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
Vvi19g394 . . . Bda09g00380 . Bpe08g01145 . . . . Cma01g01162 Cma09g00914 . Car09g00831 Sed14g0466 Cpe06g00736 Cpe02g00740 Bhi09g01960 Tan01g4493 Cmetu08g1286 . Hepe01g1323 Mch11g1137 . . . . . . . . . . . Cone15ag1130 Lsi04g01255 . Chy04g01029 . . . . . . . Bma07g01319 Bma14g00366 . Cmo01g01216 Cmo09g00908 . . . Car16g00574 . . . . . . . . . Cla05g01553 Cam05g1661 Cec05g1666 Cco05g1706 Clacu05g1655 Cmu05g1549 Cre05g1661 . . . Cme04g00784
Vvi19g395 . . . . . . Bma10g00528 . . Cmo04g00995 Cma01g01160 Cma09g00915 . Car09g00832 Sed06g1290 Cpe06g00737 Cpe02g00741 Bhi09g01959 Tan01g4494 Cmetu04g2937 . Hepe01g1322 Mch11g1139 . . . . . . . . . . Cone14ag1116 Cone15ag1131 Lsi04g01254 . Chy04g01028 . Blo07g00925 . . . . Bpe03g00809 . . . Cmo01g01215 Cmo09g00909 . . Car04g00867 Car16g00573 . Cpe01g00838 . . . . . . . Cla05g01552 Cam05g1660 Cec05g1665 Cco05g1704 Clacu05g1654 Cmu05g1548 Cre05g1660 . . . Cme04g00786
Vvi19g396 . . . . . . . . Cmo16g00930 . . . . . . . . . . . . . . . Cla10g00589 Cam10g0577 Cec10g0608 Cco10g0584 Clacu10g0608 Cmu10g1421 Cre10g0823 . . . . . Csa03g00578 . Cme06g02696 . . . . . . . . . . . . . . . . . Bhi11g00695 Tan01g1629 . . Hepe07g1115 . . . . . . . . . Lsi05g00662 . . .
Vvi19g397 Blo03g00606 . . . . . . Bma13g00965 . . . . . . . . . . . . . . . . Cla10g00588 Cam10g0575 Cec10g0606 Cco10g0582 Clacu10g0607 Cmu10g1420 Cre10g0821 . . . . . Csa03g00576 . Cme06g02687 . . . . . . . . . . . . Cma16g00825 . . Cpe14g00717 . Bhi11g00694 Tan01g1630 . . Hepe07g1116 . . . . . . . . . Lsi05g00661 . . .
Vvi19g398 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g399 Blo03g00605 . . . . . . . . . . . . . . . . . . . . . . . Cla10g00587 Cam10g0572 Cec10g0605 Cco10g0581 Clacu10g0606 Cmu10g1418 Cre10g0819 . . . . . . . . . . . . . . . . . . . . . . . . . Bhi11g00693 Tan01g1634 . . Hepe07g0540 Mch10g1151 . . . . . . . . . . . .
Vvi19g400 Blo03g00604 . Bda07g00326 . . . . Bma13g00962 . . . . . . . . . . . . . . . . Cla10g00585 Cam10g0569 Cec10g0603 Cco10g0579 Clacu10g0605 Cmu10g1417 Cre10g0818 . . . . . Csa03g00574 . Cme06g02685 . . . . . . . . Sed06g0194 . . . Cma16g00826 . . . . Bhi11g00692 Tan01g1636 Cmetu06g2161 . . Mch10g1155 . . . . . . . . Lsi05g00660 . . .
Vvi19g401 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g402 Blo03g00603 . . . . . . Bma13g00961 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme06g02683 . . . . . . . . . . . . Cma16g00829 . . Cpe14g00716 . . . . . . . . . . . . . . . Lsi05g00658 . . .
