构建进化树方法

996 Nocardiopsis
tropica
Baidu Nhomakorabea
DSM
44381T
AF105971
Nocardiopsis synnemataformans DSM 44143T Y13593
482 588Nocardiopsis
dassonvillei
subsp.
albirubida
DSM
40465T
X97882
62 Nocardiopsis dassonvillei subsp. dassonvillei DSM 43111T X97886
NCBI homepage http://www.ncbi.nlm.nih.gov/
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FIRST
EzTaxon http://147.47.212.35:8080/
OR
RDP(RIBOSOMAL DATABASE PROJECT) homepage http://www.bacterio.cict.fr/
99
Nocardiopsis baichengensis DSM 44845T AY619716
91 Nocardiopsis halophila DSM 44494T AJ421018
Actinomadura echinospora DSM 43163T AJ420135
Example2
PHYLIP---NJ
99
Nocardiopsis rosea DSM 44842T AY619713
Nocardiopsis gilva DSM 44841T AY619712 Nocardiopsis arabia DSM 45083T EF095149
Nocardiopsis composta DSM 44551T AF360734 Nocardiopsis potens DSM 45234T FM253114 Nocardiopsis chromatogenes DSM 44844T AY619715
Nocardiopsis listeri DSM 40297T X97887
924 Nocardiopsis
alkaliphila
DSM
44657T
AY230848
323
Nocardiopsis alba DSM 43377T X97883
102 264
Nocardiopsis umidischolae DSM 44362T AY036001
Unweightedpair group method with arithmetic mean(UPGMA) Neighbor joining(NJ)
Minimum evolution(ME)
Phylogenetic analysis &
Bootstrap analysis
TOOLS
MEGA-----UPGMA\NJ\MP\ME PHYLIP----NJ\MP\ML
Construction of Phylogenetic Tree
Extraction of chromosomal DNA PCR amplification of the16S rRNA gene
Assmbly of 16S rRNA gene fragments Obtain closely related sequences Multiple alignments Phylogenetic analysis Bootstrap analysis
65
Nocardiopsis ganjiahuensis DSM 45031T AY336513
38 89
40
Nocardiopsis alkaliphila DSM 44657T AY230848 Nocardiopsis listeri DSM 40297T X97887
Nocardiopsis alba DSM 43377T X97883
92
Nocardiopsis litoralis DSM 45168T EU583726
100
Nocardiopsis kunsanensis DSM 44524 AF195412
99 17 27
Nocardiopsis aegyptia DSM 44442T AJ539401 Nocardiopsis lucentensis DSM 44048T X97888
Nocardiopsis ganjiahuensis DSM 45031T AY336513
Nocardiopsis listeri DSM 40297T X97887 918
Nocardiopsis alkaliphila DSM 44657T AY230848
417
Nocardiopsis alba DSM 43377T X97883
752
Nocardiopsis composta DSM 44551T AF360734 510
Nocardiopsis potens DSM 45234T FM253114
Nocardiopsis trehalosi DSM 44380T AF105972 335
Nocardiopsis arabia DSM 45083T EF095149
Nocardiopsis tropica DSM 44381T AF105971
99
Nocardiopsis umidischolae DSM 44362T AY036001
28
96
YIM 90008
Nocardiopsis salina KCTC 19003T AY373031
62
Nocardiopsis xinjiangensis DSM 44589T AF251709
Nocardiopsis tropica DSM 44381T AF105971 1000
Nocardiopsis umidischolae DSM 44362T AY036001
Nocardiopsis litoralis DSM 45168T EU583726
1000 917 Nocardiopsis kunsanensis DSM 44524T AF195412
Multiple-sequences alignments
TOOL---CLUSTAL_X
Phylogenetic analysis &
Bootstrap analysis
METHODS
Distance-based method Maximum parsimony method (MP) Maximum likehood method(ML)
Actinomadura echinospora DSM 43163T AJ420135
BIOEDIT
Example3
PHYLIP-----MP
SEQBOOT DNAPARS CONSENSE
TREEVIEW
DNAPARS.EXE
CONSENSE.EXE
TREEVIEW.EXE
MP TREE

975 1000
Nocardiopsis quinghaiensis DSM 44739T EF597511 568
Nocardiopsis halotolerans DSM 44410T AJ290448
446 328
Nocardiopsis rosea DSM 44842T AY619713 973 995 Nocardiopsis rhodophaea DSM 44843T AY619714
BIOEDIT SEQBOOT DNADIST NEIGHBOR CONSENSE TREVIEW
A number= 4n+1>0 SEQBOOT.EXE
Outfile
infile
DNADIST.EXE
Outfile
infile
NEIGHBOR.EXE
Outtree
intree
CONSENSE.EXE
NJ TREE
1000
290 995
278
631 364
Nocardiopsis valliformis DSM 45023T AY336503 994 695 Nocardiopsis exhalans DSM 44407T AY028325
875
Nocardiopsis metallicus DSM 44598T AJ420769
Nocardiopsis exhalans DSM 44407T AY028325
866 554Nocardiopsis
valliformis
DSM
45023T
AY336503
550 Nocardiopsis metallicus DSM 44598T AJ420769
787 581
Nocardiopsis ganjiahuensis DSM 45031T AY336513
Nocardiopsis lucentensis DSM 44048T X97888
408
Nocardiopsis aegyptia DSM 44442T AJ539401
Nocardiopsis quinghaiensis DSM 44739T EF597511
526 Nocardiopsis
Nocardiopsis quinghaiensis DSM 44739T EF597511
57
Nocardiopsis halotolerans DSM 44410T AJ290448
31 35 49
42
Nocardiopsis trehalosi DSM 44380T AF105972
95
Nocardiopsis rhodophaea DSM 44843T AY619714
Nocardiopsis dassonvillei subsp. dassonvillei DSM 43111T X97886
80
Nocardiopsis dassonvillei subsp. albirubida DSM 40465T X97882
81
Nocardiopsis synnemataformans DSM 44143T Y13593
Example 1 MEGA--------NJ
Example MEGA ---------NJ
74 0.01
99 Nocardiopsis exhalans DSM 44407T AY028325
68 88
Nocardiopsis valliformis DSM 45023T AY336503 Nocardiopsis metallicus DSM 44598T AJ420769
607
Nocardiopsis xinjiangensis DSM 44589T AF251709
962
Nocardiopsis salina KCTC 19003T AY373031
YIM 90008
Nocardiopsis dassonvillei subsp. albirubida DSM 40465T X97882 811 815 Nocardiopsis synnemataformans DSM 44143T Y13593
Assmbly of 16S rRNA gene
TOOL ---SeqMan(DNASTAR)
Select your sequences here
R
A
Delete it
Obtain closely related sequences
TOOLS
NCBI http://www.ncbi.nlm.nih.gov/ RDP http://www.bacterio.cict.fr/ EzTaxon http://147.47.212.35:8080/
258
Nocardiopsis dassonvillei subsp. dassonvillei DSM 43111T X97886
169
Nocardiopsis lucentensis DSM 44048T X97888
Nocardiopsis aegyptia DSM 44442T AJ539401
Nocardiopsis gilva DSM 44841T AY619712
Nocardiopsis baichengensis DSM 44845T AY619716 928 994 Nocardiopsis halophila DSM 44494T AJ421018
Nocardiopsis chromatogenes DSM 44844T AY619715