Improving Phylogeny Reconstruction at the Strain Level Using Peptidome Datasets
Publication Date
December 29, 2016
Authors
Aitor Blanco Míguez, Jan P. Meier Kolthoff, Alberto Gutiérrez Jácome, Markus Göker, et al
Volume
12
Issue
12
Pages
e1005271
DOI
https://dx.plos.org/10.1371/journal.pcbi.1005271
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1005271
Scopus
85007574612
Mendeley
http://www.mendeley.com/research/improving-phylogeny-reconstruction-strain-level-using-peptidome-datasets
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Mendeley | Further Information

{"title"=>"Improving Phylogeny Reconstruction at the Strain Level Using Peptidome Datasets", "type"=>"journal", "authors"=>[{"first_name"=>"Aitor", "last_name"=>"Blanco-Míguez", "scopus_author_id"=>"57188733896"}, {"first_name"=>"Jan P.", "last_name"=>"Meier-Kolthoff", "scopus_author_id"=>"16309872500"}, {"first_name"=>"Alberto", "last_name"=>"Gutiérrez-Jácome", "scopus_author_id"=>"57188867177"}, {"first_name"=>"Markus", "last_name"=>"Göker", "scopus_author_id"=>"6602789910"}, {"first_name"=>"Florentino", "last_name"=>"Fdez-Riverola", "scopus_author_id"=>"35580091100"}, {"first_name"=>"Borja", "last_name"=>"Sánchez", "scopus_author_id"=>"7103257987"}, {"first_name"=>"Anália", "last_name"=>"Lourenço", "scopus_author_id"=>"7005749859"}], "year"=>2016, "source"=>"PLoS Computational Biology", "identifiers"=>{"sgr"=>"85007574612", "pmid"=>"28033346", "pui"=>"613954235", "isbn"=>"1111111111", "scopus"=>"2-s2.0-85007574612", "doi"=>"10.1371/journal.pcbi.1005271", "issn"=>"15537358"}, "id"=>"c9475ad4-4a6d-3126-9b2a-8e70827918ac", "abstract"=>"Typical bacterial strain differentiation methods are often challenged by high genetic similarity between strains. To address this problem, we introduce a novel in silico peptide fingerprinting method based on conventional wet-lab protocols that enables the identification of potential strain-specific peptides. These can be further investigated using in vitro approaches, laying a foundation for the development of biomarker detection and application-specific methods. This novel method aims at reducing large amounts of comparative peptide data to binary matrices while maintaining a high phylogenetic resolution. The underlying case study concerns the Bacillus cereus group, namely the differentiation of Bacillus thuringiensis, Bacillus anthracis and Bacillus cereus strains. Results show that trees based on cytoplasmic and extracellular peptidomes are only marginally in conflict with those based on whole proteomes, as inferred by the established Genome-BLAST Distance Phylogeny (GBDP) method. Hence, these results indicate that the two approaches can most likely be used complementarily even in other organismal groups. The obtained results confirm previous reports about the misclassification of many strains within the B. cereus group. Moreover, our method was able to separate the B. anthracis strains with high resolution, similarly to the GBDP results as benchmarked via Bayesian inference and both Maximum Likelihood and Maximum Parsimony. In addition to the presented phylogenomic applications, whole-peptide fingerprinting might also become a valuable complementary technique to digital DNA-DNA hybridization, notably for bacterial classification at the species and subspecies level in the future.", "link"=>"http://www.mendeley.com/research/improving-phylogeny-reconstruction-strain-level-using-peptidome-datasets", "reader_count"=>15, "reader_count_by_academic_status"=>{"Researcher"=>6, "Student > Ph. D. Student"=>4, "Student > Master"=>3, "Professor"=>2}, "reader_count_by_user_role"=>{"Researcher"=>6, "Student > Ph. D. Student"=>4, "Student > Master"=>3, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>3, "Chemical Engineering"=>1, "Computer Science"=>4, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>3}, "Computer Science"=>{"Computer Science"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>3}, "Chemical Engineering"=>{"Chemical Engineering"=>1}}, "reader_count_by_country"=>{"Greece"=>1, "Spain"=>1}, "group_count"=>2}

Scopus | Further Information

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