Vvi19g403 . . Bda07g00331 . . . . Bma13g00950 . . . . . . . . . . . . . . . . . . . . . . . . Cone9ag0113 . . . . . . Blo07g00921 . Bda05g00743 . . Bpe03g00808 . . . . . . Cma16g00830 . . . . . . . . . . . . . . . . . . Lsi05g00657 . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 55839805 55841800 + Bda021888.1 Bda05g00743 743
7 4375321 4377743 - Bda025412.2 Bda07g00326 326
7 4407928 4419546 + Bda025417.1 Bda07g00331 331
9 4876636 4878716 + Bda030961.1 Bda09g00380 380
9 54578078 54580772 + XM_039040916.1 Bhi09g01959 1959
9 54580587 54583428 - XM_039040915.1 Bhi09g01960 1960
11 17805109 17816112 + XM_039049829.1 Bhi11g00692 692
11 17873970 17880083 + XM_039047673.1 Bhi11g00693 693
11 18047713 18052287 - XM_039047369.1 Bhi11g00694 694
11 18047713 18052120 - XM_039047368.1 Bhi11g00695 695
3 24064019 24066091 + BLOR11784 Blo03g00603 603
3 24067007 24069941 + BLOR11785 Blo03g00604 604
3 24251974 24256961 + BLOR11786 Blo03g00605 605
3 24418534 24420815 + BLOR11787 Blo03g00606 606
7 28237792 28240103 - BLOR18853 Blo07g00921 921
7 28326005 28328167 + BLOR18857 Blo07g00925 925
7 48720604 48722726 - Bma026594.1 Bma07g01319 1319
10 6140184 6142188 - Bma004219.1 Bma10g00528 528
13 40577149 40579440 - Bma010045.1 Bma13g00950 950
13 40882863 40885208 + Bma010063.1 Bma13g00961 961
13 41003393 41005725 + Bma010065.1 Bma13g00962 962
13 41269944 41272227 - Bma010072.1 Bma13g00965 965
14 4421664 4423422 - Bma010787.1 Bma14g00366 366
3 28028211 28030227 + Bpe012717.1 Bpe03g00808 808
3 28059541 28067186 + Bpe012718.1 Bpe03g00809 809
8 13290945 13292924 - Bpe023270.1 Bpe08g01145 1145
5 24520909 24522882 + CaPI482276_05g016600.1 Cam05g1660 1660
5 24524391 24526993 - CaPI482276_05g016610.1 Cam05g1661 1661
10 8779902 8780238 - CaPI482276_10g005690.1 Cam10g0569 569
10 8786614 8792567 - CaPI482276_10g005720.1 Cam10g0572 572
10 8870182 8875063 + CaPI482276_10g005750.1 Cam10g0575 575
10 8910694 8911882 + CaPI482276_10g005770.1 Cam10g0577 577
4 4993427 4995948 - Carg00042-RA Car04g00867 867
9 5069481 5072160 + Carg12785-RA Car09g00831 831
9 5072896 5074755 - Carg12786-RA Car09g00832 832
16 3616061 3617731 + Carg05658-RA Car16g00573 573
16 3618521 3621376 - Carg05659-RA Car16g00574 574
5 25090569 25092420 + CcPI632755_05g017040.1 Cco05g1704 1704
5 25097498 25100333 - CcPI632755_05g017060.1 Cco05g1706 1706
10 7630932 7638784 - CcPI632755_10g005790.1 Cco10g0579 579
10 7664963 7670476 + CcPI632755_10g005810.1 Cco10g0581 581
10 7690287 7692599 + CcPI632755_10g005820.1 Cco10g0582 582
10 7705069 7706555 + CcPI632755_10g005840.1 Cco10g0584 584
5 27512476 27518152 + CePI673135_05g016650.1 Cec05g1665 1665
5 27519588 27522025 - CePI673135_05g016660.1 Cec05g1666 1666
10 7983501 7984646 - CePI673135_10g006030.1 Cec10g0603 603
