Mutational dynamics and phylogenetic utility of noncoding chloroplast DNA

摘要: Introns and spacers are a rich well-appreciated information source for evolutionary studies in plants. Compared to coding sequences, the mutational dynamics of introns is very different, involving frequent microstructural changes addition substitutions individual nucleotides. An understanding biology sequence change required correct application molecular characters phylogenetic analyses, including homology assessment, alignment coding, tree inference. The widely used term “indel” general, different kinds mutations, such as simple repeats, short tandem homonucleotide inversions, inverted deletions, need be distinguished. Noncoding DNA has been indispensable analyses at species level because sequences usually do not offer sufficient variability. A variety successfully applied phylogeny inference deeper levels (major lineages angiosperms land plants) past years, structure R intron spacer data sets outperforms that coding-sequence sets. In order fully utilize their potential, evolution applicability most important noncoding markers (the trnT–trnF region comprising two group I intron; trnS–G one II trnG; petD, rpl16, rps16, trnK; atpB–rbcL psbA–trnG spacers) reviewed. study argues use spectrum applications from deep-level phylogenetics speciation barcoding, aims outlining principles needed effective analysis.