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
Vvi1g521 Blo01g00775 Blo16g00760 Bda01g01789 Bda11g00191 . . . . Cmo04g01114 . Cma04g01044 . Car04g00974 . . . . Bhi07g00419 . . Lac13g1295 Hepe01g0615 . . Cla07g00519 Cam07g0554 Cec07g0607 Cco07g0579 Clacu07g0558 Cmu07g0595 Cre07g0927 . . Cone6ag0349 Cone9ag0382 Lsi04g00995 Csa05g01974 . . . . . Bda11g00191 . Bpe02g01967 Bma01g00492 Bma06g01135 . . Cmo15g00932 . Cma15g00893 . . Cpe13g00423 . Bhi12g00957 . . . Hepe02g2608 . Lcy10g1376 . . . . . . . Lsi09g00700 . Chy09g00810 Cme09g01325
Vvi1g522 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g523 . . . . . Bpe10g01007 . Bma15g00022 Cmo04g01115 . Cma04g01045 Cma04g00088 Car04g00975 . . . . Bhi07g00420 . . Lac13g1294 . . . Cla07g00517 Cam07g0553 Cec07g0606 Cco07g0578 Clacu07g0556 Cmu07g0594 Cre07g0926 Cone13ag0727 Cone19ag0730 . . Lsi04g00996 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g524 . . . . . . Bma14g01920 . . . . Cma04g00085 . Car04g00086 . . . . . . . . . . . . . . . . . . . Cone6ag0348 Cone9ag0381 . . Chy10g00215 . . Blo11g00966 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01127 . .
Vvi1g525 . . . . . . Bma14g01921 . . . . Cma04g00084 . Car04g00085 . . . . . . . . . . . . . . . . . . . Cone6ag0347 . . . Chy10g00214 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01126 . .
Vvi1g526 . . . . Bpe13g01001 . . . . . . Cma04g00083 . Car04g00084 . Cpe09g00608 Cpe01g01855 . . . . . . . . . . . . . . . . . Cone9ag0379 . Csa05g01972 . . . . . . . . . Bma06g01137 . Cmo04g02230 . Cma04g02137 . Car04g02074 . . . Bhi12g00959 . . . Hepe02g2605 . Lcy10g1600 Cla01g00649 Cam01g0678 Cec01g0671 Cco01g0697 Clacu01g0666 Cmu01g0639 Cre09g1866 Lsi09g00702 Csa05g01125 . .
Vvi1g527 Blo01g00776 Blo16g00764 Bda01g01788 Bda11g00194 Bpe13g01000 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0345 . . . . . . . . Bda11g00194 . Bpe02g01965 Bma01g00494 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g528 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone19ag0729 . . . Csa05g01971 . . . . . . . . . . . . Cmo15g00931 . Cma15g00892 . Car15g00838 Cpe13g00425 . Bhi12g00960 . . . . . Lcy10g1599 Cla01g00650 . . . . . . Lsi09g00703 . Chy09g00808 .
Vvi1g529 . Blo16g00765 . Bda11g00196 Bpe13g00998 . . . . . . . . . . . Cpe01g01856 . . . . . . . . . . . . . . . . . . . Csa05g01969 . . . . . Bda11g00196 . . . Bma06g01140 . Cmo04g02231 Cmo15g00928 Cma04g02138 Cma15g00890 Car04g02075 Car15g00836 Cpe13g00426 . Bhi12g00962 . . . . . Lcy10g1597 Cla01g00652 Cam01g0681 Cec01g0674 Cco01g0701 Clacu01g0669 Cmu01g0642 Cre09g1863 Lsi09g00705 . Chy09g00805 .
