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
Vvi1g331 . . Bda01g02066 . . Bpe10g01021 . . Cmo04g01570 Cmo18g01017 . Cma18g01006 Car04g01552 Car18g00928 Sed06g1904 Cpe09g00314 Cpe01g01336 Bhi07g01302 Tan04g0836 Cmetu09g1765 Lac13g0517 Hepe01g1174 . . Cla05g02284 Cam05g2457 Cec05g2478 Cco05g2521 Clacu05g2452 Cmu05g2313 Cre05g2431 Cone13ag0816 Cone19ag0823 Cone6ag0434 Cone9ag0451 Lsi04g00240 Csa05g02068 Chy10g01163 Cme10g00242 Blo06g01047 . . . . . Bma01g00355 . . Cmo04g02165 Cmo15g00960 Cma04g02070 Cma15g00921 . Car15g00863 Cpe13g00399 . Bhi12g00829 . . . Hepe02g2694 . Lcy10g1478 Cla01g00568 Cam01g0592 Cec01g0583 Cco01g0607 Clacu01g0587 Cmu01g0557 Cre09g1950 Lsi09g00616 . Chy09g00896 Cme09g01429
Vvi1g332 Blo01g00506 . Bda01g02065 . . . Bma14g01905 . Cmo04g01569 Cmo18g01016 . Cma18g01005 Car04g01551 Car18g00927 Sed06g1905 Cpe09g00315 Cpe01g01335 Bhi07g01301 Tan04g0834 Cmetu09g0646 Lac13g0518 Hepe01g1173 . . Cla05g02283 Cam05g2455 Cec05g2477 Cco05g2520 Clacu05g2451 Cmu05g2312 Cre05g2430 Cone13ag0815 Cone19ag0822 Cone6ag0433 Cone9ag0450 Lsi04g00239 Csa05g02067 Chy10g01164 Cme10g00241 . . Bda07g01722 . . Bpe02g02257 Bma01g00180 . . Cmo04g02170 Cmo15g00961 Cma04g02074 Cma15g00922 Car04g02012 Car15g00864 Cpe13g00398 . Bhi12g00831 . . . . . Lcy10g1477 Cla01g00569 Cam01g0595 Cec01g0584 Cco01g0610 Clacu01g0588 Cmu01g0560 Cre09g1949 Lsi09g00617 . Chy09g00895 Cme09g00772
Vvi1g333 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g334 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g335 . . . . . . . . . . . . . . . . . Bhi07g01300 Tan04g0829 . . Hepe01g1172 . . . . . . . . . . . . . . . . Cme10g00240 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g336 . . . . . . . . Cmo04g01568 . . . Car04g01550 . Sed06g1907 . Cpe01g01334 Bhi07g01299 Tan04g0827 Cmetu10g1444 Lac13g0519 . . . . . . . . . . . . . . Lsi04g00238 Csa05g02629 Chy10g01165 . . . . . . . . . . . . . . . . . Cpe04g01394 . . . . . . . . . . . . . . . . . .
Vvi1g337 . . . . . . Bma14g01906 . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0814 Cone19ag0821 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g338 Blo01g00507 . Bda01g02064 Bda11g00105 Bpe13g01106 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone19ag0819 Cone6ag0432 . . . . . . . . Bda11g00105 . Bpe02g02071 Bma01g00390 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g339 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g340 Blo01g00733 . Bda01g01847 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone9ag0449 . Csa05g02066 . . . . . . . Bpe02g02024 . . . . Cmo15g00962 . Cma15g00923 . Car15g00865 Cpe13g00397 . Bhi12g00834 . . . . . Lcy10g1475 Cla01g00570 Cam01g0596 Cec01g0585 Cco01g0611 Clacu01g0589 Cmu01g0561 Cre09g1946 Lsi09g00618 . Chy09g00894 Cme09g01427
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 54580775 54582167 - Bda004140.1 Bda01g01847 1847
