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
Vvi19g704 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g705 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g706 . . . . Bpe09g00116 . . Bma13g01125 . . Cma01g01065 Cma09g01022 Car01g00939 Car09g00926 Sed08g1410 Cpe06g00830 Cpe02g00832 Bhi09g01794 Tan01g3210 Cmetu01g2405 . . Mch11g1296 . Cla10g00435 Cam10g0434 Cec10g0456 Cco10g0445 Clacu10g0442 Cmu10g1273 Cre10g0689 . . . . Lsi02g01814 . . . . . Bda05g00687 Bda12g00975 . Bpe03g00748 . . . Cmo01g01107 Cmo09g01025 . . . . . . . . . . . . . Cla09g02092 Cam09g2178 Cec09g2244 . . . . . . Chy01g01127 Cme01g00879
Vvi19g707 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g708 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g00413 . Cme06g02761 . Blo10g00874 . . . . . . . . . . . . . Cpe14g00778 . Bhi11g00458 . . . . . . . . . . . . . . . Chy06g01899 .
Vvi19g709 . . . . Bpe09g00115 . . Bma13g01126 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g00412 . Cme06g02760 . . . Bda12g00977 . . . . . . . . . . . Cpe14g00777 . Bhi11g00457 . . . . . . . . . . . . . . . Chy06g01900 .
Vvi19g710 . . . . Bpe09g00114 . . Bma13g01127 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo10g00875 . Bda12g00978 . . . . . . . . . . . Cpe14g00776 . . . . . . . . . . . . . . . Lsi05g00513 . . .
Vvi19g711 Blo03g00498 . Bda07g00421 . Bpe09g00113 . . Bma13g01128 . . Cma01g01064 Cma09g01023 Car01g00938 Car09g00927 Sed07g2753 Cpe06g00831 Cpe02g00833 Bhi09g01795 Tan01g3211 Cmetu01g1220 . . Mch11g1299 . . . . . . . . . . . . Lsi02g01812 . . . . Blo10g00876 . Bda12g00979 Bpe11g00596 . . Bma14g00673 . Cmo01g01106 Cmo09g01026 . . . . . . . . . . . . . Cla09g02093 Cam09g2179 Cec09g2246 . . . . . . Chy01g01126 Cme01g00877
Vvi19g712 . . . . Bpe09g00112 . Bma10g00599 Bma13g01129 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo10g00877 Bda05g00675 . . . . . . . . . . . . Cpe14g00775 . . . . . . . . . . . . . . . Lsi05g00514 . . .
Vvi19g713 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 55059715 55061696 + Bda021809.1 Bda05g00675 675
5 55176861 55179124 + Bda021822.1 Bda05g00687 687
7 5397090 5400369 + Bda025516.1 Bda07g00421 421
12 40906127 40907607 - Bda009521.1 Bda12g00975 975
12 40920221 40922655 - Bda009523.1 Bda12g00977 977
12 40923489 40927273 + Bda009524.1 Bda12g00978 978
12 40933847 40936135 + Bda009525.1 Bda12g00979 979
9 48808870 48811708 + XM_039043573.1 Bhi09g01794 1794
9 48857688 48861119 + XM_039042495.1 Bhi09g01795 1795
11 10995323 10998917 + XM_039047253.1 Bhi11g00457 457
11 11000331 11004507 + XM_039047504.1 Bhi11g00458 458
3 18252935 18256091 - BLOR11679 Blo03g00498 498
10 27514834 27517436 - BLOR02664 Blo10g00874 874
10 27542831 27546354 + BLOR02665 Blo10g00875 875
10 27548914 27551412 + BLOR02666 Blo10g00876 876
10 27552268 27554099 - BLOR02667 Blo10g00877 877
10 7315744 7317727 - Bma004306.1 Bma10g00599 599
13 44352169 44355227 - Bma010254.1 Bma13g01125 1125
13 44357163 44358853 - Bma010255.1 Bma13g01126 1126
13 44360193 44363195 + Bma010256.1 Bma13g01127 1127
13 44384904 44387254 + Bma010257.1 Bma13g01128 1128
13 44388390 44390163 - Bma010258.1 Bma13g01129 1129
14 7291169 7294464 - Bma011124.1 Bma14g00673 673
3 27558817 27561816 + Bpe025391 Bpe03g00748 748
9 767824 769655 + Bpe023790.1 Bpe09g00112 112
9 770790 773115 - Bpe026199 Bpe09g00113 113
9 774631 778364 - Bpe026200 Bpe09g00114 114
9 778934 781412 + Bpe023791.1 Bpe09g00115 115
9 784937 787409 + Bpe026201 Bpe09g00116 116
11 4534956 4538165 + Bpe003961.1 Bpe11g00596 596
