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
Vvi19g1164 . Blo13g00604 . . . . Bma08g00823 . . . . . . . Sed04g3557 . . Bhi05g01988 Tan02g0021 Cmetu01g0138 Lac12g0035 Hepe02g0009 . . . . . . . . . . . . . . Csa07g01216 . . . . . . . . . . . . . . . . . Cpe15g00908 . . . . . . . . . . . . . . . . . Chy01g00847 Cme01g01496
Vvi19g1165 Blo04g00457 . . . . . Bma08g00824 . . . . . . . . . . Bhi05g01987 . . . . . . . . . . . . . . . . . . Csa07g01217 . . . . . . Bpe15g00924 . Bma03g00490 . . . . . . . . Cpe15g00909 . . . . . . . . . . . . . . . . . Chy01g00846 Cme01g01495
Vvi19g1166 . . . . . . . . . . . . . . . . Cpe16g00706 . . . . . . . Cla02g01830 Cam02g1939 Cec02g1966 Cco02g2005 Clacu02g1919 Cmu02g1868 Cre02g2181 . . . . . . . Cme11g01637 . . . . . . . . . . . . . . . . . Bhi10g00931 . . . . . . . . . . . . . . Csa06g01148 Chy11g01044 .
Vvi19g1167 . . . . . . . . . . . . . . . . Cpe16g00705 . . . . . . . Cla02g01831 Cam02g1940 Cec02g1967 Cco02g2006 Clacu02g1920 Cmu02g1869 Cre02g2182 . . . . . . . Cme11g01638 . . . . . . . Bma12g00575 Sed01g0768 . . . . . . . Cpe05g01030 Bhi10g00930 Tan05g0580 Cmetu11g1042 . Hepe08g0651 . . . . . . . . . . Csa06g01147 Chy11g01045 .
Vvi19g1168 . . . . Bpe07g00475 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo15g00637 . . . . . . Bma12g00574 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1169 . . . . . . . . . . . . . . . . Cpe16g00704 . . . . . . . Cla02g01832 Cam02g1941 Cec02g1968 Cco02g2007 Clacu02g1921 Cmu02g1870 Cre02g2183 . . . . . . . Cme11g01643 . . . . . . . . Sed05g3313 . . . . . . . Cpe05g01029 Bhi10g00929 Tan05g0579 Cmetu11g2423 . Hepe08g0653 . . . . . . . . . . Csa06g01146 Chy11g01046 .
Vvi19g1170 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo15g00639 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1171 Blo04g00455 Blo13g00605 . . Bpe07g00477 . Bma08g00825 . . . . . . . . . . Bhi05g01981 Tan02g0015 Cmetu01g1460 Lac12g0030 . . . Cla02g01833 Cam02g1942 Cec02g1969 Cco02g2008 Clacu02g1922 Cmu02g1871 Cre02g2184 . . . . . Csa07g01218 . Cme11g01645 Blo15g00640 . . . Bpe15g00926 . Bma03g00488 Bma12g00569 Sed01g0770 . . . . . . Cpe15g00910 Cpe05g01028 Bhi10g00928 Tan05g0578 Cmetu11g1511 . Hepe08g0654 . . . . . . . . . . Csa06g01145 Chy11g01047 Cme01g01493
Vvi19g1172 Blo04g00454 Blo13g00606 . . . . Bma08g00826 . . . . . . . . . . Bhi05g01979 . . Lac12g0029 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe15g00911 . . . . . . . . . . . . . . . . . . .
