3 Biotech (2018) 8:250
Molecular phylogenetic species in Alternaria pathogens infecting
pistachio and wild relatives
· Unal Sevinc
Received: 4 March 2018 / Accepted: 4 May 2018 / Published online: 10 May 2018
© Springer-Verlag GmbH Germany, part of Springer Nature 2018
Many important pathogens of crops worldwide are members of section Alternaria within the genus Alternaria. Representative
species in this section such as Alternaria alternata, Alternaria tenuissima, and Alternaria arborescens show high variability,
intermediate characters and plasticity in morphological features, which makes species identiﬁcation diﬃcult. The aim of this
study was to characterize Alternaria species associated with pistachio and wild relatives in Turkey using molecular phyloge-
netics. One hundred isolates of Alternaria spp. from pistachio and wild relatives from Turkey were investigated. In addition,
standard morphological reference isolates and Alternaria blight pathogens of pistachio from USA were included. Sequence
data from major allergen a1, ATPase, endopolygalacturanase, and anonymous regions OPA1.3 and SCAR2 were obtained.
Gene trees were estimated based on maximum parsimony, maximum-likelihood, and bayesian inference methods. Species
tree estimation was performed based on Yule speciation and strict molecular clock assumption. Among the collection of
Alternaria spp. from Turkey, only one A. arborescens isolate and three isolates which were morphologically A. alternata/A.
arborescens intermediate types, but, phylogenetically close to A. arborescens were discovered. While A. alternata and A.
tenuissima formed one phylogenetic species, A. alternata/tenuissima were phylogenetically distinct from A. arborescens.
Furthermore, a TaqI restriction site in the endopolygalacturanase gene was explored as a novel diagnosis for identiﬁcation of
A. alternata/tenuissima and A. arborescens. All these molecular phylogenetic approaches allow to distinguish morphologi-
cally similar Alternaria pathogens and molecular phylogenies of Alternaria pathogens from pistachio and wild relatives in
Turkey are described for the ﬁrst time.
Keywords Alternaria · Alternaria blight · Phylogenetics
Small-spored Alternaria species, also known as the Alter-
naria species group or section Alternaria, are a well-sup-
ported phylogenetic lineage within the genus Alternaria
(Lawrence et al. 2013; Woudenberg et al. 2013). Alternaria
alternata, A. tenuissima, and A. arborescens are the most
common morpho-species within this group (Pryor and
Michailides 2002; Lawrence et al. 2013; Woudenberg et al.
2015). These taxa are important plant pathogens around
the world. Thus, accurate identiﬁcation is important for
pathogen reports, quarantine procedures, as well as explor-
ing biodiversity. Delimitation and identiﬁcation of species
boundaries within the section Alternaria are challenging due
to similar characteristics with high variability, intermedi-
ate characters, and plasticity in their morphological features
(Rotem 1994; Simmons 2007; Tymon et al. 2016). Besides,
providing perfectly standardized environmental conditions,
ﬁnding experienced mycologists make species identiﬁca-
tion of these species challenging. Personal qualiﬁcations are
other diﬃculties for accurate identiﬁcation of these species.
In addition to considerable and overlapping morphological
similarities of A. alternata and A. tenuissima, intermediate
morphological characters have been observed between A.
Electronic supplementary material The online version of this
article (https ://doi.org/10.1007/s1320 5-018-1277-0) contains
supplementary material, which is available to authorized users.
* Hilal Ozkilinc
Department of Molecular Biology and Genetics, Faculty
of Arts and Sciences, Canakkale Onsekiz Mart University,
MSc Program in Bioengineering and Materials Engineering,
Graduate School of Natural and Applied Sciences, Canakkale
Onsekiz Mart University, Canakkale, Turkey