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
Vvi4g62 . . . . . . . . Cmo05g00109 Cmo12g00572 . Cma05g00102 . Car12g00580 Sed08g1760 Cpe07g00553 . Bhi04g00496 Tan02g1648 Cmetu03g0500 . Hepe08g1383 . Lcy13g2177 . . . . . . . Cone4ag1652 . Cone17ag0917 Cone20ag0260 . . . . Blo17g00293 Blo18g00287 . Bda13g01608 Bpe14g00257 . . . . . . . Cma12g00631 . Car05g00374 Cpe11g00082 . . . . . . . . Cla08g01021 Cam08g1470 Cec08g1048 Cco08g1172 Clacu08g1174 . Cre08g0956 Lsi08g01575 Csa02g01846 Chy03g01638 .
Vvi4g63 . Blo12g01010 Bda01g00612 . . Bpe02g00481 Bma04g00130 Bma01g02220 . . Cma01g01743 . Car09g00278 . . . Cpe06g00234 . . . . . . . Cla05g01822 Cam05g1944 Cec05g1957 Cco05g2017 Clacu05g1936 Cmu05g1817 Cre05g1943 . . . . Lsi04g01435 . . . . . . . . Bpe04g00131 . . Sed11g1842 Cmo01g01768 Cmo09g00329 Cma09g00329 . Car01g01355 . . Cpe02g00254 Bhi09g03169 Tan01g4642 Cmetu07g0953 . Hepe01g1871 Mch11g0405 . . . . . . . . . . . Cme07g00234
Vvi4g64 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone17ag0919 Cone20ag0262 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g65 . . . . . . . . . . Cma01g01742 . Car09g00279 . . . Cpe06g00235 . . . . . . . Cla05g01823 Cam05g1945 Cec05g1958 Cco05g2018 Clacu05g1937 Cmu05g1818 Cre05g1944 . . . . Lsi04g01434 . . . . . . . . . . . Sed11g1840 Cmo01g01770 . Cma09g00330 . Car01g01354 . . Cpe02g00255 Bhi09g03168 Tan01g4641 Cmetu02g0525 . Hepe01g1872 Mch11g0406 . . . . . . . . . . . Cme07g00233
Vvi4g66 Blo01g01473 . Bda01g00613 . . Bpe02g00482 . Bma01g02219 Cmo05g00108 Cmo12g00573 . Cma05g00101 . Car12g00581 Sed08g1762 Cpe07g00554 . Bhi04g00498 Tan02g1646 . . Hepe08g1384 . Lcy13g2178 . . . . . . . Cone4ag1654 Cone7ag1297 Cone17ag0920 Cone20ag0263 . . . . . . . . . . . . . . . . Cma12g00632 . Car05g00087 Cpe11g00081 . . . . . . . . . . . . . . . Lsi08g01576 Csa02g01844 Chy03g01639 .
Vvi4g67 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g68 . . . . Bpe02g01536 . . . Cmo05g00107 Cmo12g00574 . Cma05g00100 . Car12g00582 . Cpe07g00555 . Bhi04g00500 . . . Hepe08g1385 . Lcy13g2179 . . . . . . . . . Cone17ag0921 Cone20ag0264 . . . . Blo17g00292 . Bda01g01326 Bda13g01607 Bpe14g00258 . Bma01g00927 . . . . . Cma12g00634 . Car05g00086 Cpe11g00080 . . . . . . . . . . . . . . . Lsi08g01577 Csa02g01843 Chy03g01640 .
Vvi4g69 Blo01g01471 . Bda01g00614 . . Bpe02g00483 . Bma01g02218 . . Cma01g01741 . Car09g00280 . . . Cpe06g00236 . . . . . . . Cla05g01824 Cam05g1946 Cec05g1959 . Clacu05g1938 Cmu05g1819 . Cone4ag1655 Cone7ag1296 Cone17ag0922 Cone20ag0265 Lsi04g01433 . . . . . . . . . . . Sed13g1853 Cmo01g01771 Cmo09g00331 Cma09g00331 . Car01g01353 . . . Bhi09g03166 Tan01g4639 Cmetu07g0839 . Hepe01g1873 . . . . . . . . . . . . Cme07g00232
Vvi4g70 . . . . . . . . . Cmo12g00575 . . . Car12g00583 Sed08g1764 Cpe07g00556 . Bhi04g00508 Tan02g1642 Cmetu03g2033 . Hepe08g1387 . Lcy13g2180 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma12g00635 . . . . . . . . . . . . . . . . . . Lsi08g01578 Csa02g01841 . .
