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
Vvi19g604 . . . . Bpe09g00138 . Bma10g00586 Bma13g01105 Cmo16g00977 . . . . . . . . . . . . . . . Cla10g00437 Cam10g0436 Cec10g0458 Cco10g0447 Clacu10g0444 Cmu10g1275 Cre10g0691 . . Cone14ag1198 Cone15ag1218 . Csa03g00446 . Cme06g02803 Blo07g00875 . Bda05g00688 . . Bpe03g00762 . . . . . . Cma16g00939 . Car16g00903 Cpe14g00763 . Bhi11g00510 . . . . . . . . . . . . . Lsi05g00529 . Chy06g01871 .
Vvi19g605 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g606 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g607 . . Bda07g00394 . . . . . . . . . Car01g00970 Car09g00896 Sed07g2724 Cpe06g00796 Cpe02g00804 Bhi09g01727 Tan01g3153 Cmetu01g0554 . Hepe01g1229 Mch11g1238 . . . . . . . . Cone6ag0031 Cone9ag0031 . . Lsi02g01858 Csa07g00975 . . . . . . Bpe11g00572 . . Bma14g00307 . Cmo01g01142 Cmo09g00987 . . . . . . . . . . . . . Cla09g02047 Cam09g2135 Cec09g2201 . . . . . . Chy01g01082 Cme01g00963
Vvi19g608 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g609 . . . . Bpe09g00137 . Bma10g00587 Bma13g01106 Cmo16g00980 Cmo06g00879 . . . . . . . . . . . . . . Cla10g00435 Cam10g0434 Cec10g0456 Cco10g0445 Clacu10g0442 Cmu10g1273 Cre10g0689 Cone6ag0030 Cone9ag0029 Cone14ag1200 Cone15ag1220 . Csa03g00443 . Cme06g02800 Blo07g00874 . Bda05g00687 Bda12g00948 . Bpe03g00761 . . . . . . Cma16g00941 . Car16g00905 Cpe14g00765 . Bhi11g00503 Tan01g1803 . . . . . . . . . . . . Lsi05g00527 . Chy06g01874 .
Vvi19g610 . Blo03g01468 . . Bpe09g00136 Bpe08g01104 . . Cmo16g00981 . . . . . . . . . . . . . . . Cla10g00434 Cam10g0432 Cec10g0455 Cco10g0444 Clacu10g0440 Cmu10g1271 Cre10g0688 Cone6ag0029 . Cone14ag1205 Cone15ag1222 . Csa03g00442 . Cme06g02799 . Blo10g00860 . Bda12g00949 . . Bma07g01270 . Sed08g2940 . . . Cma16g00942 . Car16g00906 Cpe14g00766 . Bhi11g00501 Tan01g1805 Cmetu06g0464 . . Mch10g1392 . . . . . . . . Lsi05g00526 . Chy06g01875 .
Vvi19g611 Blo03g00526 . Bda07g00395 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe11g00573 . . Bma14g00306 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g612 . . . . Bpe09g00135 . Bma10g00588 Bma13g01107 Cmo16g00982 Cmo06g00719 . . . . . . . . . . . . . . Cla10g00433 Cam10g0431 Cec10g0454 Cco10g0443 Clacu10g0439 Cmu10g1270 Cre10g0687 Cone6ag0027 Cone9ag0026 Cone14ag1206 . . Csa03g00441 . Cme06g02787 Blo07g00873 Blo10g00861 . Bda12g00951 . Bpe03g00760 . . . . . . Cma16g00943 . Car16g00907 Cpe14g00818 . Bhi11g00499 . . . . . . . . . . . . . Lsi05g00524 . Chy06g01876 .
