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
Vvi1g431 . . . . . . . . . . . Cma04g00027 . . . . . . . . . . . . . . . . . . . Cone13ag0761 Cone19ag0765 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01021 . .
Vvi1g432 . . . . . . . . . . . . . . . . Cpe01g01849 . . . . . . . . . . . . . . Cone13ag0760 Cone19ag0764 . . . Csa05g02023 . . . . . . . . . Bma06g01109 . . . . . . . . . Bhi12g00887 . . . . . . Cla01g00608 Cam01g0636 Cec01g0628 Cco01g0655 Clacu01g0626 Cmu01g0599 Cre09g1903 Lsi09g00659 . Chy09g00851 Cme09g01384
Vvi1g433 . Blo16g00730 Bda01g01817 Bda11g00164 . . . . . . . . . . . . Cpe01g01848 . . . . . . . . . . . . . . Cone13ag0759 Cone19ag0763 Cone6ag0395 Cone9ag0421 . Csa05g02022 . . . . . Bda11g00164 . Bpe02g01993 Bma01g00466 . . . Cmo15g00996 . Cma15g00957 . Car15g00901 Cpe13g00368 . Bhi12g00905 . . . . . . Cla01g00610 Cam01g0638 Cec01g0630 Cco01g0657 Clacu01g0628 Cmu01g0601 Cre09g1901 Lsi09g00661 . Chy09g00850 Cme09g01383
Vvi1g434 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01020 . .
Vvi1g435 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe04g01371 . . . . . . . . . . . . . . . . . .
Vvi1g436 Blo01g00756 . . . . . . . . . . . . . . . Cpe01g01847 . . . . . . . . . . . . . . Cone13ag0758 Cone19ag0762 Cone6ag0393 Cone9ag0419 . Csa05g02021 . . . . . . . . . . . . Cmo15g00997 . Cma15g00958 . Car15g00902 Cpe13g00367 . Bhi12g00907 . . . . . . Cla01g00611 Cam01g0639 Cec01g0631 Cco01g0658 Clacu01g0629 Cmu01g0602 Cre09g1900 Lsi09g00662 . Chy09g00515 Cme09g01382
Vvi1g437 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g438 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0756 Cone19ag0761 . . Lsi04g01195 . Chy10g00266 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01180 . .
Vvi1g439 . . . . . . Bma14g01953 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g440 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 54337724 54343136 + Bda004109.1 Bda01g01817 1817
11 2130880 2136849 - Bda004879.1 Bda11g00164 164
12 26732402 26733502 - XM_039051126.1 Bhi12g00887 887
12 27210303 27221704 + XM_039018650.1 Bhi12g00905 905
12 27242601 27246755 - XM_039050738.1 Bhi12g00907 907
1 10156514 10173765 + BLOR00756 Blo01g00756 756
16 28415856 28428126 - BLOR21517 Blo16g00730 730
1 3858031 3863543 - Bma000642.1 Bma01g00466 466
6 47879048 47879551 - Bma024205.1 Bma06g01109 1109
14 42105587 42106281 - Bma012756.1 Bma14g01953 1953
2 21687867 21693161 + Bpe009816.1 Bpe02g01993 1993
1 6945335 6946132 + CaPI482276_01g006360.1 Cam01g0636 636
1 6965016 6974532 + CaPI482276_01g006380.1 Cam01g0638 638
1 6978278 6980791 - CaPI482276_01g006390.1 Cam01g0639 639
15 5476248 5481971 + Carg26343-RA Car15g00901 901
15 5482265 5485139 - Carg26342-RA Car15g00902 902
1 6685065 6685862 + CcPI632755_01g006550.1 Cco01g0655 655
1 6710825 6720174 + CcPI632755_01g006570.1 Cco01g0657 657
1 6724283 6726784 - CcPI632755_01g006580.1 Cco01g0658 658
1 6750288 6751085 + CePI673135_01g006280.1 Cec01g0628 628
1 6770853 6780149 + CePI673135_01g006300.1 Cec01g0630 630
1 6784330 6786841 - CePI673135_01g006310.1 Cec01g0631 631
9 5201329 5202994 + Chy9G162310.1 Chy09g00515 515
9 11303295 11313653 - Chy9G165660.1 Chy09g00850 850
9 11320443 11321176 - Chy9G165670.1 Chy09g00851 851
10 6588477 6598195 - Chy10G174600.1 Chy10g00266 266
