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
Vvi5g39 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g40 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g41 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g42 Blo01g00038 . . Bda08g00326 . . . Bma05g01001 . . . . . . . . . . . . . . . . . . . . . . . . . Cone7ag0092 . . . . . . . . . Bpe05g00802 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g43 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g44 . . . . . Bpe14g01089 . . . . Cma06g01572 Cma14g01579 Car06g01336 Car14g01390 Sed02g1128 Cpe08g00143 Cpe03g01318 Bhi01g01101 Tan10g1088 Cmetu06g1064 . Hepe05g1365 . Lcy11g1328 . . . . . . . . Cone15ag0720 . . Lsi05g01410 . . Cme06g00801 Blo02g00471 Blo07g00132 . Bda13g00226 . . Bma02g00937 . . Cmo06g01566 Cmo14g01611 . . . . . . . . . . . . . Cla05g00717 Cam05g0784 Cec05g0790 Cco05g0786 Clacu05g0774 Cmu05g0739 Cre05g0813 . Csa03g01530 Chy06g00767 .
Vvi5g45 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g46 Blo01g00037 Blo12g00030 Bda03g01189 . Bpe04g01123 . Bma04g01118 Bma05g01000 . Cmo17g00369 . . . . . . . . . . . . . . Cla06g00417 Cam06g0439 Cec06g0445 Cco06g0444 Clacu06g0426 Cmu06g0425 Cre06g1204 . Cone15ag0721 . . . Csa06g01860 . . . . . . . . . . . . . . Cma17g00380 . Car17g00351 Cpe12g00332 Cpe17g00076 Bhi12g01943 . . . . . Lcy12g0865 . . . . . . . Lsi09g01506 . . Cme11g02092
Vvi5g47 . . . . . Bpe14g01090 . . Cmo08g01253 . . . . . . . . . . . . . . . Cla06g00418 . . . . . . . . . . . . Chy11g01581 . Blo02g00472 . . Bda13g00225 . . Bma02g00936 . . . . Cma08g01288 . Car08g01155 . . . Bhi12g01942 . . . . . Lcy12g0864 . . . . . . . Lsi09g01505 . . Cme11g02091
Vvi5g48 . . Bda03g01188 . Bpe04g01122 Bpe14g01092 . . . Cmo17g00367 Cma06g01571 Cma14g01581 Car06g01335 Car14g01391 Sed02g1129 Cpe08g00144 Cpe03g01319 Bhi01g01100 Tan10g1087 Cmetu06g2518 Lac11g0974 Hepe05g1368 . Lcy11g1329 Cla06g00419 Cam06g0441 Cec06g0447 Cco06g0446 Clacu06g0428 Cmu06g0427 Cre06g1206 . Cone15ag0722 . Cone4ag0098 Lsi05g01411 Csa06g01861 . Cme06g00800 Blo02g00473 Blo07g00133 Bda11g00494 Bda13g00224 . Bpe13g00706 Bma02g00935 Bma06g01458 . Cmo06g01565 Cmo14g01612 . Cma17g00379 . Car17g00350 Cpe12g00331 . . . . . . . . Cla05g00716 Cam05g0783 Cec05g0789 Cco05g0785 Clacu05g0773 Cmu05g0738 Cre05g0812 . Csa03g01529 Chy06g00766 Cme11g02090
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 14265918 14266577 + Bda017266.1 Bda03g01188 1188
3 14292469 14306227 - Bda017267.1 Bda03g01189 1189
8 3366107 3366971 - Bda024765.1 Bda08g00326 326
11 5270703 5271813 - Bda005231.1 Bda11g00494 494
13 2849666 2850812 + Bda001102.1 Bda13g00224 224
13 2854063 2855322 + Bda001103.1 Bda13g00225 225
13 2855596 2859381 + Bda001104.1 Bda13g00226 226
1 20981951 20983747 + XM_039045031.1 Bhi01g01100 1100
1 21064857 21071140 + XM_039046270.1 Bhi01g01101 1101
12 61926513 61928009 + XM_039051240.1 Bhi12g01942 1942
12 61928102 61943533 - XM_039051239.1 Bhi12g01943 1943
1 473856 487186 - BLOR00037 Blo01g00037 37
1 500002 501031 + BLOR00038 Blo01g00038 38
2 6700954 6704730 - BLOR10201 Blo02g00471 471
2 6706311 6707541 - BLOR10202 Blo02g00472 472
