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
Vvi5g589 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g590 . . . . . Bpe14g01219 . . . . Cma06g01351 Cma14g01767 Car06g01172 Car14g01591 Sed02g1361 Cpe08g00300 Cpe03g01481 Bhi01g00741 Tan10g0765 Cmetu02g0010 . Hepe05g1602 . Lcy11g1599 . . . . . . . . . . . Lsi05g01654 . . Cme06g00556 Blo02g00596 Blo07g00239 Bda11g00606 . . Bpe13g00580 Bma02g00818 Bma06g01579 . Cmo06g01364 Cmo14g01805 . . . . . . . . . . . . . Cla05g00495 Cam05g0543 Cec05g0554 Cco05g0553 Clacu05g0540 Cmu05g0512 Cre05g0580 . Csa03g01273 Chy06g00526 .
Vvi5g591 . . . . Bpe04g00808 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g592 . . . . . Bpe14g01220 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo02g00598 . . Bda13g00095 . . Bma02g00814 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g593 Blo01g00102 Blo12g00351 Bda03g00854 Bda08g00264 Bpe04g00807 . Bma04g00755 Bma05g01081 Cmo08g01091 . . Cma14g01768 . Car14g01592 . . Cpe03g01482 Bhi01g00740 . . . . . Lcy11g1600 Cla06g00622 . . . . . . . . . . Lsi05g01655 Csa02g01109 Chy05g00369 Cme06g00555 . . . . . . . . . . Cmo14g01806 Cma08g01115 Cma17g00195 Car08g00998 Car17g00172 Cpe12g00166 Cpe17g00170 Bhi12g02255 . . . . . Lcy13g0324 Cla05g00494 . . . . . . Lsi09g01281 Csa03g01272 Chy06g00525 Cme05g00513
Vvi5g594 Blo01g00101 . . . . . . Bma05g01080 . Cmo17g00190 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe05g00871 . . . . . . . Cma17g00193 . Car17g00171 Cpe12g00165 . . . . . . . . . . . . . . . . . . .
Vvi5g595 . Blo12g00352 Bda03g00853 . Bpe04g00806 . Bma04g00754 . . Cmo17g00189 . . . . . . . . . . . . . . Cla06g00623 Cam06g0662 Cec06g0665 Cco06g0672 Clacu06g0649 Cmu06g0642 Cre06g1410 Cone14ag0894 . . . . Csa02g01108 Chy05g00368 . . . . . . . . . Sed04g1948 . . . Cma17g00192 . Car17g00170 Cpe12g00164 . Bhi12g02257 Tan06g2468 Cmetu05g0174 . . . Lcy13g0325 . . . . . . . Lsi09g01280 . . Cme05g00514
Vvi5g596 Blo01g00100 . . Bda08g00265 . . . Bma05g01079 . . Cma06g01350 . Car06g01171 . Sed02g1363 Cpe08g00301 . Bhi01g00739 Tan10g0763 Cmetu06g1429 . Hepe05g1604 . Lcy11g1601 . . . . . . . . . . . Lsi05g01657 . . Cme06g00554 . . . . Bpe05g00870 . . . . Cmo06g01363 . . . . . . . . . . . . . . . . . . . . . . Csa03g01271 Chy06g00524 .
Vvi5g597 . . . . . Bpe14g01221 . . . . Cma06g01349 Cma14g01771 Car06g01170 Car14g01593 . Cpe08g00302 . Bhi01g00738 . . . . . Lcy11g1602 . . . . . . . . . Cone7ag0290 . Lsi05g01658 . . Cme06g00553 Blo02g00600 Blo07g00240 Bda11g00607 . . . . . . Cmo06g01362 Cmo14g01807 . . . . . . . . . . . . . Cla05g00493 . . . . . . . Csa03g01270 Chy06g00523 .
