#Codoncode aligner blast search not working full#
Over the years, several classifications have been proposed for the genus Pinus based on morphological and anatomical traits ( ), isozyme loci ( ), restriction patterns of chloroplast genome (, ), sequence data from nuclear ITS (Internal Transcribed Spacer - ), mainly chloroplast organelle regions (, ) as well as the full chloroplast genome ( ). The number of species is currently estimated to be from about 110 to more than 200, but there exists disagreement about the exact numbers (, ,, ). The largest and most economically important conifer genus Pinus is widespread in the northern hemisphere. Within-species variability and high plasticity of the psbA-trnH intergenic spacer with frequent indels and inversions have been observed in angiosperms and bryophytes ( ). Sylvestris - ) puts into question the reliability of this marker for species identification purposes. In addition, observations that BLAST searches performed on psbA-trnH sequences do not always match conspecific specimens from GenBank ( P. The psbA-trnH region has been successfully used in a few phylogenetic Pinaceae studies (, ) but due to technical problems related to the sequencing of the duplicated psbA-trnH region in some pines (, , ), the use of this marker has been limited. In pines in particular, the most frequently used additional markers are the intergenic spacer psbA-trnH and more recently, the highly variable ycf1 gene (, , ). However, additional DNA regions are often needed to identify specimens at species level in plant groups that contain little variation among these markers, such as conifers ( ). DNA barcoding markers matK and rbcL are the standard markers for plants ( ).
Identification of individuals and multispecies phylogenies are usually based on established universal markers, so called DNA barcodes.
In addition, we show that matK and psbA-trnH contain contradicting phylogenetic signals in some of the most economically important pine species. In this study, we use this clade as an example to explain weak support in phylogenetic studies of closely related pine species and show that some of the most popular genetic markers, namely the chloroplast DNA barcoding sequences matK, psbA- trnH and rbcL, are not recommended for species identification purposes in European pines. One such example, which is also inconsistent in terms of biogeography, is within the subsection Pinus and includes five taxa: Pinus densiflora, P. However, phylogenetic relationships remain unresolved for certain lineages. Comprehensive phylogenies relying on complete chloroplast gene sequences are now available for the entire genus.
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