2 6768754 6769920 - BLOR10203 Blo02g00473 473
7 1807661 1811106 - BLOR18064 Blo07g00132 132
7 1815711 1816820 - BLOR18065 Blo07g00133 133
12 1992215 2001186 - BLOR04049 Blo12g00030 30
2 49202332 49203489 + Bma015725.1 Bma02g00935 935
2 49244388 49245648 + Bma015728.1 Bma02g00936 936
2 49246885 49250662 + Bma015729.1 Bma02g00937 937
4 26462746 26464306 + Bma019821.1 Bma04g01118 1118
5 48491326 48492400 - Bma022154.1 Bma05g01000 1000
5 48496707 48497270 + Bma022155.1 Bma05g01001 1001
6 51257200 51265384 - Bma024572.2 Bma06g01458 1458
4 9543590 9544988 + Bpe015802.1 Bpe04g01122 1122
4 9640879 9654081 - Bpe015803.2 Bpe04g01123 1123
5 21360937 21361966 + Bpe018215.1 Bpe05g00802 802
13 13646723 13647819 + Bpe010407.1 Bpe13g00706 706
14 8141064 8144807 - Bpe014463.1 Bpe14g01089 1089
14 8145441 8146689 - Bpe014464.2 Bpe14g01090 1090
14 8150578 8151736 - Bpe014466.1 Bpe14g01092 1092
5 6844335 6845876 + CaPI482276_05g007830.1 Cam05g0783 783
5 6857792 6863610 + CaPI482276_05g007840.1 Cam05g0784 784
6 6502737 6516733 + CaPI482276_06g004390.1 Cam06g0439 439
6 6524678 6526096 - CaPI482276_06g004410.1 Cam06g0441 441
6 9575672 9577062 + Carg25644-RA Car06g01335 1335
6 9579813 9585301 + Carg25645-RA Car06g01336 1336
8 7755681 7758086 - Carg18897-RA Car08g01155 1155
14 11743282 11749268 - Carg19611-RA Car14g01390 1390
14 11753466 11754680 - Carg19612-RA Car14g01391 1391
17 2214403 2215310 + Carg05556-RA Car17g00350 350
17 2219831 2229706 - Carg05557-RA Car17g00351 351
5 6559253 6560783 + CcPI632755_05g007850.1 Cco05g0785 785
5 6572363 6578146 + CcPI632755_05g007860.1 Cco05g0786 786
6 4883614 4897711 + CcPI632755_06g004440.1 Cco06g0444 444
6 4905637 4907044 - CcPI632755_06g004460.1 Cco06g0446 446
5 6576135 6577687 + CePI673135_05g007890.1 Cec05g0789 789
5 6590359 6596377 + CePI673135_05g007900.1 Cec05g0790 790
6 5016733 5031138 + CePI673135_06g004450.1 Cec06g0445 445
6 5039065 5040466 - CePI673135_06g004470.1 Cec06g0447 447
6 5293301 5294752 + Chy6G112940.1 Chy06g00766 766
6 5303551 5309107 + Chy6G112950.1 Chy06g00767 767
11 22383847 22392206 + Chy11G201610.1 Chy11g01581 1581
5 6554892 6556457 + ClG42_05g0077300.10 Clacu05g0773 773
5 6568093 6573904 + ClG42_05g0077400.10 Clacu05g0774 774
6 5041963 5056082 + ClG42_06g0042600.10 Clacu06g0426 426
6 5063751 5065173 - ClG42_06g0042800.10 Clacu06g0428 428
5 6696711 6699482 + ClCG05G006660.1 Cla05g00716 716
5 6709900 6717327 + ClCG05G006670.1 Cla05g00717 717
6 5071717 5095234 + ClCG06G004470.2 Cla06g00417 417
6 5086645 5088412 - ClCG06G004480.2 Cla06g00418 418
6 5093567 5095514 - ClCG06G004490.2 Cla06g00419 419
6 9833175 9834847 + CmaCh06G015710.1 Cma06g01571 1571
6 9836795 9842519 + CmaCh06G015720.1 Cma06g01572 1572
8 7797609 7799237 - CmaCh08G012880.1 Cma08g01288 1288
14 11866424 11871975 - CmaCh14G015790.1 Cma14g01579 1579
14 11876011 11877554 - CmaCh14G015810.1 Cma14g01581 1581
17 2109793 2110780 + CmaCh17G003790.1 Cma17g00379 379
17 2115307 2125582 - CmaCh17G003800.1 Cma17g00380 380
6 5322743 5323966 + MELO3C006725.2.1 Cme06g00800 800
6 5332336 5338510 + MELO3C006726.2.1 Cme06g00801 801
11 28560931 28562595 + MELO3C000030.2.1 Cme11g02090 2090
11 28567048 28569396 + MELO3C021259.2.1 Cme11g02091 2091