Vvi5g598 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 7382311 7389324 + Bda016843.1 Bda03g00853 853
3 7390250 7391356 - Bda016844.1 Bda03g00854 854
8 2698843 2700168 + Bda024691.1 Bda08g00264 264
8 2713879 2715436 + Bda024693.1 Bda08g00265 265
11 6157125 6158967 - Bda005349.1 Bda11g00606 606
11 6171112 6173370 + Bda005350.1 Bda11g00607 607
13 1282231 1285524 + Bda000947.1 Bda13g00095 95
1 13842020 13847126 - XM_039041767.1 Bhi01g00738 738
1 13856913 13859323 - XM_039022666.1 Bhi01g00739 739
1 13873377 13875058 - XM_039044843.1 Bhi01g00740 740
1 13975106 13979364 + XM_039044979.1 Bhi01g00741 741
12 72028070 72029831 + XM_039050585.1 Bhi12g02255 2255
12 72032228 72042335 - XM_039019258.1 Bhi12g02257 2257
1 1413023 1414817 - BLOR00100 Blo01g00100 100
1 1415321 1417936 + BLOR00101 Blo01g00101 101
1 1419468 1420796 - BLOR00102 Blo01g00102 102
2 11546806 11552803 - BLOR10326 Blo02g00596 596
2 11608238 11611514 - BLOR10328 Blo02g00598 598
2 11649838 11651853 + BLOR10330 Blo02g00600 600
7 2986697 2988590 - BLOR18171 Blo07g00239 239
7 2995040 2997837 + BLOR18172 Blo07g00240 240
12 19549829 19551133 + BLOR04370 Blo12g00351 351
12 19564094 19571325 - BLOR04371 Blo12g00352 352
2 44450953 44454250 + Bma015558.1 Bma02g00814 814
2 44550953 44552612 + Bma015564.1 Bma02g00818 818
4 8111670 8118764 + Bma019271.1 Bma04g00754 754
4 8119226 8120533 - Bma019272.1 Bma04g00755 755
5 49555956 49557746 - Bma022247.1 Bma05g01079 1079
5 49560713 49563328 + Bma022248.1 Bma05g01080 1080
5 49564266 49565393 - Bma022249.1 Bma05g01081 1081
6 52053979 52055859 - Bma024697.1 Bma06g01579 1579
4 5304559 5311648 + Bpe015466.1 Bpe04g00806 806
4 5312150 5313454 - Bpe015467.1 Bpe04g00807 807
4 5320944 5322330 + Bpe015468.1 Bpe04g00808 808
5 21892590 21894336 - Bpe018282.1 Bpe05g00870 870
5 21895400 21898015 + Bpe018283.1 Bpe05g00871 871
13 12943119 12944954 + Bpe010283.1 Bpe13g00580 580
14 9116818 9118476 - Bpe014582.1 Bpe14g01219 1219
14 9124844 9128129 - Bpe014583.1 Bpe14g01220 1220
14 9129673 9131092 + Bpe014584.1 Bpe14g01221 1221
5 4794489 4797152 + CaPI482276_05g005430.1 Cam05g0543 543
6 8900884 8911181 - CaPI482276_06g006620.1 Cam06g0662 662
6 8612044 8615012 - Carg06187-RA Car06g01170 1170
6 8616028 8619149 - Carg06186-RA Car06g01171 1171
6 8622919 8624421 + Carg06185-RA Car06g01172 1172
8 6865320 6866618 - Carg15876-RA Car08g00998 998
14 12910734 12912579 - Carg16596-RA Car14g01591 1591
14 12917140 12918459 + Carg16595-RA Car14g01592 1592
14 12919959 12921937 + Carg16594-RA Car14g01593 1593
17 1054367 1063037 + Carg10061-RA Car17g00170 170
17 1065041 1067626 + Carg10060-RA Car17g00171 171
