中国科学院理论物理研究所机构知识库
Advanced  
ITP OpenIR  > 理论物理所1978-2010年知识产出  > 期刊论文
题名: A fungal phylogeny based on 82 complete genomes using the composition vector method
作者: Wang, Hao ;  Xu, Zhao ;  Gao, Lei ;  Hao, Bailin
刊名: BMC EVOLUTIONARY BIOLOGY
出版日期: 2009
卷号: 9, 期号:195, 页码:-
关键词: PARACOCCIDIOIDES-BRASILIENSIS ;  PROKARYOTE PHYLOGENY ;  TREE ;  RECONSTRUCTION ;  ASCOMYCOTA ;  PLANT ;  LIFE ;  CLASSIFICATION ;  INCONGRUENCE ;  SYSTEMATICS
学科分类: Physics
通讯作者: Hao, BL , Fudan Univ, Dept Phys, T Life Res Ctr, Shanghai 200433, Peoples R China
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
英文摘要: 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.
资助者: Basic Research Program of China[2007CB814800]; Shanghai Leading Academic Discipline Project[B111]
收录类别: SCI
原文出处: 查看原文
WOS记录号: WOS:000270356700001
Citation statistics: 
内容类型: 期刊论文
URI标识: http://ir.itp.ac.cn/handle/311006/5263
Appears in Collections:理论物理所1978-2010年知识产出_期刊论文

Files in This Item: Download All
File Name/ File Size Content Type Version Access License
A fungal phylogeny based on 82 complete genomes using the composition vector method.pdf(982KB)----开放获取View Download

Recommended Citation:
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):-.
Service
 Recommend this item
 Sava as my favorate item
 Show this item's statistics
 Export Endnote File
Google Scholar
 Similar articles in Google Scholar
 [Wang, Hao]'s Articles
 [Xu, Zhao]'s Articles
 [Gao, Lei]'s Articles
CSDL cross search
 Similar articles in CSDL Cross Search
 [Wang, Hao]‘s Articles
 [Xu, Zhao]‘s Articles
 [Gao, Lei]‘s Articles
Related Copyright Policies
Null
Social Bookmarking
  Add to CiteULike  Add to Connotea  Add to Del.icio.us  Add to Digg  Add to Reddit 
文件名: A fungal phylogeny based on 82 complete genomes using the composition vector method.pdf
格式: Adobe PDF
此文件暂不支持浏览
所有评论 (0)
暂无评论
 
评注功能仅针对注册用户开放,请您登录
您对该条目有什么异议,请填写以下表单,管理员会尽快联系您。
内 容:
Email:  *
单位:
验证码:   刷新
您在IR的使用过程中有什么好的想法或者建议可以反馈给我们。
标 题:
 *
内 容:
Email:  *
验证码:   刷新

Items in IR are protected by copyright, with all rights reserved, unless otherwise indicated.

 

 

Valid XHTML 1.0!
Copyright © 2007-2017  中国科学院理论物理研究所 - Feedback
Powered by CSpace