059 6452280 - CrPI670011_01g006890.1 Cre01g0689 689
1 6577108 6579169 + CrPI670011_01g006950.1 Cre01g0695 695
1 6612576 6615571 + CrPI670011_01g006960.1 Cre01g0696 696
2 6408492 6412559 + CrPI670011_02g009290.1 Cre02g0929 929
2 6446852 6448724 + CrPI670011_02g009320.1 Cre02g0932 932
2 11798159 11800967 - CsaV3_2G014160.1 Csa02g01200 1200
2 11807087 11810939 - CsaV3_2G014170.1 Csa02g01201 1201
2 11824530 11827874 - CsaV3_2G014190.1 Csa02g01203 1203
2 11843438 11848872 + CsaV3_2G014200.1 Csa02g01204 1204
2 11854532 11859194 + CsaV3_2G014210.1 Csa02g01205 1205
2 11858997 11876436 - CsaV3_2G014220.1 Csa02g01206 1206
2 11888042 11891642 - CsaV3_2G014230.1 Csa02g01207 1207
7 5506453 5508833 - CsaV3_7G008830.1 Csa07g00784 784
7 5514315 5517582 + CsaV3_7G008840.1 Csa07g00785 785
7 5524623 5528527 - CsaV3_7G008860.1 Csa07g00787 787
7 5540440 5541682 - CsaV3_7G008880.1 Csa07g00789 789
2 5681652 5685794 + Hsped.02g05630.1 Hepe02g0563 563
2 5716118 5718096 + Hsped.02g05660.1 Hepe02g0566 566
8 10237097 10242623 - Hsped.08g10600.1 Hepe08g1060 1060
8 10285505 10287934 + Hsped.08g10620.1 Hepe08g1062 1062
10 4965744 4969326 - Lsi10G003110.1 Lsi10g00311 311
10 4994984 4998580 - Lsi10G003120.1 Lsi10g00312 312
10 5014715 5017131 - Lsi10G003130.1 Lsi10g00313 313
10 5082412 5087512 + Lsi10G003160.1 Lsi10g00316 316
10 5090291 5105489 - Lsi10G003170.1 Lsi10g00317 317
10 8367092 8373829 - Lsi10G005740.1 Lsi10g00574 574
11 17644304 17646608 - Lsi11G010290.1 Lsi11g01029 1029
11 17668923 17672337 + Lsi11G010300.1 Lsi11g01030 1030
11 17679695 17683304 - Lsi11G010320.1 Lsi11g01032 1032
11 17829396 17831517 - Lsi11G010340.1 Lsi11g01034 1034
1 2507008 2509873 + Sed0021785.1 Sed01g0333 333
1 2516289 2519064 + Sed0023862.1 Sed01g0334 334
5 37577156 37580989 + Sed0021769.2 Sed05g2583 2583
8 38624443 38626573 - Sed0010117.1 Sed08g2645 2645
10 37036147 37038384 - Sed0002499.2 Sed10g2052 2052
2 9815797 9821341 + Tan0012600.1 Tan02g0874 874
2 9881202 9884498 + Tan0011083.2 Tan02g0877 877
2 9930127 9932592 + Tan0008722.2 Tan02g0881 881
5 19644335 19647448 + Tan0002673.1 Tan05g1390 1390
5 19700127 19702303 + Tan0015267.2 Tan05g1392 1392
3 4477402 4479789 - Vvi3g466 Vvi3g466 466
3 4481839 4484778 - Vvi3g467 Vvi3g467 467
3 4488819 4491489 - Vvi3g468 Vvi3g468 468
3 4502405 4513315 - Vvi3g469 Vvi3g469 469
3 4513959 4520767 + Vvi3g470 Vvi3g470 470
3 4586629 4589079 - Vvi3g471 Vvi3g471 471
3 4593423 4601048 - Vvi3g472 Vvi3g472 472
3 4601054 4617416 - Vvi3g473 Vvi3g473 473
3 4623402 4627530 - Vvi3g474 Vvi3g474 474
3 4640644 4641895 - Vvi3g475 Vvi3g475 475
       

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