Vvi19g1173 . Blo13g00608 . . . . Bma08g00827 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 61114350 61117025 + XM_039031086.1 Bhi05g01979 1979
5 61216090 61218712 - XM_039032877.1 Bhi05g01981 1981
5 61265410 61273040 + XM_039032146.1 Bhi05g01987 1987
5 61273669 61276464 - XM_039032655.1 Bhi05g01988 1988
10 19061804 19064930 - XM_039044450.1 Bhi10g00928 928
10 19072439 19087506 - XM_039045529.1 Bhi10g00929 929
10 19158481 19161791 + XM_039045546.1 Bhi10g00930 930
10 19161760 19171194 - XM_039045543.1 Bhi10g00931 931
4 3784415 3786099 + BLOR13366 Blo04g00454 454
4 3788347 3789796 - BLOR13367 Blo04g00455 455
4 3813282 3816134 + BLOR13369 Blo04g00457 457
13 28449328 28452126 + BLOR19656 Blo13g00604 604
13 28469327 28470685 + BLOR19657 Blo13g00605 605
13 28483740 28485553 - BLOR19658 Blo13g00606 606
13 28499293 28503924 + BLOR19660 Blo13g00608 608
15 16738301 16748367 - BLOR07031 Blo15g00637 637
15 16753312 16760759 - BLOR07033 Blo15g00639 639
15 17129641 17131071 - BLOR07034 Blo15g00640 640
3 3841540 3842897 - Bma016771.1 Bma03g00488 488
3 3851248 3855512 + Bma016772.4 Bma03g00490 490
8 46030840 46033416 + Bma028218.1 Bma08g00823 823
8 46034044 46037946 - Bma028219.1 Bma08g00824 824
8 46047913 46049179 + Bma028220.1 Bma08g00825 825
8 46053656 46055432 - Bma028221.1 Bma08g00826 826
8 46094264 46095766 + Bma028223.1 Bma08g00827 827
12 24779078 24780477 - Bma007726.1 Bma12g00569 569
12 24926926 24937945 - Bma007734.2 Bma12g00574 574
12 24942210 24945500 + Bma007735.1 Bma12g00575 575
7 8120640 8128947 - Bpe021313.1 Bpe07g00475 475
7 8171923 8173316 + Bpe021315.2 Bpe07g00477 477
15 19012528 19016023 - Bpe001845.1 Bpe15g00924 924
15 19025279 19026637 + Bpe001847.1 Bpe15g00926 926
2 32483514 32487552 + CaPI482276_02g019390.1 Cam02g1939 1939
2 32487830 32490455 - CaPI482276_02g019400.1 Cam02g1940 1940
2 32500975 32512102 + CaPI482276_02g019410.1 Cam02g1941 1941
2 32518806 32526164 + CaPI482276_02g019420.1 Cam02g1942 1942
2 33000390 33004411 + CcPI632755_02g020050.1 Cco02g2005 2005
2 33004690 33007311 - CcPI632755_02g020060.1 Cco02g2006 2006
2 33017619 33028447 + CcPI632755_02g020070.1 Cco02g2007 2007
2 33035249 33039185 + CcPI632755_02g020080.1 Cco02g2008 2008
2 37499822 37503854 + CePI673135_02g019660.1 Cec02g1966 1966
2 37504132 37506757 - CePI673135_02g019670.1 Cec02g1967 1967
2 37516053 37527032 + CePI673135_02g019680.1 Cec02g1968 1968
2 37533770 37537700 + CePI673135_02g019690.1 Cec02g1969 1969
1 7424717 7429378 + Chy1G008460.1 Chy01g00846 846
1 7431108 7433502 - Chy1G008470.1 Chy01g00847 847
11 14898237 14902278 + Chy11G196240.1 Chy11g01044 1044
11 14902559 14905096 - Chy11G196250.1 Chy11g01045 1045
11 14923094 14948806 + Chy11G196260.1 Chy11g01046 1046
11 14949199 14952274 + Chy11G196270.1 Chy11g01047 1047
2 32741987 32746022 + ClG42_02g0191900.10 Clacu02g1919 1919
2 32746301 32748930 - ClG42_02g0192000.10 Clacu02g1920 1920
2 32756565 32767410 + ClG42_02g0192100.10 Clacu02g1921 1921
2 32774216 32781475 + ClG42_02g0192200.10 Clacu02g1922 1922
2 33446333 33450818 + ClCG02G018710.2 Cla02g01830 1830
2 33450777 33453556 - ClCG02G018720.1 Cla02g01831 1831
2 33460980 33472140 + ClCG02G018730.2 Cla02g01832 1832
2 33478656 33486223 + ClCG02G018740.1 Cla02g01833 1833
1 19617312 19620141 - MELO3C012590.2.1 Cme01g01493 1493
1 19667710 19672548 + MELO3C012592.2.1 Cme01g01495 1495