1 56858899 56860112 - Bda004390.1 Bda01g02064 2064
1 56861897 56865711 + Bda004391.2 Bda01g02065 2065
1 56870333 56870974 + Bda004392.1 Bda01g02066 2066
7 32234531 32242073 - Bda028629.2 Bda07g01722 1722
11 1283749 1288544 + Bda004808.1 Bda11g00105 105
7 39920194 39928028 + XM_039037154.1 Bhi07g01299 1299
7 39920709 39928028 + XM_039037155.1 Bhi07g01300 1300
7 39938804 39943611 + XM_039035395.1 Bhi07g01301 1301
7 39952239 39953448 + XM_039037237.1 Bhi07g01302 1302
12 25356803 25357823 - XM_039019490.1 Bhi12g00829 829
12 25440326 25455713 - XM_039018741.1 Bhi12g00831 831
12 25509084 25511268 + XM_039051032.1 Bhi12g00834 834
1 5606478 5609613 - BLOR00506 Blo01g00506 506
1 5610374 5612473 + BLOR00507 Blo01g00507 507
1 9527240 9528760 + BLOR00733 Blo01g00733 733
6 33805550 33806233 + BLOR17630 Blo06g01047 1047
1 1660202 1664071 - Bma000345.1 Bma01g00180 180
1 2921103 2921756 + Bma000527.1 Bma01g00355 355
1 3216533 3220451 + Bma000564.1 Bma01g00390 390
14 40730751 40740729 - Bma012692.1 Bma14g01905 1905
14 40756036 40762728 + Bma012693.2 Bma14g01906 1906
2 21855912 21857317 - Bpe009846.1 Bpe02g02024 2024
2 22228090 22232131 - Bpe009892.1 Bpe02g02071 2071
2 23458204 23461839 + Bpe010074.2 Bpe02g02257 2257
10 15649727 15650413 + Bpe003327.1 Bpe10g01021 1021
13 16631536 16636336 - Bpe010784.1 Bpe13g01106 1106
1 6388716 6389375 - CaPI482276_01g005920.1 Cam01g0592 592
1 6422586 6428705 - CaPI482276_01g005950.1 Cam01g0595 595
1 6441966 6443812 + CaPI482276_01g005960.1 Cam01g0596 596
5 32450793 32454984 + CaPI482276_05g024550.1 Cam05g2455 2455
5 32462682 32463353 + CaPI482276_05g024570.1 Cam05g2457 2457
4 9003448 9011281 + Carg01850-RA Car04g01550 1550
4 9012788 9016136 + Carg01849-RA Car04g01551 1551
4 9020547 9021239 + Carg01848-RA Car04g01552 1552
4 15929985 15936228 - Carg26601-RA Car04g02012 2012
15 5069055 5069510 - Carg24931-RA Car15g00863 863
15 5087679 5095931 - Carg24930-RA Car15g00864 864
15 5099048 5100293 + Carg24929-RA Car15g00865 865
18 10009449 10013531 + Carg19053-RA Car18g00927 927
18 10020882 10021514 + Carg19054-RA Car18g00928 928
1 6113811 6114470 - CcPI632755_01g006070.1 Cco01g0607 607
1 6149597 6153298 - CcPI632755_01g006100.1 Cco01g0610 610
1 6167421 6169243 + CcPI632755_01g006110.1 Cco01g0611 611
5 33519928 33523744 + CcPI632755_05g025200.1 Cco05g2520 2520
5 33531829 33532500 + CcPI632755_05g025210.1 Cco05g2521 2521
1 6157171 6157830 - CePI673135_01g005830.1 Cec01g0583 583
1 6187467 6198921 - CePI673135_01g005840.1 Cec01g0584 584
1 6212042 6213884 + CePI673135_01g005850.1 Cec01g0585 585
5 35856568 35860380 + CePI673135_05g024770.1 Cec05g2477 2477
5 35868487 35869158 + CePI673135_05g024780.1 Cec05g2478 2478
9 11710560 11711784 - Chy9G166100.1 Chy09g00894 894
9 11717889 11727809 + Chy9G166110.1 Chy09g00895 895
9 11745725 11746363 + Chy9G166120.1 Chy09g00896 896
10 16491906 16492595 - Chy10G183570.1 Chy10g01163 1163
10 16500756 16504823 - Chy10G183580.1 Chy10g01164 1164
