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
Vvi2g572 . . . . . . . Bma14g00061 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy04g00034 . . . . . . Bpe11g00293 . . . . Cmo19g00396 . . . . . . Bhi05g00568 Tan07g1907 . Lac11g2349 Hepe06g1723 . Lcy12g1883 Cla09g01201 Cam09g1269 Cec09g1283 . . . Cre09g1229 . . . Cme04g00043
Vvi2g573 . . . . . . . . . . Cma02g01579 . Car02g01343 . . . Cpe05g00211 . . . . . . . . . . . . . . Cone8ag0437 Cone12ag0422 . . . . Chy04g00035 . . . Bda07g00129 Bda09g00688 Bpe08g00872 Bpe11g00360 . . Sed01g4061 Cmo02g01621 Cmo19g00395 . . . . . . Bhi05g00566 Tan07g1908 Cmetu04g1824 Lac11g2350 Hepe06g1725 . . Cla09g01200 Cam09g1268 Cec09g1282 Cco09g1316 . . Cre09g1228 . Csa03g04668 . Cme04g00044
Vvi2g574 . . . . . . Bma07g00986 . Cmo06g00850 Cmo16g01145 . . . . Sed07g1309 Cpe14g00906 . Bhi11g00095 Tan01g2117 Cmetu06g1743 . Hepe06g1072 Mch10g1608 . Cla10g00202 Cam10g0208 Cec10g0213 Cco10g0214 Clacu10g0211 Cmu10g1054 Cre10g0462 Cone8ag0438 Cone12ag0423 . . Lsi07g01243 . . Cme06g02514 . Blo19g00158 . Bda09g00689 Bpe08g00871 . . . . . . Cma06g00827 Cma16g01096 . Car16g01038 . . . . . . . . . . . . . . . . . Csa03g00217 Chy06g02103 .
Vvi2g575 . . Bda06g01304 . . . . . Cmo06g00851 . Cma02g01580 . Car02g01344 . . . Cpe05g00210 Bhi11g00096 . . . . Mch10g1609 . Cla10g00201 . . . . . . Cone8ag0440 Cone12ag0425 Cone6ag0626 Cone9ag0627 Lsi07g01242 . Chy04g00037 Cme06g02513 Blo03g00818 . Bda07g00128 Bda09g00691 Bpe08g00866 Bpe11g00359 . . . Cmo02g01622 Cmo19g00393 Cma06g00828 Cma16g01095 . Car16g01036 Cpe08g00701 . Bhi05g00563 . . . . . Lcy12g1885 Cla09g01197 . . . . . . . Csa03g04665 Chy06g02104 Cme04g00046
Vvi2g576 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g577 Blo02g01008 . . Bda08g00612 Bpe05g00544 . . . Cmo06g00852 Cmo16g01144 . . . . Sed02g1450 Cpe14g00904 . Bhi11g00097 Tan01g2119 Cmetu06g1039 . Hepe06g1069 Mch10g1610 . Cla10g00200 Cam10g0206 Cec10g0211 Cco10g0212 Clacu10g0209 Cmu10g1052 Cre10g0460 . Cone12ag0426 . . Lsi07g01241 . . Cme06g02512 . . Bda07g00053 . . . . . . . . Cma06g00829 Cma16g01094 . Car16g01035 . . . . . . . . . . . . . . . . . Csa03g00215 Chy06g02105 .
Vvi2g578 . Blo03g00133 Bda06g01303 . . Bpe07g00202 . . Cmo06g00853 . . . . . . . . Bhi11g00099 . . . Hepe06g1068 Mch10g1611 . Cla10g00199 Cam10g0205 Cec10g0210 Cco10g0211 Clacu10g0208 Cmu10g1051 Cre10g0459 Cone8ag0441 . . . Lsi07g01239 . . Cme06g02510 . . . . . . . Bma12g00197 . . . Cma06g00830 . . . . . . . . . . . . . . . . . . . . Csa03g00213 Chy06g02107 .
Vvi2g579 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy04g00040 . Blo03g00821 . Bda07g00127 . . Bpe11g00358 . . . . Cmo19g00390 . . . . . . . . . . . . . Cla09g01192 Cam09g1259 Cec09g1274 Cco09g1310 . . Cre09g1223 . Csa03g04662 . Cme04g00049
Vvi2g580 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo03g00822 . . . . . . . . . Cmo19g00389 . . . . . . . . . . . . . Cla09g01190 Cam09g1256 Cec09g1271 . . . Cre09g1218 . . . .
