Plastid DNA Variation of the Endemic Species Oxytropis Glandulosa Turcz

Turkish Journal of Botany Turk J Bot (2018) 42: 38-50 http://journals.tubitak.gov.tr/botany/ © TÜBİTAK Research Article doi:10.3906/bot-1706-11 Plastid DNA variation of the endemic species Oxytropis glandulosa Turcz. (Fabaceae) 1, 1 1 2 3 2 Alla KHOLINA *, Marina KOZYRENKO , Elena ARTYUKOVA , Denis SANDANOV , Inessa SELYUTINA , Daba CHIMITOV 1 Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia 2 Institute of General and Experimental Biology, Siberian Branch of the Russian Academy of Sciences, Ulan-Ude, Russia 3 Central Siberian Botanical Garden, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Received: 06.06.2017 Accepted/Published Online: 15.09.2017 Final Version: 11.01.2018 Abstract: Oxytropis glandulosa Turcz. (Fabaceae) is a rare perennial plant endemic to Buryatia (Russia). We sequenced three intergenic spacers (the psbA–trnH, trnL–trnF, and trnS–trnG) of chloroplast DNA (cpDNA) in specimens of four populations from two geographic regions (Barguzin and Yeravna depressions) within this species range. The levels of haplotype and nucleotide diversity varied in the range of 0.133–0.911 and 0.0002–0.0059, respectively. The highest values of these parameters are characteristic of populations located in the Barguzin depression. Variable sites detected within the intergenic spacers allowed the identification of eleven haplotypes; nine of them were found in the populations from the Barguzin depression and only two haplotypes were found in the populations from the Yeravna depression. No common haplotypes for all four populations were found. A high level of population differentiation (ΦST = 0.758, P < 0.0001) and the absence of evidence for isolation by distance were also found in O. glandulosa. Genealogical and phylogenetic analyses and Bayesian analysis of the genetic structure showed a clear division of the studied populations of O. glandulosa into three major lineages. Key words: Oxytropis glandulosa, endemic, genetic diversity, intergenic spacer region, cpDNA 1. Introduction and Chimitov, 2013). O. glandulosa belongs to the section As habitat fragmentation increases throughout the Polyadena Bunge (Malyshev, 2008). The species occurs world it has many important ecological and genetic in two isolated depressions more than 150 km distant consequences for endemic plant populations. There are from each other and separated by mountain ridges. The profound consequences for species genetic patterns as a representatives of the populations from the Barguzin result of this fragmentation and it is crucial to understand depression are diploids (Konichenko and Selyutina, the characteristics of fragmented populations to provide 2013) and the representatives of the populations from adequate management, particularly where the populations the Yeravna depression are tetraploids (Zhukova, 1983). and species are endangered. Knowledge of the population O. glandulosa habitats mostly are affected by plowing and genetic structure of narrowly occurring endemic plants grazing (Peshkova, 2008). is of great importance for the purpose of conservation The chloroplast genome is useful in providing of the existing populations (Ellstrand and Elam, 1993). information on the inference of the evolutionary patterns The analysis of variation in plant genomes with different and processes in plants (Raubeson and Jansen, 2005). modes of inheritance can provide valuable information At lower taxonomic levels, noncoding regions of the on the genetic structure of current populations and on chloroplast DNA (cpDNA) are phylogenetically more the evolutionary forces that have shaped the current informative than coding regions because they are under distribution of genetic variation (Pleines et al., 2009 and fewer functional constraints and evolve more rapidly references therein). (Gielly and Taberlet, 1994). Analysis of the chloroplast Oxytropis glandulosa Turcz. (Fabaceae) is a rare plant genome provides the resolution of controversial taxonomic species endemic to Buryatia (region of Russia located in and phylogenetic issues. The analysis of the cpDNA data the south-central part of Siberia along the eastern shore reveals considerable divergence of closely related species of Lake Baikal). The species is included in the Red Data of the genus Oxytropis DC., O. chankaensis Jurtz. and O. Book of the Russian Federation (Peshkova, 2008) and the oxyphylla (Pall.) DC. (Artyukova and Kozyrenko, 2012). Red Data Book of the Republic of Buryatia (Sandanov The phylogenetic relationships of the species and sections * Correspondence: [email protected] 38 KHOLINA et al. / Turk J Bot of the genus Oxytropis from Asian Russia were clarified 2.3. Data analysis on the basis of sequence comparison of the noncoding For each individual, sequence data for the three regions regions of cpDNA (Kholina et al., 2016). were combined. The rate of plastid DNA evolution is In this study, we used sequence data for three noncoding very slow, and differences between substitution and indel regions (the psbA–trnH, trnL–trnF, and trnS–trnG) of mutation rates are unlikely to affect the resolution of the cpDNA to estimate the level of genetic diversity and intraspecific phylogenetic relationships (Gonzales et al., population structure of O. glandulosa. 