9 36288772 36291138 + CaPI482276_09g021780.1 Cam09g2178 2178
9 36297751 36300383 + CaPI482276_09g021790.1 Cam09g2179 2179
10 6701670 6703480 + CaPI482276_10g004340.1 Cam10g0434 434
1 9058156 9062089 - Carg23342-RA Car01g00938 938
1 9064827 9067519 - Carg23341-RA Car01g00939 939
9 5710879 5713677 + Carg24748-RA Car09g00926 926
9 5716181 5719220 + Carg24747-RA Car09g00927 927
10 5252259 5254171 + CcPI632755_10g004450.1 Cco10g0445 445
9 39317654 39320015 + CePI673135_09g022440.1 Cec09g2244 2244
9 39327031 39329663 + CePI673135_09g022460.1 Cec09g2246 2246
10 5443618 5445999 + CePI673135_10g004560.1 Cec10g0456 456
1 12907022 12910000 - Chy1G011260.1 Chy01g01126 1126
1 12950520 12952770 - Chy1G011270.1 Chy01g01127 1127
6 22843939 22846560 - Chy6G124270.1 Chy06g01899 1899
6 22848802 22854193 - Chy6G124280.1 Chy06g01900 1900
10 5498248 5500171 + ClG42_10g0044200.10 Clacu10g0442 442
9 38448092 38450454 + ClCG09G021490.2 Cla09g02092 2092
9 38457010 38460387 + ClCG09G021500.1 Cla09g02093 2093
10 5854919 5857332 + ClCG10G004630.1 Cla10g00435 435
1 7877245 7881874 - CmaCh01G010640.1 Cma01g01064 1064
1 7883658 7886841 - CmaCh01G010650.1 Cma01g01065 1065
9 5251076 5254849 + CmaCh09G010220.1 Cma09g01022 1022
9 5256657 5260021 + CmaCh09G010230.1 Cma09g01023 1023
1 9990894 9994335 - MELO3C024962.2.1 Cme01g00877 877
1 10016618 10019938 - MELO3C024961.2.1 Cme01g00879 879
6 34829477 34833054 + MELO3C014108.2.1 Cme06g02760 2760
6 34834759 34838474 + MELO3C014109.2.1 Cme06g02761 2761
1 14150254 14153175 + PI0026995.1 Cmetu01g1220 1220
1 14124398 14127714 + PI0025900.1 Cmetu01g2405 2405
1 9195914 9199591 - CmoCh01G011060.1 Cmo01g01106 1106
1 9201609 9204747 - CmoCh01G011070.1 Cmo01g01107 1107
9 5479046 5481947 + CmoCh09G010250.1 Cmo09g01025 1025
9 5485903 5489282 + CmoCh09G010260.1 Cmo09g01026 1026
10 5635138 5637059 + CmPI595203_10g012730.1 Cmu10g1273 1273
2 5323013 5326138 + Cp4.1LG02g00500.1 Cpe02g00832 832
2 5329466 5333346 + Cp4.1LG02g00490.1 Cpe02g00833 833
6 5336291 5341775 + Cp4.1LG06g08260.1 Cpe06g00830 830
6 5343375 5348123 + Cp4.1LG06g08210.1 Cpe06g00831 831
14 6109843 6116698 + Cp4.1LG14g07730.1 Cpe14g00775 775
14 6113840 6118591 - Cp4.1LG14g07810.1 Cpe14g00776 776
14 6120218 6124287 + Cp4.1LG14g07750.1 Cpe14g00777 777
14 6125046 6129461 + Cp4.1LG14g07760.1 Cpe14g00778 778
10 6556431 6558241 + CrPI670011_10g006890.1 Cre10g0689 689
3 3491456 3495209 + CsaV3_3G004120.1 Csa03g00412 412
3 3496805 3500437 + CsaV3_3G004130.1 Csa03g00413 413
2 23915048 23918650 - Lsi02G018120.1 Lsi02g01812 1812
2 23927549 23931279 - Lsi02G018140.1 Lsi02g01814 1814
5 6430307 6435658 + Lsi05G005130.1 Lsi05g00513 513
5 6435213 6452901 - Lsi05G005140.1 Lsi05g00514 514
11 9172298 9176634 + MC11g1073 Mch11g1296 1296
11 9181037 9184359 + MC11g1075 Mch11g1299 1299
7 42586501 42590480 - Sed0025611.1 Sed07g2753 2753
8 28736423 28742536 + Sed0024116.2 Sed08g1410 1410
1 86247332 86249528 + Tan0008463.1 Tan01g3210 3210
1 86306617 86310447 + Tan0005531.1 Tan01g3211 3211
19 9010620 9015289 - Vvi19g704 Vvi19g704 704
19 9015338 9023045 - Vvi19g705 Vvi19g705 705
19 9025801 9029915 - Vvi19g706 Vvi19g706 706
19 9040135 9050827 + Vvi19g707 Vvi19g707 707
19 9051362 9053928 - Vvi19g708 Vvi19g708 708
19 9054783 9058957 - Vvi19g709 Vvi19g709 709
19 9060514 9063661 + Vvi19g710 Vvi19g710 710
19 9068110 9071818 + Vvi19g711 Vvi19g711 711
19 9072484 9077519 - Vvi19g712 Vvi19g712 712
19 9077801 9082842 - Vvi19g713 Vvi19g713 713
       

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