Vvi4g71 Blo01g01469 . Bda01g00617 . . Bpe02g00486 . . . . . . . . . . . . . . . . . . Cla05g01825 Cam05g1947 Cec05g1960 Cco05g2019 Clacu05g1939 Cmu05g1820 Cre05g1945 Cone4ag1657 . . . . . . . . . . . . . . . . Cmo01g01772 . . . . . . . Bhi09g03164 . . . Hepe01g1874 Mch11g0407 . . . . . . . . . . . Cme07g00231
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 33133442 33143248 + Bda032906 Bda01g00612 612
1 33147436 33150612 + Bda002636.1 Bda01g00613 613
1 33151911 33152480 - Bda002637.1 Bda01g00614 614
1 33163066 33165299 - Bda002639.1 Bda01g00617 617
1 48863701 48865387 - Bda003561.2 Bda01g01326 1326
13 39601813 39604207 + Bda000478.1 Bda13g01607 1607
13 39607183 39612912 + Bda000479.1 Bda13g01608 1608
4 12470418 12476581 - XM_039028577.1 Bhi04g00496 496
4 12566308 12569993 + XM_039028864.1 Bhi04g00498 498
4 12570126 12575506 - XM_039028860.1 Bhi04g00500 500
4 12653903 12656359 + XM_039028450.1 Bhi04g00508 508
9 80978202 80982534 + XM_039044038.1 Bhi09g03164 3164
9 80986761 80988230 + XM_039042852.1 Bhi09g03166 3166
9 80989536 80993108 - XM_039040201.1 Bhi09g03168 3168
9 80994211 80998698 - XM_039042008.1 Bhi09g03169 3169
1 53946276 53949416 + BLOR01469 Blo01g01469 1469
1 53958415 53958984 + BLOR01471 Blo01g01471 1471
1 53960017 53970019 - BLOR01473 Blo01g01473 1473
12 28067473 28068933 + BLOR05029 Blo12g01010 1010
17 3076413 3078114 + BLOR16113 Blo17g00292 292
17 3087616 3092472 + BLOR16114 Blo17g00293 293
18 3015280 3018826 + BLOR08775 Blo18g00287 287
1 9069693 9070914 + Bma001156.2 Bma01g00927 927
1 79149209 79149802 + Bma003068.1 Bma01g02218 2218
1 79151088 79154466 - Bma003069.1 Bma01g02219 2219
1 79158579 79163630 - Bma030287 Bma01g02220 2220
4 1025360 1026799 - Bma018576.1 Bma04g00130 130
2 3114840 3116766 + Bpe008321.1 Bpe02g00481 481
2 3120763 3123876 + Bpe008322.2 Bpe02g00482 482
2 3125161 3125730 - Bpe008323.1 Bpe02g00483 483
2 3139492 3144142 - Bpe008325.1 Bpe02g00486 486
2 18472366 18474047 - Bpe009388.2 Bpe02g01536 1536
4 878469 879907 - Bpe014850.1 Bpe04g00131 131
14 2673485 2679140 - Bpe006911.1 Bpe14g00257 257
14 2688643 2690987 - Bpe006912.1 Bpe14g00258 258
5 28371390 28374731 + CaPI482276_05g019440.1 Cam05g1944 1944
5 28376702 28379771 + CaPI482276_05g019450.1 Cam05g1945 1945
5 28381674 28382597 - CaPI482276_05g019460.1 Cam05g1946 1946
5 28387360 28391014 - CaPI482276_05g019470.1 Cam05g1947 1947
8 20954724 20962788 + CaPI482276_08g014700.1 Cam08g1470 1470
1 11977412 11986283 + Carg10684-RA Car01g01353 1353
1 11987639 11991020 - Carg10683-RA Car01g01354 1354
1 11992172 11996652 - Carg10682-RA Car01g01355 1355
5 436930 438822 + Carg11920-RA Car05g00086 86
5 439275 443243 - Carg11918-RA Car05g00087 87
