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
Vvi2g312 . . . . . . . . . . Cma02g01443 Cma15g01234 Car02g01211 Car15g01111 . . Cpe05g00343 . . . . . . . . . . . . . . Cone8ag0298 Cone12ag0304 . . . Csa05g00272 Chy09g01236 . . . . . . . . . . Cmo02g01479 Cmo15g01297 . . . . . Cpe13g00152 Bhi12g00274 . . Lac11g2079 Hepe06g1537 . Lcy12g1640 . . . . . . . Lsi09g00248 . . Cme09g01770
Vvi2g313 . . . . . . . Bma14g00701 . . Cma02g01444 . Car02g01212 . . . Cpe05g00342 . . . . . . . . . . . . . . Cone8ag0299 Cone12ag0305 . . . Csa05g00273 Chy09g01235 . Blo03g00340 . Bda07g00481 . . . . . . Cmo02g01481 . . . . . . . Bhi12g00272 . . . Hepe06g1538 . Lcy12g1641 Cla01g00256 Cam01g0262 Cec01g0254 Cco01g0267 Clacu01g0260 Cmu01g0249 Cre09g2260 Lsi09g00249 . . Cme09g01769
Vvi2g314 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g00276 Chy09g01233 . . . . . . . . . . . . . . . . . . Bhi12g00270 . . Lac11g2084 Hepe06g1539 . Lcy12g1643 Cla01g00257 Cam01g0264 Cec01g0255 Cco01g0270 Clacu01g0263 Cmu01g0252 Cre09g2257 Lsi09g00252 . . Cme09g01768
Vvi2g315 . . . . . . . . . . Cma02g01447 . Car02g01215 . . . Cpe05g00340 . . . . . . . . . . . . . . Cone8ag0300 . . . . Csa05g00277 Chy09g01232 . . . . . . . . . . Cmo02g01484 . . . . . . . Bhi12g00269 . . Lac11g2086 Hepe06g1540 . Lcy12g1646 Cla01g00258 Cam01g0265 Cec01g0256 Cco01g0271 Clacu01g0264 Cmu01g0253 Cre09g2256 Lsi09g00253 . . Cme09g01767
Vvi2g316 . . . . . Bpe07g00105 . . . . . . . . . . . Bhi11g00395 . . . . . . . . . . . . . . . . Cone9ag0787 Lsi07g01416 Csa05g00148 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g317 Blo02g01111 Blo03g00217 Bda06g00113 Bda08g00368 Bpe05g00647 Bpe07g00106 . . Cmo06g01033 . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0782 Cone9ag0786 . . . Cme06g02703 . . Bda07g00480 . . . . Bma12g00073 . . . Cma06g01013 . Car06g00850 . Cpe08g00597 . . . . . . . . . . . . . . . . Csa03g00375 . .
Vvi2g318 . . . . . . . . . Cmo16g00643 . . . . . . . . . . . . . . Cla07g00771 Cam07g0830 Cec07g0885 Cco07g0862 Clacu07g0807 Cmu07g0813 Cre07g1167 . . . . . . . Cme07g01629 Blo03g00339 . Bda07g00479 . . . . . . . . . Cma16g00594 . . . . . . . . . . . . . . . . . . . Csa04g00595 Chy07g01216 .
