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Phylogenetic Relationship and Genetic Differentiation of Populus Caspica and Populus Alba Using Cpdna and ITS Noncoding Sequences

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Phylogenetic Relationship and Genetic Differentiation of Populus Caspica and Populus Alba Using Cpdna and ITS Noncoding Sequences J. For. Res. https://doi.org/10.1007/s11676-018-0785-4 ORIGINAL PAPER Phylogenetic relationship and genetic differentiation of Populus caspica and Populus alba using cpDNA and ITS noncoding sequences 1 2 2 Hamed Yousefzadeh • Abasalt Hosseinzadeh Colagar • Effat Yousefi • 2 3 Maryam Badbar • Gregor Kozlowski Received: 8 October 2016 / Accepted: 18 September 2017 Ó Northeast Forestry University and Springer-Verlag GmbH Germany, part of Springer Nature 2018 Abstract Populus caspica Bornm. (section Leuce and caspica individuals. Conflicts between topologies from ITS subsection Albida), one of the most endangered endemic and plastid genomes were observed. High differentiation of tree species in the Hyrcanian Forest in Iran, has numerous P. caspica from the other Populus species shown in this morphological characteristics that are closely similar to study confirmed the diverging taxonomic status of this Populus alba; to clarify their taxonomic relatedness and endangered species. We recommend in situ conservation genetic differentiation and thus inform conservation measures (e.g., protected areas) for at least several popu- strategies, we used the noncoding regions of chloroplast lations of this species, especially in the plain regions of the DNA (cpDNA; trnL-F and trnH-psbA) and the internal Hyrcanian forest. transcribed spacer (ITS). Leaf samples were collected from six populations across northern Iran. cpDNA and ITS Keywords Endangered endemic species Á DNA fragments were amplified by universal primers using the barcoding Á Hyrcanian forest Á Taxonomic status PCR technique and directed sequencing. The results showed that P. caspica is genetically differentiated from P. alba, and two ITS variants were detected within some P. Introduction Very important forest trees such as aspens, cottonwoods, Project funding: This project is supported by grant funding from the and poplars, belong in the genus Populus (Salicaceae), Tarbiat Modares University and Mazandaran University. commonly called poplars, they are mainly distributed in northern subtropical forests and play a significant ecolog- The online version is available at http://www.springerlink.com ical role as an indicator species in these regions (Dickmann Corresponding editor: Hu Yanbo. et al. 2001; Hamzeh and Dayanandan 2004). They are long-lived trees characterized by a dioecious breeding Electronic supplementary material The online version of this system and wind dispersal of pollen and seeds, and are also article (https://doi.org/10.1007/s11676-018-0785-4) contains supple- mentary material, which is available to authorized users. commonly used as the model species for tree genomics (Tuskan et al. 2006). & Hamed Yousefzadeh The Hyrcanian forest in northern Iran is located between [email protected] the Caspian Sea and the Alborz Mountains. These forests & Abasalt Hosseinzadeh Colagar comprise 15% of the Iranian forests and represent 1.1% of [email protected] the country’s land area (Yousefzadeh et al. 2012). This 1 Department of Environmental Science, Faculty of Natural region has a unique rich biodiversity and is home to many Resources, Tarbiat Modares University, Tehran, Iran endemic species. Although recognized as a refuge for many 2 Department of Molecular and Cell Biology, Faculty of Basic Arco-Tertiary relict plants, many forest habitats, and Science, University of Mazandaran, Babolsar, Iran especially the riverine vegetation in the Caspian forest, 3 Department of Biology and Botanic Garden, University of have been greatly degraded by human activities (Leest- Fribourg, Fribourg, Switzerland mans 2005; Akhani et al. 2010). 123 H. Yousefzadeh et al. Populus caspica Bornm., one of the most-endangered (Fukuda et al. 2011; Yousefzadeh et al. 2012; Tang et al. relict tree species of the Hyrcanian forest (Fallah et al. 2015). Therefore, we used the ITS regions of nuclear 2012), is a fast-growing hygrophytic tree, distributed ribosomal DNA to trace potential hybridizations events throughout the Hyrcanian forest from the plains to 1400 m within a population of P. caspica by comparing bootstrap above sea level. Unfortunately, many of these habitats have support for lineages resolved by independent topologies been destroyed because of land-use changes, illegal and combined trees. exploitation and habitat fragmentation (Colagar et al. The main objectives of this study were (1) to differen- 2013). Large-scale interspecific hybridization and high tiate the two closely related species P. caspica and P. alba levels of morphological variation among poplars have (section Leuce) and (2) to place P. caspica preliminarily resulted