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
Vvi1g351 . . . Bda11g00161 . . . . Cmo04g01564 . . . Car04g01545 . Sed07g2111 . Cpe01g01331 Bhi07g01289 Tan04g0818 Cmetu10g0877 Lac13g0528 Hepe01g1166 . . Cla05g02277 Cam05g2448 Cec05g2469 Cco05g2513 Clacu05g2443 Cmu05g2305 Cre05g2423 Cone13ag0804 Cone19ag0809 . . Lsi04g00228 Csa05g02061 Chy10g01172 Cme10g00232 . . . Bda11g00161 . . . . . . Cmo15g01032 . Cma15g00987 . Car15g00927 Cpe13g00392 . Bhi12g00840 . . . . . Lcy10g1470 Cla01g00575 Cam01g0601 Cec01g0592 Cco01g0616 Clacu01g0594 Cmu01g0567 Cre09g1940 Lsi09g00623 . Chy09g00598 Cme09g01422
Vvi1g352 . . . . . . . . . Cmo18g01007 . . . . . . . . . . . . . . Cla05g02276 Cam05g2447 Cec05g2468 Cco05g2512 Clacu05g2442 Cmu05g2304 Cre05g2422 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g353 . . . Bda11g00160 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0426 . . Csa05g02060 . . . . . Bda11g00160 . . . . . . Cmo15g00968 . . . Car15g00872 Cpe13g00391 . Bhi12g00843 . . . . . Lcy10g1469 Cla01g00576 Cam01g0602 Cec01g0593 Cco01g0617 Clacu01g0595 Cmu01g0568 Cre09g1939 Lsi09g00624 . Chy09g00888 Cme09g01421
Vvi1g354 Blo01g00735 . . Bda11g00159 Bpe13g01075 . Bma14g01908 Bma15g00064 Cmo04g01562 Cmo18g01006 . Cma18g00997 Car04g01544 Car18g00920 . Cpe09g00320 Cpe01g01329 Bhi07g01288 . . . . . . Cla05g02275 . . . . . . Cone13ag0803 Cone19ag0808 Cone6ag0425 . Lsi04g00224 Csa05g02059 Chy10g01174 Cme10g00230 . Blo11g00752 . Bda11g00159 Bpe11g01621 Bpe02g02022 . . . Cmo04g02173 . Cma04g02078 . Car04g02015 . . . Bhi12g00845 . . . . . Lcy10g1468 Cla01g00577 . . . . . . Lsi09g00625 . Chy09g00887 Cme09g01420
Vvi1g355 . . . . . . Bma14g01909 . Cmo04g01561 Cmo18g01005 . Cma18g00996 Car04g01543 Car18g00919 Sed07g2115 Cpe09g00321 Cpe01g01328 Bhi07g01287 Tan04g0813 Cmetu10g0970 Lac13g0531 . . . Cla05g02274 Cam05g2444 Cec05g2465 Cco05g2509 Clacu05g2439 Cmu05g2302 Cre05g2420 Cone13ag0802 Cone19ag0807 . . Lsi04g00223 Csa05g02642 Chy10g01175 Cme10g00229 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g356 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g357 Blo01g00736 . Bda01g01845 . . . . . . . . . . . . . Cpe01g01801 . . . . . . . . . . . . . . . . Cone6ag0424 Cone9ag0446 . Csa05g02058 . . . . . . . Bpe02g02021 Bma01g00443 . . Cmo04g02174 Cmo15g00969 Cma04g02079 Cma15g00929 Car04g02016 Car15g00873 Cpe13g00390 . Bhi12g00846 . . . . . Lcy10g1467 Cla01g00578 Cam01g0605 Cec01g0595 Cco01g0619 Clacu01g0597 Cmu01g0570 Cre09g1937 Lsi09g00626 . Chy09g00886 Cme09g01419