Vvi19g613 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 55176861 55179124 + Bda021822.1 Bda05g00687 687
5 55183225 55199592 + Bda021823.1 Bda05g00688 688
7 4904633 4909639 - Bda025479.1 Bda07g00394 394
7 4911968 4915943 + Bda033840 Bda07g00395 395
12 40545553 40555696 - Bda009494.1 Bda12g00948 948
12 40578890 40580486 - Bda009496.1 Bda12g00949 949
12 40590110 40593752 + Bda009498.2 Bda12g00951 951
9 46933938 46938670 - XM_039041823.1 Bhi09g01727 1727
11 11821890 11827042 - XM_039048144.1 Bhi11g00499 499
11 11865057 11867754 + XM_039049214.1 Bhi11g00501 501
11 11902514 11905738 + XM_039048696.1 Bhi11g00503 503
11 12016018 12022317 + XM_039047422.1 Bhi11g00510 510
3 19961694 19963786 + BLOR11707 Blo03g00526 526
3 41309034 41310028 - BLOR12649 Blo03g01468 1468
7 27396932 27400319 - BLOR18805 Blo07g00873 873
7 27445258 27447316 + BLOR18806 Blo07g00874 874
7 27461134 27466858 + BLOR18807 Blo07g00875 875
10 27149716 27151084 - BLOR02650 Blo10g00860 860
10 27159181 27162853 + BLOR02651 Blo10g00861 861
7 48260017 48261032 + Bma026537.1 Bma07g01270 1270
10 7205863 7211372 - Bma004293.1 Bma10g00586 586
10 7213464 7215084 - Bma004294.2 Bma10g00587 587
10 7220605 7223911 + Bma004295.1 Bma10g00588 588
13 43992531 43994301 - Bma010231.1 Bma13g01105 1105
13 44003268 44004261 - Bma010232.1 Bma13g01106 1106
13 44028849 44032363 + Bma010233.1 Bma13g01107 1107
14 3845070 3847140 - Bma010729.1 Bma14g00306 306
14 3851211 3854144 + Bma010730.1 Bma14g00307 307
3 27637758 27641037 - Bpe012670.1 Bpe03g00760 760
3 27647006 27648967 + Bpe012671.1 Bpe03g00761 761
3 27651940 27667092 + Bpe012672.2 Bpe03g00762 762
8 13097880 13098875 + Bpe023231.1 Bpe08g01104 1104
9 910747 914147 - Bpe026204 Bpe09g00135 135
9 925409 926541 + Bpe023810.2 Bpe09g00136 136
9 931435 933433 + Bpe023811.1 Bpe09g00137 137
9 935337 941232 + Bpe023812.1 Bpe09g00138 138
11 4385920 4390207 - Bpe003938.1 Bpe11g00572 572
11 4391744 4393824 + Bpe003939.1 Bpe11g00573 573
9 35908478 35912806 - CaPI482276_09g021350.1 Cam09g2135 2135
10 6658452 6664096 - CaPI482276_10g004310.1 Cam10g0431 431
10 6692502 6694815 + CaPI482276_10g004320.1 Cam10g0432 432
10 6701670 6703480 + CaPI482276_10g004340.1 Cam10g0434 434
10 6726187 6732100 + CaPI482276_10g004360.1 Cam10g0436 436
1 9250159 9254375 + Carg22392-RA Car01g00970 970
9 5535318 5539514 - Carg12850-RA Car09g00896 896
16 7371523 7377395 - Carg22351-RA Car16g00903 903
16 7396051 7398831 - Carg22349-RA Car16g00905 905
16 7419118 7420111 - Carg22348-RA Car16g00906 906
16 7429862 7434581 + Carg22347-RA Car16g00907 907
10 5212577 5218216 - CcPI632755_10g004430.1 Cco10g0443 443
