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We present 14 microsatellite loci that were isolated from little spotted kiwi (LSK, Apteryx owenii). All loci cross-amplify in all kiwi species currently recognized except for one locus in a single species. Little spotted kiwi exhibited lower variation at these loci (mean number of alleles, H E) than other kiwi species, despite the markers having been developed for polymorphism in LSK and a far greater number of LSK genotyped than kiwi of other species. Reliable cross-species amplification and polymorphism make these markers promising new tools for the management of New Zealand’s threatened kiwi.

The use of beneficial organisms to help control pests and pathogens in field and greenhouse crops is constantly increasing. Insects and mites are commonly used as beneficial organisms and, nowadays, rearing companies have to produce them in large quantities. Because of the peculiarities of laboratory culture conditions, the quality of lab-reared organisms generally degrades over time. To maintain high fitness levels, cultures are refreshed with field specimens at regular intervals. However, this bears the risk of contaminating laboratory cultures with species or strains other than the intended natural enemy. To ensure that the correct species is produced and also to facilitate surveys after field release, we have developed a diagnostic microarray for identification of beneficial species. Probes have been designed from the different haplotypes of a fragment of the mitochondrial cytochrome oxidase I (COI) gene of each species. Hybridization of labeled PCR amplicons of COI on the microarray chip all...

The conservation status of small breeding areas of the Goosander (Mergus merganser merganser) in Central Europe is unclear. Geographic isolation of these areas suggests restricted gene flow to and from large North-European populations. On the other hand, migrating Goosanders from northern Europe join the Central European breeding population for wintering. To evaluate the conservation status of the small breeding areas we assessed the genetic structure of M. merganser populations in Europe by examining two nuclear marker systems (microsatellites and Single Nucleotide Polymorphisms, SNP) and mitochondrial (mtDNA) control region sequence variation for Goosanders in 11 sampling areas representing three of five distinct breeding areas and two subspecies (M. m. merganser and M. m. americanus). Overall population differentiation estimates including both subspecies were high, both based on mtDNA (\(\Upphi_{\rm ST}=0.899;\,P

To attract insects for sexual reproduction, some fungi can induce the formation of pseudoflowers on their hosts. Pseudoflowers are rosettes of yellow host leaves upon which the fungus presents gametes in sweet nectar. Eleven species of the fungus complex Uromyces pisi can induce pseudoflowers on the host Euphorbia cyparissias. The taxonomy of these species is based on the choice of the alternate host, a species of Fabaceae as well as on teliospore morphology on the Fabaceae hosts. Morphological identification of the fungi on E. cyparissias is impossible. To identify the fungal species on infected E. cyparissias, we compared sequences from the ITS region of the rDNA to the DNA from five identified fungal species on Fabaceae. From 43 specimens on E. cyparissias, collected in 1997-99 in Switzerland, 24 specimens could be identified as U. pisi s. str. and 16 specimens as U. striatus. Two specimens were identified as U. laburni and U. loti respectively, and one specimen could not be identified. We therefore conclude that fungal pseudoflowers are typically induced by U. pisi s. str. on U. striatus in Switzerland, although other species do sometimes occur. The ITS sequences were then used to reconstruct the phylogenetic relationship among species in the U. pisi complex and two closely related microcyclic rust species of the complex Uromyces scutellatus. Phylogenetic analyses indicated that the microcyclic species may be descendants from macrocyclic U. pisi s.l. ancestors. The ITS region sequenced in this study was found to be appropriate for answering phylogenetic, as well as ecological questions, and provided valuable markers for future studies.

The plant Euphorbia cyparissiasis commonly infected by rust fungi of the species complex Uromyces pisi.When infected, E. cyparissias is unable to flower, but instead is induced by the fungus to form pseudoflowers. Pseudoflowers are rosettes of yellow leaves upon which the fungus presents its gametes in a sweet-smelling fungal nectar. We hypothesized that the fungi, as they are heterothallic, are dependent on insect visitation to cross-fertilize their mating types. We confirmed that insects are required with an insect exclusion experiment. We further hypothesized that pseudoflowers of U. pisi interact with uninfected true host flowers through insects during their period of co-‘‘flowering’’ in early spring. We conducted artificial array experiments in the field to test whether the two species share insects and whether they influenced each other’s insect visitation. Insects moved between true flowers and pseudoflowers, but true flowers received more visits over all. Pseudoflowers and true flowers did not influence each other’s visitation rates in mixtures. However, shorter visits were observed on pseudoflowers in mixtures than monocultures, suggesting that true flowers might be competitors for pseudoflowers. Further experiments are needed to determine whether the similarity of pseudoflowers to true flowers is adaptive. For over a hundred years studies have accumulated describing and discussing heterothallic rust fungi (fungi with more than one mating type) that present their haploid fungal gametes (spermatia) in a sweet-smelling, sug