1 6578626 6579423 + ClG42_01g0062600.10 Clacu01g0626 626
1 6598368 6607885 + ClG42_01g0062800.10 Clacu01g0628 628
1 6611917 6615942 - ClG42_01g0062900.10 Clacu01g0629 629
1 6938460 6939572 + ClCG01G006240.2 Cla01g00608 608
1 6958059 6968515 + ClCG01G006260.2 Cla01g00610 610
1 6971551 6977069 - ClCG01G006270.2 Cla01g00611 611
4 128255 131619 - CmaCh04G000270.1 Cma04g00027 27
15 5149949 5155968 + CmaCh15G009570.1 Cma15g00957 957
15 5156070 5160114 - CmaCh15G009580.1 Cma15g00958 958
9 19064520 19068759 + MELO3C005303.2.1 Cme09g01382 1382
9 19069914 19080528 - MELO3C005304.2.1 Cme09g01383 1383
9 19085694 19090301 - MELO3C005305.2.1 Cme09g01384 1384
15 5360888 5366987 + CmoCh15G009960.1 Cmo15g00996 996
15 5367188 5370905 - CmoCh15G009970.1 Cmo15g00997 997
1 6535463 6535811 + CmPI595203_01g005990.1 Cmu01g0599 599
1 6555213 6564730 + CmPI595203_01g006010.1 Cmu01g0601 601
1 6568758 6572786 - CmPI595203_01g006020.1 Cmu01g0602 602
6 1907214 1908518 + Conep06aG0040100.1 Cone6ag0393 393
6 1910739 1916882 - Conep06aG0040300.1 Cone6ag0395 395
9 1932780 1933999 + Conep09aG0042900.1 Cone9ag0419 419
9 1937140 1943091 - Conep09aG0043100.1 Cone9ag0421 421
13 7151598 7153863 - Conep13aG0078000.1 Cone13ag0756 756
13 7164452 7165443 + Conep13aG0078200.1 Cone13ag0758 758
13 7165806 7168431 - Conep13aG0078300.1 Cone13ag0759 759
13 7168916 7169705 - Conep13aG0078400.1 Cone13ag0760 760
13 7181430 7185576 + Conep13aG0078600.1 Cone13ag0761 761
19 6193732 6196140 - Conep19aG0078200.1 Cone19ag0761 761
19 6205811 6207874 + Conep19aG0078300.1 Cone19ag0762 762
19 6208338 6210148 - Conep19aG0078400.1 Cone19ag0763 763
19 6211351 6212662 - Conep19aG0078500.1 Cone19ag0764 764
19 6216865 6220790 + Conep19aG0078700.1 Cone19ag0765 765
1 15750457 15753753 + Cp4.1LG01g18470.1 Cpe01g01847 1847
1 15752575 15759075 - Cp4.1LG01g18540.1 Cpe01g01848 1848
1 15762963 15764382 - Cp4.1LG01g18500.1 Cpe01g01849 1849
4 11141487 11144903 - Cp4.1LG04g13710.1 Cpe04g01371 1371
13 3972656 3976528 + Cp4.1LG13g03720.1 Cpe13g00367 367
13 3977980 3983307 - Cp4.1LG13g03800.1 Cpe13g00368 368
9 37741638 37744157 + CrPI670011_09g019000.1 Cre09g1900 1900
9 37748333 37757553 - CrPI670011_09g019010.1 Cre09g1901 1901
9 37776928 37777725 - CrPI670011_09g019030.1 Cre09g1903 1903
5 9706836 9716154 - CsaV3_5G013260.1 Csa05g01020 1020
5 9720731 9731562 - CsaV3_5G013270.1 Csa05g01021 1021
5 12210665 12222452 - CsaV3_5G015040.1 Csa05g01180 1180
5 23588558 23592756 + CsaV3_5G028400.1 Csa05g02021 2021
5 23594214 23605089 - CsaV3_5G028410.1 Csa05g02022 2022
5 23610918 23612310 - CsaV3_5G028420.1 Csa05g02023 2023
4 18020606 18026383 + Lsi04G011950.1 Lsi04g01195 1195
9 7369430 7369963 + Lsi09G006590.1 Lsi09g00659 659
9 7383415 7395024 + Lsi09G006610.1 Lsi09g00661 661
9 7396949 7401092 - Lsi09G006620.1 Lsi09g00662 662
1 4650631 4654857 - Vvi1g431 Vvi1g431 431
1 4661912 4662737 + Vvi1g432 Vvi1g432 432
1 4665983 4672737 + Vvi1g433 Vvi1g433 433
1 4673766 4683777 + Vvi1g434 Vvi1g434 434
1 4685929 4687708 - Vvi1g435 Vvi1g435 435
1 4689630 4694454 - Vvi1g436 Vvi1g436 436
1 4707474 4710202 - Vvi1g437 Vvi1g437 437
1 4717257 4721940 + Vvi1g438 Vvi1g438 438
1 4722595 4723256 + Vvi1g439 Vvi1g439 439
1 4732748 4737395 + Vvi1g440 Vvi1g440 440
       

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