The genome of a songbird

The zebra finch is an important model organism in several fields1,2 with unique relevance to human neuroscience3,4. Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other animals and lacking in the chicken5—the only bird with a sequenced genome until now6. Here we present a structural, functional and comparative analysis of the genome sequence of the zebra finch (Taeniopygia guttata), which is a songbird belonging to the large avian order Passeriformes7. We find that the overall structures of the genomes are similar in zebra finch and chicken, but they differ in many intrachromosomal rearrangements, lineage-specific gene family expansions, the number of long-terminal-repeat-based retrotransposons, and mechanisms of sex chromosome dosage compensation. We show that song behaviour engages gene regulatory networks in the zebra finch brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets. We also show evidence for rapid molecular evolution in the songbird lineage of genes that are regulated during song experience. These results indicate an active involvement of the genome in neural processes underlying vocal communication and identify potential genetic substrates for the evolution and regulation of this behaviour

Molecular evolution of genes in avian genomes

Nam K, Mugal C, Nabholz B, et al. Molecular evolution of genes in avian genomes. Genome Biology. 2010;11(6): R68.Background: Obtaining a draft genome sequence of the zebra finch (Taeniopygia guttata), the second bird genome to be sequenced, provides the necessary resource for whole-genome comparative analysis of gene sequence evolution in a non-mammalian vertebrate lineage. To analyze basic molecular evolutionary processes during avian evolution, and to contrast these with the situation in mammals, we aligned the protein-coding sequences of 8,384 1:1 orthologs of chicken, zebra finch, a lizard and three mammalian species. Results: We found clear differences in the substitution rate at fourfold degenerate sites, being lowest in the ancestral bird lineage, intermediate in the chicken lineage and highest in the zebra finch lineage, possibly reflecting differences in generation time. We identified positively selected and/or rapidly evolving genes in avian lineages and found an overrepresentation of several functional classes, including anion transporter activity, calcium ion binding, cell adhesion and microtubule cytoskeleton. Conclusions: Focusing specifically on genes of neurological interest and genes differentially expressed in the unique vocal control nuclei of the songbird brain, we find a number of positively selected genes, including synaptic receptors. We found no evidence that selection for beneficial alleles is more efficient in regions of high recombination; in fact, there was a weak yet significant negative correlation between ω and recombination rate, which is in the direction predicted by the Hill-Robertson effect if slightly deleterious mutations contribute to protein evolution. These findings set the stage for studies of functional genetics of avian genes

The genome of a songbird

The zebra finch is an important model organism in several fields with unique relevance to human neuroscience. Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other animals and lacking in the chickenthe only bird with a sequenced genome until now. Here we present a structural, functional and comparative analysis of the genome sequence of the zebra finch (Taeniopygia guttata), which is a songbird belonging to the large avian order Passeriformes. We find that the overall structures of the genomes are similar in zebra finch and chicken, but they differ in many intrachromosomal rearrangements, lineage-specific gene family expansions, the number of long-terminal-repeat- based retrotransposons, and mechanisms of sex chromosome dosage compensation. We show that song behaviour engages gene regulatory networks in the zebra finch brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets. We also show evidence for rapid molecular evolution in the songbird lineage of genes that are regulated during song experience. These results indicate an active involvement of the genome in neural processes underlying vocal communication and identify potential genetic substrates for the evolution and regulation of this behaviour. © 2010 Macmillan Publishers Limited. All rights reserved

A Mutant Strain of <i>Chlamydomonas reinhardtii</i> Lacking the Chloroplast Photosystem II <i>psbI</i> Gene Grows Photoautotrophically

The product of the chloroplast psbI gene is associated with the photosystem II reaction center. To gain insights into the function of this polypeptide, we have disrupted its gene in Chlamydomonas reinhardtii with an aadA expression cassette that confers resistance to spectinomycin through biolistic transformation. The transformants are still able to grow photoautotrophically in dim light, but not in high light, and they remain photosensitive when grown on acetate containing medium. The amounts of photosystem II complex and oxygen evolving activity are both reduced to 10-20% of wild-type levels in these psbI-deficient mutants. It appears that the PsbI polypeptide plays a role in the stability of photosystem II and possibly also in modulating electron transport or energy transfer in this complex