Vvi2g581 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0620 . Cone6ag0624 Cone9ag0626 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 43714033 43720081 + Bda023157.1 Bda06g01303 1303
6 43720937 43722737 - Bda023158.1 Bda06g01304 1304
7 814650 820903 + Bda033826 Bda07g00053 53
7 1560373 1622143 + Bda025192.1 Bda07g00127 127
7 1623078 1624854 - Bda025193.1 Bda07g00128 128
7 1633263 1633907 + Bda025194.1 Bda07g00129 129
8 6257264 6259326 - Bda029074.1 Bda08g00612 612
9 10776701 10781450 - Bda031348.1 Bda09g00688 688
9 10795466 10798467 + Bda031349.1 Bda09g00689 689
9 10842602 10844807 + Bda031352.1 Bda09g00691 691
5 13760169 13762973 - XM_039032307.1 Bhi05g00563 563
5 13974033 13980988 + XM_039033021.1 Bhi05g00566 566
5 14085517 14088581 + XM_039031589.1 Bhi05g00568 568
11 2262627 2266886 + XM_039047214.1 Bhi11g00095 95
11 2317523 2322003 + XM_039047884.1 Bhi11g00096 96
11 2322704 2325371 - XM_039047882.1 Bhi11g00097 97
11 2358396 2364106 - XM_039048795.1 Bhi11g00099 99
2 39179899 39181994 + BLOR10738 Blo02g01008 1008
3 3825223 3829590 + BLOR11314 Blo03g00133 133
3 33622228 33623881 + BLOR11999 Blo03g00818 818
3 33691231 33701785 - BLOR12002 Blo03g00821 821
3 33713497 33725408 - BLOR12003 Blo03g00822 822
19 6306740 6319371 + BLOR09501 Blo19g00158 158
7 38249238 38252241 - Bma026144.1 Bma07g00986 986
12 2629956 2633941 - Bma007083.1 Bma12g00197 197
14 774532 775506 - Bma030636 Bma14g00061 61
5 19630262 19632319 + Bpe017961.2 Bpe05g00544 544
7 1389464 1393807 - Bpe021012.1 Bpe07g00202 202
8 11027339 11029513 - Bpe022989.1 Bpe08g00866 866
8 11103941 11106967 - Bpe022994.1 Bpe08g00871 871
8 11116354 11121121 + Bpe022995.1 Bpe08g00872 872
11 2150793 2151153 - Bpe003668.1 Bpe11g00293 293
11 2637839 2697530 + Bpe003732.1 Bpe11g00358 358
11 2698435 2700254 - Bpe003733.1 Bpe11g00359 359
11 2702473 2714202 + Bpe003734.1 Bpe11g00360 360
9 14680665 14692860 + CaPI482276_09g012560.1 Cam09g1256 1256
9 14709197 14715882 + CaPI482276_09g012590.1 Cam09g1259 1259
9 14918944 14924742 + CaPI482276_09g012680.1 Cam09g1268 1268
9 14936034 14938438 + CaPI482276_09g012690.1 Cam09g1269 1269
10 3750354 3757812 + CaPI482276_10g002050.1 Cam10g0205 205
10 3763299 3765628 + CaPI482276_10g002060.1 Cam10g0206 206
10 3783935 3787083 - CaPI482276_10g002080.1 Cam10g0208 208
2 8880816 8885563 - Carg08810-RA Car02g01343 1343
2 8890867 8892892 + Carg08811-RA Car02g01344 1344
16 8891222 8893732 + Carg23239-RA Car16g01035 1035
16 8894098 8897204 - Carg23240-RA Car16g01036 1036
16 8903653 8905918 - Carg23242-RA Car16g01038 1038
9 14673925 14766498 + CcPI632755_09g013100.1 Cco09g1310 1310
9 14947959 14954122 + CcPI632755_09g013160.1 Cco09g1316 1316
10 2187042 2195635 + CcPI632755_10g002110.1 Cco10g0211 211
10 2201128 2203460 + CcPI632755_10g002120.1 Cco10g0212 212
10 2230461 2233659 - CcPI632755_10g002140.1 Cco10g0214 214
9 14822261 14834522 + CePI673135_09g012710.1 Cec09g1271 1271
9 14866538 14931519 + CePI673135_09g012740.1 Cec09g1274 1274
9 15097639 15103065 + CePI673135_09g012820.1 Cec09g1282 1282
9 15124001 15126431 + CePI673135_09g012830.1 Cec09g1283 1283
10 2286783 2295357 + CePI673135_10g002100.1 Cec10g0210 210
10 2300858 2303188 + CePI673135_10g002110.1 Cec10g0211 211
10 2333718 2336913 - CePI673135_10g002130.1 Cec10g0213 213
