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Wang, Hao; Xu, Zhao; Gao, Lei; Hao, Bailin; Hao, BL , Fudan Univ, Dept Phys, T Life Res Ctr, Shanghai 200433, Peoples R China
A fungal phylogeny based on 82 complete genomes using the composition vector method
Source PublicationBMC EVOLUTIONARY BIOLOGY
KeywordParacoccidioides-brasiliensis Prokaryote Phylogeny Tree Reconstruction Ascomycota Plant Life Classification Incongruence Systematics
AbstractBackground: Molecular phylogenetics and phylogenomics have greatly revised and enriched the fungal systematics in the last two decades. Most of the analyses have been performed by comparing single or multiple orthologous gene regions. Sequence alignment has always been an essential element in tree construction. These alignment-based methods (to be called the standard methods hereafter) need independent verification in order to put the fungal Tree of Life (TOL) on a secure footing. The ever-increasing number of sequenced fungal genomes and the recent success of our newly proposed alignment-free composition vector tree (CVTree, see Methods) approach have made the verification feasible. Results: In all, 82 fungal genomes covering 5 phyla were obtained from the relevant genome sequencing centers. An unscaled phylogenetic tree with 3 outgroup species was constructed by using the CVTree method. Overall, the resultant phylogeny infers all major groups in accordance with standard methods. Furthermore, the CVTree provides information on the placement of several currently unsettled groups. Within the sub-phylum Pezizomycotina, our phylogeny places the Dothideomycetes and Eurotiomycetes as sister taxa. Within the Sordariomycetes, it infers that Magnaporthe grisea and the Plectosphaerellaceae are closely related to the Sordariales and Hypocreales, respectively. Within the Eurotiales, it supports that Aspergillus nidulans is the early-branching species among the 8 aspergilli. Within the Onygenales, it groups Histoplasma and Paracoccidioides together, supporting that the Ajellomycetaceae is a distinct clade from Onygenaceae. Within the sub-phylum Saccharomycotina, the CVTree clearly resolves two clades: (1) species that translate CTG as serine instead of leucine (the CTG clade) and ( 2) species that have undergone whole-genome duplication (the WGD clade). It places Candida glabrata at the base of the WGD clade. Conclusion: Using different input data and methodology, the CVTree approach is a good complement to the standard methods. The remarkable consistency between them has brought about more confidence to the current understanding of the fungal branch of TOL.
2009
ISSN1471-2148
Volume9Issue:195Pages:-
Subject AreaPhysics
Indexed BySCI
Funding OrganizationBasic Research Program of China[2007CB814800]; Shanghai Leading Academic Discipline Project[B111] ; Basic Research Program of China[2007CB814800]; Shanghai Leading Academic Discipline Project[B111] ; Basic Research Program of China[2007CB814800]; Shanghai Leading Academic Discipline Project[B111] ; Basic Research Program of China[2007CB814800]; Shanghai Leading Academic Discipline Project[B111]
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Cited Times:119[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.itp.ac.cn/handle/311006/5263
Collection理论物理所科研产出_SCI论文
Corresponding AuthorHao, BL , Fudan Univ, Dept Phys, T Life Res Ctr, Shanghai 200433, Peoples R China
Recommended Citation
GB/T 7714
Wang, Hao,Xu, Zhao,Gao, Lei,et al. A fungal phylogeny based on 82 complete genomes using the composition vector method[J]. BMC EVOLUTIONARY BIOLOGY,2009,9(195):-.
APA Wang, Hao,Xu, Zhao,Gao, Lei,Hao, Bailin,&Hao, BL , Fudan Univ, Dept Phys, T Life Res Ctr, Shanghai 200433, Peoples R China.(2009).A fungal phylogeny based on 82 complete genomes using the composition vector method.BMC EVOLUTIONARY BIOLOGY,9(195),-.
MLA Wang, Hao,et al."A fungal phylogeny based on 82 complete genomes using the composition vector method".BMC EVOLUTIONARY BIOLOGY 9.195(2009):-.
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