STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design

BackgroundMicrosatellites (MSs) are DNA markers with high analytical power, which are widely used in population genetics, genetic mapping, and forensic studies. Currently available software solutions for high-throughput MS design (i) have shortcomings in detecting and distinguishing imperfect and perfect MSs, (ii) lack often necessary interactive design steps, and (iii) do not allow for the development of primers for multiplex amplifications. We present a set of new tools implemented as extensions to the STADEN package, which provides the backbone functionality for flexible sequence analysis workflows. The possibility to assemble overlapping reads into unique contigs (provided by the base functionality of the STADEN package) is important to avoid developing redundant markers, a feature missing from most other similar tools.ResultsOur extensions to the STADEN package provide the following functionality to facilitate microsatellite (and also minisatellite) marker design: The new modules (i) integrate the state-of-the-art tandem repeat detection and analysis software PHOBOS into workflows, (ii) provide two separate repeat detection steps with different search criteria one for masking repetitive regions during assembly of sequencing reads and the other for designing repeat-flanking primers for MS candidate loci, (iii) incorporate the widely used primer design program PRIMER3 into STADEN workflows, enabling the interactive design and visualization of flanking primers for microsatellites, and (iv) provide the functionality to find optimal locus- and primer pair combinations for multiplex primer design. Furthermore, our extensions include a module for storing analysis results in an SQLite database, providing a transparent solution for data access from within as well as from outside of the STADEN Package.ConclusionThe STADEN package is enhanced by our modules into a highly flexible, high-throughput, interactive tool for conventional and multiplex microsatellite marker design. It gives the user detailed control over the workflow, enabling flexible combinations of manual and automated analysis steps. The software is available under the OpenBSD License [1,2]. The high efficiency of our automated marker design workflow has been confirmed in three microsatellite development projects

Inter-annual variability of transparent exopolymer particles in the Arctic Ocean reveals high sensitivity to ecosystem changes

Transparent exopolymer particles (TEP) are a class of marine gel particles and important links between surface ocean biology and atmospheric processes. Derived from marine microorganisms, these particles can facilitate the biological pumping of carbon dioxide to the deep sea, or act as cloud condensation and ice nucleation particles in the atmosphere. Yet, environmental controls on TEP abundance in the ocean are poorly known. Here, we investigated some of these controls during the first multiyear time-series on TEP abundance for the Fram Strait, the Atlantic gateway to the Central Arctic Ocean. Data collected at the Long-Term Ecological Research observatory HAUSGARTEN during 2009 to 2014 indicate a strong biological control with highest abundance co-occurring with the prymnesiophyte Phaeocystis pouchetii. Higher occurrence of P. pouchetii in the Arctic Ocean has previously been related to northward advection of warmer Atlantic waters, which is expected to increase in the future. Our study highlights the role of plankton key species in driving climate relevant processes; thus, changes in plankton distribution need to be accounted for when estimating the ocean’s biogeochemical response to global change

Summertime plankton ecology in Fram Strait - a compilation of long- and short-term observations

Between Greenland and Spitsbergen, Fram Strait is a region where cold ice-covered Polar Water exits the Arctic Ocean with the East Greenland Current (EGC) and warm Atlantic Water enters the Arctic Ocean with the West Spitsbergen Current (WSC). In this compilation, we present two different data sets from plankton ecological observations in Fram Strait: (1) long-term measurements of satellite-derived (1998–2012) and in situ chlorophyll a (chl a) measurements (mainly summer cruises, 1991–2012) plus protist compositions (a station in WSC, eight summer cruises, 1998–2011); and (2) short-term measurements of a multidisciplinary approach that includes traditional plankton investigations, remote sensing, zooplankton, microbiological and molecular studies, and biogeochemical analyses carried out during two expeditions in June/July in the years 2010 and 2011. Both summer satellite-derived and in situ chl a concentrations showed slight trends towards higher values in the WSC since 1998 and 1991, respectively. In contrast, no trends were visible in the EGC. The protist composition in the WSC showed differences for the summer months: a dominance of diatoms was replaced by a dominance of Phaeocystis pouchetii and other small pico- and nanoplankton species. The observed differences in eastern Fram Strait were partially due to a warm anomaly in the WSC. Although changes associated with warmer water temperatures were observed, further long-term investigations are needed to distinguish between natural variability and climate change in Fram Strait. Results of two summer studies in 2010 and 2011 revealed the variability in plankton ecology in Fram Strait

Bewertung der genetischen Diversität des Kolonie-formenden Prymnesiophyten Phaeocystis antarctica

This thesis provides a detailed insight into genetic diversity among and between Phaeocystis antarctica populations from different regions of the Southern Ocean and the gene flow between them. Genetic, physiological and ecological results are discussed in a broader view giving valuable insights into the ecology of this keystone species in the Southern Ocean. This work is opening a new field of research on P. antarctica, which can be termed 'ecophysiological genetics'. By combining genetic data with results from ecological investigations and physiological experiments, a broader understanding of ecosystem functioning will also direct future studies

Estimation of genetic diversity in the colony forming polar prymnesiophyte species Phaeocystis antarctica

This thesis provides a detailed insight into genetic diversity among and between Phaeocystis antarctica populations from different regions of the Southern Ocean and the gene flow between them. Genetic, physiological and ecological results are discussed in a broader view giving valuable insights into the ecology of this keystone species in the Southern Ocean. This work is opening a new field of research on P. antarctica, which can be termed 'ecophysiological genetics'. By combining genetic data with results from ecological investigations and physiological experiments, a broader understanding of ecosystem functioning will also direct future studies