10 16507098 16513929 - Chy10G183590.1 Chy10g01165 1165
1 6033807 6034466 - ClG42_01g0058700.10 Clacu01g0587 587
1 6061526 6073614 - ClG42_01g0058800.10 Clacu01g0588 588
1 6086784 6088627 + ClG42_01g0058900.10 Clacu01g0589 589
5 32663702 32667833 + ClG42_05g0245100.10 Clacu05g2451 2451
5 32675096 32675767 + ClG42_05g0245200.10 Clacu05g2452 2452
1 6371348 6372007 - ClCG01G005820.1 Cla01g00568 568
1 6398937 6411668 - ClCG01G005830.1 Cla01g00569 569
1 6424633 6426476 + ClCG01G005840.1 Cla01g00570 570
5 34454610 34459093 + ClCG05G022550.1 Cla05g02283 2283
5 34468113 34468784 + ClCG05G022560.1 Cla05g02284 2284
4 13998165 13998824 - CmaCh04G020700.1 Cma04g02070 2070
4 14113165 14117879 - CmaCh04G020740.1 Cma04g02074 2074
15 4816638 4817243 - CmaCh15G009210.1 Cma15g00921 921
15 4832643 4841297 - CmaCh15G009220.1 Cma15g00922 922
15 4845021 4846427 + CmaCh15G009230.1 Cma15g00923 923
18 8436359 8440977 + CmaCh18G010050.1 Cma18g01005 1005
18 8448747 8449379 + CmaCh18G010060.1 Cma18g01006 1006
9 9423613 9430174 - MELO3C002995.2.1 Cme09g00772 772
9 19470828 19472268 - MELO3C005345.2.1 Cme09g01427 1427
9 19506424 19507287 + MELO3C005347.2.1 Cme09g01429 1429
10 1578014 1586378 + MELO3C012265.2.1 Cme10g00240 240
10 1587597 1592213 + MELO3C012264.2.1 Cme10g00241 241
10 1599888 1600577 + MELO3C012263.2.1 Cme10g00242 242
9 15552929 15559830 + PI0028144.2 Cmetu09g0646 646
9 14868673 14870365 + PI0026173.1 Cmetu09g1765 1765
10 20523768 20531194 - PI0027934.1 Cmetu10g1444 1444
4 8015730 8025815 + CmoCh04G015680.1 Cmo04g01568 1568
4 8025863 8029409 + CmoCh04G015690.1 Cmo04g01569 1569
4 8033450 8034142 + CmoCh04G015700.1 Cmo04g01570 1570
4 15685821 15686501 - CmoCh04G021650.1 Cmo04g02165 2165
4 15800030 15806032 - CmoCh04G021700.1 Cmo04g02170 2170
15 4993753 4994355 - CmoCh15G009600.1 Cmo15g00960 960
15 5006819 5015280 - CmoCh15G009610.1 Cmo15g00961 961
15 5018979 5020239 + CmoCh15G009620.1 Cmo15g00962 962
18 10990716 10999687 + CmoCh18G010160.1 Cmo18g01016 1016
18 11007067 11007699 + CmoCh18G010170.1 Cmo18g01017 1017
1 5990560 5991219 - CmPI595203_01g005570.1 Cmu01g0557 557
1 6026291 6030392 - CmPI595203_01g005600.1 Cmu01g0560 560
1 6043435 6045264 + CmPI595203_01g005610.1 Cmu01g0561 561
5 32401651 32405382 + CmPI595203_05g023120.1 Cmu05g2312 2312
5 32413511 32414182 + CmPI595203_05g023130.1 Cmu05g2313 2313
6 2093899 2095268 - Conep06aG0044200.1 Cone6ag0432 432
6 2096562 2101265 + Conep06aG0044300.1 Cone6ag0433 433
6 2113743 2114465 + Conep06aG0044400.1 Cone6ag0434 434
9 2087084 2088985 - Conep09aG0045900.1 Cone9ag0449 449
9 2092575 2097455 + Conep09aG0046000.1 Cone9ag0450 450
9 2106541 2107293 + Conep09aG0046100.1 Cone9ag0451 451
13 7463004 7467743 - Conep13aG0084000.1 Cone13ag0814 814
13 7471033 7474432 + Conep13aG0084100.1 Cone13ag0815 815
13 7482893 7483612 + Conep13aG0084200.1 Cone13ag0816 816
19 6514639 6516402 - Conep19aG0084200.1 Cone19ag0819 819
