Phylogenetic position of Phlojodicarpus villosus (Apiaceae) based on ITS and trnH-psbA nucleotide sequences

Abstract

The aim of our work was to obtain chloroplast (trnH-psbA) and nuclear (ITS1-ITS2) DNA nucleotide sequences and identify the phylogenetic position of Phlojodicarpus villosus (Apiaceae). This species of vascular plants is represented in the Urals by isolated relic populations and is included in the regional Red Data Books. There is no data on P. villosus nucleotide sequences in the international open genetic databases. We studied two herbarium specimens of P. villosus, one collected from the Ural part of its range in the Komi Republic (Northern Urals) and the second collected from the main part of its range in the Magadan Region (Kolyma Highlands). Combining nuclear and chloroplast markers made it possible to reliably determine phylogenetic position of P. villosus within the tribe Selineae (subfamily Apioideae, family Apiaceae). We found ITS1-ITS2 and trnH-psbA nucleotide sequences to be sufficiently informative to identify specimens of this genus. High polymorphism of P. villosus sequences obtained from different parts of its range (Northern Urals and Kolyma Highlands) and the presence of evolutionary events (deletions) require more detail study of P. villosus and other Phlojodicarpus taxa by DNA barcoding methods.

The use of DNA barcoding for the identification of giant hogweeds in the European North-East of Russia

“…Based on the comparison of H. sosnowskyi plant sequences with the only available in genetic databases H. mantegazzianum sample, we found the use of the ETS sequence for species distinction upon involving more H. mantegazzianum samples as promising (Shadrin et al, 2021).…”

“…As a result, the samples that we previously identified as H. sosnowskyi (Shadrin et al, 2021) were divided into four groups after reidentification using a set of features (Table 1):…”

“…In the last decade, in order to identify systematically complex plants, alongside with traditional taxonomy methods DNA barcoding of plants has been widely used, which enables identification of organisms based on short fragments of the DNA sequence (Hebert et al, 2003;Kress, 2017). In order to barcode representatives of the plant kingdom the following is used: rbcL and matK genes, intergenic spacer trnH-psbA of chloroplast DNA (cpDNA), sequence ITS1-5.8s-ITS2 of the ribosomal nuclear DNA cluster (nrDNA) (Shneyer, Rodionov, 2018;Shekhovtsov et al, 2019;Shadrin, 2021). By now, the most detailed description of the molecular phylogenetic relationships, as well as the origin and migration of representatives of the Apiaceae family has been carried out using the ITS region of nrDNA (Downie et al, 2001(Downie et al, , 2010Banasiak et al, 2013).…”

“…is a large family of flowering plants comprised of compound species complexes with a high level of morphological variability (Kljuykov et al, 2018). The most popular classification for Umbelliferae at present is a system based on the anatomy and morphology of the fruit (Pimenov, Leonov, 1993; Pimenov, 2012; Valuyskikh et al, 2021). The classification system presented is not absolute and at times fails to accurately reflect relationships within the family (Downie et al, 2010).…”

“…By now, the most detailed description of the molecular phylogenetic relationships, as well as the origin and migration of representatives of the Apiaceae family has been carried out using the ITS region of nrDNA (Downie et al, 2001, 2010; Banasiak et al, 2013). To identify a number of subtaxa of the Apiaceae family, an attempt was made to use the cpDNA trn H- psb A intergenic spacer region (Degtjareva et al, 2012), as well as a combination of ITS and trn H- psb A sequences (Liu et al, 2014; Valuyskikh, Shadrin, 2021). Another work declared high conservation of the intergenic spacer psb A -trn H to act as a limitation for the identification of representatives of the Heracleum genus and related taxa (Logacheva et al, 2007).…”