5 2136289 2142219 + Carg09285-RA Car05g00374 374
9 1513208 1517060 + Carg21743-RA Car09g00278 278
9 1518082 1521396 + Carg21742-RA Car09g00279 279
9 1522198 1522908 - Carg21741-RA Car09g00280 280
12 3870510 3874029 - Carg23968-RA Car12g00580 580
12 3879676 3883525 + Carg23967-RA Car12g00581 581
12 3883564 3887122 - Carg23965-RA Car12g00582 582
12 3895924 3897504 + Carg23964-RA Car12g00583 583
5 29290532 29293676 + CcPI632755_05g020170.1 Cco05g2017 2017
5 29295526 29298592 + CcPI632755_05g020180.1 Cco05g2018 2018
5 29300528 29310102 - CcPI632755_05g020190.1 Cco05g2019 2019
8 23484820 23492760 + CcPI632755_08g011720.1 Cco08g1172 1172
5 31644580 31647956 + CePI673135_05g019570.1 Cec05g1957 1957
5 31649808 31652872 + CePI673135_05g019580.1 Cec05g1958 1958
5 31654799 31659414 - CePI673135_05g019590.1 Cec05g1959 1959
5 31660549 31664200 - CePI673135_05g019600.1 Cec05g1960 1960
8 22357171 22364457 + CePI673135_08g010480.1 Cec08g1048 1048
3 18257683 18263527 - Chy3G066180.1 Chy03g01638 1638
3 18272225 18275543 + Chy3G066190.1 Chy03g01639 1639
3 18276116 18277825 - Chy3G066200.1 Chy03g01640 1640
5 28575156 28578537 + ClG42_05g0193600.10 Clacu05g1936 1936
5 28580429 28583498 + ClG42_05g0193700.10 Clacu05g1937 1937
5 28585456 28590044 - ClG42_05g0193800.10 Clacu05g1938 1938
5 28591173 28594840 - ClG42_05g0193900.10 Clacu05g1939 1939
8 21726395 21733732 + ClG42_08g0117400.10 Clacu08g1174 1174
5 30145240 30148986 + ClCG05G017770.1 Cla05g01822 1822
5 30150315 30153982 + ClCG05G017780.1 Cla05g01823 1823
5 30155602 30156676 - ClCG05G017790.2 Cla05g01824 1824
5 30159414 30165882 - ClCG05G017800.1 Cla05g01825 1825
8 22915567 22924275 + ClCG08G010180.2 Cla08g01021 1021
1 11772069 11780861 + CmaCh01G017410.1 Cma01g01741 1741
1 11782071 11786053 - CmaCh01G017420.1 Cma01g01742 1742
1 11786758 11791097 - CmaCh01G017430.1 Cma01g01743 1743
5 423448 425367 + CmaCh05G001000.1 Cma05g00100 100
5 425784 429880 - CmaCh05G001010.1 Cma05g00101 101
5 433008 438960 + CmaCh05G001020.1 Cma05g00102 102
9 1359537 1363872 + CmaCh09G003290.1 Cma09g00329 329
9 1363986 1367588 + CmaCh09G003300.1 Cma09g00330 330
9 1368135 1370760 - CmaCh09G003310.1 Cma09g00331 331
12 3344586 3351257 - CmaCh12G006310.1 Cma12g00631 631
12 3354955 3358902 + CmaCh12G006320.1 Cma12g00632 632
12 3359268 3362034 - CmaCh12G006340.1 Cma12g00634 634
12 3372350 3373944 + CmaCh12G006350.1 Cma12g00635 635
7 1519211 1522750 + MELO3C016865.2.1 Cme07g00231 231
7 1526109 1527525 + MELO3C016864.2.1 Cme07g00232 232
7 1528374 1532179 - MELO3C016862.2.1 Cme07g00233 233
7 1533270 1536715 - MELO3C016861.2.1 Cme07g00234 234
2 1908463 1911882 + PI0027080.1 Cmetu02g0525 525
3 651376 657826 + PI0010087.1 Cmetu03g0500 500