4 326972 331701 - Chy4G067520.1 Chy04g00034 34
4 331704 337027 - Chy4G067530.1 Chy04g00035 35
4 358198 361882 + Chy4G067550.1 Chy04g00037 37
4 368153 444914 - Chy4G067580.1 Chy04g00040 40
6 25206342 25211734 + Chy6G126310.1 Chy06g02103 2103
6 25217613 25221150 + Chy6G126320.1 Chy06g02104 2104
6 25222541 25224851 - Chy6G126330.1 Chy06g02105 2105
6 25233310 25238389 - Chy6G126350.1 Chy06g02107 2107
10 2494872 2503359 + ClG42_10g0020800.10 Clacu10g0208 208
10 2508822 2511090 + ClG42_10g0020900.10 Clacu10g0209 209
10 2529346 2532513 - ClG42_10g0021100.10 Clacu10g0211 211
9 14737591 14749316 + ClCG09G012500.2 Cla09g01190 1190
9 14759850 14834471 + ClCG09G012520.1 Cla09g01192 1192
9 14876219 14878931 - ClCG09G012560.1 Cla09g01197 1197
9 14964704 14969730 + ClCG09G012590.1 Cla09g01200 1200
9 14972513 14984309 + ClCG09G012610.2 Cla09g01201 1201
10 2309531 2318071 + ClCG10G002040.2 Cla10g00199 199
10 2323515 2326076 + ClCG10G002060.1 Cla10g00200 200
10 2326448 2329951 - ClCG10G002070.2 Cla10g00201 201
10 2344226 2348396 - ClCG10G002080.1 Cla10g00202 202
2 8969120 8973857 - CmaCh02G015790.1 Cma02g01579 1579
2 8978183 8980847 + CmaCh02G015800.1 Cma02g01580 1580
6 4485780 4489566 + CmaCh06G008270.1 Cma06g00827 827
6 4498750 4501714 + CmaCh06G008280.1 Cma06g00828 828
6 4502013 4504134 - CmaCh06G008290.1 Cma06g00829 829
6 4508247 4512979 - CmaCh06G008300.1 Cma06g00830 830
16 8427258 8430320 + CmaCh16G010940.1 Cma16g01094 1094
16 8430207 8433910 - CmaCh16G010950.1 Cma16g01095 1095
16 8437627 8442933 - CmaCh16G010960.1 Cma16g01096 1096
4 282628 284869 - MELO3C003342.2.1 Cme04g00043 43
4 286264 293188 - MELO3C003343.2.1 Cme04g00044 44
4 311634 314120 + MELO3C003345.2.1 Cme04g00046 46
4 317258 393583 - MELO3C003359.2.1 Cme04g00049 49
6 32158929 32164551 + MELO3C013885.2.1 Cme06g02510 2510
6 32172958 32176042 + MELO3C013887.2.1 Cme06g02512 2512
6 32176348 32180676 - MELO3C013888.2.1 Cme06g02513 2513
6 32185468 32192119 - MELO3C013889.2.1 Cme06g02514 2514
4 33161393 33166781 + PI0019119.1 Cmetu04g1824 1824
6 29230317 29233299 - PI0024717.1 Cmetu06g1039 1039
6 29214584 29218932 + PI0026730.1 Cmetu06g1743 1743
2 9341993 9346720 - CmoCh02G016210.1 Cmo02g01621 1621
2 9352986 9355453 + CmoCh02G016220.1 Cmo02g01622 1622
6 4760229 4764170 + CmoCh06G008500.1 Cmo06g00850 850
6 4774596 4777803 + CmoCh06G008510.1 Cmo06g00851 851
6 4777784 4780072 - CmoCh06G008520.1 Cmo06g00852 852
6 4783711 4789298 - CmoCh06G008530.1 Cmo06g00853 853
16 8164765 8168300 + CmoCh16G011440.1 Cmo16g01144 1144
16 8174550 8178866 - CmoCh16G011450.1 Cmo16g01145 1145
19 4502717 4507341 + CmoCh19G003890.1 Cmo19g00389 389
19 4514446 4585145 + CmoCh19G003900.1 Cmo19g00390 390
19 4588525 4592446 - CmoCh19G003930.1 Cmo19g00393 393
19 4597208 4599677 + CmoCh19G003950.1 Cmo19g00395 395
19 4601356 4603857 + CmoCh19G003960.1 Cmo19g00396 396
10 2645825 2654312 + CmPI595203_10g010510.1 Cmu10g1051 1051
10 2659778 2662046 + CmPI595203_10g010520.1 Cmu10g1052 1052
10 2680326 2683494 - CmPI595203_10g010540.1 Cmu10g1054 1054
6 3123090 3124210 + Conep06aG0064300.1 Cone6ag0624 624
6 3169346 3171559 - Conep06aG0064500.1 Cone6ag0626 626
8 2740923 2745311 - Conep08aG0045400.1 Cone8ag0437 437
8 2751960 2755447 + Conep08aG0045500.1 Cone8ag0438 438
