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
Vvi5g849 . . . . . Bpe14g01296 . . . . . . . Car14g01676 Sed02g1471 . Cpe03g01572 Bhi01g00060 Tan10g0556 Cmetu06g1480 . . . Lcy11g1747 . . . . . . . . . . Cone4ag0385 Lsi05g01815 . . Cme06g00408 . . . Bda13g00025 . . Bma02g01213 . . . Cmo14g01921 . . . . . . . . . . . . . Cla05g00370 Cam05g0403 Cec05g0408 Cco05g0408 Clacu05g0398 Cmu05g0383 Cre05g0445 . Csa03g01126 Chy06g00392 .
Vvi5g850 . . . . . Bpe14g01297 . . . . Cma06g01264 Cma14g01874 Car06g01086 Car14g01677 . Cpe08g00383 Cpe03g01573 . . . . . . . . . . . . . . . . . Cone4ag0386 . . . Cme06g00407 . . . Bda13g00024 . . . . . Cmo06g01273 Cmo14g01923 . . . . . . . . . . . . . Cla05g00369 Cam05g0402 Cec05g0407 Cco05g0407 Clacu05g0397 Cmu05g0382 Cre05g0444 . Csa03g01125 Chy06g00391 .
Vvi5g851 . . . . . . . . . Cmo17g00118 . . . . . . . . . . . . . . Cla06g00740 Cam06g0791 Cec06g0797 . Clacu06g0790 Cmu06g0764 Cre06g1544 . . . . . . . . . . . . . . . . . . . . Cma17g00115 . Car17g00102 Cpe12g00101 . . . . . . . . . . . . . . . Lsi09g01160 . . Cme05g00659
Vvi5g852 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g853 Blo01g00318 . Bda03g01115 Bda08g00024 Bpe04g01060 . Bma04g01043 Bma05g01277 . Cmo17g00117 . Cma14g01876 . Car14g01678 . . Cpe03g01574 . . . . . . . Cla06g00741 Cam06g0794 Cec06g0799 . Clacu06g0793 Cmu06g0766 Cre06g1547 Cone14ag0211 Cone15ag0232 . . Lsi05g01816 . Chy05g00544 Cme06g00406 . . . . Bpe05g01132 . . . Sed02g1473 . Cmo14g01924 . Cma17g00114 . Car17g00101 Cpe12g00100 . Bhi12g01513 Tan06g2323 Cmetu05g1421 . . . Lcy13g0447 Cla05g00368 Cam05g0401 Cec05g0406 Cco05g0406 Clacu05g0396 Cmu05g0381 Cre05g0443 Lsi09g01159 Csa03g01124 Chy06g00390 Cme05g00692
Vvi5g854 . . . . . . . . . . Cma06g01262 . Car06g01085 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo06g01271 . . . . . . . . . . . . . . . . . . . . . . . Chy06g00389 .
Vvi5g855 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme06g00403 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g856 . . . . . Bpe14g01298 . . . . . Cma14g01878 . Car14g01680 . Cpe08g00384 Cpe03g01575 . . . . . . . . . . . . . . Cone14ag0212 Cone15ag0233 . . Lsi05g01818 . . . . . . . . . . . . . Cmo14g01926 . . . . . . . . . . . . . . . . . . . . . Csa03g01121 . .