3 621990 624151 - PI0008395.1 Cmetu03g2033 2033
7 23273805 23275463 - PI0026649.1 Cmetu07g0839 839
7 23263688 23267184 + PI0025265.1 Cmetu07g0953 953
1 13097629 13101939 + CmoCh01G017680.1 Cmo01g01768 1768
1 13104874 13106949 + CmoCh01G017700.1 Cmo01g01770 1770
1 13108213 13109236 - CmoCh01G017710.1 Cmo01g01771 1771
1 13111731 13119881 - CmoCh01G017720.1 Cmo01g01772 1772
5 431215 434668 + CmoCh05G001070.1 Cmo05g00107 107
5 435080 439145 - CmoCh05G001080.1 Cmo05g00108 108
5 442455 448859 + CmoCh05G001090.1 Cmo05g00109 109
9 1425940 1429754 + CmoCh09G003290.1 Cmo09g00329 329
9 1434610 1436122 - CmoCh09G003310.1 Cmo09g00331 331
12 3523915 3530367 - CmoCh12G005720.1 Cmo12g00572 572
12 3535069 3538907 + CmoCh12G005730.1 Cmo12g00573 573
12 3539266 3541247 - CmoCh12G005740.1 Cmo12g00574 574
12 3551680 3553398 + CmoCh12G005750.1 Cmo12g00575 575
5 28292724 28296109 + CmPI595203_05g018170.1 Cmu05g1817 1817
5 28298004 28301073 + CmPI595203_05g018180.1 Cmu05g1818 1818
5 28303025 28307606 - CmPI595203_05g018190.1 Cmu05g1819 1819
5 28308733 28312391 - CmPI595203_05g018200.1 Cmu05g1820 1820
4 12444961 12446392 - Conep04aG0170500.1 Cone4ag1652 1652
4 12452269 12455133 + Conep04aG0170700.1 Cone4ag1654 1654
4 12458681 12459329 - Conep04aG0170800.1 Cone4ag1655 1655
4 12468043 12471396 - Conep04aG0171000.1 Cone4ag1657 1657
7 9542880 9543458 + Conep07aG0133500.1 Cone7ag1296 1296
7 9546190 9549545 - Conep07aG0133600.1 Cone7ag1297 1297
17 7210527 7215023 - Conep17aG0094200.1 Cone17ag0917 917
17 7217623 7225840 - Conep17aG0094400.1 Cone17ag0919 919
17 7228621 7231565 + Conep17aG0094500.1 Cone17ag0920 920
17 7231823 7234509 - Conep17aG0094600.1 Cone17ag0921 921
17 7238358 7238996 - Conep17aG0094700.1 Cone17ag0922 922
20 1160549 1164965 - Conep20aG0027100.1 Cone20ag0260 260
20 1167402 1172567 - Conep20aG0027300.1 Cone20ag0262 262
20 1174797 1177768 + Conep20aG0027400.1 Cone20ag0263 263
20 1178108 1180570 - Conep20aG0027500.1 Cone20ag0264 264
20 1183009 1183650 - Conep20aG0027600.1 Cone20ag0265 265
2 1309064 1313503 + Cp4.1LG02g06320.1 Cpe02g00254 254
2 1314013 1317975 + Cp4.1LG02g06300.1 Cpe02g00255 255
6 1244611 1248474 + Cp4.1LG06g02230.1 Cpe06g00234 234
6 1249186 1252740 + Cp4.1LG06g02290.1 Cpe06g00235 235
6 1253255 1254546 - Cp4.1LG06g02330.1 Cpe06g00236 236
7 3667796 3668233 - Cp4.1LG07g06230.1 Cpe07g00553 553
7 3672603 3676232 + Cp4.1LG07g06330.1 Cpe07g00554 554
7 3675794 3680767 - Cp4.1LG07g06190.1 Cpe07g00555 555
7 3688407 3690100 + Cp4.1LG07g06310.1 Cpe07g00556 556
11 425117 429441 + Cp4.1LG11g00120.1 Cpe11g00080 80
11 428553 432986 - Cp4.1LG11g00050.1 Cpe11g00081 81
11 436428 442576 + Cp4.1LG11g00080.1 Cpe11g00082 82
