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
Vvi2g732 . . Bda06g01255 . . Bpe07g00237 . . Cmo06g00634 Cmo16g01239 . . . . . Cpe14g00988 . . . . . . . . Cla10g00125 Cam10g0125 Cec10g0135 Cco10g0135 Clacu10g0130 Cmu10g0977 Cre10g0388 . Cone12ag0559 . . Lsi07g01160 . . Cme06g02440 . . . . . . . Bma12g00238 . . . Cma06g00625 Cma16g01191 Car06g00560 Car16g01123 . . . . . . . . . . . . . . . . . Csa03g00132 Chy06g02174 .
Vvi2g733 . . . . . . . Bma14g00062 . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0494 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g734 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g735 . . . . . . . Bma14g00063 . . Cma02g01638 . Car02g01397 . . . Cpe05g00156 . . . . . . . . . . . . . . . Cone12ag0492 . . . . Chy04g00128 . . Blo19g00258 . . . . . . Sed01g4142 Cmo02g01683 Cmo19g00228 . . . . . Cpe15g00188 Bhi05g00442 Tan07g2012 Cmetu04g2268 Lac11g2452 Hepe06g1803 . Lcy12g1975 Cla09g01090 Cam09g1143 Cec09g1153 Cco09g1169 . . Cre09g1106 . Csa03g04577 . Cme04g00151
Vvi2g736 . . . . . . Bma07g00907 . . . Cma02g01639 . Car02g01398 . . . Cpe05g00155 . . . . . . . . . . . . . . . . . . . . Chy04g00129 . . . . . . . . . Sed08g2776 Cmo02g01684 . . . . . . . Bhi05g00441 Tan07g2013 Cmetu04g3093 Lac11g2453 Hepe06g1804 . Lcy12g1976 Cla09g01089 Cam09g1142 Cec09g1152 Cco09g1168 . . Cre09g1105 . Csa03g04576 . Cme04g00152
Vvi2g737 . . . . . . . Bma14g00064 Cmo06g00633 Cmo16g01240 Cma02g01640 . Car02g01399 . . Cpe14g00989 Cpe05g00154 . . . . . . . Cla10g00124 Cam10g0124 Cec10g0134 Cco10g0134 Clacu10g0129 Cmu10g0976 Cre10g0387 Cone8ag0496 Cone12ag0558 . . Lsi07g01159 . Chy04g00130 Cme06g02439 . . . . . . . . . Cmo02g01685 . Cma06g00624 Cma16g01193 Car06g00559 Car16g01124 . . Bhi05g00440 Tan07g2015 . . Hepe06g0987 . . Cla09g01088 . Cec09g1151 Cco09g1167 . . Cre09g1104 . Csa03g04575 Chy06g02175 Cme04g00153
Vvi2g738 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g739 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g740 . . . . . . . . Cmo06g00629 . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi07g01157 . . Cme06g02437 . . . . . . . . . . . Cma06g00621 . Car06g00555 . . . . . . . . . . . . . . . . . . Csa03g00129 Chy06g02177 .