Vvi5g857 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g858 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 11579960 11594335 - Bda017164.1 Bda03g01115 1115
8 216428 225766 + Bda024415.2 Bda08g00024 24
13 450224 454322 - Bda000866.1 Bda13g00024 24
13 455910 457988 - Bda000867.1 Bda13g00025 25
1 1229452 1232676 - XM_039022140.1 Bhi01g00060 60
12 48888975 48893062 - XM_039050534.1 Bhi12g01513 1513
1 3896104 3900937 + BLOR00318 Blo01g00318 318
2 54178395 54180731 + Bma016054.1 Bma02g01213 1213
4 18937438 18945167 - Bma019670.1 Bma04g01043 1043
5 52107049 52110983 + Bma031242 Bma05g01277 1277
4 7901883 7910328 - Bpe015729.1 Bpe04g01060 1060
5 23628494 23632610 + Bpe018550.1 Bpe05g01132 1132
14 9902897 9904949 + Bpe014652.1 Bpe14g01296 1296
14 9906783 9910628 + Bpe014653.1 Bpe14g01297 1297
14 9922351 9927859 - Bpe014654.1 Bpe14g01298 1298
5 3684479 3687620 - CaPI482276_05g004010.1 Cam05g0401 401
5 3690728 3696879 - CaPI482276_05g004020.1 Cam05g0402 402
5 3701339 3704810 - CaPI482276_05g004030.1 Cam05g0403 403
6 10731712 10733412 + CaPI482276_06g007910.1 Cam06g0791 791
6 10820727 10823586 + CaPI482276_06g007940.1 Cam06g0794 794
6 8144746 8149640 + Carg06274-RA Car06g01085 1085
6 8151950 8157866 - Carg06273-RA Car06g01086 1086
14 13347127 13351103 + Carg16511-RA Car14g01676 1676
14 13352227 13357532 + Carg16510-RA Car14g01677 1677
14 13357611 13361337 + Carg16509-RA Car14g01678 1678
14 13364029 13370622 - Carg16507-RA Car14g01680 1680
17 589407 593347 - Carg10131-RA Car17g00101 101
17 598620 600326 - Carg10130-RA Car17g00102 102
5 3338371 3341542 - CcPI632755_05g004060.1 Cco05g0406 406
5 3346886 3352671 - CcPI632755_05g004070.1 Cco05g0407 407
5 3357193 3360679 - CcPI632755_05g004080.1 Cco05g0408 408
5 3330354 3333495 - CePI673135_05g004060.1 Cec05g0406 406
5 3336970 3342556 - CePI673135_05g004070.1 Cec05g0407 407
5 3347155 3350662 - CePI673135_05g004080.1 Cec05g0408 408
6 9604722 9606422 + CePI673135_06g007970.1 Cec06g0797 797
6 9696863 9699701 + CePI673135_06g007990.1 Cec06g0799 799
5 5864131 5867612 + Chy5G095900.1 Chy05g00544 544
6 2621835 2631486 + Chy6G109170.1 Chy06g00389 389
6 2633372 2636574 - Chy6G109180.1 Chy06g00390 390
6 2637972 2643379 - Chy6G109190.1 Chy06g00391 391
6 2645754 2649405 - Chy6G109200.1 Chy06g00392 392
5 3398492 3401626 - ClG42_05g0039600.10 Clacu05g0396 396
5 3404140 3410722 - ClG42_05g0039700.10 Clacu05g0397 397
5 3415178 3418656 - ClG42_05g0039800.10 Clacu05g0398 398
6 9366172 9367872 + ClG42_06g0079000.10 Clacu06g0790 790
6 9456970 9459782 + ClG42_06g0079300.10 Clacu06g0793 793
5 3350295 3353950 - ClCG05G003550.1 Cla05g00368 368
5 3357633 3363201 - ClCG05G003560.1 Cla05g00369 369
5 3365633 3371133 - ClCG05G003570.2 Cla05g00370 370
6 9639592 9641292 + ClCG06G007625.1 Cla06g00740 740
6 9727949 9735660 + ClCG06G007630.2 Cla06g00741 741
6 8390476 8396515 + CmaCh06G012620.1 Cma06g01262 1262
6 8399165 8405456 - CmaCh06G012640.1 Cma06g01264 1264
14 13282083 13291930 + CmaCh14G018740.1 Cma14g01874 1874
14 13292824 13296881 + CmaCh14G018760.1 Cma14g01876 1876
14 13298814 13305985 - CmaCh14G018780.1 Cma14g01878 1878
17 554584 558562 - CmaCh17G001140.1 Cma17g00114 114
17 563805 565508 - CmaCh17G001150.1 Cma17g00115 115
5 7176356 7178062 - MELO3C023086.2.1 Cme05g00659 659
5 7987236 7991251 + MELO3C020466.2.1 Cme05g00692 692
6 2573969 2581624 + MELO3C006332.2.1 Cme06g00403 403
