English
 
User Manual Privacy Policy Disclaimer Contact us
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT
  A phylogenetic analysis of the Brassicales clade based on an alignment-free sequence comparison method.

Hatje, K., & Kollmar, M. (2012). A phylogenetic analysis of the Brassicales clade based on an alignment-free sequence comparison method. Frontiers in Plant Science, 3: 192. doi:10.3389/fpls.2012.00192.

Item is

Basic

show hide
Item Permalink: http://hdl.handle.net/11858/00-001M-0000-000F-F103-0 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0029-6934-E
Genre: Journal Article

Files

show Files
hide Files
:
1546205.pdf (Publisher version), 2MB
Name:
1546205.pdf
Description:
-
Visibility:
Public
MIME-Type / Checksum:
application/pdf / [MD5]
Technical Metadata:
Copyright Date:
-
Copyright Info:
-
License:
-

Creators

show
hide
 Creators:
Hatje, K.1, Author              
Kollmar, M.1, Author              
Affiliations:
1Research Group of Systems Biology of Motor Proteins, MPI for biophysical chemistry, Max Planck Society, ou_578570              

Content

show
hide
Free keywords: -
 Abstract: Phylogenetic analyses reveal the evolutionary derivation of species. A phylogenetic tree can be inferred from multiple sequence alignments of proteins or genes. The alignment of whole genome sequences of higher eukaryotes is a computational intensive and ambitious task as is the computation of phylogenetic trees based on these alignments. To overcome these limitations, we here used an alignment-free method to compare genomes of the Brassicales clade. For each nucleotide sequence a Chaos Game Representation (CGR) can be computed, which represents each nucleotide of the sequence as a point in a square defined by the four nucleotides as vertices. Each CGR is therefore a unique fingerprint of the underlying sequence. If the CGRs are divided by grid lines each grid square denotes the occurrence of oligonucleotides of a specific length in the sequence (Frequency Chaos Game Representation, FCGR). Here, we used distance measures between FCGRs to infer phylogenetic trees of Brassicales species. Three types of data were analyzed because of their different characteristics: (A) Whole genome assemblies as far as available for species belonging to the Malvidae taxon. (B) EST data of species of the Brassicales clade. (C) Mitochondrial genomes of the Rosids branch, a supergroup of the Malvidae. The trees reconstructed based on the Euclidean distance method are in general agreement with single gene trees. The Fitch–Margoliash and Neighbor joining algorithms resulted in similar to identical trees. Here, for the first time we have applied the bootstrap re-sampling concept to trees based on FCGRs to determine the support of the branchings. FCGRs have the advantage that they are fast to calculate, and can be used as additional information to alignment based data and morphological characteristics to improve the phylogenetic classification of species in ambiguous cases.

Details

show
hide
Language(s): eng - English
 Dates: 2012-08-29
 Publication Status: Published online
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: Peer
 Identifiers: DOI: 10.3389/fpls.2012.00192
 Degree: -

Event

show

Legal Case

show

Project information

show

Source 1

show
hide
Title: Frontiers in Plant Science
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: -
Pages: - Volume / Issue: 3 Sequence Number: 192 Start / End Page: - Identifier: -