Molecular evolution and phylogenetic utility of non-coding DNA: applications from species to deep level questions

Abstract

The analysis of non-coding DNA in evolutionary studies of plants is witnessing an ever-increasing 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 non-coding sequences available in EMBL/GenBank. For example, trnL intron sequences have so far been published for approximately 30% of all 450,000 species of land plants. Similar numbers can be found for nrITS sequences. Nevertheless, recent years have also witnessed a trend to look for new non-coding markers in all three genomic compartments of plants. Organellar and nuclear genomes of plants are made up to a large extent by non-coding sequences. There is a broad spectrum of different non-coding genomic regions such as introns, spacers, satellite regions. Therefore, non-coding DNA constitutes an immense source of information which will be accessible through the more and more completely sequenced genomes. The information content of non-coding 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 non-coding 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 non-coding DNA markers at the same time requires a careful implementation of analytical tools in order to deal with the complexity of evolutionary patterns in non-coding sequences that are largely caused by frequent micro-structural mutations in addition to substitutions of nucleotides. To explore the potential of non-coding genomic regions and recent developments for their analysis were the objectives of a workshop ‘‘Molecular evolution and phylogenetic utility of non-coding DNA: applications from species to deep level questions’’ that was held during the T. Borsch (&) Botanischer Garten und Botanisches Museum Berlin-Dahlem und Institut fur Biologie/Botanik, Freie Universitat Berlin, Konigin-Luise Str. 6-8, 14195 Berlin, Germany e-mail: t.borsch@bgbm.org