Molecular evolution and phylogenetic utility of no

Authors: Thomas Borsch Dietmar Quandt Marcus Koch

Publish Date: 2009/02/07

Volume: 282, Issue: 3-4, Pages: 107-108

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Abstract

The analysis of noncoding DNA in evolutionary studies of plants is witnessing an everincreasing popularity in addition to the widespread application of sequences of protein coding genes like plastid rbcL and matK mitochondrial coxI and matR or the 18 and 26S parts of the nuclear ribosomal array For the chloroplast genome the use of universal primers annealing to highly conserved tandemly repeated tRNA genes allowed the routine amplification and sequencing of variable chloroplast spacers and the trnL intron since the beginning of the 1990s Protocols for other spacers followed shortly after facilitated by the availability of several completely sequenced green plant plastid genomes At around the same time the use of nuclear internal transcribed spacer ITS sequences was proposed for phylogenetic analyses This has led to a large proportion of noncoding sequences available in EMBL/GenBank For example trnL intron sequences have so far been published for approximately 30 of all 450000 species of land plants Similar numbers can be found for nrITS sequences Nevertheless recent years have also witnessed a trend to look for new noncoding markers in all three genomic compartments of plantsOrganellar and nuclear genomes of plants are made up to a large extent by noncoding sequences There is a broad spectrum of different noncoding genomic regions such as introns spacers satellite regions Therefore noncoding DNA constitutes an immense source of information which will be accessible through the more and more completely sequenced genomes The information content of noncoding DNA has been predominantly used for phylogeny reconstruction among closely related species or genera and in population level studies for example to create haplotype networks or in the form of fragment size analyses of microsatellites More recently the application of noncoding DNA for phylogeny reconstruction at deeper levels became more prominent because well resolved and statistically highly supported angiosperm trees could be inferred based on relatively few nucleotides of plastid spacers and introns This growing awareness for the potential of noncoding DNA markers at the same time requires a careful implementation of analytical tools in order to deal with the complexity of evolutionary patterns in noncoding sequences that are largely caused by frequent microstructural mutations in addition to substitutions of nucleotidesTo explore the potential of noncoding genomic regions and recent developments for their analysis were the objectives of a workshop “Molecular evolution and phylogenetic utility of noncoding DNA applications from species to deep level questions” that was held during the 17th International Symposium on Biodiversity and Evolutionary Botany of the German Botanical Society in Bonn in September 2006 The prominent results of this workshop are published in the present volumeScot Kelchner deals with the specifics of models and model selection for noncoding DNA as they are required for all Bayesian and likelihood approaches to evolutionary questions Models provide fundamental pictures on evolutionary patterns in character partitions and in our case into the molecular evolution of genomic regions David Morrison outlines the process of hypothesis testing in phylogenetic sequence alignment that is connected to viewing indels as mutational events that comprise multiple nucleotides at once Helga Ochoterena then provides a parsimony perspective on homology in coding as compared to noncoding DNA sequences This is of particular relevance in the context of aligning length variable sequences The principle of parsimony here provides the basis for a widely used approach to assess homology Thomas Borsch and Dietmar Quandt examine the large body of data now existing on introns and spacers of the chloroplast genome as tools for phylogeny reconstruction in land plants Aims of their study are to evaluate the state of knowledge on finding the best performing markers with respect to resolution and support of the trees to be inferred and to evaluate pitfalls and possibilities in widely used genomic regions Nadja Korotkova et al apply noncoding sequences of the petD group II intron to reconstructing relationships within the angiosperm order Malpighiales which exhibits a notoriously difficult phylogenetic problem connected to the analysis of a rapid radiation Marcus Koch et al investigate structural dynamics of trnF pseudogenes in various chloroplast genomes of cruciferous plants and discuss its application in plant evolution on species and population level Using mosses as an example Ute Wahrmund et al compare the phylogenetic structure in several structurally different noncoding regions of the mitochondrial genome to chloroplast loci Mitochondrial markers in plants are considerably less understood as compared to plastid markers but especially mitochondrial introns appear to hold great promises Miriam Calonje et al focus on noncoding genomic regions in the nuclear genome and their potential for evolutionary analyses Important issues are the biology of the nuclear ribosomal DNA with its consequences on the molecular evolution of the widely applied ITS region but also on the state of knowledge on other currently available noncoding markers in the nuclear genome Thekla Pleines et al discuss the infraspecific variability that can be found in many noncoding regions and its application to phylogeographic and speciation studies In fact noncoding DNA is the major source for information in any population genetic application

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