Vvi2g319 . . . . . . . . . . . Cma15g01230 . Car15g01108 . . . . . . . . . . . . . . . . . . . Cone6ag0780 Cone9ag0785 . Csa05g00278 Chy09g01231 . Blo03g00338 . . . . . . . . . Cmo15g01294 . . . . . Cpe13g00154 Bhi12g00268 . . . . . Lcy12g1647 Cla01g00259 Cam01g0266 Cec01g0257 Cco01g0272 Clacu01g0265 Cmu01g0254 Cre09g2255 Lsi09g00254 . . Cme09g01766
Vvi2g320 Blo02g01110 Blo03g00212 Bda06g00112 Bda08g00516 Bpe05g00646 Bpe07g00107 . Bma14g00667 . . Cma02g01449 Cma15g01228 Car02g01216 Car15g01107 . . Cpe05g00339 . . . . . . . Cla10g00365 Cam10g0377 Cec10g0397 Cco10g0390 Clacu10g0383 Cmu10g1218 Cre10g0632 Cone8ag0301 Cone12ag0307 . . . Csa05g00279 Chy09g01230 . . . . . . Bpe11g00603 Bma05g00820 Bma12g00075 . Cmo02g01485 Cmo15g01292 . . . . . Cpe13g00155 Bhi12g00265 . . . . . Lcy12g1649 Cla01g00260 . Cec01g0258 Cco01g0273 . . Cre09g2254 Lsi09g00255 . . Cme09g01765
Vvi2g321 . . . . . . . . . . Cma02g01450 . Car02g01217 . . . Cpe05g00338 . . . . . . . . . . . . . . Cone8ag0303 . . . . Csa05g00280 Chy09g01229 . . . . . Bpe08g01484 . . . . Cmo02g01486 . . . . . . . Bhi12g00262 . . . . . . Cla01g00261 Cam01g0267 Cec01g0259 Cco01g0274 Clacu01g0266 Cmu01g0255 Cre09g2252 Lsi09g00256 . . Cme09g01764
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 1821514 1824979 - Bda023307.2 Bda06g00112 112
6 1833650 1834973 + Bda023308.1 Bda06g00113 113
7 6041395 6043413 + Bda025581.1 Bda07g00479 479
7 6046376 6048330 + Bda025582.1 Bda07g00480 480
7 6059234 6062173 + Bda025583.1 Bda07g00481 481
8 3763014 3765614 - Bda024809.1 Bda08g00368 368
8 5209324 5215824 + Bda024971.3 Bda08g00516 516
11 9391907 9394356 + XM_039050074.1 Bhi11g00395 395
12 7926288 7933565 - XM_039020272.1 Bhi12g00262 262
12 7946452 7957660 - XM_039018817.1 Bhi12g00265 265
12 7989430 7993450 + XM_039050520.1 Bhi12g00268 268
12 7994078 7997796 - XM_039019928.1 Bhi12g00269 269
12 8011455 8017240 - XM_039018801.1 Bhi12g00270 270
12 8064592 8070480 + XM_039019865.1 Bhi12g00272 272
12 8071236 8082358 + XM_039019868.1 Bhi12g00274 274
2 42104405 42121049 - BLOR10840 Blo02g01110 1110
2 42174461 42177554 + BLOR10841 Blo02g01111 1111
3 4890960 4893194 + BLOR11393 Blo03g00212 212
3 4926281 4945686 + BLOR11398 Blo03g00217 217
3 7275154 7280161 + BLOR11519 Blo03g00338 338
3 7331260 7333078 + BLOR11520 Blo03g00339 339
3 7366291 7369689 + BLOR11521 Blo03g00340 340
5 45530211 45536440 - Bma021926.2 Bma05g00820 820
12 1284561 1287701 - Bma006943.1 Bma12g00073 73
12 1396479 1399466 + Bma006947.1 Bma12g00075 75
14 7234114 7240163 + Bma011116.1 Bma14g00667 667
14 7654083 7657011 + Bma011156.1 Bma14g00701 701
5 20266918 20273180 - Bpe018061.2 Bpe05g00646 646
5 20283349 20286402 + Bpe018062.1 Bpe05g00647 647
7 746844 747928 - Bpe026039 Bpe07g00105 105
7 750204 753344 - Bpe020919.2 Bpe07g00106 106
7 763497 769568 + Bpe020920.1 Bpe07g00107 107
8 15554978 15558246 + Bpe023597.1 Bpe08g01484 1484
11 4582905 4589036 - Bpe003968.1 Bpe11g00603 603
