NDLI: Toward an Efficient Method of Identifying Core Genes for Evolutionary and Functional Microbial Phylogenies

Content Provider	PubMed Central
Author	Nicola, Segata Huttenhower, Curtis
Editor	Gibas, Cynthia
Copyright Year	2011
Abstract	Microbial community metagenomes and individual microbial genomes are becoming increasingly accessible by means of high-throughput sequencing. Assessing organismal membership within a community is typically performed using one or a few taxonomic marker genes such as the 16S rDNA, and these same genes are also employed to reconstruct molecular phylogenies. There is thus a growing need to bioinformatically catalog strongly conserved core genes that can serve as effective taxonomic markers, to assess the agreement among phylogenies generated from different core gene, and to characterize the biological functions enriched within core genes and thus conserved throughout large microbial clades. We present a method to recursively identify core genes (i.e. genes ubiquitous within a microbial clade) in high-throughput from a large number of complete input genomes. We analyzed over 1,100 genomes to produce core gene sets spanning 2,861 bacterial and archaeal clades, ranging in size from one to >2,000 genes in inverse correlation with the α-diversity (total phylogenetic branch length) spanned by each clade. These cores are enriched as expected for housekeeping functions including translation, transcription, and replication, in addition to significant representations of regulatory, chaperone, and conserved uncharacterized proteins. In agreement with previous manually curated core gene sets, phylogenies constructed from one or more of these core genes agree with those built using 16S rDNA sequence similarity, suggesting that systematic core gene selection can be used to optimize both comparative genomics and determination of microbial community structure. Finally, we examine functional phylogenies constructed by clustering genomes by the presence or absence of orthologous gene families and show that they provide an informative complement to standard sequence-based molecular phylogenies.
Related Links	http://dx.doi.org/10.1371/journal.pone.0024704
Starting Page	24704
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	9
Volume Number	6
Language	English
Publisher	Public Library of Science
Publisher Date	2011-09-01
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	Biochemistry, Genetics and Molecular Biology(all) Agricultural and Biological Sciences(all) Medicine(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Toward an Efficient Method of Identifying Core Genes for Evolutionary and Functional Microbial Phylogenies

attract: A Method for Identifying Core Pathways That Define Cellular Phenotypes

An Efficient Method for Identifying Gene Fusions by Targeted RNA Sequencing from Fresh Frozen and FFPE Samples

A P-Norm Robust Feature Extraction Method for Identifying Differentially Expressed Genes

A Novel Prioritization Method in Identifying Recurrent Venous Thromboembolism-Related Genes

Covariation of Branch Lengths in Phylogenies of Functionally Related Genes

An Approach for Identifying Brainstem Dopaminergic Pathways Using Resting State Functional MRI

An Efficient Computational Method for Calculating Ligand Binding Affinities

Assessing Trait Covariation and Morphological Integration on Phylogenies Using Evolutionary Covariance Matrices

Toward an Efficient Method of Identifying Core Genes for Evolutionary and Functional Microbial Phylogenies

Similar Documents

Toward an Efficient Method of Identifying Core Genes for Evolutionary and Functional Microbial Phylogenies

attract: A Method for Identifying Core Pathways That Define Cellular Phenotypes

An Efficient Method for Identifying Gene Fusions by Targeted RNA Sequencing from Fresh Frozen and FFPE Samples

A P-Norm Robust Feature Extraction Method for Identifying Differentially Expressed Genes

A Novel Prioritization Method in Identifying Recurrent Venous Thromboembolism-Related Genes

Covariation of Branch Lengths in Phylogenies of Functionally Related Genes

An Approach for Identifying Brainstem Dopaminergic Pathways Using Resting State Functional MRI

An Efficient Computational Method for Calculating Ligand Binding Affinities

Assessing Trait Covariation and Morphological Integration on Phylogenies Using Evolutionary Covariance Matrices

Toward an Efficient Method of Identifying Core Genes for Evolutionary and Functional Microbial Phylogenies