Application of gene sequences in plant phylogenetic inferences

Abstract

Molecular phylogenetic is the branch of phylogeny that analyzes hereditary molecular diversity, mainly in DNA sequences, to growth data on an organism's evolutionary relationships. Due to the taxonomic levels of the study, various molecular markers are applied in molecular phylogeny. The selection of molecular instrument is of paramount matter to ensure that a proper level of variation is meliorated to response the phylogenetic question. In this review, we have been trying to discuss about gene markers that used in the plant phylogeny at various taxonomic levels. The current gene markers that are used in phylogeny include: the ribosomal nuclear genes, low copy nuclear genes and the extra-nuclear genome (mitochondrial and chloroplastic genomes). Conserved regions could be used at higher taxonomic levels in phylogenetics studies and regions with more changes could be applied between closely related taxa. Researchers should identify regions with the enough variation rate to investigate phylogenetic relationships. DNA barcoding methods rely on the usage of chloroplast gene sequences. Because of the low evolutionary rates of chloroplast genes, there are few choices appropriate, for molecular studies on angiosperms at low taxonomic levels and DNA barcoding of species. Low-copy nuclear genes are most useful at the interspecific and intraspecific levels where cpDNA and/or nrDNA cannot provide adequate resolution. Evidence offers that for more strong reconstruction of phylogeny, several discrete genes are needed. Now, uses of next generation sequencing (NGS) techniques are reported. Techniques for NGS are an alternative to prevalent methods that let access to hundreds of DNA regions.