Vvi2g741 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 43034794 43037911 - Bda023094.1 Bda06g01255 1255
5 9232758 9238743 + XM_039032225.1 Bhi05g00440 440
5 9242804 9246376 + XM_039033123.1 Bhi05g00441 441
5 9259741 9265069 + XM_039031344.1 Bhi05g00442 442
19 14923368 14928386 + BLOR09601 Blo19g00258 258
7 32404841 32407926 + Bma026000.1 Bma07g00907 907
12 3074021 3076803 + Bma007129.1 Bma12g00238 238
14 777369 780856 + Bma010468.1 Bma14g00062 62
14 783017 785038 - Bma030637 Bma14g00063 63
14 788781 793408 - Bma010469.1 Bma14g00064 64
7 1685557 1688534 + Bpe021048.1 Bpe07g00237 237
9 11933658 11956179 + CaPI482276_09g011420.1 Cam09g1142 1142
9 11965698 11969802 + CaPI482276_09g011430.1 Cam09g1143 1143
10 2812691 2817526 + CaPI482276_10g001240.1 Cam10g0124 124
10 2817951 2822233 - CaPI482276_10g001250.1 Cam10g0125 125
2 9185851 9190081 - Carg08864-RA Car02g01397 1397
2 9192004 9195037 - Carg08865-RA Car02g01398 1398
2 9195983 9201102 - Carg08866-RA Car02g01399 1399
6 3151279 3153246 - Carg23408-RA Car06g00555 555
6 3160924 3166098 + Carg23404-RA Car06g00559 559
6 3166470 3169913 - Carg23403-RA Car06g00560 560
16 9645823 9650618 + Carg23586-RA Car16g01123 1123
16 9650808 9655322 - Carg23585-RA Car16g01124 1124
9 11316447 11331331 + CcPI632755_09g011670.1 Cco09g1167 1167
9 11336264 11338874 + CcPI632755_09g011680.1 Cco09g1168 1168
9 11348412 11352414 + CcPI632755_09g011690.1 Cco09g1169 1169
10 1220216 1225104 + CcPI632755_10g001340.1 Cco10g0134 134
10 1225190 1230012 - CcPI632755_10g001350.1 Cco10g0135 135
9 11351286 11365167 + CePI673135_09g011510.1 Cec09g1151 1151
9 11366244 11374031 + CePI673135_09g011520.1 Cec09g1152 1152
9 11383519 11388666 + CePI673135_09g011530.1 Cec09g1153 1153
10 1234836 1239704 + CePI673135_10g001340.1 Cec10g0134 134
10 1240233 1244518 - CePI673135_10g001350.1 Cec10g0135 135
4 1153902 1157774 - Chy4G068460.1 Chy04g00128 128
4 1164875 1167924 - Chy4G068470.1 Chy04g00129 129
4 1169547 1178651 - Chy4G068480.1 Chy04g00130 130
6 26027206 26031286 + Chy6G127020.1 Chy06g02174 2174
6 26032096 26035667 - Chy6G127030.1 Chy06g02175 2175
6 26036833 26045912 + Chy6G127050.1 Chy06g02177 2177
10 1536087 1540951 + ClG42_10g0012900.10 Clacu10g0129 129
10 1541095 1545854 - ClG42_10g0013000.10 Clacu10g0130 130
9 11569360 11582300 + ClCG09G011600.2 Cla09g01088 1088
9 11584425 11594147 + ClCG09G011610.1 Cla09g01089 1089
9 11603080 11607398 + ClCG09G011620.1 Cla09g01090 1090
10 1268952 1275174 + ClCG10G001250.1 Cla10g00124 124
10 1274994 1283082 - ClCG10G001260.1 Cla10g00125 125
2 9286411 9289480 - CmaCh02G016380.1 Cma02g01638 1638
2 9291591 9294584 - CmaCh02G016390.1 Cma02g01639 1639
2 9295412 9303960 - CmaCh02G016400.1 Cma02g01640 1640
6 3033803 3035823 - CmaCh06G006210.1 Cma06g00621 621
6 3042042 3048624 + CmaCh06G006240.1 Cma06g00624 624
6 3049081 3052521 - CmaCh06G006250.1 Cma06g00625 625
16 9092792 9099412 + CmaCh16G011910.1 Cma16g01191 1191
16 9100070 9104393 - CmaCh16G011930.1 Cma16g01193 1193
4 1148942 1153580 - MELO3C003441.2.1 Cme04g00151 151
4 1159567 1162943 - MELO3C003442.2.1 Cme04g00152 152
4 1163943 1174347 - MELO3C003443.2.1 Cme04g00153 153
6 31420025 31421962 - MELO3C013817.2.1 Cme06g02437 2437
6 31429038 31434138 + MELO3C013820.2.1 Cme06g02439 2439