10 7996235 7997975 - CePI673135_10g006050.1 Cec10g0605 605
10 8039025 8044338 - CePI673135_10g006060.1 Cec10g0606 606
10 8092666 8100408 + CePI673135_10g006080.1 Cec10g0608 608
4 15287779 15289803 + Chy4G077460.1 Chy04g01028 1028
4 15290585 15293146 - Chy4G077470.1 Chy04g01029 1029
5 24707864 24709838 + ClG42_05g0165400.10 Clacu05g1654 1654
5 24711133 24713709 - ClG42_05g0165500.10 Clacu05g1655 1655
10 8062088 8070220 - ClG42_10g0060500.10 Clacu10g0605 605
10 8112131 8117630 + ClG42_10g0060600.10 Clacu10g0606 606
10 8179980 8184907 + ClG42_10g0060700.10 Clacu10g0607 607
10 8207261 8220684 + ClG42_10g0060800.10 Clacu10g0608 608
5 26091435 26097092 + ClCG05G014930.1 Cla05g01552 1552
5 26098172 26101100 - ClCG05G014940.2 Cla05g01553 1553
10 8526476 8534618 - ClCG10G006210.1 Cla10g00585 585
10 8581655 8587838 + ClCG10G006230.1 Cla10g00587 587
10 8655015 8661619 + ClCG10G006250.2 Cla10g00588 588
10 8683965 8697391 + ClCG10G006260.1 Cla10g00589 589
1 8469317 8470977 + CmaCh01G011600.1 Cma01g01160 1160
1 8472072 8474738 - CmaCh01G011620.1 Cma01g01162 1162
9 4556959 4562566 + CmaCh09G009140.1 Cma09g00914 914
9 4563203 4565054 - CmaCh09G009150.1 Cma09g00915 915
16 4622233 4625084 + CmaCh16G008250.1 Cma16g00825 825
16 4630689 4633204 + CmaCh16G008260.1 Cma16g00826 826
16 4685724 4688661 + CmaCh16G008290.1 Cma16g00829 829
16 4694253 4696455 + CmaCh16G008300.1 Cma16g00830 830
4 9523254 9526434 + MELO3C018147.2.1 Cme04g00784 784
4 9530437 9532559 - MELO3C018145.2.1 Cme04g00786 786
6 33953314 33958899 + MELO3C014040.2.1 Cme06g02683 2683
6 34054933 34061417 + MELO3C014045.2.1 Cme06g02685 2685
6 34075330 34079515 + MELO3C014047.2.1 Cme06g02687 2687
6 34152204 34157997 + MELO3C014051.2.1 Cme06g02696 2696
4 25227928 25229980 + PI0000565.1 Cmetu04g2937 2937
6 24960343 24963345 - PI0014016.1 Cmetu06g2161 2161
8 16253954 16256094 + PI0020832.1 Cmetu08g1286 1286
1 9800539 9802199 + CmoCh01G012150.1 Cmo01g01215 1215
1 9802995 9805872 - CmoCh01G012160.1 Cmo01g01216 1216
4 5008549 5011190 - CmoCh04G009950.1 Cmo04g00995 995
9 4754143 4756754 + CmoCh09G009080.1 Cmo09g00908 908
9 4757566 4759362 - CmoCh09G009090.1 Cmo09g00909 909
16 5759386 5761945 + CmoCh16G009300.1 Cmo16g00930 930
5 24421703 24423677 + CmPI595203_05g015480.1 Cmu05g1548 1548
5 24424971 24427559 - CmPI595203_05g015490.1 Cmu05g1549 1549
10 8182503 8190599 - CmPI595203_10g014170.1 Cmu10g1417 1417
10 8232692 8238200 + CmPI595203_10g014180.1 Cmu10g1418 1418
10 8299431 8304364 + CmPI595203_10g014200.1 Cmu10g1420 1420
10 8326687 8340098 + CmPI595203_10g014210.1 Cmu10g1421 1421
9 485071 486529 + Conep09aG0011300.1 Cone9ag0113 113
14 9305244 9307752 - Conep14aG0113800.1 Cone14ag1116 1116
15 9215057 9216623 + Conep15aG0115600.1 Cone15ag1130 1130
