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
Vvi2g52 . . . . . . . Bma14g00595 . Cmo16g00627 . . . . . Cpe14g00489 . . . . . . . . Cla07g00743 Cam07g0795 Cec07g0861 Cco07g0830 Clacu07g0776 Cmu07g0783 Cre07g1135 . . Cone6ag0816 Cone9ag0816 . . . Cme07g01610 . . . . . . . . . . . . Cma16g00578 . . . . . . . . . . . . . . . . . . . Csa04g00615 Chy07g01196 .
Vvi2g53 . . . . . . Bma07g01675 Bma14g00618 . Cmo16g00626 Cma02g01421 Cma15g01255 Car02g01190 Car15g01132 . Cpe14g00488 Cpe05g00364 . . . . . . . Cla07g00739 Cam07g0792 Cec07g0857 Cco07g0827 Clacu07g0773 Cmu07g0782 Cre07g1133 Cone8ag0272 Cone12ag0279 Cone6ag0817 . . Csa05g00235 Chy09g01265 Cme07g01609 . Blo19g00348 Bda07g00473 Bda09g00023 . Bpe11g00651 . . . Cmo02g01454 Cmo15g01321 . Cma16g00577 . . . Cpe13g00130 Bhi12g00182 . . Lac11g2040 Hepe06g1508 . Lcy12g1604 Cla01g00224 Cam01g0232 Cec01g0223 Cco01g0233 Clacu01g0227 Cmu01g0220 Cre09g2290 Lsi09g00211 Csa04g00616 Chy07g01195 Cme09g01804
Vvi2g54 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g55 Blo02g01125 Blo03g00230 Bda06g00124 Bda08g00500 Bpe05g00664 Bpe07g00091 . . . Cmo16g00625 . . . . . Cpe14g00487 Cpe05g00634 . . . . . . . Cla07g00738 Cam07g0791 Cec07g0856 Cco07g0826 Clacu07g0772 Cmu07g0781 Cre07g1132 . . Cone14ag0046 . . . . Cme07g01608 . . Bda07g01911 . . . Bma05g00838 Bma12g00061 . Cmo02g01105 . . Cma16g00576 . . . . . . . . . . . . . . . . . . . Csa04g00618 Chy07g01194 .
Vvi2g56 . . . . . . . . . . Cma02g01000 . . . . . . . . . . . . . . . . . . . . . . . . . . Chy09g01268 . . . . . . . . . . Cmo02g01450 . . . . . . . Bhi12g00177 . . . . . Lcy12g1599 Cla01g00219 Cam01g0226 Cec01g0217 Cco01g0227 Clacu01g0221 Cmu01g0214 Cre09g2295 Lsi09g00206 . . Cme09g01809
Vvi2g57 . . . . . . . . . . Cma02g01417 . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g00230 Chy09g01269 . . . . . . . . . . Cmo02g01449 Cmo15g01324 . . . . . . Bhi12g00176 . . Lac11g2036 Hepe06g1504 . Lcy12g1598 Cla01g00217 Cam01g0224 Cec01g0215 Cco01g0223 Clacu01g0219 Cmu01g0212 Cre09g2296 Lsi09g00204 . . Cme09g01810
Vvi2g58 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g59 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0270 . . . . . Chy09g01270 . . . Bda07g00471 . . Bpe11g00649 . . . Cmo02g01448 . . . . . . . Bhi12g00175 . . . . . Lcy12g1597 Cla01g00215 Cam01g0222 Cec01g0213 Cco01g0221 Clacu01g0216 Cmu01g0210 Cre09g2298 Lsi09g00202 . . Cme09g01813
Vvi2g60 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g61 Blo02g01126 . Bda06g00125 Bda08g00499 Bpe05g00665 Bpe07g00090 . . Cmo06g01077 . Cma02g01416 Cma15g01257 Car02g01186 Car15g01134 . . Cpe05g00366 . . . . . . . . . . . . . . Cone8ag0269 Cone12ag0275 Cone6ag0819 Cone9ag0818 . Csa05g00229 Chy09g01271 . . . . . . . . Bma12g00060 . Cmo02g01447 Cmo15g01325 . . Car06g00886 . . Cpe13g00128 Bhi12g00174 . . Lac11g2034 Hepe06g1503 . Lcy12g1596 Cla01g00212 Cam01g0217 Cec01g0211 Cco01g0215 Clacu01g0212 Cmu01g0206 Cre09g2301 Lsi09g00200 . . Cme09g01814
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 1930880 1932280 - Bda023319.1 Bda06g00124 124
6 1938775 1940465 + Bda023320.1 Bda06g00125 125
7 5992326 5994132 + Bda025572.1 Bda07g00471 471