in great difficulty in the classification of species in within the genus Populus using sequence data from the systematic and comparative evolutionary research. plastid and nuclear genome. Populus caspica has very similar morphological features with P. alba and is differentiated mainly by the inflorescence and petiole sizes; the petiole of P. caspica is 10–15 cm long Materials and methods (P. alba 10 cm) and inflorescence is 20 cm long (P. alba 10–15 cm). Populus alba has many ridges in its bark and Plant material, DNA extraction, PCR grows in the sun, tolerates almost any soils, wet or dry, and is and sequencing distributed in the river areas of southern Europe, north Africa and central Asia; this species can be found in active flood- Leaves were collected from six small populations of P. plains (Hamzeh and Dayanandan 2004). Populus caspica, caspica along an east to west gradient of the Hyrcanian with few ridges in its bark (Rechinger 1982), is distributed Forest, northern Iran (Appendix 1 in Electronic Supple- exclusively in the Hyrcanian Forest with other relict tree mentary Material), stored on ice and then brought to the lab species, such as Alnus glutinosa, Pterocarya fraxinifolia, and and frozen in liquid nitrogen and milled to a fine powder. Quercus castaneifolia. Because of the many morphological Total DNA was extracted from the ground powder using a similarities between these two species, the taxonomic status combination of the cetyltrimethylammonium bromide of P. caspica is disputed. In fact, some botanists argue that P. (CTAB) and SDS-potassium acetate (Colagar et al. 2010). caspica and P. alba belong to the same species (Rechinger Before PCR, the DNA extract was electrophoresed in 1% 1982). When morphological similarities prevent accurate agarose. The cpDNA noncoding regions trnL-F and trnH- plant identification (Brinegar 2009), several molecular psbA intergenic spacer (IGS) were amplified by PCR using markers have been applied to differentiate the species (Khasa the conditions described by Yousefzadeh et al. (2014) and et al. 2003; Cervera et al. 2004; Wan et al. 2013). specific primers UEUFF (50-GGTTCAAGTCCCTCTATC The trnL-trnF (GAA) in the chloroplast genome is CC-30) as the direct primer and UEUFR (50ATTTGAA suitable for accurate identification of species at the CTGGTGACACGAG-30) as the reverse primer. intraspecific level (Kojoma et al. 2002; Yi et al. 2004; Holt The trnH-psbA region was amplified with forward pri- et al. 2004). The length of these regions is another mer trnH-GUG (50-CGCGCATGGTGGATTCACAATCC- advantage as they are usually shorter than 700 bp (based 30) and reverse primer psbA(50-GTTATGCATGAACG- upon most species examined to date) and can thus be TAATGCTC-30). The ITS region was amplified using ITS1 directly amplified and sequenced (Tsai et al. 2006). (50-TCCGTAGGTGAACCTGCGG-30) as the direct primer The trnH-psbA intergenic spacer is another sequence and ITS4 (50-TCCTCCGCTTATTGATATGC-30) as the candidate for resolving lower level relationships (Nitta and reverse primer, which was designed by Taberlet et al. O’Grady 2008; Akbarzadeh Roshan et al. 2013). These two (1991) as a universal primer; the PCR conditions that were regions can be amplified by universal primers (Taberlet used were described by Yousefzadeh et al. (2012). et al. 1991; Pirie et al. 2007); hence, they have been the PCR products were separated by electrophoresis in 1% most widely used for phylogenetic studies in plants agarose. The Taq-PCR products were direct-sequenced by (Quandt et al. 2004). Conflicts between topologies have MWG DNA sequencing services (MWG Co., Ebersberg, often been discovered from different plastid and nuclear Germany). The gel electrophoresis and staining were per- genomes. The internal transcribed spacer (ITS) genomes formed by Green and Sambrook (2012) methods. have been interpreted in different ways, such as lineage sorting or reticulation (Wendel and Doyle 1998). ITS Phylogenetic analysis regions of nuclear ribosomal DNA have been frequently used for phylogenetic analysis of plants at lower taxonomic Electropherograms of the trnL-F sequences were further levels because of their universality, easy amplification, checked by eye using the Chromas software program ver- biparental inheritance and intragenomic uniformity sion 2.33. The boundaries of sequences were determined 123 Phylogenetic relationship and genetic differentiation of Populus caspica and Populus alba… via comparison with samples of Populus in searches by 288 positions of trnH-psbA, there were 17 parsimony Hamzeh and Dayanandan (2004) for trnL-F and NCBI positions for P. caspica, whereas only three sites were sequence data for trnH-psbA and ITS. Multiple sequence observed for NCBI under the study species. The trnL- alignment was performed using ClustalW2 in MEGA 6 F fragments and sequencing analysis revealed that trnL- (Tamura et al. 2013). F of P. caspica and P. alba was 315 bp long; 28%
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