19 6518330 6520447 - Conep19aG0084400.1 Cone19ag0821 821
19 6521678 6525345 + Conep19aG0084500.1 Cone19ag0822 822
19 6531965 6532687 + Conep19aG0084600.1 Cone19ag0823 823
1 8026755 8034839 + Cp4.1LG01g13880.1 Cpe01g01334 1334
1 8036232 8040092 + Cp4.1LG01g13770.1 Cpe01g01335 1335
1 8043945 8044643 + Cp4.1LG01g13720.1 Cpe01g01336 1336
4 11273317 11283609 + Cp4.1LG04g14000.1 Cpe04g01394 1394
9 1860482 1863299 - Cp4.1LG09g03130.1 Cpe09g00314 314
9 1871329 1876542 - Cp4.1LG09g03150.1 Cpe09g00315 315
13 4316033 4317635 - Cp4.1LG13g07010.1 Cpe13g00397 397
13 4320461 4328920 + Cp4.1LG13g06970.1 Cpe13g00398 398
13 4345738 4348440 + Cp4.1LG13g07020.1 Cpe13g00399 399
5 35726171 35729984 + CrPI670011_05g024300.1 Cre05g2430 2430
5 35738128 35738799 + CrPI670011_05g024310.1 Cre05g2431 2431
9 38293911 38295784 - CrPI670011_09g019460.1 Cre09g1946 1946
9 38319174 38320745 + CrPI670011_09g019490.1 Cre09g1949 1949
9 38347711 38348370 + CrPI670011_09g019500.1 Cre09g1950 1950
5 23963010 23964553 - CsaV3_5G028850.1 Csa05g02066 2066
5 23969057 23982085 + CsaV3_5G028860.1 Csa05g02067 2067
5 23999272 24000781 + CsaV3_5G028870.1 Csa05g02068 2068
5 27419065 27425913 - CsaV3_5G034480.1 Csa05g02629 2629
1 76874994 76882867 + Hsped.01g11720.1 Hepe01g1172 1172
1 76884507 76889282 + Hsped.01g11730.1 Hepe01g1173 1173
1 76898686 76899354 + Hsped.01g11740.1 Hepe01g1174 1174
2 74801818 74802810 + Hsped.02g26940.1 Hepe02g2694 2694
13 3783891 3784579 - Lag0040313.1 Lac13g0517 517
13 3792807 3797066 - Lag0040314.1 Lac13g0518 518
13 3799035 3807121 - Lag0040315.1 Lac13g0519 519
10 38786814 38789466 - Maker00006912 Lcy10g1475 1475
10 38815660 38830034 + Maker00006979 Lcy10g1477 1477
10 38872447 38873100 + Maker00006953 Lcy10g1478 1478
4 2412687 2422106 + Lsi04G002380.1 Lsi04g00238 238
4 2424176 2428553 + Lsi04G002390.1 Lsi04g00239 239
4 2436913 2437575 + Lsi04G002400.1 Lsi04g00240 240
9 6751781 6752440 - Lsi09G006160.1 Lsi09g00616 616
9 6787713 6800028 - Lsi09G006170.1 Lsi09g00617 617
9 6809593 6811662 + Lsi09G006180.1 Lsi09g00618 618
6 43400180 43401217 - Sed0002254.1 Sed06g1904 1904
6 43413232 43418551 - Sed0014262.1 Sed06g1905 1905
6 43421790 43430955 - Sed0008110.2 Sed06g1907 1907
4 7030918 7038964 + Tan0008373.3 Tan04g0827 827
4 7030918 7038964 + Tan0008373.5 Tan04g0829 829
4 7040403 7045461 + Tan0015225.1 Tan04g0834 834
4 7061303 7062376 + Tan0022003.1 Tan04g0836 836
1 3422551 3423477 - Vvi1g331 Vvi1g331 331
1 3429410 3441168 - Vvi1g332 Vvi1g332 332
1 3444538 3445414 - Vvi1g333 Vvi1g333 333
1 3449470 3450097 - Vvi1g334 Vvi1g334 334
1 3450806 3467015 - Vvi1g335 Vvi1g335 335
1 3467055 3473568 - Vvi1g336 Vvi1g336 336
1 3485711 3512371 + Vvi1g337 Vvi1g337 337
1 3514021 3515031 + Vvi1g338 Vvi1g338 338
1 3517779 3520132 + Vvi1g339 Vvi1g339 339
1 3520167 3521895 + Vvi1g340 Vvi1g340 340
       

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