7 6001310 6007118 - Bda025574.1 Bda07g00473 473
7 36541976 36542818 - Bda028886.1 Bda07g01911 1911
8 5079124 5080750 - Bda024950.1 Bda08g00499 499
8 5089754 5091262 + Bda024951.1 Bda08g00500 500
9 376251 377396 - Bda030542.1 Bda09g00023 23
12 4990682 4992798 - XM_039020082.1 Bhi12g00174 174
12 5039072 5040866 + XM_039051150.1 Bhi12g00175 175
12 5041900 5044368 + XM_039018349.1 Bhi12g00176 176
12 5085708 5087470 - XM_039051153.1 Bhi12g00177 177
12 5453931 5463806 - XM_039018419.1 Bhi12g00182 182
2 42531761 42533192 - BLOR10855 Blo02g01125 1125
2 42559296 42561008 + BLOR10856 Blo02g01126 1126
3 5107299 5108743 - BLOR11411 Blo03g00230 230
19 22551928 22558488 + BLOR09691 Blo19g00348 348
5 45748871 45750157 - Bma021948.1 Bma05g00838 838
7 52310148 52310610 + Bma026972.1 Bma07g01675 1675
12 1167462 1170041 - Bma006931.1 Bma12g00060 60
12 1182126 1183482 + Bma006932.1 Bma12g00061 61
14 6455251 6455998 + Bma011031.1 Bma14g00595 595
14 6679680 6685771 + Bma011058.1 Bma14g00618 618
5 20364210 20365736 - Bpe018077.1 Bpe05g00664 664
5 20369429 20371022 + Bpe018078.1 Bpe05g00665 665
7 656852 658540 - Bpe020903.1 Bpe07g00090 90
7 662075 663418 + Bpe020904.1 Bpe07g00091 91
11 4994545 4996414 + Bpe004005.1 Bpe11g00649 649
11 5005700 5011518 - Bpe004007.1 Bpe11g00651 651
1 2508658 2510320 - CaPI482276_01g002170.1 Cam01g0217 217
1 2531690 2532199 - CaPI482276_01g002220.1 Cam01g0222 222
1 2539123 2543349 - CaPI482276_01g002240.1 Cam01g0224 224
1 2547330 2550122 - CaPI482276_01g002260.1 Cam01g0226 226
1 2582596 2591474 - CaPI482276_01g002320.1 Cam01g0232 232
7 19832187 19833635 + CaPI482276_07g007910.1 Cam07g0791 791
7 19836005 19848438 - CaPI482276_07g007920.1 Cam07g0792 792
7 19956890 19957680 + CaPI482276_07g007950.1 Cam07g0795 795
2 8080915 8083153 - Carg02562-RA Car02g01186 1186
2 8096251 8104131 - Carg02558-RA Car02g01190 1190
6 6893392 6895604 - Carg20863-RA Car06g00886 886
15 8921630 8929555 + Carg16610-RA Car15g01132 1132
15 8943571 8945633 + Carg21258-RA Car15g01134 1134
1 2113183 2114839 - CcPI632755_01g002150.1 Cco01g0215 215
1 2143720 2145580 - CcPI632755_01g002210.1 Cco01g0221 221
1 2154373 2154612 - CcPI632755_01g002230.1 Cco01g0223 223
1 2163193 2163504 - CcPI632755_01g002270.1 Cco01g0227 227
1 2197241 2206128 - CcPI632755_01g002330.1 Cco01g0233 233
7 19104936 19106384 + CcPI632755_07g008260.1 Cco07g0826 826
7 19108723 19121136 - CcPI632755_07g008270.1 Cco07g0827 827
7 19215599 19216389 + CcPI632755_07g008300.1 Cco07g0830 830
1 2106908 2108567 - CePI673135_01g002110.1 Cec01g0211 211
1 2118255 2120649 + CePI673135_01g002130.1 Cec01g0213 213
1 2131371 2132976 + CePI673135_01g002150.1 Cec01g0215 215
1 2142242 2144867 - CePI673135_01g002170.1 Cec01g0217 217
1 2177929 2186287 - CePI673135_01g002230.1 Cec01g0223 223
7 21027495 21028960 + CePI673135_07g008560.1 Cec07g0856 856
7 21031355 21043713 - CePI673135_07g008570.1 Cec07g0857 857
7 21104009 21104805 + CePI673135_07g008610.1 Cec07g0861 861
7 16798172 16799618 + Chy7G140240.1 Chy07g01194 1194
7 16804249 16813027 - Chy7G140250.1 Chy07g01195 1195
7 16821501 16822281 + Chy7G140260.1 Chy07g01196 1196
9 14687245 14696057 + Chy9G169810.1 Chy09g01265 1265