10 5243342 5245636 + CcPI632755_10g004440.1 Cco10g0444 444
10 5252259 5254171 + CcPI632755_10g004450.1 Cco10g0445 445
10 5277351 5283294 + CcPI632755_10g004470.1 Cco10g0447 447
9 38929833 38934161 - CePI673135_09g022010.1 Cec09g2201 2201
10 5399467 5405145 - CePI673135_10g004540.1 Cec10g0454 454
10 5435455 5437744 + CePI673135_10g004550.1 Cec10g0455 455
10 5443618 5445999 + CePI673135_10g004560.1 Cec10g0456 456
10 5470014 5475887 + CePI673135_10g004580.1 Cec10g0458 458
1 12232454 12233821 - Chy1G010820.1 Chy01g01082 1082
6 22580639 22586538 - Chy6G123990.1 Chy06g01871 1871
6 22602081 22603990 - Chy6G124020.1 Chy06g01874 1874
6 22611055 22612744 - Chy6G124030.1 Chy06g01875 1875
6 22629322 22636030 + Chy6G124040.1 Chy06g01876 1876
10 5455623 5461259 - ClG42_10g0043900.10 Clacu10g0439 439
10 5489405 5491682 + ClG42_10g0044000.10 Clacu10g0440 440
10 5498248 5500171 + ClG42_10g0044200.10 Clacu10g0442 442
10 5522848 5528783 + ClG42_10g0044400.10 Clacu10g0444 444
9 38039951 38044888 - ClCG09G021030.2 Cla09g02047 2047
10 5809593 5815229 - ClCG10G004600.2 Cla10g00433 433
10 5845994 5848618 + ClCG10G004620.1 Cla10g00434 434
10 5854919 5857332 + ClCG10G004630.1 Cla10g00435 435
10 5879448 5886639 + ClCG10G004650.2 Cla10g00437 437
16 7205169 7211246 - CmaCh16G009390.1 Cma16g00939 939
16 7238076 7240891 - CmaCh16G009410.1 Cma16g00941 941
16 7260086 7261353 - CmaCh16G009420.1 Cma16g00942 942
16 7269003 7274618 + CmaCh16G009430.1 Cma16g00943 943
1 11251426 11255772 + MELO3C024898.2.1 Cme01g00963 963
6 35108962 35117914 - MELO3C014134.2.1 Cme06g02787 2787
6 35203988 35206541 + MELO3C014138.2.1 Cme06g02799 2799
6 35213739 35216904 + MELO3C014139.2.1 Cme06g02800 2800
6 35242146 35248937 + MELO3C014142.2.1 Cme06g02803 2803
1 12726197 12730621 - PI0018198.1 Cmetu01g0554 554
6 26896206 26898988 - PI0018186.1 Cmetu06g0464 464
1 9379979 9384195 + CmoCh01G011420.1 Cmo01g01142 1142
6 3663619 3668028 + CmoCh06G007190.1 Cmo06g00719 719
6 5003302 5006507 - CmoCh06G008790.1 Cmo06g00879 879
9 5239100 5245055 - CmoCh09G009870.1 Cmo09g00987 987
16 6646603 6652531 - CmoCh16G009770.1 Cmo16g00977 977
16 6691881 6694651 - CmoCh16G009800.1 Cmo16g00980 980
16 6714689 6715930 - CmoCh16G009810.1 Cmo16g00981 981
16 6726015 6730845 + CmoCh16G009820.1 Cmo16g00982 982
10 5592451 5598087 - CmPI595203_10g012700.1 Cmu10g1270 1270
10 5626310 5628587 + CmPI595203_10g012710.1 Cmu10g1271 1271
10 5635138 5637059 + CmPI595203_10g012730.1 Cmu10g1273 1273
10 5659645 5665592 + CmPI595203_10g012750.1 Cmu10g1275 1275
6 172101 175961 - Conep06aG0002700.1 Cone6ag0027 27
6 182398 184090 + Conep06aG0002900.1 Cone6ag0029 29
6 185853 189524 + Conep06aG0003000.1 Cone6ag0030 30