15 9216898 9219655 - Conep15aG0115700.1 Cone15ag1131 1131
1 4968442 4969179 - Cp4.1LG01g08390.1 Cpe01g00838 838
2 4715946 4719017 + Cp4.1LG02g01390.1 Cpe02g00740 740
2 4719642 4721311 - Cp4.1LG02g01300.1 Cpe02g00741 741
6 4616374 4618930 + Cp4.1LG06g07250.1 Cpe06g00736 736
6 4619316 4625219 - Cp4.1LG06g07370.1 Cpe06g00737 737
14 4784342 4785053 + Cp4.1LG14g00020.1 Cpe14g00716 716
14 4815002 4833483 + Cp4.1LG14g00010.1 Cpe14g00717 717
5 27553752 27555728 + CrPI670011_05g016600.1 Cre05g1660 1660
5 27557150 27559589 - CrPI670011_05g016610.1 Cre05g1661 1661
10 8695081 8702714 - CrPI670011_10g008180.1 Cre10g0818 818
10 8763118 8768338 + CrPI670011_10g008190.1 Cre10g0819 819
10 8800940 8805371 + CrPI670011_10g008210.1 Cre10g0821 821
10 8835213 8838656 + CrPI670011_10g008230.1 Cre10g0823 823
3 4925550 4930927 - CsaV3_3G005740.1 Csa03g00574 574
3 4956424 4960057 - CsaV3_3G005760.1 Csa03g00576 576
3 4980160 4983994 - CsaV3_3G005780.1 Csa03g00578 578
1 78417462 78419367 + Hsped.01g13220.1 Hepe01g1322 1322
1 78420092 78422817 - Hsped.01g13230.1 Hepe01g1323 1323
7 5704211 5708908 - Hsped.07g05400.1 Hepe07g0540 540
7 19573266 19577919 + Hsped.07g11150.1 Hepe07g1115 1115
7 19616143 19616731 + Hsped.07g11160.1 Hepe07g1116 1116
4 19545430 19551277 + Lsi04G012540.1 Lsi04g01254 1254
4 19552123 19555652 - Lsi04G012550.1 Lsi04g01255 1255
5 8442605 8452212 + Lsi05G006570.1 Lsi05g00657 657
5 8511256 8516197 + Lsi05G006580.1 Lsi05g00658 658
5 8555816 8557751 + Lsi05G006600.1 Lsi05g00660 660
5 8594106 8598038 + Lsi05G006610.1 Lsi05g00661 661
5 8610068 8621748 - Lsi05G006620.1 Lsi05g00662 662
10 8661778 8665661 - MC10g0980 Mch10g1151 1151
10 8729090 8733482 + MC10g0982 Mch10g1155 1155
11 7973001 7973831 + MC11g0938 Mch11g1137 1137
11 7978021 7980201 - MC11g0940 Mch11g1139 1139
6 1436334 1441193 - Sed0008638.1 Sed06g0194 194
6 36907829 36915959 + Sed0007185.2 Sed06g1290 1290
14 4679838 4682157 - Sed0024493.1 Sed14g0466 466
1 16520407 16520948 - Tan0001156.1 Tan01g1629 1629
1 16521086 16523146 - Tan0014839.1 Tan01g1630 1630
1 16662416 16663688 + Tan0011198.1 Tan01g1634 1634
1 16863709 16871643 + Tan0007013.1 Tan01g1636 1636
1 110503265 110506103 + Tan0012664.1 Tan01g4493 4493
1 110506780 110509742 - Tan0009895.1 Tan01g4494 4494
19 5068258 5077130 + Vvi19g394 Vvi19g394 394
19 5085858 5089101 - Vvi19g395 Vvi19g395 395
19 5137988 5156157 - Vvi19g396 Vvi19g396 396
19 5156207 5159153 - Vvi19g397 Vvi19g397 397
19 5167088 5172317 + Vvi19g398 Vvi19g398 398
19 5187118 5188831 + Vvi19g399 Vvi19g399 399
19 5188832 5190518 + Vvi19g400 Vvi19g400 400
19 5198059 5199853 - Vvi19g401 Vvi19g401 401
19 5214959 5225074 - Vvi19g402 Vvi19g402 402
19 5225077 5232195 - Vvi19g403 Vvi19g403 403
       

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