1 19673329 19676073 - MELO3C012593.2.1 Cme01g01496 1496
11 24236403 24240771 + MELO3C019630.2.1 Cme11g01637 1637
11 24240102 24243844 - MELO3C019629.2.1 Cme11g01638 1638
11 24293435 24310356 + MELO3C019622.2.1 Cme11g01643 1643
11 24315395 24318702 + MELO3C019621.2.1 Cme11g01645 1645
1 7142661 7145694 - PI0011723.1 Cmetu01g0138 138
1 7097844 7100350 - PI0008091.2 Cmetu01g1460 1460
11 8546813 8549368 + PI0019607.1 Cmetu11g1042 1042
11 8487868 8491183 - PI0009049.1 Cmetu11g1511 1511
11 8496559 8530228 - PI0010032.1 Cmetu11g2423 2423
2 32604252 32608287 + CmPI595203_02g018680.1 Cmu02g1868 1868
2 32608566 32611195 - CmPI595203_02g018690.1 Cmu02g1869 1869
2 32618830 32629675 + CmPI595203_02g018700.1 Cmu02g1870 1870
2 32636481 32643740 + CmPI595203_02g018710.1 Cmu02g1871 1871
5 6737489 6740495 - Cp4.1LG05g10290.1 Cpe05g01028 1028
5 6743169 6759278 - Cp4.1LG05g10320.1 Cpe05g01029 1029
5 6762928 6766492 + Cp4.1LG05g10250.1 Cpe05g01030 1030
15 8703370 8706914 + Cp4.1LG15g09020.1 Cpe15g00908 908
15 8705304 8711494 - Cp4.1LG15g09130.1 Cpe15g00909 909
15 8713480 8716141 + Cp4.1LG15g09040.1 Cpe15g00910 910
15 8716946 8720053 - Cp4.1LG15g09140.1 Cpe15g00911 911
16 7228718 7241335 - Cp4.1LG16g07130.1 Cpe16g00704 704
16 7243944 7247345 + Cp4.1LG16g07030.1 Cpe16g00705 705
16 7245926 7250278 - Cp4.1LG16g07070.1 Cpe16g00706 706
2 35453233 35457209 + CrPI670011_02g021810.1 Cre02g2181 2181
2 35457488 35460110 - CrPI670011_02g021820.1 Cre02g2182 2182
2 35470144 35480991 + CrPI670011_02g021830.1 Cre02g2183 2183
2 35487802 35491711 + CrPI670011_02g021840.1 Cre02g2184 2184
6 9545350 9549020 - CsaV3_6G013430.1 Csa06g01145 1145
6 9553079 9570338 - CsaV3_6G013440.1 Csa06g01146 1146
6 9578918 9582262 + CsaV3_6G013450.1 Csa06g01147 1147
6 9582363 9586590 - CsaV3_6G013460.1 Csa06g01148 1148
7 11938379 11940788 + CsaV3_7G023050.1 Csa07g01216 1216
7 11941684 11947918 - CsaV3_7G023060.1 Csa07g01217 1217
7 11974425 11977379 + CsaV3_7G023070.1 Csa07g01218 1218
2 270278 272700 - Hsped.02g00090.1 Hepe02g0009 9
8 5791737 5793816 - Hsped.08g06510.1 Hepe08g0651 651
8 5813364 5822057 + Hsped.08g06530.1 Hepe08g0653 653
8 5829050 5832498 + Hsped.08g06540.1 Hepe08g0654 654
12 442075 444575 + Lag0014401.1 Lac12g0029 29
12 448178 450082 - Lag0014402.1 Lac12g0030 30
12 495742 498461 + Lag0014407.1 Lac12g0035 35
1 5721913 5726284 - Sed0000958.1 Sed01g0768 768
1 5741691 5744658 + Sed0015076.2 Sed01g0770 770
4 44954066 44958015 + Sed0007161.1 Sed04g3557 3557
5 42467690 42482795 + Sed0009726.1 Sed05g3313 3313
2 571209 573821 - Tan0003439.2 Tan02g0015 15
2 592143 594575 - Tan0000086.1 Tan02g0021 21
5 4195205 4198795 - Tan0006387.2 Tan05g0578 578
5 4204377 4219778 - Tan0015241.1 Tan05g0579 579
5 4232166 4235056 + Tan0003691.1 Tan05g0580 580
19 23279324 23283793 + Vvi19g1164 Vvi19g1164 1164
19 23284513 23291080 - Vvi19g1165 Vvi19g1165 1165
19 23305997 23313302 + Vvi19g1166 Vvi19g1166 1166
19 23313348 23318736 - Vvi19g1167 Vvi19g1167 1167
19 23319002 23339683 + Vvi19g1168 Vvi19g1168 1168
19 23341371 23351231 + Vvi19g1169 Vvi19g1169 1169
19 23353907 23383396 + Vvi19g1170 Vvi19g1170 1170
19 23387999 23390312 + Vvi19g1171 Vvi19g1171 1171
19 23399296 23401496 - Vvi19g1172 Vvi19g1172 1172
19 23412508 23437714 + Vvi19g1173 Vvi19g1173 1173
       

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