1 2923747 2936221 - CaPI482276_01g002620.1 Cam01g0262 262
1 2948973 2955460 + CaPI482276_01g002640.1 Cam01g0264 264
1 2959214 2962559 + CaPI482276_01g002650.1 Cam01g0265 265
1 2963569 2967552 - CaPI482276_01g002660.1 Cam01g0266 266
1 2972893 2992076 + CaPI482276_01g002670.1 Cam01g0267 267
7 20755662 20756925 + CaPI482276_07g008300.1 Cam07g0830 830
10 6051991 6054092 - CaPI482276_10g003770.1 Cam10g0377 377
2 8222284 8223006 - Carg02537-RA Car02g01211 1211
2 8223720 8229049 - Carg02536-RA Car02g01212 1212
2 8238905 8242309 + Carg02533-RA Car02g01215 1215
2 8243561 8254119 + Carg02532-RA Car02g01216 1216
2 8256739 8260630 + Carg02531-RA Car02g01217 1217
6 6669385 6671238 + Carg20900-RA Car06g00850 850
15 8740997 8749899 - Carg16635-RA Car15g01107 1107
15 8752859 8756463 + Carg16634-RA Car15g01108 1108
15 8766488 8773839 + Carg16631-RA Car15g01111 1111
1 2552844 2565337 - CcPI632755_01g002670.1 Cco01g0267 267
1 2576987 2583592 + CcPI632755_01g002700.1 Cco01g0270 270
1 2587299 2590662 + CcPI632755_01g002710.1 Cco01g0271 271
1 2591683 2595517 - CcPI632755_01g002720.1 Cco01g0272 272
1 2597935 2610636 + CcPI632755_01g002730.1 Cco01g0273 273
1 2613560 2619524 + CcPI632755_01g002740.1 Cco01g0274 274
7 19996615 19997878 + CcPI632755_07g008620.1 Cco07g0862 862
10 4572826 4574925 - CcPI632755_10g003900.1 Cco10g0390 390
1 2529611 2542124 - CePI673135_01g002540.1 Cec01g0254 254
1 2554865 2561366 + CePI673135_01g002550.1 Cec01g0255 255
1 2565154 2568522 + CePI673135_01g002560.1 Cec01g0256 256
1 2569531 2573447 - CePI673135_01g002570.1 Cec01g0257 257
1 2579132 2589059 + CePI673135_01g002580.1 Cec01g0258 258
1 2593715 2597816 + CePI673135_01g002590.1 Cec01g0259 259
7 21881040 21883564 + CePI673135_07g008850.1 Cec07g0885 885
10 4769583 4774351 - CePI673135_10g003970.1 Cec10g0397 397
7 16956280 16966070 + Chy7G140460.1 Chy07g01216 1216
9 14371808 14375931 - Chy9G169450.1 Chy09g01229 1229
9 14379765 14388609 - Chy9G169460.1 Chy09g01230 1230
9 14393191 14396475 + Chy9G169470.1 Chy09g01231 1231
9 14397832 14401471 - Chy9G169480.1 Chy09g01232 1232
9 14404394 14407582 - Chy9G169490.1 Chy09g01233 1233
9 14416039 14422735 + Chy9G169510.1 Chy09g01235 1235
9 14423112 14428261 + Chy9G169520.1 Chy09g01236 1236
1 2542867 2555447 - ClG42_01g0026000.10 Clacu01g0260 260
1 2568117 2574829 + ClG42_01g0026300.10 Clacu01g0263 263
1 2578383 2581707 + ClG42_01g0026400.10 Clacu01g0264 264
1 2582719 2586704 - ClG42_01g0026500.10 Clacu01g0265 265
1 2592009 2611198 + ClG42_01g0026600.10 Clacu01g0266 266
7 20465559 20473502 + ClG42_07g0080700.10 Clacu07g0807 807
10 4841765 4843866 - ClG42_10g0038300.10 Clacu10g0383 383
1 2598063 2610990 - ClCG01G002620.2 Cla01g00256 256
1 2621154 2632051 + ClCG01G002640.2 Cla01g00257 257
1 2635629 2639471 + ClCG01G002660.1 Cla01g00258 258
1 2641705 2644308 - ClCG01G002670.2 Cla01g00259 259
1 2650124 2660305 + ClCG01G002680.2 Cla01g00260 260
1 2662225 2671633 + ClCG01G002700.2 Cla01g00261 261
7 21581591 21589892 + ClCG07G008090.2 Cla07g00771 771