Vvi1g530 . . . . . . Bma14g01900 . . . . Cma04g00071 . Car04g00066 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 54067146 54075326 + Bda004076.1 Bda01g01788 1788
1 54078102 54079212 + Bda004077.1 Bda01g01789 1789
11 2424202 2425451 - Bda004908.1 Bda11g00191 191
11 2469745 2479357 - Bda004913.1 Bda11g00194 194
11 2483040 2516486 - Bda004915.1 Bda11g00196 196
7 18690274 18700135 - XM_039036354.1 Bhi07g00419 419
7 18705919 18712940 - XM_039036814.1 Bhi07g00420 420
12 28993572 28997770 - XM_039018607.1 Bhi12g00957 957
12 29191964 29194076 + XM_039019297.1 Bhi12g00959 959
12 29201631 29204454 - XM_039019311.1 Bhi12g00960 960
12 29217118 29250268 - XM_039051311.1 Bhi12g00962 962
1 11203616 11204763 - BLOR00775 Blo01g00775 775
1 11223594 11233750 - BLOR00776 Blo01g00776 776
11 21844441 21847798 + BLOR03842 Blo11g00966 966
16 31347563 31350341 - BLOR21547 Blo16g00760 760
16 31668661 31669359 - BLOR21551 Blo16g00764 764
16 31851098 31858895 - BLOR21552 Blo16g00765 765
1 4041082 4042179 - Bma000669.1 Bma01g00492 492
1 4050224 4057074 - Bma000671.1 Bma01g00494 494
6 48241241 48242728 - Bma024232.1 Bma06g01135 1135
6 48253282 48254819 - Bma024234.1 Bma06g01137 1137
6 48278403 48309519 - Bma024237.1 Bma06g01140 1140
14 40659658 40660050 - Bma012688.1 Bma14g01900 1900
14 40983192 40991032 + Bma012710.1 Bma14g01920 1920
14 40991707 40993055 - Bma012711.1 Bma14g01921 1921
15 264536 269500 + Bma012991.1 Bma15g00022 22
2 21515527 21522703 + Bpe009788.1 Bpe02g01965 1965
2 21529086 21530203 + Bpe009790.1 Bpe02g01967 1967
10 15501028 15505862 - Bpe003312.1 Bpe10g01007 1007
13 15726131 15758691 + Bpe010681.1 Bpe13g00998 998
13 15761711 15770593 + Bpe010683.1 Bpe13g01000 1000
13 15774491 15775391 + Bpe010684.1 Bpe13g01001 1001
1 7494878 7496600 + CaPI482276_01g006780.1 Cam01g0678 678
1 7517382 7542040 - CaPI482276_01g006810.1 Cam01g0681 681
7 8316642 8322296 + CaPI482276_07g005530.1 Cam07g0553 553
7 8355557 8361599 + CaPI482276_07g005540.1 Cam07g0554 554
4 355734 356126 - Carg22014-RA Car04g00066 66
4 447227 449287 + Carg27434-RA Car04g00084 84
4 450969 453691 + Carg27433-RA Car04g00085 85
4 455024 458689 - Carg27432-RA Car04g00086 86
4 5619449 5621050 - Carg00150-RA Car04g00974 974
4 5621595 5628942 - Carg00151-RA Car04g00975 975
4 16873933 16876123 + Carg25248-RA Car04g02074 2074
4 16878000 16913457 - Carg25249-RA Car04g02075 2075
15 4788303 4820195 + Carg01319-RA Car15g00836 836
15 4824438 4826861 + Carg01317-RA Car15g00838 838
1 7272316 7273996 + CcPI632755_01g006970.1 Cco01g0697 697
1 7295640 7319281 - CcPI632755_01g007010.1 Cco01g0701 701
7 7771909 7777659 + CcPI632755_07g005780.1 Cco07g0578 578
7 7811630 7817852 + CcPI632755_07g005790.1 Cco07g0579 579
1 7329971 7331628 + CePI673135_01g006710.1 Cec01g0671 671
1 7352950 7377508 - CePI673135_01g006740.1 Cec01g0674 674
7 8096630 8102327 + CePI673135_07g006060.1 Cec07g0606 606
7 8140467 8150579 + CePI673135_07g006070.1 Cec07g0607 607
9 10754304 10779702 + Chy9G165210.1 Chy09g00805 805
9 10788988 10793957 + Chy9G165240.1 Chy09g00808 808
9 10818115 10819913 + Chy9G165260.1 Chy09g00810 810
10 5459576 5471916 + Chy10G174080.1 Chy10g00214 214
10 5472752 5477270 - Chy10G174090.1 Chy10g00215 215
1 7144064 7145761 + ClG42_01g0066600.10 Clacu01g0666 666
1 7166978 7191474 - ClG42_01g0066900.10 Clacu01g0669 669
7 7521580 7527267 + ClG42_07g0055600.10 Clacu07g0556 556
7 7567476 7573479 + ClG42_07g0055800.10 Clacu07g0558 558
1 7536696 7539334 + ClCG01G006660.1 Cla01g00649 649
1 7541016 7543409 - ClCG01G006670.1 Cla01g00650 650
1 7559368 7584998 - ClCG01G006690.1 Cla01g00652 652
7 7649275 7657595 + ClCG07G005405.1 Cla07g00517 517
7 7696412 7702420 + ClCG07G005420.1 Cla07g00519 519
4 339796 342959 - CmaCh04G000710.1 Cma04g00071 71
4 414220 416780 + CmaCh04G000830.1 Cma04g00083 83
4 418288 420964 + CmaCh04G000840.1 Cma04g00084 84
4 419964 425964 - CmaCh04G000850.1 Cma04g00085 85