Vvi1g358 . . . . . . Bma14g01910 . . Cmo18g01004 . Cma18g00995 . Car18g00918 Sed06g1949 Cpe09g00322 Cpe01g01327 Bhi07g01286 Tan04g0812 Cmetu10g0150 Lac13g0532 Hepe01g1164 . . Cla05g02273 Cam05g2443 Cec05g2464 Cco05g2508 Clacu05g2438 Cmu05g2301 Cre05g2419 . . Cone6ag0423 Cone9ag0445 Lsi04g00222 Csa05g02643 Chy10g01176 Cme10g00228 . . Bda07g01725 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g359 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g360 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 54548431 54564863 + Bda004138.1 Bda01g01845 1845
7 32298413 32306937 + Bda033993 Bda07g01725 1725
11 2076684 2079188 - Bda004872.1 Bda11g00159 159
11 2096834 2098716 + Bda004874.1 Bda11g00160 160
11 2101318 2110007 - Bda004875.2 Bda11g00161 161
7 39671896 39678669 - XM_039037022.1 Bhi07g01286 1286
7 39682089 39685901 + XM_039037264.1 Bhi07g01287 1287
7 39686539 39689343 - XM_039037253.1 Bhi07g01288 1288
7 39743759 39744898 - XM_039036827.1 Bhi07g01289 1289
12 25671299 25673210 - XM_039018332.1 Bhi12g00840 840
12 25707273 25714618 - XM_039050707.1 Bhi12g00843 843
12 25807532 25810423 + XM_039050601.1 Bhi12g00845 845
12 25815302 25829018 - XM_039051234.1 Bhi12g00846 846
1 9566872 9569145 + BLOR00735 Blo01g00735 735
1 9569808 9583674 - BLOR00736 Blo01g00736 736
11 10204153 10211841 + BLOR03628 Blo11g00752 752
1 3677881 3684552 - Bma000621.1 Bma01g00443 443
14 40794714 40796341 + Bma012695.1 Bma14g01908 1908
14 40802141 40802984 - Bma012696.1 Bma14g01909 1909
14 40808001 40818683 + Bma012697.1 Bma14g01910 1910
15 775609 779565 - Bma013037.1 Bma15g00064 64
2 21831700 21838748 + Bpe009843.1 Bpe02g02021 2021
2 21840515 21842768 - Bpe009844.1 Bpe02g02022 2022
11 12354878 12359824 + Bpe004936.1 Bpe11g01621 1621
13 16329234 16331676 + Bpe010752.1 Bpe13g01075 1075
1 6501590 6503099 - CaPI482276_01g006010.1 Cam01g0601 601
1 6506701 6514164 - CaPI482276_01g006020.1 Cam01g0602 602
1 6528412 6535284 - CaPI482276_01g006050.1 Cam01g0605 605
5 32374670 32380766 - CaPI482276_05g024430.1 Cam05g2443 2443
5 32387487 32389765 + CaPI482276_05g024440.1 Cam05g2444 2444
5 32402963 32405342 - CaPI482276_05g024470.1 Cam05g2447 2447
5 32407796 32408657 - CaPI482276_05g024480.1 Cam05g2448 2448
4 8975053 8976027 + Carg01857-RA Car04g01543 1543
4 8977076 8979418 - Carg01856-RA Car04g01544 1544
4 8983318 8984483 - Carg01855-RA Car04g01545 1545
4 15963145 15965527 + Carg26598-RA Car04g02015 2015
4 15967608 15974322 - Carg26597-RA Car04g02016 2016
15 5148150 5154932 - Carg24922-RA Car15g00872 872
15 5158187 5166380 - Carg24921-RA Car15g00873 873
15 6229544 6230641 - Carg27854-RA Car15g00927 927
18 9960513 9966646 - Carg19044-RA Car18g00918 918
18 9969195 9969949 + Carg19045-RA Car18g00919 919
18 9971576 9973937 - Carg19046-RA Car18g00920 920