8 2761272 2764036 + Conep08aG0045700.1 Cone8ag0440 440
8 2773256 2776761 - Conep08aG0045800.1 Cone8ag0441 441
8 6109588 6119046 - Conep08aG0064100.1 Cone8ag0620 620
9 2982164 2983166 + Conep09aG0064000.1 Cone9ag0626 626
9 2988239 2990743 - Conep09aG0064100.1 Cone9ag0627 627
12 2511124 2511639 - Conep12aG0043700.1 Cone12ag0422 422
12 2512886 2516387 + Conep12aG0043800.1 Cone12ag0423 423
12 2521804 2524450 + Conep12aG0044000.1 Cone12ag0425 425
12 2526705 2529823 - Conep12aG0044100.1 Cone12ag0426 426
5 1162533 1165137 - Cp4.1LG05g01890.1 Cpe05g00210 210
5 1169844 1174678 + Cp4.1LG05g01960.1 Cpe05g00211 211
8 5462444 5465657 + Cp4.1LG08g07000.1 Cpe08g00701 701
14 7612220 7616732 + Cp4.1LG14g09000.1 Cpe14g00904 904
14 7622538 7628111 - Cp4.1LG14g09050.1 Cpe14g00906 906
9 14822857 14835109 + CrPI670011_09g012180.1 Cre09g1218 1218
9 14856757 14916613 + CrPI670011_09g012230.1 Cre09g1223 1223
9 15078931 15085105 + CrPI670011_09g012280.1 Cre09g1228 1228
9 15097996 15100416 + CrPI670011_09g012290.1 Cre09g1229 1229
10 3612890 3621560 + CrPI670011_10g004590.1 Cre10g0459 459
10 3627033 3629364 + CrPI670011_10g004600.1 Cre10g0460 460
10 3645780 3648939 - CrPI670011_10g004620.1 Cre10g0462 462
3 1729664 1735193 + CsaV3_3G002130.1 Csa03g00213 213
3 1743127 1745945 + CsaV3_3G002150.1 Csa03g00215 215
3 1755058 1761459 - CsaV3_3G002170.1 Csa03g00217 217
3 40505043 40575692 + CsaV3_3G049680.1 Csa03g04662 4662
3 40583456 40585386 - CsaV3_3G049710.1 Csa03g04665 4665
3 40605454 40612381 + CsaV3_3G049740.1 Csa03g04668 4668
6 59034659 59040620 + Hsped.06g10680.1 Hepe06g1068 1068
6 59046041 59048872 + Hsped.06g10690.1 Hepe06g1069 1069
6 59082446 59087133 - Hsped.06g10720.1 Hepe06g1072 1072
6 68214151 68217514 - Hsped.06g17230.1 Hepe06g1723 1723
6 68224331 68231836 - Hsped.06g17250.1 Hepe06g1725 1725
11 39542678 39546651 - Lag0032987.1 Lac11g2349 2349
11 39549924 39554773 - Lag0032988.1 Lac11g2350 2350
12 40013098 40015418 - Maker00037896 Lcy12g1883 1883
12 40047851 40050942 + Maker00038039 Lcy12g1885 1885
7 18129267 18138038 + Lsi07G012390.1 Lsi07g01239 1239
7 18144380 18146877 + Lsi07G012410.1 Lsi07g01241 1241
7 18148597 18153491 - Lsi07G012420.1 Lsi07g01242 1242
7 18166398 18171334 - Lsi07G012430.1 Lsi07g01243 1243
10 16156956 16160225 + MC10g1274 Mch10g1608 1608
10 16173353 16177771 + MC10g1275 Mch10g1609 1609
10 16177917 16180651 - MC10g1276 Mch10g1610 1610
10 16185385 16190211 - MC10g1277 Mch10g1611 1611
1 69566470 69575951 - Sed0017522.1 Sed01g4061 4061
2 50550350 50553798 + Sed0014728.1 Sed02g1450 1450
7 9851384 9855775 + Sed0006691.1 Sed07g1309 1309
1 24379188 24383718 + Tan0004811.1 Tan01g2117 2117
1 24413004 24415843 - Tan0002953.1 Tan01g2119 2119
7 70617551 70620330 - Tan0014667.1 Tan07g1907 1907
7 70625678 70632595 - Tan0022453.1 Tan07g1908 1908
2 5715972 5719517 - Vvi2g572 Vvi2g572 572
2 5723376 5725314 - Vvi2g573 Vvi2g573 573
2 5757585 5775765 + Vvi2g574 Vvi2g574 574
2 5785738 5790833 + Vvi2g575 Vvi2g575 575
2 5798021 5798307 + Vvi2g576 Vvi2g576 576
2 5804012 5807077 - Vvi2g577 Vvi2g577 577
2 5811387 5820436 - Vvi2g578 Vvi2g578 578
2 5826769 5900307 - Vvi2g579 Vvi2g579 579
2 5915694 5997069 - Vvi2g580 Vvi2g580 580
2 5999580 6000966 - Vvi2g581 Vvi2g581 581
       

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