ITS2 sequence-structure analysis in phylogenetics: A how-to manual for molecular systematics

被引：162

作者：

Schultz, Joerg ^{[1
]}

Wolf, Matthias ^{[1
]}

机构：

[1] Univ Wurzburg, Dept Bioinformat, Bioctr, D-97074 Wurzburg, Germany

来源：

MOLECULAR PHYLOGENETICS AND EVOLUTION | 2009年 / 52卷 / 02期

关键词：

Internal transcribed spacer 2; ITS2; Phylogeny; Molecular systematics; Phylogenetics; Secondary structure; RNA; Non-coding RNA; Sequence-structure alignment; Scoring matrix; Substitution model; Compensatory base change; CBC; Species concept; SECONDARY STRUCTURE; EVOLUTIONARY; DATABASE; PREDICTION; ALIGNMENT;

D O I：

10.1016/j.ympev.2009.01.008

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The information that can be obtained from the secondary structure of the nuclear ribosomal internal transcribed spacer 2 (ITS2) is substantial, and yet many studies exploit this information inconsistently or inappropriately. This review introduces a remedy in the form of a flowchart where we detail the steps involved in estimating structure-based phylogenetic trees from ITS2 data. The pipeline described consists of the ITS2 Database, 4SALE, the CBCAnalyzer, and ProfDistS. Based on these tools, we describe how to utilize ITS2 sequence and secondary structure information together with an ITS2 specific scoring matrix and an ITS2 specific substitution model. The phylogenetic results thus obtained have been shown to be more reliable than approaches based on primary sequence data alone. Moreover, compensatory base changes (CBCs) in ITS2 sequence-structure pairs are identified as a possible marker for distinguishing species. (C) 2009 Elsevier Inc. All rights reserved.

引用

页码：520 / 523

页数：4

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