1 6227698 6229190 - CcPI632755_01g006160.1 Cco01g0616 616
1 6234542 6241918 - CcPI632755_01g006170.1 Cco01g0617 617
1 6256227 6263094 - CcPI632755_01g006190.1 Cco01g0619 619
5 33444587 33450691 - CcPI632755_05g025080.1 Cco05g2508 2508
5 33455041 33457347 + CcPI632755_05g025090.1 Cco05g2509 2509
5 33470553 33472786 - CcPI632755_05g025120.1 Cco05g2512 2512
5 33477236 33478097 - CcPI632755_05g025130.1 Cco05g2513 2513
1 6281125 6282679 - CePI673135_01g005920.1 Cec01g0592 592
1 6288210 6295426 - CePI673135_01g005930.1 Cec01g0593 593
1 6309647 6316237 - CePI673135_01g005950.1 Cec01g0595 595
5 35782961 35789086 - CePI673135_05g024640.1 Cec05g2464 2464
5 35793487 35795701 + CePI673135_05g024650.1 Cec05g2465 2465
5 35808947 35811245 - CePI673135_05g024680.1 Cec05g2468 2468
5 35814432 35815086 - CePI673135_05g024690.1 Cec05g2469 2469
9 7044533 7047065 - Chy9G163140.1 Chy09g00598 598
9 11633683 11640901 + Chy9G166020.1 Chy09g00886 886
9 11643862 11646200 - Chy9G166030.1 Chy09g00887 887
9 11650895 11656693 + Chy9G166040.1 Chy09g00888 888
10 16547627 16548467 + Chy10G183660.1 Chy10g01172 1172
10 16557729 16559976 + Chy10G183680.1 Chy10g01174 1174
10 16560786 16562523 - Chy10G183690.1 Chy10g01175 1175
10 16565788 16573182 + Chy10G183700.1 Chy10g01176 1176
1 6146633 6148142 - ClG42_01g0059400.10 Clacu01g0594 594
1 6151981 6159192 - ClG42_01g0059500.10 Clacu01g0595 595
1 6173456 6180324 - ClG42_01g0059700.10 Clacu01g0597 597
5 32587641 32593754 - ClG42_05g0243800.10 Clacu05g2438 2438
5 32600666 32602921 + ClG42_05g0243900.10 Clacu05g2439 2439
5 32616242 32618665 - ClG42_05g0244200.10 Clacu05g2442 2442
5 32621093 32621951 - ClG42_05g0244300.10 Clacu05g2443 2443
1 6488237 6490085 - ClCG01G005890.1 Cla01g00575 575
1 6493802 6501363 - ClCG01G005900.2 Cla01g00576 576
1 6507054 6509602 + ClCG01G005910.1 Cla01g00577 577
1 6515610 6522478 - ClCG01G005920.2 Cla01g00578 578
5 34378248 34384835 - ClCG05G022460.2 Cla05g02273 2273
5 34391549 34393796 + ClCG05G022465.1 Cla05g02274 2274
5 34394583 34397262 - ClCG05G022470.1 Cla05g02275 2275
5 34404743 34409842 - ClCG05G022490.2 Cla05g02276 2276
5 34412005 34413496 - ClCG05G022500.1 Cla05g02277 2277
4 14146147 14148841 + CmaCh04G020780.1 Cma04g02078 2078
4 14149911 14157370 - CmaCh04G020790.1 Cma04g02079 2079
15 4899027 4906222 - CmaCh15G009290.1 Cma15g00929 929
15 5661808 5663052 - CmaCh15G009870.1 Cma15g00987 987
18 8388108 8394716 - CmaCh18G009950.1 Cma18g00995 995
18 8396902 8397829 + CmaCh18G009960.1 Cma18g00996 996
18 8398722 8401477 - CmaCh18G009970.1 Cma18g00997 997
9 19397169 19405618 + MELO3C005338.2.1 Cme09g01419 1419
9 19407451 19410539 - MELO3C005339.2.1 Cme09g01420 1420