4 439365 444623 - CmaCh04G000880.1 Cma04g00088 88
4 5406146 5409704 - CmaCh04G010440.1 Cma04g01044 1044
4 5411304 5417647 - CmaCh04G010450.1 Cma04g01045 1045
4 14936388 14938711 + CmaCh04G021370.1 Cma04g02137 2137
4 14939546 14949310 - CmaCh04G021380.1 Cma04g02138 2138
15 4532496 4567020 + CmaCh15G008900.1 Cma15g00890 890
15 4570537 4578245 + CmaCh15G008920.1 Cma15g00892 892
15 4578980 4581206 + CmaCh15G008930.1 Cma15g00893 893
9 18307921 18309619 - MELO3C005259.2.1 Cme09g01325 1325
4 5678248 5681169 - CmoCh04G011140.1 Cmo04g01114 1114
4 5681933 5688903 - CmoCh04G011150.1 Cmo04g01115 1115
4 16667124 16669172 + CmoCh04G022300.1 Cmo04g02230 2230
4 16670417 16679967 - CmoCh04G022310.1 Cmo04g02231 2231
15 4724624 4759913 + CmoCh15G009280.1 Cmo15g00928 928
15 4764971 4767394 + CmoCh15G009310.1 Cmo15g00931 931
15 4772103 4773813 + CmoCh15G009320.1 Cmo15g00932 932
1 7114087 7115769 + CmPI595203_01g006390.1 Cmu01g0639 639
1 7136992 7161469 - CmPI595203_01g006420.1 Cmu01g0642 642
7 7680189 7685877 + CmPI595203_07g005940.1 Cmu07g0594 594
7 7726070 7732077 + CmPI595203_07g005950.1 Cmu07g0595 595
6 1666813 1678316 + Conep06aG0035100.1 Cone6ag0345 345
6 1690256 1692269 + Conep06aG0035300.1 Cone6ag0347 347
6 1692728 1695864 - Conep06aG0035400.1 Cone6ag0348 348
6 1701845 1703549 + Conep06aG0035700.1 Cone6ag0349 349
9 1730248 1731092 + Conep09aG0038700.1 Cone9ag0379 379
9 1732722 1735848 - Conep09aG0038900.1 Cone9ag0381 381
9 1739152 1740579 + Conep09aG0039200.1 Cone9ag0382 382
13 7009193 7012898 + Conep13aG0075100.1 Cone13ag0727 727
19 6008821 6011278 - Conep19aG0075000.1 Cone19ag0729 729
19 6012152 6015758 + Conep19aG0075100.1 Cone19ag0730 730
1 15801390 15803575 + Cp4.1LG01g18550.1 Cpe01g01855 1855
1 15804509 15839860 - Cp4.1LG01g18580.1 Cpe01g01856 1856
9 4239934 4244106 + Cp4.1LG09g05790.1 Cpe09g00608 608
13 4559343 4564556 - Cp4.1LG13g06670.1 Cpe13g00423 423
13 4567063 4569483 - Cp4.1LG13g06520.1 Cpe13g00425 425
13 4572387 4610611 - Cp4.1LG13g06540.1 Cpe13g00426 426
7 8918312 8924026 + CrPI670011_07g009260.1 Cre07g0926 926
7 8959367 8965668 + CrPI670011_07g009270.1 Cre07g0927 927
9 37156090 37179414 + CrPI670011_09g018630.1 Cre09g1863 1863
9 37195434 37197081 - CrPI670011_09g018660.1 Cre09g1866 1866
5 11490783 11492726 + CsaV3_5G014490.1 Csa05g01125 1125
5 11496294 11503340 + CsaV3_5G014500.1 Csa05g01126 1126
5 11499822 11506322 - CsaV3_5G014510.1 Csa05g01127 1127
5 23063998 23088729 + CsaV3_5G027880.1 Csa05g01969 1969
5 23094044 23097000 + CsaV3_5G027900.1 Csa05g01971 1971
5 23097481 23099780 - CsaV3_5G027910.1 Csa05g01972 1972
5 23120797 23123210 + CsaV3_5G027930.1 Csa05g01974 1974
1 67509120 67511672 - Hsped.01g06150.1 Hepe01g0615 615
2 73320756 73323069 - Hsped.02g26050.1 Hepe02g2605 2605
2 73381933 73384157 + Hsped.02g26080.1 Hepe02g2608 2608
13 11884933 11890057 + Lag0041090.1 Lac13g1294 1294
13 11892874 11898797 + Lag0041091.1 Lac13g1295 1295
10 37058213 37059964 + Maker00008368 Lcy10g1376 1376
10 40400557 40432375 + Maker00039883 Lcy10g1597 1597
10 40445924 40448314 + Maker00039468 Lcy10g1599 1599
10 40449517 40453424 - Maker00039197 Lcy10g1600 1600
4 10880452 10890703 - Lsi04G009950.1 Lsi04g00995 995
4 10907338 10913756 - Lsi04G009960.1 Lsi04g00996 996
9 7925012 7928453 - Lsi09G007000.1 Lsi09g00700 700
9 7962579 7964679 + Lsi09G007020.1 Lsi09g00702 702
9 7967748 7970141 - Lsi09G007030.1 Lsi09g00703 703
9 7983305 8008188 - Lsi09G007050.1 Lsi09g00705 705
1 5765350 5767833 - Vvi1g521 Vvi1g521 521
1 5781885 5784954 - Vvi1g522 Vvi1g522 522
1 5786196 5797731 - Vvi1g523 Vvi1g523 523
1 5806546 5811465 + Vvi1g524 Vvi1g524 524
1 5816680 5821580 - Vvi1g525 Vvi1g525 525
1 5829739 5832049 - Vvi1g526 Vvi1g526 526
1 5836229 5846190 - Vvi1g527 Vvi1g527 527
1 5847647 5850416 - Vvi1g528 Vvi1g528 528
1 5854871 5917506 - Vvi1g529 Vvi1g529 529
1 5922275 5931486 + Vvi1g530 Vvi1g530 530
       

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