Application of gene sequences in plant phylogenetic inferences

Molecular phylogenetic is the branch of phylogeny that analyzes hereditary molecular diversity, mainly in DNA sequences, to increase 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 respond the phylogenetic question. In this review, we have been trying to discuss about gene markers used in the plant phylogeny at various taxonomic levels. The current gene markers 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. One of the most common sequences for studying the phylogenetic relationships at the generic and infrageneric taxonomic levels in plants is the internal transcribed spacer (ITS) region of the 18S–5.8S–26S nuclear ribosomal cistron. Chloroplastic gene sequences have been used extensively at the family level and above but chloroplast non-coding sequences such as introns and intergenic spacers are used more frequently at lower taxonomic levels. 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 strongly 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.