5 pages; International audience; This article documents the addition of 411 microsatellite marker loci and 15 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Acanthopagrus schlegeli, Anopheles lesteri, Aspergillus clavatus, Aspergillus flavus, Aspergillus fumigatus, Aspergillus oryzae, Aspergillus terreus, Branchiostoma japonicum, Branchiostoma belcheri, Colias behrii, Coryphopterus personatus, Cynogolssus semilaevis, Cynoglossus semilaevis, Dendrobium officinale, Dendrobium officinale, Dysoxylum malabaricum, Metrioptera roeselii, Myrmeciza exsul, Ochotona thibetana, Neosartorya fischeri, Nothofagus pumilio, Onychodactylus fischeri, Phoenicopterus roseus, Salvia officinalis L., Scylla paramamosain, Silene latifo, Sula sula, and Vulpes vulpes. These loci were cross-tested on the following species: Aspergillus giganteus, Colias pelidne, Colias interior, Colias meadii, Colias eurytheme, Coryphopterus lipernes, Coryphopterus glaucofrenum, Coryphopterus eidolon, Gnatholepis thompsoni, Elacatinus evelynae, Dendrobium loddigesii Dendrobium devonianum, Dysoxylum binectariferum, Nothofagus antarctica, Nothofagus dombeyii, Nothofagus nervosa, Nothofagus obliqua, Sula nebouxii, and Sula variegata. This article also documents the addition of 39 sequencing primer pairs and 15 allele specific primers or probes for Paralithodes camtschaticus.

Botanica Helvetica, 116 (2), ISSN:0253-1453, ISSN:1420-9063

Infections with mycobacteria are an important issue in public health care. Here we present a "proof-of-principle" concept for the identification of 37 different Mycobacterium species using 5' exonuclease real-time PCR and DNA microarray based on the region upstream of the 65 kDa heat shock protein. With our two PCR probes, one complementary to all mycobacteria species, the other specific for the M. tbc-complex, 34 species were properly classified by real-time PCR. After reamplification and hybridization to a DNA microarray, all species showed a specific pattern. All 10 blindly tested positive cultures revealed a positive real-time PCR signal with the genus probe. After reamplification and hybridization, six samples could unambiguously be identified. One sample showed a mixture of presumably three species-specific patterns and sequencing the 16S rRNA confirmed the presence of a mixture. The hybridization results of three specimens could not be interpreted because the signal to background ratio was not sufficient. Two samples considered as negative controls (LAL Reagent Water (Cambrex) and DNA of Candida albicans) gave neither a genus nor a M. tbc-complex positive PCR signal. Based on these results we consider our method to be a promising tool for the rapid identification of different mycobacteria species, with the advantage of possible identification of mixed infections or contaminations.

Homogeneous probe hybridization is a prerequisite for the robust design of microarrays. Elaborate algorithms were developed to select for probe sets with uniform melting temperatures (Tm). However, at least short oligonucleotides (20 bp) show large variation in the on-chip hybridization efficiency even if designed with state-of-the-art algorithms. This variation can be explained by steric effects and interferences on the solid surface as well as by chemical conditions that may deviate from conditions used to develop the algorithms. We designed 412 random 13mer duplexes to study the differences between the Tm of nearest-neighbor algorithms and the Tm values measured by dissociation analysis in polymerase chain reaction (PCR) and 1X SSC buffer. We tested the effects of theoretical vs empirical Tm values on the hybridization variation of 40 duplexes on-chip. Although the empirical approach resulted in a slightly better prediction of hybridization efficiency, less than one-fifth (17%) of the observed variation could be explained by the factor Tm alone. We conclude that state-of-the-art algorithms can be used for a first selection of short oligonucleotide probes, but that it is then necessary to perform an on-chip selection to obtain a probe set with a uniform hybridization behavior.