5 31602676 31606619 + CrPI670011_05g019430.1 Cre05g1943 1943
5 31607906 31610956 + CrPI670011_05g019440.1 Cre05g1944 1944
5 31612885 31622067 - CrPI670011_05g019450.1 Cre05g1945 1945
8 22718362 22725584 + CrPI670011_08g009560.1 Cre08g0956 956
2 17600161 17602308 - CsaV3_2G025610.1 Csa02g01841 1841
2 17613594 17615301 + CsaV3_2G025630.1 Csa02g01843 1843
2 17615885 17619168 - CsaV3_2G025640.1 Csa02g01844 1844
2 17626933 17633135 + CsaV3_2G025660.1 Csa02g01846 1846
1 83621962 83627915 + Hsped.01g18710.1 Hepe01g1871 1871
1 83629064 83632783 + Hsped.01g18720.1 Hepe01g1872 1872
1 83634345 83635945 - Hsped.01g18730.1 Hepe01g1873 1873
1 83639488 83644984 - Hsped.01g18740.1 Hepe01g1874 1874
8 16242666 16248395 - Hsped.08g13830.1 Hepe08g1383 1383
8 16272162 16276682 + Hsped.08g13840.1 Hepe08g1384 1384
8 16277432 16279436 - Hsped.08g13850.1 Hepe08g1385 1385
8 16299497 16305449 + Hsped.08g13870.1 Hepe08g1387 1387
13 40705786 40711783 - Maker00025211 Lcy13g2177 2177
13 40724993 40728471 + Maker00025184 Lcy13g2178 2178
13 40728928 40734580 - Maker00025173 Lcy13g2179 2179
13 40743513 40746836 + Maker00025355 Lcy13g2180 2180
4 22064089 22076570 + Lsi04G014330.1 Lsi04g01433 1433
4 22077897 22081839 - Lsi04G014340.1 Lsi04g01434 1434
4 22082217 22086901 - Lsi04G014350.1 Lsi04g01435 1435
8 23770854 23777649 - Lsi08G015750.1 Lsi08g01575 1575
8 23788966 23793239 + Lsi08G015760.1 Lsi08g01576 1576
8 23793283 23796853 - Lsi08G015770.1 Lsi08g01577 1577
8 23814098 23816989 + Lsi08G015780.1 Lsi08g01578 1578
11 2547929 2553289 + MC11g0325 Mch11g0405 405
11 2554305 2558347 + MC11g0326 Mch11g0406 406
11 2559563 2568409 - MC11g0327 Mch11g0407 407
8 32462019 32467766 - Sed0027567.1 Sed08g1760 1760
8 32477861 32481989 + Sed0002101.2 Sed08g1762 1762
8 32496725 32500684 + Sed0007074.1 Sed08g1764 1764
11 33169813 33178860 - Sed0023083.1 Sed11g1840 1840
11 33179913 33184881 - Sed0018803.2 Sed11g1842 1842
13 23494419 23496435 - Sed0016841.1 Sed13g1853 1853
1 112289744 112291302 + Tan0022698.1 Tan01g4639 4639
1 112292728 112296061 - Tan0022559.2 Tan01g4641 4641
1 112296982 112301127 - Tan0008914.1 Tan01g4642 4642
2 76879104 76882042 - Tan0013379.1 Tan02g1642 1642
2 76953602 76958109 - Tan0015174.2 Tan02g1646 1646
2 77164058 77170116 + Tan0010805.1 Tan02g1648 1648
4 700691 706374 - Vvi4g62 Vvi4g62 62
4 710288 715166 - Vvi4g63 Vvi4g63 63
4 716416 725089 - Vvi4g64 Vvi4g64 64
4 727411 730203 + Vvi4g65 Vvi4g65 65
4 736444 742154 + Vvi4g66 Vvi4g66 66
4 743661 745109 - Vvi4g67 Vvi4g67 67
4 746922 749384 - Vvi4g68 Vvi4g68 68
4 763541 764099 - Vvi4g69 Vvi4g69 69
4 773915 775796 + Vvi4g70 Vvi4g70 70
4 781101 787349 - Vvi4g71 Vvi4g71 71
       

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