6 2586059 2586440 - MELO3C032616.2.1 Cme06g00406 406
6 2589960 2596189 - MELO3C006335.2.1 Cme06g00407 407
6 2598129 2601984 - MELO3C006336.2.1 Cme06g00408 408
5 16798076 16801583 - PI0007513.1 Cmetu05g1421 1421
6 2799220 2803196 - PI0002727.1 Cmetu06g1480 1480
6 9587341 9593301 + CmoCh06G012710.1 Cmo06g01271 1271
6 9595662 9601584 - CmoCh06G012730.1 Cmo06g01273 1273
14 14267482 14271447 + CmoCh14G019210.1 Cmo14g01921 1921
14 14273940 14277859 + CmoCh14G019230.1 Cmo14g01923 1923
14 14277938 14282097 + CmoCh14G019240.1 Cmo14g01924 1924
14 14284340 14291079 - CmoCh14G019260.1 Cmo14g01926 1926
17 626941 632820 - CmoCh17G001170.1 Cmo17g00117 117
17 638459 640162 - CmoCh17G001180.1 Cmo17g00118 118
5 3236460 3239594 - CmPI595203_05g003810.1 Cmu05g0381 381
5 3242110 3248691 - CmPI595203_05g003820.1 Cmu05g0382 382
5 3253144 3256623 - CmPI595203_05g003830.1 Cmu05g0383 383
6 9183678 9185378 + CmPI595203_06g007640.1 Cmu06g0764 764
6 9274389 9277238 + CmPI595203_06g007660.1 Cmu06g0766 766
4 1748186 1750205 + Conep04aG0039800.1 Cone4ag0385 385
4 1751768 1755540 + Conep04aG0039900.1 Cone4ag0386 386
14 983243 986788 + Conep14aG0021500.1 Cone14ag0211 211
14 989128 992216 - Conep14aG0021600.1 Cone14ag0212 212
15 1087857 1091424 + Conep15aG0023600.1 Cone15ag0232 232
15 1091499 1094587 - Conep15aG0023700.1 Cone15ag0233 233
3 12166732 12170331 + Cp4.1LG03g18300.1 Cpe03g01572 1572
3 12171462 12176090 + Cp4.1LG03g18340.1 Cpe03g01573 1573
3 12177231 12181337 + Cp4.1LG03g18400.1 Cpe03g01574 1574
3 12184187 12190372 - Cp4.1LG03g18180.1 Cpe03g01575 1575
8 2396973 2403770 + Cp4.1LG08g02910.1 Cpe08g00383 383
8 2405944 2412326 - Cp4.1LG08g02870.1 Cpe08g00384 384
12 600806 604750 - Cp4.1LG12g01060.1 Cpe12g00100 100
12 611007 612716 - Cp4.1LG12g01020.1 Cpe12g00101 101
5 4020069 4023207 - CrPI670011_05g004430.1 Cre05g0443 443
5 4026740 4032317 - CrPI670011_05g004440.1 Cre05g0444 444
5 4036842 4040315 - CrPI670011_05g004450.1 Cre05g0445 445
6 10398871 10400571 + CrPI670011_06g015440.1 Cre06g1544 1544
6 10500386 10503277 + CrPI670011_06g015470.1 Cre06g1547 1547
3 8844664 8851651 + CsaV3_3G011210.1 Csa03g01121 1121
3 8855847 8859672 - CsaV3_3G011240.1 Csa03g01124 1124
3 8860576 8866942 - CsaV3_3G011250.1 Csa03g01125 1125
3 8868191 8872550 - CsaV3_3G011260.1 Csa03g01126 1126
11 41289278 41293286 + Maker00031360 Lcy11g1747 1747
13 5295364 5299066 + Maker00023620 Lcy13g0447 447
5 25401579 25405395 + Lsi05G018150.1 Lsi05g01815 1815
5 25409712 25422202 + Lsi05G018160.1 Lsi05g01816 1816
5 25425282 25444556 - Lsi05G018180.1 Lsi05g01818 1818
9 18594961 18599101 - Lsi09G011590.1 Lsi09g01159 1159
9 18638525 18640216 - Lsi09G011600.1 Lsi09g01160 1160
2 50715290 50720041 + Sed0000115.1 Sed02g1471 1471
2 50729127 50733047 + Sed0024789.1 Sed02g1473 1473
6 74508297 74512244 - Tan0012528.1 Tan06g2323 2323
10 4468141 4472397 - Tan0019332.1 Tan10g0556 556
5 11503638 11518716 + Vvi5g849 Vvi5g849 849
5 11545075 11551320 + Vvi5g850 Vvi5g850 850
5 11589342 11591070 - Vvi5g851 Vvi5g851 851
5 11603121 11606724 - Vvi5g852 Vvi5g852 852
5 11625679 11636150 + Vvi5g853 Vvi5g853 853
5 11700908 11750474 - Vvi5g854 Vvi5g854 854
5 11753656 11754177 - Vvi5g855 Vvi5g855 855
5 11754227 11759310 - Vvi5g856 Vvi5g856 856
5 11790522 11790729 + Vvi5g857 Vvi5g857 857
5 11800869 11810878 - Vvi5g858 Vvi5g858 858
       

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