Studied RNAr 16S
(SequenceX)
5’
3’
(a)
Sequence
databases
Leucobacter
ACACGTGAGCAACCTGCCCTTCACTCTGGGATAAGCACTGGAAACGGTGTCTAATACTGGATATGCACAATGATCGCATGGTCTGTTGTGG
Cryobacterium
ACACGTGAGCAATCTGCCCTTGACTCTGGGATAAGCGTTGGAAACGACGTCTAATACCGGATACGACCTTTGGAGGCATC-TCTGGGGGTG
Microcella
ACACGTGAGTAACCTGCCCTTGACTCTGGGATAAGCGTTGGAAACGACGTCTAATACCGGATACGAGCTGAGACCGCATGGTCATTAGCTG
Salinibacterium
ACACGTGAGTAACCTGCCCTTGACTCTGGAATAAGCGTTGGAAACGACGTCTAATACCGGATACGAGCTTCCGCCGCATGGTGAGGAGCTG
Bacillus
ACACGTGAGTAACCTGCCCCTGACTCTGGGATAAGCGTTGGAAACGACGTCTAATACTGGATATGACTGCCGGCCGCATGGTCTGGTGGTG
Actinobacteria
ACACGTGAGCAATCTGCCCTTGACTCTGGGATAAGCGTTGGAAACGACGTCTAATACCGGATACGACCCTCGGAGGCATCTCCTGGGGGTG
Frigoribacterium
ACACGTGAGTAACCTGCCCTTGACTCTGGGATAAGCGCTAGAAATGGCGTCTAATACCGGATACGAGCTTCAGCCGCATGGCTAGGAGTTG
Actinobacterium
ACACGTGAGTAACCTGCCCTTGACTCTGGGATAACTGCTAGAAATGGTAGCTAATACCGGATACGACCCTCGGCGGCATCGCCAGGGGGTG
SequenceX
ACACGTGAGTAACCTGCCCCCGACTCTGGGATAACTGCTAGAAATGGTAGCTAATACCGGATATGACGACTGGCCGCATGGTCTGGTCGTG
Clavibacter
ACACGTGAGTAACCTGCCCCCGACTCTGGGATAACTGCTAGAAATGGTAGCTAATACCGGATATGACGATTGGCCGCATGGTCTGGTCGTG
Curtobacterium
ACACGTGAGTAACCTGCCCCCGACTCTGGGATAACTGCTAGAAATGGTAGCTAATACCGGATATGACGACTGGCCGCATGGTCTGGTCGTG
(b & c)
(d & e)
BLAST
Clustal omega, MAFFT...
DNAdist…
(f)
NJ,ML…
Actinobacteria
Cryobacterium
Salinibacterium
Microcella
Leucobacter
Frigoribacterium
Actinobacterium
Bacillus
Clavibacter
Curtobacterium
SequenceX
0.01
Fig. 6.8
Key steps in phylogenetic analysis. (a) Similarity search for sequences homologous to
the sequence of interest in the sequence databases, (b) extraction of counterparts from closely
related species, (c) multiple alignment of sequences, (d) filtering the alignment so that only
regions where homology between sites is reliable remain, (e) construction of a distance matrix, (f)
reconstruction of the phylogenetic tree and identification of the closest known relatives (see
explanations in the text), the distance scale for the phylogenetic tree represents 1 % of difference
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