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
Vvi5g49 . . . . . Bpe14g01093 . . . . Cma06g01570 Cma14g01582 Car06g01334 Car14g01392 Sed02g1130 Cpe08g00145 Cpe03g01320 Bhi01g01099 Tan10g1086 Cmetu06g0386 . Hepe05g1369 . Lcy11g1330 . . . . . . . . . Cone7ag0094 Cone4ag0099 Lsi05g01412 . . Cme06g00798 Blo02g00474 . . Bda13g00223 . . Bma02g00934 . . Cmo06g01564 Cmo14g01614 . . . . . . . . . . . . . Cla05g00715 Cam05g0782 Cec05g0788 Cco05g0784 Clacu05g0772 Cmu05g0737 Cre05g0811 . Csa03g01528 Chy06g00765 .
Vvi5g50 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g51 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g52 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g53 . . . . . Bpe14g01095 . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0711 . . . . . . . . . . Bda13g00221 . . Bma02g00932 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g54 . . . . . . . . . . Cma06g01565 Cma14g01586 Car06g01330 Car14g01396 Sed02g1134 Cpe08g00148 Cpe03g01323 Bhi01g01095 Tan10g1082 Cmetu06g1740 . . . Lcy11g1333 . . . . . . . . . . . Lsi05g01417 . . Cme06g00794 . Blo07g00138 Bda11g00497 . . . . Bma06g01462 . Cmo06g01561 Cmo14g01616 . . . . . . . . . . . . . Cla05g00711 Cam05g0777 Cec05g0785 Cco05g0779 Clacu05g0768 Cmu05g0734 Cre05g0808 . Csa03g01523 Chy06g00759 .
Vvi5g55 Blo01g00034 . Bda03g01185 Bda08g00331 Bpe04g01118 . Bma04g01123 Bma05g00995 . Cmo17g00362 . . . . . . . . . . . . . . Cla06g00423 Cam06g0445 Cec06g0452 Cco06g0451 Clacu06g0432 Cmu06g0431 Cre06g1210 Cone14ag0714 Cone15ag0726 . . . Csa06g01866 Chy11g01577 . . . . . Bpe05g00799 . . . Sed04g3089 . . Cma08g01281 Cma17g00372 Car08g01149 Car17g00347 Cpe12g00327 Cpe17g00072 Bhi12g01939 Tan06g2774 Cmetu11g0774 Lac11g0967 Hepe03g0040 . Lcy12g0857 . . . . . . . Lsi09g01500 . . Cme11g02086
Vvi5g56 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g57 . Blo12g00069 Bda03g01184 . Bpe04g01117 . Bma04g01124 . Cmo08g01246 Cmo17g00361 . . . . . . . . . . . . . . Cla06g00425 Cam06g0447 Cec06g0454 Cco06g0453 Clacu06g0434 Cmu06g0435 Cre06g1212 Cone14ag0715 . . . . Csa06g01868 Chy11g01575 . . . . . . . . . Sed04g3092 . . Cma08g01280 Cma17g00371 Car08g01147 Car17g00346 Cpe12g00326 Cpe17g00070 Bhi12g01937 Tan06g2770 Cmetu11g1821 Lac11g0966 Hepe03g0042 . Lcy12g0854 . . . . . . . Lsi09g01495 . . Cme11g02084
Vvi5g58 . . . . . . . . . . . Cma14g01587 . Car14g01397 . . Cpe03g01324 Bhi01g01094 . . . . . Lcy11g1334 . . . . . . . . . . Cone4ag0103 . . . Cme06g00793 . Blo07g00140 . . . Bpe13g00700 . Bma06g01464 . . Cmo14g01617 . . . . . . . . . . . . . Cla05g00710 . . Cco05g0778 Clacu05g0767 Cmu05g0733 Cre05g0807 . Csa03g01522 Chy06g00758 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 14069675 14071451 + Bda017259.1 Bda03g01184 1184