9 14713630 14715667 + Chy9G169840.1 Chy09g01268 1268
9 14716754 14718506 + Chy9G169850.1 Chy09g01269 1269
9 14720241 14722055 - Chy9G169860.1 Chy09g01270 1270
9 14724250 14725884 + Chy9G169870.1 Chy09g01271 1271
1 2125688 2127337 - ClG42_01g0021200.10 Clacu01g0212 212
1 2147264 2149124 - ClG42_01g0021600.10 Clacu01g0216 216
1 2157238 2160342 - ClG42_01g0021900.10 Clacu01g0219 219
1 2164493 2167473 - ClG42_01g0022100.10 Clacu01g0221 221
1 2199212 2207956 - ClG42_01g0022700.10 Clacu01g0227 227
7 19489641 19491089 + ClG42_07g0077200.10 Clacu07g0772 772
7 19493445 19505885 - ClG42_07g0077300.10 Clacu07g0773 773
7 19617270 19618180 + ClG42_07g0077600.10 Clacu07g0776 776
1 2149664 2151615 - ClCG01G002190.1 Cla01g00212 212
1 2172056 2173916 - ClCG01G002220.1 Cla01g00215 215
1 2182029 2185133 - ClCG01G002240.2 Cla01g00217 217
1 2189284 2192264 - ClCG01G002247.1 Cla01g00219 219
1 2227591 2236994 - ClCG01G002290.2 Cla01g00224 224
7 20578252 20580234 + ClCG07G007760.1 Cla07g00738 738
7 20587102 20597396 - ClCG07G007770.2 Cla07g00739 739
7 20713383 20714473 + ClCG07G007810.2 Cla07g00743 743
2 5952271 5953886 + CmaCh02G010000.1 Cma02g01000 1000
2 8175229 8177585 - CmaCh02G014160.1 Cma02g01416 1416
2 8178427 8180164 + CmaCh02G014170.1 Cma02g01417 1417
2 8188238 8196671 - CmaCh02G014210.1 Cma02g01421 1421
15 7968799 7973237 + CmaCh15G012550.1 Cma15g01255 1255
15 7986896 7989548 + CmaCh15G012570.1 Cma15g01257 1257
16 2975322 2977698 + CmaCh16G005760.1 Cma16g00576 576
16 2980222 2988524 - CmaCh16G005770.1 Cma16g00577 577
16 2989374 2990696 + CmaCh16G005780.1 Cma16g00578 578
7 21875859 21878905 + MELO3C016332.2.1 Cme07g01608 1608
7 21881148 21891536 - MELO3C016333.2.1 Cme07g01609 1609
7 21898295 21899523 + MELO3C016334.2.1 Cme07g01610 1610
9 22411185 22420289 + MELO3C005719.2.1 Cme09g01804 1804
9 22438605 22439338 + MELO3C028070.2.1 Cme09g01809 1809
9 22438939 22444579 + MELO3C000695.2.1 Cme09g01810 1810
9 22458367 22460180 - MELO3C005724.2.1 Cme09g01813 1813
9 22462902 22465190 + MELO3C005725.2.1 Cme09g01814 1814
2 6688987 6690318 - CmoCh02G011050.1 Cmo02g01105 1105
2 8523586 8525874 - CmoCh02G014470.1 Cmo02g01447 1447
2 8526968 8528553 + CmoCh02G014480.1 Cmo02g01448 1448
2 8530879 8532464 + CmoCh02G014490.1 Cmo02g01449 1449
2 8534415 8536153 + CmoCh02G014500.1 Cmo02g01450 1450
2 8544205 8552336 - CmoCh02G014540.1 Cmo02g01454 1454
6 8334492 8336948 - CmoCh06G010770.1 Cmo06g01077 1077
15 9072018 9079680 + CmoCh15G013210.1 Cmo15g01321 1321
15 9086648 9092249 - CmoCh15G013240.1 Cmo15g01324 1324
15 9091970 9094887 + CmoCh15G013250.1 Cmo15g01325 1325
16 3075880 3078064 + CmoCh16G006250.1 Cmo16g00625 625
16 3081469 3089597 - CmoCh16G006260.1 Cmo16g00626 626
16 3091845 3092844 + CmoCh16G006270.1 Cmo16g00627 627
1 2078839 2080488 - CmPI595203_01g002060.1 Cmu01g0206 206
1 2100390 2102251 - CmPI595203_01g002100.1 Cmu01g0210 210
1 2110313 2113422 - CmPI595203_01g002120.1 Cmu01g0212 212
1 2117568 2120550 - CmPI595203_01g002140.1 Cmu01g0214 214
1 2152290 2161033 - CmPI595203_01g002200.1 Cmu01g0220 220
7 19700188 19701636 + CmPI595203_07g007810.1 Cmu07g0781 781
7 19703980 19716430 - CmPI595203_07g007820.1 Cmu07g0782 782