11 28568490 28582744 - MELO3C021258.2.1 Cme11g02092 2092
6 5542496 5548893 + PI0014518.3 Cmetu06g1064 1064
6 5530619 5532127 + PI0005721.1 Cmetu06g2518 2518
6 11028323 11029878 + CmoCh06G015650.1 Cmo06g01565 1565
6 11030037 11038141 + CmoCh06G015660.1 Cmo06g01566 1566
8 7912858 7914240 - CmoCh08G012530.1 Cmo08g01253 1253
14 12794804 12800418 - CmoCh14G016110.1 Cmo14g01611 1611
14 12805350 12806755 - CmoCh14G016120.1 Cmo14g01612 1612
17 2255107 2256077 + CmoCh17G003670.1 Cmo17g00367 367
17 2261116 2272213 - CmoCh17G003690.1 Cmo17g00369 369
5 6410926 6412491 + CmPI595203_05g007380.1 Cmu05g0738 738
5 6424129 6429940 + CmPI595203_05g007390.1 Cmu05g0739 739
6 4836104 4851021 + CmPI595203_06g004250.1 Cmu06g0425 425
6 4857912 4859332 - CmPI595203_06g004270.1 Cmu06g0427 427
4 473724 475437 - Conep04aG0010000.1 Cone4ag0098 98
7 406150 407759 - Conep07aG0009200.1 Cone7ag0092 92
15 4004611 4008249 - Conep15aG0073400.1 Cone15ag0720 720
15 4016550 4021523 + Conep15aG0073500.1 Cone15ag0721 721
15 4027841 4030111 - Conep15aG0073600.1 Cone15ag0722 722
3 10720656 10726297 - Cp4.1LG03g11890.1 Cpe03g01318 1318
3 10730902 10732156 - Cp4.1LG03g11900.1 Cpe03g01319 1319
8 932112 937637 - Cp4.1LG08g05310.1 Cpe08g00143 143
8 939405 941099 - Cp4.1LG08g05270.1 Cpe08g00144 144
12 2190645 2192926 + Cp4.1LG12g03320.1 Cpe12g00331 331
12 2196254 2207031 - Cp4.1LG12g03390.1 Cpe12g00332 332
17 432623 446206 + Cp4.1LG17g00280.1 Cpe17g00076 76
5 7201861 7203397 + CrPI670011_05g008120.1 Cre05g0812 812
5 7215969 7221759 + CrPI670011_05g008130.1 Cre05g0813 813
6 5896621 5909457 + CrPI670011_06g012040.1 Cre06g1204 1204
6 5917369 5918797 - CrPI670011_06g012060.1 Cre06g1206 1206
3 11362956 11365199 + CsaV3_3G015290.1 Csa03g01529 1529
3 11377961 11384362 + CsaV3_3G015300.1 Csa03g01530 1530
6 16769900 16782950 + CsaV3_6G028500.1 Csa06g01860 1860
6 16783402 16791738 - CsaV3_6G028510.1 Csa06g01861 1861
5 62266997 62273270 - Hsped.05g13650.1 Hepe05g1365 1365
5 62322167 62323967 - Hsped.05g13680.1 Hepe05g1368 1368
11 10736993 10738144 + Lag0031612.1 Lac11g0974 974
11 36900838 36907207 - Maker00032074 Lcy11g1328 1328
11 36917052 36918975 - Maker00031450 Lcy11g1329 1329
12 11985169 11986342 + Maker00024815 Lcy12g0864 864
12 11997852 12002031 - Maker00024819 Lcy12g0865 865
5 22033559 22040079 - Lsi05G014100.1 Lsi05g01410 1410
5 22051870 22053690 - Lsi05G014110.1 Lsi05g01411 1411
9 23101471 23102970 + Lsi09G015050.1 Lsi09g01505 1505
9 23102767 23118562 - Lsi09G015060.1 Lsi09g01506 1506
2 48475031 48482159 - Sed0008581.2 Sed02g1128 1128
2 48492949 48494949 - Sed0010981.1 Sed02g1129 1129
10 10214516 10216376 + Tan0012224.1 Tan10g1087 1087
10 10255731 10263132 + Tan0004320.1 Tan10g1088 1088
5 441758 444928 - Vvi5g39 Vvi5g39 39
5 454098 454377 + Vvi5g40 Vvi5g40 40
5 455084 464858 + Vvi5g41 Vvi5g41 41
5 480373 483103 - Vvi5g42 Vvi5g42 42
5 483213 487376 - Vvi5g43 Vvi5g43 43
5 487689 494963 - Vvi5g44 Vvi5g44 44
5 496251 501848 - Vvi5g45 Vvi5g45 45
5 507912 523990 + Vvi5g46 Vvi5g46 46
5 524036 525474 - Vvi5g47 Vvi5g47 47
5 530083 531773 - Vvi5g48 Vvi5g48 48
       

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