6 31434582 31438606 - MELO3C013821.2.1 Cme06g02440 2440
4 32270236 32274981 + PI0025260.1 Cmetu04g2268 2268
4 32259774 32263587 + PI0023573.1 Cmetu04g3093 3093
2 9660909 9664548 - CmoCh02G016830.1 Cmo02g01683 1683
2 9666502 9669581 - CmoCh02G016840.1 Cmo02g01684 1684
2 9670417 9679311 - CmoCh02G016850.1 Cmo02g01685 1685
6 3128236 3130203 - CmoCh06G006290.1 Cmo06g00629 629
6 3138763 3144626 + CmoCh06G006330.1 Cmo06g00633 633
6 3144349 3148499 - CmoCh06G006340.1 Cmo06g00634 634
16 8874330 8879187 + CmoCh16G012390.1 Cmo16g01239 1239
16 8879499 8883695 - CmoCh16G012400.1 Cmo16g01240 1240
19 1551956 1556025 + CmoCh19G002280.1 Cmo19g00228 228
10 1687103 1691970 + CmPI595203_10g009760.1 Cmu10g0976 976
10 1692114 1696869 - CmPI595203_10g009770.1 Cmu10g0977 977
8 3515012 3520054 + Conep08aG0051500.1 Cone8ag0494 494
8 3532227 3537670 - Conep08aG0051700.1 Cone8ag0496 496
12 3316819 3319240 - Conep12aG0051300.1 Cone12ag0492 492
12 4015990 4022593 + Conep12aG0057900.1 Cone12ag0558 558
12 4049597 4054924 + Conep12aG0058000.1 Cone12ag0559 559
5 801123 807358 + Cp4.1LG05g00470.1 Cpe05g00154 154
5 808152 811275 + Cp4.1LG05g00400.1 Cpe05g00155 155
5 813470 816398 + Cp4.1LG05g00440.1 Cpe05g00156 156
14 8343639 8348155 + Cp4.1LG14g09930.1 Cpe14g00988 988
14 8347870 8352782 - Cp4.1LG14g09980.1 Cpe14g00989 989
15 1531627 1535688 + Cp4.1LG15g01830.1 Cpe15g00188 188
9 11509437 11520416 + CrPI670011_09g011040.1 Cre09g1104 1104
9 11522774 11532220 + CrPI670011_09g011050.1 Cre09g1105 1105
9 11541615 11545705 + CrPI670011_09g011060.1 Cre09g1106 1106
10 2647396 2652331 + CrPI670011_10g003870.1 Cre10g0387 387
10 2652465 2657010 - CrPI670011_10g003880.1 Cre10g0388 388
3 995851 1000002 - CsaV3_3G001290.1 Csa03g00129 129
3 1012745 1017526 - CsaV3_3G001320.1 Csa03g00132 132
3 39806582 39817079 + CsaV3_3G048810.1 Csa03g04575 4575
3 39818018 39821740 + CsaV3_3G048820.1 Csa03g04576 4576
3 39827304 39831499 + CsaV3_3G048830.1 Csa03g04577 4577
6 57589689 57595138 + Hsped.06g09870.1 Hepe06g0987 987
6 69128689 69133156 - Hsped.06g18030.1 Hepe06g1803 1803
6 69139781 69144280 - Hsped.06g18040.1 Hepe06g1804 1804
11 40714212 40718640 - Lag0033090.1 Lac11g2452 2452
11 40725933 40728957 - Lag0033091.1 Lac11g2453 2453
12 41143160 41146798 - Maker00038114 Lcy12g1975 1975
12 41156855 41160365 - Maker00038036 Lcy12g1976 1976
7 17042753 17047677 - Lsi07G011570.1 Lsi07g01157 1157
7 17052474 17059551 + Lsi07G011590.1 Lsi07g01159 1159
7 17060223 17065057 - Lsi07G011600.1 Lsi07g01160 1160
1 70230790 70234889 - Sed0015752.1 Sed01g4142 4142
8 39347894 39351570 + Sed0023739.2 Sed08g2776 2776
7 71844760 71848654 - Tan0001333.1 Tan07g2012 2012
7 71855468 71859008 - Tan0006283.1 Tan07g2013 2013
7 71862458 71870506 - Tan0006773.2 Tan07g2015 2015
2 8991156 9003680 + Vvi2g732 Vvi2g732 732
2 9012194 9017414 + Vvi2g733 Vvi2g733 733
2 9039187 9039439 - Vvi2g734 Vvi2g734 734
2 9053547 9055651 - Vvi2g735 Vvi2g735 735
2 9124645 9137039 - Vvi2g736 Vvi2g736 736
2 9137679 9153416 - Vvi2g737 Vvi2g737 737
2 9164517 9172074 + Vvi2g738 Vvi2g738 738
2 9179292 9192139 + Vvi2g739 Vvi2g739 739
2 9220340 9222116 + Vvi2g740 Vvi2g740 740
2 9295260 9321129 + Vvi2g741 Vvi2g741 741
       

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