9 19414925 19421136 + MELO3C005340.2.1 Cme09g01421 1421
9 19425640 19427527 + MELO3C005341.2.1 Cme09g01422 1422
10 1521716 1527269 - MELO3C012277.2.1 Cme10g00228 228
10 1529539 1531830 + MELO3C012276.2.1 Cme10g00229 229
10 1531870 1534812 - MELO3C012275.2.1 Cme10g00230 230
10 1542325 1544128 - MELO3C012273.2.1 Cme10g00232 232
10 20595768 20601231 + PI0011883.1 Cmetu10g0150 150
10 20575173 20576318 + PI0016745.1 Cmetu10g0877 877
10 20590422 20592593 - PI0007615.1 Cmetu10g0970 970
4 7985923 7986981 + CmoCh04G015610.1 Cmo04g01561 1561
4 7987916 7990370 - CmoCh04G015620.1 Cmo04g01562 1562
4 7994290 8003077 - CmoCh04G015640.1 Cmo04g01564 1564
4 15831220 15833984 + CmoCh04G021730.1 Cmo04g02173 2173
4 15835295 15842389 - CmoCh04G021740.1 Cmo04g02174 2174
15 5069926 5076457 - CmoCh15G009680.1 Cmo15g00968 968
15 5077555 5085890 - CmoCh15G009690.1 Cmo15g00969 969
15 6248734 6249928 - CmoCh15G010320.1 Cmo15g01032 1032
18 10947226 10955408 - CmoCh18G010040.1 Cmo18g01004 1004
18 10949546 10957141 + CmoCh18G010050.1 Cmo18g01005 1005
18 10958254 10960935 - CmoCh18G010060.1 Cmo18g01006 1006
18 10964982 10967069 - CmoCh18G010070.1 Cmo18g01007 1007
1 6103259 6104768 - CmPI595203_01g005670.1 Cmu01g0567 567
1 6108344 6115816 - CmPI595203_01g005680.1 Cmu01g0568 568
1 6130079 6136947 - CmPI595203_01g005700.1 Cmu01g0570 570
5 32325652 32331743 - CmPI595203_05g023010.1 Cmu05g2301 2301
5 32338628 32340883 + CmPI595203_05g023020.1 Cmu05g2302 2302
5 32354200 32356426 - CmPI595203_05g023040.1 Cmu05g2304 2304
5 32359049 32359910 - CmPI595203_05g023050.1 Cmu05g2305 2305
6 2055320 2058888 - Conep06aG0043300.1 Cone6ag0423 423
6 2059367 2063092 + Conep06aG0043400.1 Cone6ag0424 424
6 2063811 2066364 - Conep06aG0043500.1 Cone6ag0425 425
6 2067289 2071405 + Conep06aG0043600.1 Cone6ag0426 426
9 2061289 2065909 - Conep09aG0045500.1 Cone9ag0445 445
9 2066193 2070246 + Conep09aG0045600.1 Cone9ag0446 446
13 7405557 7406338 + Conep13aG0082800.1 Cone13ag0802 802
13 7406610 7409694 - Conep13aG0082900.1 Cone13ag0803 803
13 7411392 7413355 - Conep13aG0083000.1 Cone13ag0804 804
19 6463964 6464885 + Conep19aG0083000.1 Cone19ag0807 807
19 6465061 6467906 - Conep19aG0083100.1 Cone19ag0808 808
19 6469136 6470809 - Conep19aG0083200.1 Cone19ag0809 809
1 7991857 7994150 - Cp4.1LG01g13860.1 Cpe01g01327 1327
1 7996970 7998132 + Cp4.1LG01g13870.1 Cpe01g01328 1328
1 7998923 8001357 - Cp4.1LG01g13800.1 Cpe01g01329 1329
1 8005319 8010107 - Cp4.1LG01g13840.1 Cpe01g01331 1331
1 14976747 14984233 + Cp4.1LG01g18190.1 Cpe01g01801 1801
9 1913703 1916426 + Cp4.1LG09g03180.1 Cpe09g00320 320
9 1917650 1918233 - Cp4.1LG09g03280.1 Cpe09g00321 321