Use of Surface Acoustic Waves for Crack Detection on Railway Track Components&mdash;Laboratory Tests

The present work investigates the technical feasibility of a condition monitoring setup aiming at the detection of gauge corner cracks (aka head checks) in pearlitic railway rails, using a wayside (i.e., stationary) setup with surface acoustic waves (SAW) as its detection principle. The experimental SAW setup consists of a pitch-catch setup using piezo transducers equipped with comb adaptors to excite and measure narrowband Rayleigh waves with a center frequency of 1 MHz. SAW experiments were performed on a rail subjected to cyclic loading in a 1:1 wheel&ndash;rail test rig yielding the specific rolling contact fatigue, i.e., head checks. Elastodynamic finite integration technique (EFIT) simulations were performed to analyze the surface and bulk wave propagation in the rail and to predict the signals at specific receiver positions. SAW transmission and reflection scenarios at cracks were analyzed numerically via modelled variations of gauge corner crack configurations according to number of cracks (0&ndash;3) and depth (0, 0.5 mm and 1 mm). The numerical and the experimental results each show a clear correlation between the appearance and intensity of head check damage and the wave attenuation in transmission mode

Use of Surface Acoustic Waves for Crack Detection on Railway Track Components—Laboratory Tests

The present work investigates the technical feasibility of a condition monitoring setup aiming at the detection of gauge corner cracks (aka head checks) in pearlitic railway rails, using a wayside (i.e., stationary) setup with surface acoustic waves (SAW) as its detection principle. The experimental SAW setup consists of a pitch-catch setup using piezo transducers equipped with comb adaptors to excite and measure narrowband Rayleigh waves with a center frequency of 1 MHz. SAW experiments were performed on a rail subjected to cyclic loading in a 1:1 wheel–rail test rig yielding the specific rolling contact fatigue, i.e., head checks. Elastodynamic finite integration technique (EFIT) simulations were performed to analyze the surface and bulk wave propagation in the rail and to predict the signals at specific receiver positions. SAW transmission and reflection scenarios at cracks were analyzed numerically via modelled variations of gauge corner crack configurations according to number of cracks (0–3) and depth (0, 0.5 mm and 1 mm). The numerical and the experimental results each show a clear correlation between the appearance and intensity of head check damage and the wave attenuation in transmission mode

Full SNP dataset

Provided is the SNP dataset file for guppies distributed across northen trinidad

Optimization of next-generation sequencing transcriptome annotation for species lacking sequenced genomes

Next‐generation sequencing methods, such as RNA‐seq, have permitted the exploration of gene expression in a range of organisms which have been studied in ecological contexts but lack a sequenced genome. However, the efficacy and accuracy of RNA‐seq annotation methods using reference genomes from related species have yet to be robustly characterized. Here we conduct a comprehensive power analysis employing RNA‐seq data from Drosophila melanogaster in conjunction with 11 additional genomes from related Drosophila species to compare annotation methods and quantify the impact of evolutionary divergence between transcriptome and the reference genome. Our analyses demonstrate that, regardless of the level of sequence divergence, direct genome mapping (DGM), where transcript short reads are aligned directly to the reference genome, significantly outperforms the widely used de novo and guided assembly‐based methods in both the quantity and accuracy of gene detection. Our analysis also reveals that DGM recovers a more representative profile of Gene Ontology functional categories, which are often used to interpret emergent patterns in genomewide expression analyses. Lastly, analysis of available primate RNA‐seq data demonstrates the applicability of our observations across diverse taxa. Our quantification of annotation accuracy and reduced gene detection associated with sequence divergence thus provides empirically derived guidelines for the design of future gene expression studies in species without sequenced genomes