7 19831839 19832635 + CmPI595203_07g007830.1 Cmu07g0783 783
6 4145736 4146613 - Conep06aG0084000.1 Cone6ag0816 816
6 4153681 4159026 + Conep06aG0084100.1 Cone6ag0817 817
6 4171400 4175376 + Conep06aG0084300.1 Cone6ag0819 819
8 1560906 1562530 - Conep08aG0028400.1 Cone8ag0269 269
8 1563364 1565517 + Conep08aG0028500.1 Cone8ag0270 270
8 1570872 1578629 - Conep08aG0028700.1 Cone8ag0272 272
9 3925558 3926223 - Conep09aG0083400.1 Cone9ag0816 816
9 3947341 3949503 + Conep09aG0083600.1 Cone9ag0818 818
12 1480057 1481706 - Conep12aG0028700.1 Cone12ag0275 275
12 1493637 1501389 - Conep12aG0029100.1 Cone12ag0279 279
14 299694 300952 + Conep14aG0004800.1 Cone14ag0046 46
5 2040696 2048264 + Cp4.1LG05g03210.1 Cpe05g00364 364
5 2062288 2064865 + Cp4.1LG05g03050.1 Cpe05g00366 366
5 3882787 3885617 + Cp4.1LG05g06270.1 Cpe05g00634 634
13 925518 927905 - Cp4.1LG13g01330.1 Cpe13g00128 128
13 939807 947162 - Cp4.1LG13g01340.1 Cpe13g00130 130
14 3093115 3095845 + Cp4.1LG14g02280.1 Cpe14g00487 487
14 3098193 3106242 - Cp4.1LG14g02250.1 Cpe14g00488 488
14 3108368 3109272 + Cp4.1LG14g02260.1 Cpe14g00489 489
7 23052331 23053776 + CrPI670011_07g011320.1 Cre07g1132 1132
7 23056507 23068508 - CrPI670011_07g011330.1 Cre07g1133 1133
7 23180318 23181291 + CrPI670011_07g011350.1 Cre07g1135 1135
9 42128871 42137870 + CrPI670011_09g022900.1 Cre09g2290 2290
9 42164778 42165911 + CrPI670011_09g022950.1 Cre09g2295 2295
9 42171240 42178653 + CrPI670011_09g022960.1 Cre09g2296 2296
9 42183498 42186319 - CrPI670011_09g022980.1 Cre09g2298 2298
9 42207983 42209638 + CrPI670011_09g023010.1 Cre09g2301 2301
4 4069326 4070699 - CsaV3_4G006150.1 Csa04g00615 615
4 4078163 4088463 + CsaV3_4G006160.1 Csa04g00616 616
4 4089954 4094047 - CsaV3_4G006180.1 Csa04g00618 618
5 1400483 1403241 - CsaV3_5G002290.1 Csa05g00229 229
5 1405040 1409109 + CsaV3_5G002300.1 Csa05g00230 230
5 1426967 1436539 - CsaV3_5G002350.1 Csa05g00235 235
6 65650825 65655739 - Hsped.06g15030.1 Hepe06g1503 1503
6 65662859 65665065 + Hsped.06g15040.1 Hepe06g1504 1504
6 65689040 65700546 - Hsped.06g15080.1 Hepe06g1508 1508
11 36011159 36012733 - Lag0032672.1 Lac11g2034 2034
11 36041776 36043590 - Lag0032674.1 Lac11g2036 2036
11 36098162 36109741 - Lag0032678.1 Lac11g2040 2040
12 36140178 36143082 - Maker00029230 Lcy12g1596 1596
12 36148719 36150502 + Maker00029304 Lcy12g1597 1597
12 36152353 36154157 - Maker00029329 Lcy12g1598 1598
12 36157895 36159690 - Maker00029410 Lcy12g1599 1599
12 36224113 36237831 - Maker00029303 Lcy12g1604 1604
9 2116532 2120898 - Lsi09G002000.1 Lsi09g00200 200
9 2130851 2133103 + Lsi09G002020.1 Lsi09g00202 202
9 2142119 2144832 - Lsi09G002040.1 Lsi09g00204 204
9 2152547 2154989 - Lsi09G002060.1 Lsi09g00206 206
9 2194576 2205782 - Lsi09G002110.1 Lsi09g00211 211
2 596474 597740 - Vvi2g52 Vvi2g52 52
2 621476 631791 + Vvi2g53 Vvi2g53 53
2 634436 638469 - Vvi2g54 Vvi2g54 54
2 659540 661587 + Vvi2g55 Vvi2g55 55
2 662066 666143 - Vvi2g56 Vvi2g56 56
2 666667 672560 - Vvi2g57 Vvi2g57 57
2 674197 674380 + Vvi2g58 Vvi2g58 58
2 678146 679886 + Vvi2g59 Vvi2g59 59
2 685299 688031 - Vvi2g60 Vvi2g60 60
2 706021 708527 + Vvi2g61 Vvi2g61 61
       

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