17 1068128 1069420 - Carg10059-RA Car17g00172 172
5 4460480 4463416 + CcPI632755_05g005530.1 Cco05g0553 553
6 7435432 7448714 - CcPI632755_06g006720.1 Cco06g0672 672
5 4476568 4479530 + CePI673135_05g005540.1 Cec05g0554 554
6 7478143 7488601 - CePI673135_06g006650.1 Cec06g0665 665
5 3904214 3925617 + Chy5G094140.1 Chy05g00368 368
5 3929425 3930717 - Chy5G094150.1 Chy05g00369 369
6 3554361 3557955 - Chy6G110510.1 Chy06g00523 523
6 3560200 3562019 - Chy6G110520.1 Chy06g00524 524
6 3562906 3564207 - Chy6G110530.1 Chy06g00525 525
6 3577945 3580262 + Chy6G110540.1 Chy06g00526 526
5 4497977 4500850 + ClG42_05g0054000.10 Clacu05g0540 540
6 7461470 7472229 - ClG42_06g0064900.10 Clacu06g0649 649
5 4476295 4495478 - ClCG05G004690.2 Cla05g00493 493
5 4499662 4504823 - ClCG05G004710.2 Cla05g00494 494
5 4522990 4525863 + ClCG05G004720.2 Cla05g00495 495
6 7606407 7607699 + ClCG06G006595.1 Cla06g00622 622
6 7610775 7621118 - ClCG06G006600.2 Cla06g00623 623
6 8854599 8857303 - CmaCh06G013490.1 Cma06g01349 1349
6 8859046 8861306 - CmaCh06G013500.1 Cma06g01350 1350
6 8864470 8865972 + CmaCh06G013510.1 Cma06g01351 1351
8 6916716 6918014 - CmaCh08G011150.1 Cma08g01115 1115
14 12835090 12836973 - CmaCh14G017670.1 Cma14g01767 1767
14 12842347 12843666 + CmaCh14G017680.1 Cma14g01768 1768
14 12845873 12847269 + CmaCh14G017710.1 Cma14g01771 1771
17 1007778 1016423 + CmaCh17G001920.1 Cma17g00192 192
17 1019394 1021976 + CmaCh17G001930.1 Cma17g00193 193
17 1022473 1023765 - CmaCh17G001950.1 Cma17g00195 195
5 4722555 4724227 + MELO3C014269.2.1 Cme05g00513 513
5 4727587 4738308 - MELO3C014268.2.1 Cme05g00514 514
6 3497459 3501196 - MELO3C006481.2.1 Cme06g00553 553
6 3503904 3506092 - MELO3C006482.2.1 Cme06g00554 554
6 3506603 3508116 - MELO3C006483.2.1 Cme06g00555 555
6 3522933 3525495 + MELO3C006484.2.1 Cme06g00556 556
2 18057645 18060958 + PI0025304.1 Cmetu02g0010 10
5 18930467 18941084 - PI0009502.3 Cmetu05g0174 174
6 3750943 3752785 - PI0018480.1 Cmetu06g1429 1429
6 10070709 10073292 - CmoCh06G013620.1 Cmo06g01362 1362
6 10075432 10077498 - CmoCh06G013630.1 Cmo06g01363 1363
6 10081418 10082920 + CmoCh06G013640.1 Cmo06g01364 1364
8 7004141 7005439 - CmoCh08G010910.1 Cmo08g01091 1091
14 13817519 13819502 - CmoCh14G018050.1 Cmo14g01805 1805
14 13824099 13825418 + CmoCh14G018060.1 Cmo14g01806 1806
14 13827129 13829354 + CmoCh14G018070.1 Cmo14g01807 1807
17 1112695 1122025 + CmoCh17G001890.1 Cmo17g00189 189
17 1124073 1126658 + CmoCh17G001900.1 Cmo17g00190 190
5 4341457 4344330 + CmPI595203_05g005120.1 Cmu05g0512 512
6 7267934 7278701 - CmPI595203_06g006420.1 Cmu06g0642 642
