Utility of ITS region sequence and structure for molecular identification of Tilia species from Hyrcanian forests, Iran

Abstract

Nucleotide sequences from the internal transcribed spacers (ITS) of nuclear ribosomal DNA and 5.8S gene were used to infer the phylogeny of Tilia species (represented by 13 distinct populations) growing in different geographical areas of Hyrcanian forests in northern Iran. Four well-supported lineages were revealed, including that of a new species, T. hyrcana, with stellate trichomes on both sides of the leaves and petiole. T. hyrcana is a wellsupported cladospecies, with the ITS sequence and secondary structure following the diagnosable phylogenetic species concept, and is also characterized by a distinct morphology. A controversial species is Tilia rubra subsp. caucasica, with three different forms-an assemblage of taxa characterized by a lack of stellate trichomes on leaves-while Tilia begonifolia is distinguished by stellate trichomes on the underside of both leaves and petiole. The fourth lineage group, T. dastyla, is characterized by the presence of trichomes on the style. A single taxon found in the west of the Hyrcanian forest region is similar to T. begonifolia, but due to the former being located in a distinct group, a reassessment of the diagnostic morphology is recommended. ITS sequence data also suggested a closer relationship between T. rubra and T. begonifolia. Compensatory base change analysis was not strong enough to separate individual species within the Tilia genus. In general, the study supports the utility of ITS sequence data and secondary structure as accessory taxonomic characteristics with which to help clarify the systematics of the Tilia genus.

The Short ITS2 Sequence Serves as an Efficient Taxonomic Sequence Tag in Comparison with the Full-Length ITS

“…For the 12861 samples, ITS and ITS2 could identify 97.5% and 93.8% of genera, respectively, by the BLAST method. The full-length ITS could identify approximately 89.2% of the species, and the mini-DNA barcode ITS2 successfully identified approximately 79.2% of the species, which is higher than the CBOL proposed plant combination of matK and rbcL (70%) [4, 5]. …”

“…The ITS sequence contains enough variable sites for species identification in many samples [5–9], but ITS could not be amplified from approximately 12% of herbarium samples [3], because ITS1 is too variable to guarantee reliable alignments and contains variable indels (insertions/deletions) at this taxonomic level. Additionally, multiple functional copies exist in many taxa.…”

Ancient woodlands in the limelight: delineation and genetic structure of ancient woodland species Tilia cordata and Tilia platyphyllos (Tiliaceae) in the UK

“…Earlier genetic studies using chloroplast PCR-RFLP markers (Fineschi et al 2003), RAPD markers, (Hosseinzadeh Colagar et al 2013;Liesebach and Sinkó 2008); and the ITS regions (Yousefzadeh et al 2012) were successful in determining various levels of genetic diversity. However, RAPDs are dominant markers and therefore restrict population genetic analyses, while chloroplast and ITS regions are generally conserved and may not differentiate the two UK species.…”

Phylogenetic relationship and genetic differentiation of Populus caspica and Populus alba using cpDNA and ITS noncoding sequences

“…The Hyrcanian forest in northern Iran is located between the Caspian Sea and the Alborz Mountains. These forests comprise 15% of the Iranian forests and represent 1.1% of the country's land area (Yousefzadeh et al 2012). This region has a unique rich biodiversity and is home to many endemic species.…”