2008). Each insertion or deletion, regardless of its size, was coded as a single mutational event in all analyses 2. Material and methods (Simmons and Ochoterena, 2000). The values of pairwise genetic distances (F 2.1. Population sampling ST) among the populations, the number Narrow endemic O. glandulosa is restricted to areas within of haplotypes, the haplotype diversity (h), and nucleotide the Barguzin and Yeravna depressions. Currently only diversity (π) were calculated using the Arlequin v. 3.5 ten different localities of O. glandulosa are known, most program (Excoffier and Lischer, 2010). To calculate the of which are small and represented by a few individuals. partitioning of genetic variation within and among the Thus, the material for the study was collected only from populations and/or population groups (fixation indices Φ , Φ , Φ ), we performed analyses of molecular four populations, which are large enough for sampling ST CT SC without damaging of the populations. Leaves from variance (AMOVA; implemented in Arlequin). Gene flow (N ) and the degree of divergence among the populations randomly selected plants approximately 100 m apart m on the basis of nucleotide substitutions (K ) were defined were collected. Sample size, population code, and the S in the DnaSP v. 5.0 program (Librado and Rozas, 2009). geographic coordinates for each population are given in We used the Mantel test with 10,000 permutations Table 1. One accession of O. triphylla (Pall.) DC. (Russia, to analyze the relationships between the matrices of Buryatia, Barguzin depression, Kurumkansky District, genetic (F ) and geographic distances using Arlequin. near the village of Sahuli, 575 m a.s.l., 54.45°N, 110.45°E), ST Phylogenetic analyses were carried out by the maximum from the section Xerobia Bunge, was used as an outgroup likelihood (ML), neighbor joining (NJ), and maximum for phylogenetic analyses. parsimony (MP) methods implemented in the PAUP v. 2.2. DNA extraction, amplification, and sequencing 4.0b10 software package (Swofford, 2002). For the ML Individual preparations of total DNA were extracted and MP analyses, heuristic searches were performed using from the leaf tissues using the method described by tree-bisection-reconnection (TBR) branch swapping and Artyukova et al. (2004). We sequenced three intergenic 10 random sequence addition replicates. The GTR + I + G spacer regions of the chloroplast genome: psbA–trnH, model was selected as the optimal setting for the ML and NJ trnL–trnF, and trnS–trnG. The research was done using analyses by Modeltest 3.6 (Posada and Crandall, 1998). The equipment of the Instrumental Centre of Biotechnology statistical significance of the branching order was assessed and Gene Engineering of FSCEATB FEB RAS. Double- by bootstrap analysis with 1000 alternative trees (bootstrap stranded templates for direct sequencing were amplified percentage, BP). BP values below 50% were not considered. on a thermal cycler UNO II 48 (Biometra, Germany) Two datasets were generated: a matrix containing data using the PCR parameters and universal primers, reaction from the cpDNA regions of the 49 accessions of O. conditions, and temperature regimes recommended for glandulosa and one accession of O. triphylla, and a matrix these regions (Taberlet et al., 1991; Shaw et al., 2005). The containing the sequences of O. glandulosa haplotypes G1– PCR products were sequenced using a BigDye terminator G11 and the sequences of Oxytropis species (haplotypes v. 3.1 sequencing standard kit (Applied Biosystems, USA). H1–H79 except H2, H19, H23, H29, H31, H39–H41, H45, Sequencing was carried out in both directions under H52, H55, H56) and the accessions of Astragalus chinensis cyclic sequencing conditions and with the same pairs L.f. (LM653160, LM653197, LM653234) and A. davuricus of primers as those used for amplification. In addition, (Pall.) DC. (LM653161, LM653198, LM653235) from our internal primers were used for sequencing of the trnL– previous study (Kholina et al., 2016). The genealogical trnF and trnS–trnG regions (Taberlet et al., 1991; Shaw et relationships of haplotypes were determined using the al., 2005). The sequences were analysed on an ABI PRISM

Load more