9 1920747 1927079 + Cp4.1LG09g03190.1 Cpe09g00322 322
13 4255029 4262700 + Cp4.1LG13g06990.1 Cpe13g00390 390
13 4264059 4270941 + Cp4.1LG13g07000.1 Cpe13g00391 391
13 4273988 4275916 + Cp4.1LG13g06950.1 Cpe13g00392 392
5 35651941 35658025 - CrPI670011_05g024190.1 Cre05g2419 2419
5 35661440 35663739 + CrPI670011_05g024200.1 Cre05g2420 2420
5 35677037 35679332 - CrPI670011_05g024220.1 Cre05g2422 2422
5 35683735 35684596 - CrPI670011_05g024230.1 Cre05g2423 2423
9 38198575 38206508 + CrPI670011_09g019370.1 Cre09g1937 1937
9 38219740 38226989 + CrPI670011_09g019390.1 Cre09g1939 1939
9 38232428 38233974 + CrPI670011_09g019400.1 Cre09g1940 1940
5 23886788 23895690 + CsaV3_5G028770.1 Csa05g02058 2058
5 23897339 23900408 - CsaV3_5G028780.1 Csa05g02059 2059
5 23904759 23915993 + CsaV3_5G028790.1 Csa05g02060 2060
5 23919734 23922343 + CsaV3_5G028800.1 Csa05g02061 2061
5 27469623 27473068 - CsaV3_5G034610.1 Csa05g02642 2642
5 27476230 27482283 + CsaV3_5G034620.1 Csa05g02643 2643
1 76759850 76767309 - Hsped.01g11640.1 Hepe01g1164 1164
1 76807572 76808623 - Hsped.01g11660.1 Hepe01g1166 1166
13 3856459 3857316 + Lag0040324.1 Lac13g0528 528
13 3879797 3883186 - Lag0040327.1 Lac13g0531 531
13 3887189 3894070 + Lag0040328.1 Lac13g0532 532
10 38606400 38611565 + Maker00006874 Lcy10g1467 1467
10 38633280 38636189 - Maker00006887 Lcy10g1468 1468
10 38657887 38668866 + Maker00006871 Lcy10g1469 1469
10 38687833 38689574 + Maker00006876 Lcy10g1470 1470
4 2315617 2322316 - Lsi04G002220.1 Lsi04g00222 222
4 2325985 2329161 + Lsi04G002230.1 Lsi04g00223 223
4 2329328 2332527 - Lsi04G002240.1 Lsi04g00224 224
4 2348394 2349607 - Lsi04G002280.1 Lsi04g00228 228
9 6868209 6870420 - Lsi09G006230.1 Lsi09g00623 623
9 6875626 6882952 - Lsi09G006240.1 Lsi09g00624 624
9 6888963 6891500 + Lsi09G006250.1 Lsi09g00625 625
9 6893948 6901644 - Lsi09G006260.1 Lsi09g00626 626
6 43683678 43693529 - Sed0022508.1 Sed06g1949 1949
7 36625854 36627864 + Sed0020371.1 Sed07g2111 2111
7 36674475 36680885 - Sed0026108.2 Sed07g2115 2115
4 6909534 6916140 - Tan0004607.1 Tan04g0812 812
4 6922533 6925851 + Tan0021197.1 Tan04g0813 813
4 6957987 6959355 - Tan0018566.2 Tan04g0818 818
1 3675467 3676903 + Vvi1g351 Vvi1g351 351
1 3678831 3683638 + Vvi1g352 Vvi1g352 352
1 3698335 3709017 - Vvi1g353 Vvi1g353 353
1 3716033 3718950 + Vvi1g354 Vvi1g354 354
1 3720066 3721588 - Vvi1g355 Vvi1g355 355
1 3727772 3730367 + Vvi1g356 Vvi1g356 356
1 3730701 3738630 - Vvi1g357 Vvi1g357 357
1 3742314 3754441 + Vvi1g358 Vvi1g358 358
1 3757150 3759858 - Vvi1g359 Vvi1g359 359
1 3776553 3777948 + Vvi1g360 Vvi1g360 360
       

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