10 4876225 4881303 - ClCG10G003890.1 Cla10g00365 365
2 8301676 8308645 - CmaCh02G014430.1 Cma02g01443 1443
2 8309259 8314608 - CmaCh02G014440.1 Cma02g01444 1444
2 8324254 8327813 + CmaCh02G014470.1 Cma02g01447 1447
2 8329891 8339200 + CmaCh02G014490.1 Cma02g01449 1449
2 8340173 8345437 + CmaCh02G014500.1 Cma02g01450 1450
6 6850415 6852265 + CmaCh06G010130.1 Cma06g01013 1013
15 7788595 7799299 - CmaCh15G012280.1 Cma15g01228 1228
15 7802621 7805264 + CmaCh15G012300.1 Cma15g01230 1230
15 7815763 7823358 + CmaCh15G012340.1 Cma15g01234 1234
16 3067069 3078588 + CmaCh16G005940.1 Cma16g00594 594
6 34236721 34243832 - MELO3C014057.2.1 Cme06g02703 2703
7 22049471 22053510 + MELO3C016353.2.1 Cme07g01629 1629
9 22111984 22118806 - MELO3C005677.2.1 Cme09g01764 1764
9 22120259 22129700 - MELO3C005678.2.1 Cme09g01765 1765
9 22133600 22137427 + MELO3C005679.2.1 Cme09g01766 1766
9 22137939 22142229 - MELO3C005680.2.1 Cme09g01767 1767
9 22144116 22150079 - MELO3C005681.2.1 Cme09g01768 1768
9 22155779 22159373 + MELO3C005683.2.1 Cme09g01769 1769
9 22162821 22167271 + MELO3C005684.2.1 Cme09g01770 1770
2 8662590 8669969 - CmoCh02G014790.1 Cmo02g01479 1479
2 8670506 8675816 - CmoCh02G014810.1 Cmo02g01481 1481
2 8685654 8689673 + CmoCh02G014840.1 Cmo02g01484 1484
2 8690950 8702048 + CmoCh02G014850.1 Cmo02g01485 1485
2 8702845 8708475 + CmoCh02G014860.1 Cmo02g01486 1486
6 8075295 8077148 + CmoCh06G010330.1 Cmo06g01033 1033
15 8874563 8884199 - CmoCh15G012920.1 Cmo15g01292 1292
15 8888176 8891713 + CmoCh15G012940.1 Cmo15g01294 1294
15 8901972 8909214 + CmoCh15G012970.1 Cmo15g01297 1297
16 3169527 3174128 + CmoCh16G006430.1 Cmo16g00643 643
1 2495775 2508382 - CmPI595203_01g002490.1 Cmu01g0249 249
1 2521076 2527786 + CmPI595203_01g002520.1 Cmu01g0252 252
1 2531335 2534659 + CmPI595203_01g002530.1 Cmu01g0253 253
1 2535671 2539658 - CmPI595203_01g002540.1 Cmu01g0254 254
1 2544963 2564135 + CmPI595203_01g002550.1 Cmu01g0255 255
7 20679570 20680833 + CmPI595203_07g008130.1 Cmu07g0813 813
10 4982685 4984786 - CmPI595203_10g012180.1 Cmu10g1218 1218
6 3974084 3976835 + Conep06aG0080300.1 Cone6ag0780 780
6 3984304 3987756 + Conep06aG0080500.1 Cone6ag0782 782
8 1722075 1726675 - Conep08aG0031300.1 Cone8ag0298 298
8 1728235 1731404 - Conep08aG0031400.1 Cone8ag0299 299
8 1736277 1739668 + Conep08aG0031500.1 Cone8ag0300 300
8 1741996 1749116 + Conep08aG0031600.1 Cone8ag0301 301
8 1751422 1755112 + Conep08aG0031800.1 Cone8ag0303 303
9 3765739 3768236 + Conep09aG0080200.1 Cone9ag0785 785
9 3769883 3772988 + Conep09aG0080300.1 Cone9ag0786 786
9 3773745 3775415 - Conep09aG0080400.1 Cone9ag0787 787
12 1657111 1661510 - Conep12aG0031700.1 Cone12ag0304 304
12 1662642 1666787 - Conep12aG0031800.1 Cone12ag0305 305
12 1672115 1679184 + Conep12aG0032000.1 Cone12ag0307 307
5 1882941 1890649 - Cp4.1LG05g03250.1 Cpe05g00338 338
5 1891504 1899271 - Cp4.1LG05g03300.1 Cpe05g00339 339
5 1903575 1909566 - Cp4.1LG05g03260.1 Cpe05g00340 340