3 14072695 14075373 + Bda017260.2 Bda03g01185 1185
8 3402194 3405089 - Bda033800 Bda08g00331 331
11 5296767 5303444 - Bda005234.1 Bda11g00497 497
13 2813593 2816732 - Bda001099.1 Bda13g00221 221
13 2840474 2843738 + Bda001101.1 Bda13g00223 223
1 20740526 20742208 + XM_039025878.1 Bhi01g01094 1094
1 20751302 20758496 + XM_039050550.1 Bhi01g01095 1095
1 20942329 20953475 + XM_039046225.1 Bhi01g01099 1099
12 61613139 61615707 + XM_039020238.1 Bhi12g01937 1937
12 61680272 61684613 + XM_039019748.1 Bhi12g01939 1939
1 437461 448439 + BLOR00034 Blo01g00034 34
2 6775107 6778440 - BLOR10204 Blo02g00474 474
7 1858289 1872005 - BLOR18070 Blo07g00138 138
7 1889369 1892021 - BLOR18072 Blo07g00140 140
12 4693297 4695397 + BLOR04088 Blo12g00069 69
2 49097852 49099983 - Bma015722.1 Bma02g00932 932
2 49192328 49195329 + Bma015724.1 Bma02g00934 934
4 27103114 27104908 - Bma019828.1 Bma04g01123 1123
4 27107290 27109939 - Bma031129 Bma04g01124 1124
5 48448068 48450962 + Bma022148.2 Bma05g00995 995
6 51289671 51296662 - Bma024576.1 Bma06g01462 1462
6 51303810 51305235 - Bma024578.1 Bma06g01464 1464
4 9197984 9199771 + Bpe015795.2 Bpe04g01117 1117
4 9201094 9203746 + Bpe015796.1 Bpe04g01118 1118
5 21338717 21341568 + Bpe018212.1 Bpe05g00799 799
13 13609083 13610495 + Bpe010401.1 Bpe13g00700 700
14 8157451 8160469 - Bpe014467.1 Bpe14g01093 1093
14 8176687 8179886 + Bpe014469.1 Bpe14g01095 1095
5 6765620 6776741 + CaPI482276_05g007770.1 Cam05g0777 777
5 6822561 6828655 + CaPI482276_05g007820.1 Cam05g0782 782
6 6588004 6591457 - CaPI482276_06g004450.1 Cam06g0445 445
6 6620918 6623070 - CaPI482276_06g004470.1 Cam06g0447 447
6 9498805 9506085 + Carg23732-RA Car06g01330 1330
6 9566094 9571144 + Carg25643-RA Car06g01334 1334
8 7724388 7725626 + Carg18889-RA Car08g01147 1147
8 7731068 7733875 + Carg18891-RA Car08g01149 1149
14 11760068 11764665 - Carg19613-RA Car14g01392 1392
14 11785716 11792931 - Carg19617-RA Car14g01396 1396
14 11794261 11796408 - Carg19618-RA Car14g01397 1397
17 2166046 2168149 + Carg05552-RA Car17g00346 346
17 2171435 2176398 + Carg05553-RA Car17g00347 347
5 6481821 6482741 + CcPI632755_05g007780.1 Cco05g0778 778
5 6485621 6492311 + CcPI632755_05g007790.1 Cco05g0779 779
5 6537198 6543531 + CcPI632755_05g007840.1 Cco05g0784 784
6 4974892 4979172 - CcPI632755_06g004510.1 Cco06g0451 451
6 5006541 5008698 - CcPI632755_06g004530.1 Cco06g0453 453
5 6499112 6509907 + CePI673135_05g007850.1 Cec05g0785 785
5 6554381 6560475 + CePI673135_05g007880.1 Cec05g0788 788
6 5109794 5113259 - CePI673135_06g004520.1 Cec06g0452 452
6 5139440 5141559 - CePI673135_06g004540.1 Cec06g0454 454
6 5226589 5228124 + Chy6G112860.1 Chy06g00758 758
6 5229343 5236607 + Chy6G112870.1 Chy06g00759 759
