Genome trees constructed using five different approaches suggest new major bacterial clades View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2001-10-23

AUTHORS

Yuri I Wolf, Igor B Rogozin, Nick V Grishin, Roman L Tatusov, Eugene V Koonin

ABSTRACT

BackgroundThe availability of multiple complete genome sequences from diverse taxa prompts the development of new phylogenetic approaches, which attempt to incorporate information derived from comparative analysis of complete gene sets or large subsets thereof. Such attempts are particularly relevant because of the major role of horizontal gene transfer and lineage-specific gene loss, at least in the evolution of prokaryotes.ResultsFive largely independent approaches were employed to construct trees for completely sequenced bacterial and archaeal genomes: i) presence-absence of genomes in clusters of orthologous genes; ii) conservation of local gene order (gene pairs) among prokaryotic genomes; iii) parameters of identity distribution for probable orthologs; iv) analysis of concatenated alignments of ribosomal proteins; v) comparison of trees constructed for multiple protein families. All constructed trees support the separation of the two primary prokaryotic domains, bacteria and archaea, as well as some terminal bifurcations within the bacterial and archaeal domains. Beyond these obvious groupings, the trees made with different methods appeared to differ substantially in terms of the relative contributions of phylogenetic relationships and similarities in gene repertoires caused by similar life styles and horizontal gene transfer to the tree topology. The trees based on presence-absence of genomes in orthologous clusters and the trees based on conserved gene pairs appear to be strongly affected by gene loss and horizontal gene transfer. The trees based on identity distributions for orthologs and particularly the tree made of concatenated ribosomal protein sequences seemed to carry a stronger phylogenetic signal. The latter tree supported three potential high-level bacterial clades,: i) Chlamydia-Spirochetes, ii) Thermotogales-Aquificales (bacterial hyperthermophiles), and ii) Actinomycetes-Deinococcales-Cyanobacteria. The latter group also appeared to join the low-GC Gram-positive bacteria at a deeper tree node. These new groupings of bacteria were supported by the analysis of alternative topologies in the concatenated ribosomal protein tree using the Kishino-Hasegawa test and by a census of the topologies of 132 individual groups of orthologous proteins. Additionally, the results of this analysis put into question the sister-group relationship between the two major archaeal groups, Euryarchaeota and Crenarchaeota,and suggest instead that Euryarchaeota might be a paraphyletic group with respect to Crenarchaeota.ConclusionsWe conclude that, the extensive horizontal gene flow and lineage-specific gene loss notwithstanding, extension of phylogenetic analysis to the genome scale has the potential of uncovering deep evolutionary relationships between prokaryotic lineages. More... »

PAGES

8

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2148-1-8

DOI

http://dx.doi.org/10.1186/1471-2148-1-8

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1035042918

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/11734060


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90 genome
91 genome scale
92 genome sequence
93 genome trees
94 group
95 grouping
96 horizontal gene flow
97 horizontal gene transfer
98 identity distribution
99 independent approaches
100 individual groups
101 information
102 large subset
103 latter group
104 latter tree
105 life style
106 lineage-specific gene loss
107 lineages
108 local gene order
109 loss
110 major archaeal groups
111 major bacterial clades
112 major role
113 method
114 multiple complete genome sequences
115 multiple protein families
116 new grouping
117 new phylogenetic approach
118 nodes
119 obvious grouping
120 order
121 orthologous clusters
122 orthologous genes
123 orthologous proteins
124 orthologs
125 pairs
126 parameters
127 paraphyletic group
128 phylogenetic analysis
129 phylogenetic approach
130 phylogenetic relationships
131 phylogenetic signal
132 potential
133 probable orthologs
134 prokaryotes
135 prokaryotic domains
136 prokaryotic genomes
137 prokaryotic lineages
138 prompts
139 protein
140 protein family
141 protein sequences
142 protein trees
143 questions
144 relationship
145 relative contribution
146 repertoire
147 respect
148 results
149 ribosomal protein sequences
150 ribosomal proteins
151 role
152 scale
153 separation
154 sequence
155 set
156 signals
157 similar life styles
158 similarity
159 sister-group relationship
160 strong phylogenetic signal
161 style
162 subset
163 such attempts
164 terminal bifurcation
165 terms
166 test
167 topology
168 transfer
169 tree nodes
170 tree topology
171 trees
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