6 191380 195691 + Conep06aG0003100.1 Cone6ag0031 31
9 128238 132403 - Conep09aG0002600.1 Cone9ag0026 26
9 139349 143098 + Conep09aG0002900.1 Cone9ag0029 29
9 147216 147728 + Conep09aG0003100.1 Cone9ag0031 31
14 9742909 9747876 - Conep14aG0122200.1 Cone14ag1198 1198
14 9754714 9757429 - Conep14aG0122400.1 Cone14ag1200 1200
14 9809900 9810889 - Conep14aG0123700.1 Cone14ag1205 1205
14 9812542 9816434 - Conep14aG0123800.1 Cone14ag1206 1206
15 9685401 9690563 - Conep15aG0124700.1 Cone15ag1218 1218
15 9698256 9701237 - Conep15aG0124900.1 Cone15ag1220 1220
15 9719898 9721412 - Conep15aG0125100.1 Cone15ag1222 1222
2 5147191 5151428 - Cp4.1LG02g00700.1 Cpe02g00804 804
6 5093591 5100393 - Cp4.1LG06g08600.1 Cpe06g00796 796
14 5988947 5994845 - Cp4.1LG14g07690.1 Cpe14g00763 763
14 6011940 6014771 - Cp4.1LG14g07660.1 Cpe14g00765 765
14 6028325 6029605 - Cp4.1LG14g07700.1 Cpe14g00766 766
14 6556851 6560228 + Cp4.1LG14g08130.1 Cpe14g00818 818
10 6515505 6521188 - CrPI670011_10g006870.1 Cre10g0687 687
10 6547289 6549630 + CrPI670011_10g006880.1 Cre10g0688 688
10 6556431 6558241 + CrPI670011_10g006890.1 Cre10g0689 689
10 6580513 6586451 + CrPI670011_10g006910.1 Cre10g0691 691
3 3723776 3732326 - CsaV3_3G004410.1 Csa03g00441 441
3 3747292 3750073 + CsaV3_3G004420.1 Csa03g00442 442
3 3754227 3757829 + CsaV3_3G004430.1 Csa03g00443 443
3 3770282 3776818 + CsaV3_3G004460.1 Csa03g00446 446
7 8602038 8606363 + CsaV3_7G018660.1 Csa07g00975 975
1 77529399 77533818 + Hsped.01g12290.1 Hepe01g1229 1229
2 24348822 24350342 + Lsi02G018580.1 Lsi02g01858 1858
5 6550848 6558649 - Lsi05G005240.1 Lsi05g00524 524
5 6578882 6581387 + Lsi05G005260.1 Lsi05g00526 526
5 6601183 6604350 + Lsi05G005270.1 Lsi05g00527 527
5 6616638 6634792 + Lsi05G005290.1 Lsi05g00529 529
10 12945909 12978517 + MC10g1110 Mch10g1392 1392
11 8768449 8773376 - MC11g1024 Mch11g1238 1238
7 42409825 42414340 - Sed0014342.1 Sed07g2724 2724
8 40156396 40158255 + Sed0019251.1 Sed08g2940 2940
1 19270946 19274349 - Tan0001050.2 Tan01g1803 1803
1 19299309 19301463 - Tan0011874.1 Tan01g1805 1805
1 85081560 85085887 - Tan0018216.1 Tan01g3153 3153
19 7676336 7684445 - Vvi19g604 Vvi19g604 604
19 7685298 7696805 + Vvi19g605 Vvi19g605 605
19 7696807 7699656 - Vvi19g606 Vvi19g606 606
19 7709733 7714248 - Vvi19g607 Vvi19g607 607
19 7716740 7719369 - Vvi19g608 Vvi19g608 608
19 7719372 7721709 - Vvi19g609 Vvi19g609 609
19 7730104 7732118 - Vvi19g610 Vvi19g610 610
19 7739873 7759142 + Vvi19g611 Vvi19g611 611
19 7760185 7767468 + Vvi19g612 Vvi19g612 612
19 7769885 7772078 + Vvi19g613 Vvi19g613 613
       

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