6 5274970 5283767 + Chy6G112930.1 Chy06g00765 765
11 22299323 22301793 + Chy11G201550.1 Chy11g01575 1575
11 22324863 22328080 + Chy11G201570.1 Chy11g01577 1577
5 6477907 6479440 + ClG42_05g0076700.10 Clacu05g0767 767
5 6482293 6489137 + ClG42_05g0076800.10 Clacu05g0768 768
5 6533217 6539273 + ClG42_05g0077200.10 Clacu05g0772 772
6 5126609 5130060 - ClG42_06g0043200.10 Clacu06g0432 432
6 5156942 5158065 - ClG42_06g0043400.10 Clacu06g0434 434
5 6617465 6619336 + ClCG05G006600.2 Cla05g00710 710
5 6622189 6629033 + ClCG05G006610.2 Cla05g00711 711
5 6673000 6679430 + ClCG05G006650.1 Cla05g00715 715
6 5159093 5163468 - ClCG06G004530.2 Cla06g00423 423
6 5190980 5192733 - ClCG06G004550.1 Cla06g00425 425
6 9802241 9809457 + CmaCh06G015650.1 Cma06g01565 1565
6 9823081 9827983 + CmaCh06G015700.1 Cma06g01570 1570
8 7763821 7765984 + CmaCh08G012800.1 Cma08g01280 1280
8 7769430 7772883 + CmaCh08G012810.1 Cma08g01281 1281
14 11883541 11888036 - CmaCh14G015820.1 Cma14g01582 1582
14 11908869 11917497 - CmaCh14G015860.1 Cma14g01586 1586
14 11918416 11919202 - CmaCh14G015870.1 Cma14g01587 1587
17 2070159 2073082 + CmaCh17G003710.1 Cma17g00371 371
17 2077279 2081605 + CmaCh17G003720.1 Cma17g00372 372
6 5253143 5254781 + MELO3C006719.2.1 Cme06g00793 793
6 5255899 5263804 + MELO3C006720.2.1 Cme06g00794 794
6 5302520 5308969 + MELO3C006723.2.1 Cme06g00798 798
11 28497449 28500728 + MELO3C021265.2.1 Cme11g02084 2084
11 28515753 28519850 + MELO3C021263.2.1 Cme11g02086 2086
6 5511264 5518244 + PI0018083.1 Cmetu06g0386 386
6 5469482 5476477 + PI0012623.1 Cmetu06g1740 1740
11 3689144 3693308 - PI0028725.1 Cmetu11g0774 774
11 3712451 3715562 - PI0028848.1 Cmetu11g1821 1821
6 11002632 11004264 + CmoCh06G015610.1 Cmo06g01561 1561
6 11018587 11023396 + CmoCh06G015640.1 Cmo06g01564 1564
8 7880787 7883180 + CmoCh08G012460.1 Cmo08g01246 1246
14 12813775 12818419 - CmoCh14G016140.1 Cmo14g01614 1614
14 12840467 12848855 - CmoCh14G016160.1 Cmo14g01616 1616
14 12851007 12853603 - CmoCh14G016170.1 Cmo14g01617 1617
17 2214492 2216966 + CmoCh17G003610.1 Cmo17g00361 361
17 2221405 2226063 + CmoCh17G003620.1 Cmo17g00362 362
5 6333836 6335369 + CmPI595203_05g007330.1 Cmu05g0733 733
5 6338231 6345076 + CmPI595203_05g007340.1 Cmu05g0734 734
5 6389206 6395262 + CmPI595203_05g007370.1 Cmu05g0737 737
6 4920685 4924134 - CmPI595203_06g004310.1 Cmu06g0431 431
6 4960033 4961156 - CmPI595203_06g004350.1 Cmu06g0435 435
4 479318 481483 - Conep04aG0010100.1 Cone4ag0099 99
4 492888 494376 - Conep04aG0010700.1 Cone4ag0103 103
7 413970 416698 - Conep07aG0009400.1 Cone7ag0094 94
14 3881608 3884423 + Conep14aG0072700.1 Cone14ag0711 711
14 3900353 3903953 - Conep14aG0073000.1 Cone14ag0714 714
14 3909825 3913429 - Conep14aG0073100.1 Cone14ag0715 715