5 1919338 1924748 + Cp4.1LG05g03350.1 Cpe05g00342 342
5 1925321 1929553 + Cp4.1LG05g03370.1 Cpe05g00343 343
8 3928485 3931021 - Cp4.1LG08g00790.1 Cpe08g00597 597
13 1101675 1109061 - Cp4.1LG13g01560.1 Cpe13g00152 152
13 1119453 1123073 - Cp4.1LG13g01570.1 Cpe13g00154 154
13 1128693 1138916 + Cp4.1LG13g01520.1 Cpe13g00155 155
7 24004179 24006681 + CrPI670011_07g011670.1 Cre07g1167 1167
9 41717831 41723965 - CrPI670011_09g022520.1 Cre09g2252 2252
9 41728792 41738657 - CrPI670011_09g022540.1 Cre09g2254 2254
9 41744501 41748347 + CrPI670011_09g022550.1 Cre09g2255 2255
9 41749351 41752715 - CrPI670011_09g022560.1 Cre09g2256 2256
9 41756466 41763131 - CrPI670011_09g022570.1 Cre09g2257 2257
9 41776089 41788682 + CrPI670011_09g022600.1 Cre09g2260 2260
10 5894149 5898733 - CrPI670011_10g006320.1 Cre10g0632 632
3 3168304 3174708 - CsaV3_3G003750.1 Csa03g00375 375
4 3933297 3937054 - CsaV3_4G005950.1 Csa04g00595 595
5 825128 827971 + CsaV3_5G001480.1 Csa05g00148 148
5 1667723 1680846 - CsaV3_5G002720.1 Csa05g00272 272
5 1682202 1688061 - CsaV3_5G002730.1 Csa05g00273 273
5 1696655 1699805 + CsaV3_5G002760.1 Csa05g00276 276
5 1702605 1706459 + CsaV3_5G002770.1 Csa05g00277 277
5 1705295 1711094 - CsaV3_5G002780.1 Csa05g00278 278
5 1714005 1724614 + CsaV3_5G002790.1 Csa05g00279 279
5 1725517 1732590 + CsaV3_5G002800.1 Csa05g00280 280
6 66068120 66075809 - Hsped.06g15370.1 Hepe06g1537 1537
6 66077822 66085824 - Hsped.06g15380.1 Hepe06g1538 1538
6 66094043 66098464 + Hsped.06g15390.1 Hepe06g1539 1539
6 66109463 66113012 + Hsped.06g15400.1 Hepe06g1540 1540
11 36668934 36681892 - Lag0032717.1 Lac11g2079 2079
11 36718923 36722070 + Lag0032722.1 Lac11g2084 2084
11 36740959 36744422 + Lag0032724.1 Lac11g2086 2086
12 36758193 36763706 - Maker00029482 Lcy12g1640 1640
12 36767458 36771626 - Maker00029403 Lcy12g1641 1641
12 36794929 36800554 + Maker00029476 Lcy12g1643 1643
12 36825631 36829154 + Maker00029358 Lcy12g1646 1646
12 36833591 36838075 - Maker00029411 Lcy12g1647 1647
12 36857745 36861444 + Maker00029320 Lcy12g1649 1649
7 20685879 20691820 - Lsi07G014160.1 Lsi07g01416 1416
9 2593995 2600596 - Lsi09G002480.1 Lsi09g00248 248
9 2601143 2606810 - Lsi09G002490.1 Lsi09g00249 249
9 2621808 2625174 + Lsi09G002520.1 Lsi09g00252 252
9 2632115 2636144 + Lsi09G002530.1 Lsi09g00253 253
9 2637874 2640398 - Lsi09G002540.1 Lsi09g00254 254
9 2644587 2658237 + Lsi09G002550.1 Lsi09g00255 255
9 2660989 2669751 + Lsi09G002560.1 Lsi09g00256 256
2 2898045 2908205 - Vvi2g312 Vvi2g312 312
2 2915651 2921109 - Vvi2g313 Vvi2g313 313
2 2924151 2929030 + Vvi2g314 Vvi2g314 314
2 2935650 2939145 + Vvi2g315 Vvi2g315 315
2 2940010 2941068 + Vvi2g316 Vvi2g316 316
2 2943364 2948362 - Vvi2g317 Vvi2g317 317
2 2967215 2971090 - Vvi2g318 Vvi2g318 318
2 2972654 2976285 - Vvi2g319 Vvi2g319 319
2 2977849 2988157 + Vvi2g320 Vvi2g320 320
2 2989813 2995888 + Vvi2g321 Vvi2g321 321
       

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