42 research outputs found
Development of Nuclear Microsatellites for the Arcto-Tertiary Tree Zelkova carpinifolia (Ulmaceae) Using 454 Pyrosequencing
Premise of the study: The current study aimed at developing nuclear
microsatellite markers for the relict tree species Zelkova carpinifolia, which
is threatened in its natural range in the South Caucasus. Methods and Results:
Pyrosequencing of an enriched microsatellite library on the Roche FLX platform
using the 454 Titanium kit produced 86,058 sequence reads, most of which
contained short tandem repeats. Eighty microsatellite loci identified using
the software package QDD version 1 were selected and tested for proper PCR
amplification. Of these, 13 allowed proper amplification and were shown to be
polymorphic among a sample of 25 Z. carpinifolia specimens from various
geographic origins. Conclusions: The set of microsatellite markers will be
suitable for the assessment of genetic diversity in Z. carpinifolia. They will
allow for an examination of phylogeographic patterns as well as of population
structure and gene flow within this species
Evidence for nonallopatric speciation among closely related sympatric Heliotropium species in the Atacama Desert
The genetic structure of populations of closely related, sympatric species may
hold the signature of the geographical mode of the speciation process. In
fully allopatric speciation, it is expected that genetic differentiation
between species is homogeneously distributed across the genome. In
nonallopatric speciation, the genomes may remain undifferentiated to a large
extent. In this article, we analyzed the genetic structure of five sympatric
species from the plant genus Heliotropium in the Atacama Desert. We used
amplified fragment length polymorphisms (AFLPs) to characterize the genetic
structure of these species and evaluate their genetic differentiation as well
as the number of loci subject to positive selection using divergence outlier
analysis (DOA). The five species form distinguishable groups in the genetic
space, with zones of overlap, indicating that they are possibly not completely
isolated. Among-species differentiation accounts for 35% of the total genetic
differentiation (FST = 0.35), and FST between species pairs is positively
correlated with phylogenetic distance. DOA suggests that few loci are subject
to positive selection, which is in line with a scenario of nonallopatric
speciation. These results support the idea that sympatric species of
Heliotropium sect. Cochranea are under an ongoing speciation process,
characterized by a fluctuation of population ranges in response to pulses of
arid and humid periods during Quaternary times
Analysis of nuclear microsatellites reveals limited differentiation between Colchic and Hyrcanian populations of the wind-pollinated relict tree Zelkova carpinifolia (Ulmaceae)
Premise of the study: The Caucasus represents one of the world’s biodiversity hotspots and includes the climatic refugia Hyrcan on the southern coast of the Caspian Sea and Colchis on the eastern coast of the Black Sea, where different species survived during the Quaternary climatic oscillations. We evaluated the genetic diversity of the relict tree Zelkova carpinifolia shared between the two refugia and distributed throughout the Caucasus and adjacent areas.Methods: Specimens were collected from 30 geographical sites in Azerbaijan, Georgia, Iran, and Turkey and screened for variability at eight nuclear microsatellite loci. The genetic diversity among and within populations was assessed using a set of statistical measures.Key results: We detected 379 different genotypes from a total of 495 individuals with varying degrees of clonal reproduction at the different sites. Low to intermediate levels of genetic diversity were observed at all sites, and strong differentiation between sampling sites was absent. In addition, we observed no clear genetic differentiation between the Colchis and Hyrcan. Bayesian clustering of the genotypes revealed three populations with high levels of admixture between the sampling sites.Conclusions: The lack of strong genetic structure of studied populations of Z. carpinifolia contrasts with a previous study based on chloroplast markers and suggests that long-distance pollen dispersal is an important factor of gene flow among populations of Z. carpinifolia. The present study does not reveal any particular site with particularly isolated genotypes that would deserve more attention for conservation purposes than others, although some sites should be considered for further investigation
Soil Saprobic Fungi Differ in Their Response to Gradually and Abruptly Delivered Copper
The overwhelming majority of studies examining environmental change deliver treatments abruptly, although, in fact, many important changes are gradual. One example of a gradually increasing environmental stressor is heavy metal contamination. Essential heavy metals, such as copper, play an important role within cells of living organisms but are toxic at higher concentrations. In our study, we focus on the effects of copper pollution on filamentous soil fungi, key players in terrestrial ecosystem functioning. We hypothesize that fungi exposed to gradually increasing copper concentrations have higher chances for physiological acclimation and will maintain biomass production and accumulate less copper, compared to fungi abruptly exposed to the highest copper concentration. To test this hypothesis, we conducted an experiment with 17 fungal isolates exposed to gradual and abrupt copper addition. Contrary to our hypothesis, we find diverse idiosyncratic responses, such that for many fungi gradually increasing copper concentrations have more severe effects (stronger growth inhibition and higher copper accumulation) than an abrupt increase. While a number of environmental change studies have accumulated evidence based on the magnitude of changes, the results of our study imply that the rate of change can be an important factor to consider in future studies in ecology, environmental science, and environmental management
Genomic Structure of and Genome-Wide Recombination in the Saccharomyces cerevisiae S288C Progenitor Isolate EM93
The diploid isolate EM93 is the main ancestor to the widely used Saccharomyces cerevisiae haploid laboratory strain, S288C. In this study, we generate a high-resolution overview of the genetic differences between EM93 and S288C. We show that EM93 is heterozygous for >45,000 polymorphisms, including large sequence polymorphisms, such as deletions and a Saccharomyces paradoxus introgression. We also find that many large sequence polymorphisms (LSPs) are associated with Ty-elements and sub-telomeric regions. We identified 2,965 genetic markers, which we then used to genotype 120 EM93 tetrads. In addition to deducing the structures of all EM93 chromosomes, we estimate that the average EM93 meiosis produces 144 detectable recombination events, consisting of 87 crossover and 31 non-crossover gene conversion events. Of the 50 polymorphisms showing the highest levels of non-crossover gene conversions, only three deviated from parity, all of which were near heterozygous LSPs. We find that non-telomeric heterozygous LSPs significantly reduce meiotic recombination in adjacent intervals, while sub-telomeric LSPs have no discernable effect on recombination. We identified 203 recombination hotspots, relatively few of which are hot for both non-crossover gene conversions and crossovers. Strikingly, we find that recombination hotspots show limited conservation. Some novel hotspots are found adjacent to heterozygous LSPs that eliminate other hotspots, suggesting that hotspots may appear and disappear relatively rapidly
Species tree of Heliotropium sect. Cochranea
Species tree of Heliotropium sect. Cochranea generated with star-BEAS
normalizedExpressionLevels
Expression levels of the transcriptomic contigs after normalisation of the cDNA librar
Data from: "Transcriptome sequences for Campanula gentilis" in Genomic Resources Notes accepted 1 April 2015 – 31 May 2015
In this report, we present the transcriptome of a single accession of Campanula gentilis Kovanda, obtained through the sequencing of both a normalized and a non-normalized cDNA library generated from stem and leaf tissue. The resources we provide include the raw sequence reads, the assembled contigs, the putative open reading frames, the contig/ORF annotations and the normalized as well as non-normalized expression levels