15 4129871 4133803 - Conep15aG0074100.1 Cone15ag0726 726
3 10737515 10742770 - Cp4.1LG03g11860.1 Cpe03g01320 1320
3 10764177 10772017 - Cp4.1LG03g11880.1 Cpe03g01323 1323
3 10772938 10775095 - Cp4.1LG03g11910.1 Cpe03g01324 1324
8 945945 952320 - Cp4.1LG08g05300.1 Cpe08g00145 145
8 967576 974832 - Cp4.1LG08g05290.1 Cpe08g00148 148
12 2150194 2153529 + Cp4.1LG12g03160.1 Cpe12g00326 326
12 2155518 2157685 + Cp4.1LG12g03230.1 Cpe12g00327 327
17 412642 413775 + Cp4.1LG17g00230.1 Cpe17g00070 70
17 417449 420802 + Cp4.1LG17g00240.1 Cpe17g00072 72
5 7123343 7124873 + CrPI670011_05g008070.1 Cre05g0807 807
5 7127722 7134563 + CrPI670011_05g008080.1 Cre05g0808 808
5 7180039 7186128 + CrPI670011_05g008110.1 Cre05g0811 811
6 5983263 5986724 - CrPI670011_06g012100.1 Cre06g1210 1210
6 6014174 6016367 - CrPI670011_06g012120.1 Cre06g1212 1212
3 11300106 11302305 + CsaV3_3G015220.1 Csa03g01522 1522
3 11303211 11310993 + CsaV3_3G015230.1 Csa03g01523 1523
3 11346374 11353496 + CsaV3_3G015280.1 Csa03g01528 1528
6 16831535 16835977 - CsaV3_6G028560.1 Csa06g01866 1866
6 16857636 16860664 - CsaV3_6G028580.1 Csa06g01868 1868
3 478916 482940 - Hsped.03g00400.1 Hepe03g0040 40
3 501621 504514 - Hsped.03g00420.1 Hepe03g0042 42
5 62339899 62345160 - Hsped.05g13690.1 Hepe05g1369 1369
11 10650627 10651786 - Lag0031604.1 Lac11g0966 966
11 10660091 10663929 + Lag0031605.1 Lac11g0967 967
11 36936938 36942565 - Maker00031979 Lcy11g1330 1330
11 36994772 37003412 - Maker00032014 Lcy11g1333 1333
11 37008414 37010224 - Maker00032020 Lcy11g1334 1334
12 11806709 11808148 + Maker00024845 Lcy12g0854 854
12 11843620 11849152 + Maker00024962 Lcy12g0857 857
5 22079149 22087335 - Lsi05G014120.1 Lsi05g01412 1412
5 22127433 22139041 - Lsi05G014170.1 Lsi05g01417 1417
9 22993337 22994697 + Lsi09G014950.1 Lsi09g01495 1495
9 23028473 23033646 + Lsi09G015000.1 Lsi09g01500 1500
2 48506697 48511339 - Sed0024233.1 Sed02g1130 1130
2 48549599 48557740 - Sed0007022.2 Sed02g1134 1134
4 41882846 41887093 - Sed0000513.1 Sed04g3089 3089
4 41905597 41909080 - Sed0013117.2 Sed04g3092 3092
6 79897245 79900246 + Tan0021101.2 Tan06g2770 2770
6 79920422 79924436 + Tan0018371.2 Tan06g2774 2774
10 10104961 10114545 + Tan0002031.2 Tan10g1082 1082
10 10177598 10189558 + Tan0000823.1 Tan10g1086 1086
5 538907 542600 - Vvi5g49 Vvi5g49 49
5 542605 545201 - Vvi5g50 Vvi5g50 50
5 556698 558344 - Vvi5g51 Vvi5g51 51
5 572859 573024 + Vvi5g52 Vvi5g52 52
5 602814 610049 + Vvi5g53 Vvi5g53 53
5 615165 645269 - Vvi5g54 Vvi5g54 54
5 648108 653215 - Vvi5g55 Vvi5g55 55
5 658341 667959 + Vvi5g56 Vvi5g56 56
5 668028 671203 - Vvi5g57 Vvi5g57 57
5 672866 674782 - Vvi5g58 Vvi5g58 58
       

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