Using cascading Bloom filters to improve the memory usage for de Brujin graphs

De Brujin graphs are widely used in bioinformatics for processing next-generation sequencing data. Due to a very large size of NGS datasets, it is essential to represent de Bruijn graphs compactly, and several approaches to this problem have been proposed recently. In this work, we show how to reduce the memory required by the algorithm of [3] that represents de Brujin graphs using Bloom filters. Our method requires 30% to 40% less memory with respect to the method of [3], with insignificant impact to construction time. At the same time, our experiments showed a better query time compared to [3]. This is, to our knowledge, the best practical representation for de Bruijn graphs.Comment: 12 pages, submitte

Evolutionary history of wild barley (Hordeum vulgare subsp. spontaneum) analyzed using multilocus sequence data and paleodistribution modeling

PubMedID: 24586028Studies of Hordeum vulgare subsp. spontaneum, the wild progenitor of cultivated barley, have mostly relied on materials collected decades ago and maintained since then ex situ in germplasm repositories. We analyzed spatial genetic variation in wild barley populations collected rather recently, exploring sequence variations at seven single-copy nuclear loci, and inferred the relationships among these populations and toward the genepool of the crop. The wild barley collection covers the whole natural distribution area from the Mediterraneanto Middle Asia. Incontrast to earlier studies, Bayesian assignment analyses revealed three population clusters, in the Levant, Turkey, and east of Turkey, respectively. Genetic diversity was exceptionally high in the Levant, while eastern populations were depleted of private alleles. Species distribution modeling based on climate parameters and extant occurrence points of the taxon inferred suitable habitat conditions during the ice-age, particularly in the Levant and Turkey. Together with the ecologically wide range of habitats, they might contribute to structured but long-term stable populations in this region and their high genetic diversity. For recently collected individuals, Bayesian assignment to geographic clusters was generally unambiguous, but materials from genebanks often showed accessions that were not placed according to their assumed geographic origin or showed traces of introgression from cultivated barley. We assign this to gene flow among accessions during ex situ maintenance. Evolutionary studies based on such materials might therefore result in wrong conclusions regarding the history of the species or the origin and mode of domestication of the crop, depending on the accessions included. © The Author(s) 2014.Massachusetts Department of Fish and Game: JA 1938/

EURALLIVEG: Establishment of a European core collection by cryopreservation and virus elimination in garlic

A European project named EURALLIVEG (Vegetative Allium, Europe’s Core Collection, safe & sound) was performed under Council Regulation EC 870/2004 from 2007 until 2011. It was coordinated by IPK. The main focus of the project was the development of a European integrated Allium Core collection provided by national collections of Germany, Czech Republic, Poland, Italy, France, and Nordic countries. This collection was designed as a part of the European Genebank Integrated System (AEGIS) of the European Cooperative Program for Plant Genetic Resources (ECPGR). The project consists of five work packages: documentation, molecular screening, cryopreservation, virus elimination, and coordination. Main aim was identification of a core collection of the 200 most important garlic accessions. This collection was cryopreserved using vitrification, which is the most economic way for long term storage. A Cryobanks Network was organized by three project partners. This system ensures safe storage of material by adopting a safety duplicate strategy. The documentation of the collection used passport and characterization data, pictures and other information. In addition genetic fingerprinting with AFLP markers was conducted. In the project, the garlic accessions were introduced into meristem culture for virus elimination. Of the viruses present in garlic, Onion Yellow Dwarf (OYDV) and Leek Yellow Stripe (LYSV) Viruses are most harmful. Therefore, because of the impossibility to do all treatments and tests on all germplasm, it was decided to test the major part of the collection on OYDV and LYSV only. However, a specific part with higher priority (backbone subset) was examined for five viruses. Virus detection used ELISA testing

Phylogeny, geographic distribution, and new taxonomic circumscription of the Crocus reticulatus species group (Iridaceae)

Recent phylogenetic analyses proved several infrageneric units within the genus Crocus to be para- or polyphyletic. In an attempt to arrive at a system of Crocus that closely reflects species relationships, we provide here phylogenetic, morphometric, geographic, and nomenclatorial data for the species of a narrower-defined, monophyletic Crocus series Reticulati. We sequenced the ETS and ITS regions of the nuclear ribosomal DNA in 9 Reticulati and 19 outgroup species. Three chloroplast loci (trnL–F, rps16–trnQ, matK–trnK) were sequenced in the newly defined series Reticulati species and 1 outgroup. Data were analyzed with Bayesian and parsimony algorithms. The phylogenies resulted in 2 clearly separated, geographically defined species groups within the series Reticulati. The southern one comprises only the taxa from Turkey, while the species of the second group are distributed from Italy in the west through the areas north of the Black Sea to the Caucasus in the east. To arrive at monophyletic species we describe here C. danubensis sp. nov., C. filis-maculatis sp. nov., and C. orphei sp. nov. as new species, and we define C. reticulatus s.s. to comprise only the populations in the area north and east of the Black Sea. © TÜBİTAK