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A fungal phylogeny based on 82 complete genomes using the composition vector method
Wang, Hao; Xu, Zhao; Gao, Lei; Hao, Bailin; Hao, BL , Fudan Univ, Dept Phys, T Life Res Ctr, Shanghai 200433, Peoples R China
2009
发表期刊BMC EVOLUTIONARY BIOLOGY
ISSN1471-2148
卷号9期号:195页码:-
摘要Background: 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.
部门归属[Wang, H; Xu, Z; Hao, BL] Fudan Univ, Dept Phys, T Life Res Ctr, Shanghai 200433, Peoples R China; [Gao, L] Univ Calif Riverside, Dept Bot & Plant Sci, Riverside, CA 92521 USA; [Hao, BL] Acad Sinica, Inst Theoret Phys, Beijing 100190, Peoples R China; [Hao, BL] Santa Fe Inst, Santa Fe, NM 87501 USA
关键词Paracoccidioides-brasiliensis Prokaryote Phylogeny Tree Reconstruction Ascomycota Plant Life Classification Incongruence Systematics
学科领域Physics
资助者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] ; 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] ; 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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收录类别SCI
资助者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] ; 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] ; Basic Research Program of China[2007CB814800]; Shanghai Leading Academic Discipline Project[B111] ; Basic Research Program of China[2007CB814800]; Shanghai Leading Academic Discipline Project[B111]
WOS记录号WOS:000270356700001
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被引频次:113[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.itp.ac.cn/handle/311006/5263
专题理论物理所SCI论文
通讯作者Hao, BL , Fudan Univ, Dept Phys, T Life Res Ctr, Shanghai 200433, Peoples R China
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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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