7 1247880 1250618 + Conep07aG0029700.1 Cone7ag0290 290
14 7083928 7091513 + Conep14aG0091100.1 Cone14ag0894 894
3 11717702 11720497 - Cp4.1LG03g10200.1 Cpe03g01481 1481
3 11725168 11729885 + Cp4.1LG03g10330.1 Cpe03g01482 1482
8 1915454 1916956 - Cp4.1LG08g03660.1 Cpe08g00300 300
8 1920735 1923365 + Cp4.1LG08g03810.1 Cpe08g00301 301
8 1925041 1927412 + Cp4.1LG08g03790.1 Cpe08g00302 302
12 1072243 1080956 + Cp4.1LG12g01570.1 Cpe12g00164 164
12 1082960 1085548 + Cp4.1LG12g01580.1 Cpe12g00165 165
12 1086048 1087340 - Cp4.1LG12g01600.1 Cpe12g00166 166
17 1082441 1083739 + Cp4.1LG17g01610.1 Cpe17g00170 170
5 5139883 5142852 + CrPI670011_05g005800.1 Cre05g0580 580
6 8349934 8360377 - CrPI670011_06g014100.1 Cre06g1410 1410
2 10840551 10857023 + CsaV3_2G013240.1 Csa02g01108 1108
2 10872284 10874288 - CsaV3_2G013250.1 Csa02g01109 1109
3 9716725 9720433 - CsaV3_3G012700.1 Csa03g01270 1270
3 9721512 9724447 - CsaV3_3G012710.1 Csa03g01271 1271
3 9724996 9726644 - CsaV3_3G012720.1 Csa03g01272 1272
3 9739627 9742123 + CsaV3_3G012730.1 Csa03g01273 1273
5 65707098 65710509 - Hsped.05g16020.1 Hepe05g1602 1602
5 65740222 65742335 + Hsped.05g16040.1 Hepe05g1604 1604
11 39831454 39834680 - Maker00031554 Lcy11g1599 1599
11 39858277 39859584 + Maker00031998 Lcy11g1600 1600
11 39861960 39864398 + Maker00031330 Lcy11g1601 1601
11 39869953 39875877 + Maker00031635 Lcy11g1602 1602
13 3526403 3527695 + Maker00024035 Lcy13g0324 324
13 3530326 3538636 - Maker00023734 Lcy13g0325 325
5 24195892 24198942 - Lsi05G016540.1 Lsi05g01654 1654
5 24219412 24223810 + Lsi05G016550.1 Lsi05g01655 1655
5 24227287 24228781 + Lsi05G016570.1 Lsi05g01657 1657
5 24230059 24237030 + Lsi05G016580.1 Lsi05g01658 1658
9 20635402 20646765 + Lsi09G012800.1 Lsi09g01280 1280
9 20651591 20652883 - Lsi09G012810.1 Lsi09g01281 1281
2 49899224 49902162 - Sed0013440.1 Sed02g1361 1361
2 49921585 49926447 + Sed0016634.1 Sed02g1363 1363
4 34146338 34161611 - Sed0002710.1 Sed04g1948 1948
6 77334956 77349896 + Tan0013685.1 Tan06g2468 2468
10 6322954 6325454 - Tan0018564.1 Tan10g0763 763
10 6357473 6360630 + Tan0021464.1 Tan10g0765 765
5 6344963 6348222 + Vvi5g589 Vvi5g589 589
5 6348744 6352561 - Vvi5g590 Vvi5g590 590
5 6360868 6369087 - Vvi5g591 Vvi5g591 591
5 6369615 6377812 - Vvi5g592 Vvi5g592 592
5 6388675 6390727 + Vvi5g593 Vvi5g593 593
5 6392294 6394940 - Vvi5g594 Vvi5g594 594
5 6397284 6408271 - Vvi5g595 Vvi5g595 595
5 6409646 6411676 + Vvi5g596 Vvi5g596 596
5 6424262 6430178 + Vvi5g597 Vvi5g597 597
5 6435127 6441609 + Vvi5g598 Vvi5g598 598
       

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