Low diversity,activity, and density of transposable elements in five avian genomes

In this study, we conducted the activity, diversity, and density analysis of transposable elements (TEs) across five avian genomes (budgerigar, chicken, turkey, medium ground finch, and zebra finch) to explore the potential reason of small genome sizes of birds. We found that these avian genomes exhibited low density of TEs by about 10% of genome coverages and low diversity of TEs with the TE landscapes dominated by CR1 and ERV elements, and contrasting proliferation dynamics both between TE types and between species were observed across the five avian genomes. Phylogenetic analysis revealed that CR1 clade was more diverse in the family structure compared with R2 clade in birds; avian ERVs were classified into four clades (alpha, beta, gamma, and ERV-L) and belonged to three classes of ERV with an uneven distributed in these lineages. The activities of DNA and SINE TEs were very low in the evolution history of avian genomes; most LINEs and LTRs were ancient copies with a substantial decrease of activity in recent, with only LTRs and LINEs in chicken and zebra finch exhibiting weak activity in very recent, and very few TEs were intact; however, the recent activity may be underestimated due to the sequencing/assembly technologies in some species. Overall, this study demonstrates low diversity, activity, and density of TEs in the five avian species; highlights the differences of TEs in these lineages; and suggests that the current and recent activity of TEs in avian genomes is very limited, which may be one of the reasons of small genome sizes in birds.     

The evolutionary relationship of avian and mammalian myosin heavy-chain genes

Summary Sequence comparisons of avian and mammalian skeletal and cardiac myosin heavy-chain isoforms are used to examine the evolutionary relationships of sarcomeric myosin multigene families. Mammalian fast-myosin heavy-chain isoforms forms from different species, with comparable developmental expression, are more similar to each other than they are to other fast isoforms within the same genome. In contrast, the developmentally regulated chicken fast isoforms are more similar to each other than they are to myosin heavy-chain isoforms in other species. Extensive regions of nucleotide identity among the chicken fast myosin heavy chains and in the mouse and rat α- and β-cardiac myosin heavy-chain sequences suggest that geneconversion-like mechanisms have played a major role in the concerted evolution of these gene families. We also conclude that the chicken fast myosin heavy-chain multigene family has undergone recent expansion subsequent to the divergence of birds and mammals and that both the developmental regulation and the specialization of myosin isoforms have likely developed independently in birds and mammals.     

The mtDNA sequence of the ostrich and the divergence between paleognathous and neognathous birds

The complete mitochondrial DNA (mtDNA) molecule of the ostrich, Struthio camelus, was sequenced. The size of the molecule is 16,591 nucleotides. Since the ostrich represents the paleognathous birds, comparison with the mtDNA of the neognathous chicken, the only avian species reported so far in databases, made it possible to identify common and, probably, general avian mtDNA characteristics. Relative to other vertebrates, the avian NADH6 and tRNA-Glu genes are positioned upstream of the control region rather than the cytochrome b gene. The NADH3 gene of the ostrich is terminated by a stop codon at position 207. Thus, the gene is about 140 nucleotides shorter than in other vertebrates. The sequence for L-strand origin of replication is missing in both birds, and four transfer RNA genes of the two avian mtDNAs deviate from common characteristics of tRNAs of vertebrate mtDNAs by having an adenine (and not a thymidine) at position 8. Due to the absence of suitable fossils, most paleontological datings of avian divergences are conjectural. Molecular dating of the divergence between the ostrich and the chicken indicates that these two avian lineages separated 80-90 MYA. Phylogenetic analysis of complete cytochrome b genes of six avian orders showed that Passeriformes represent the earliest divergence among recent birds, contradicting the commonly accepted notion of a basal position of the Palaeognathae among recent birds.      

Short-day experience is not a prerequisite for the termination of photorefractoriness in the reproductive cycle of baya weaver,Ploceus philippinus

In most photoperiodic avian forms (irrespective of temperate or tropical distribution) including the baya weaver,Ploceus philippinus, seasonal reproduction comes to an end due to the development of a photoperiodically controlled photorefractory phase when birds cease to respond to the stimulatory effect of long days. In the present paper photoperiodic control of the termination of photorefractory phase has been examined by studying the effect of short-day exposure lasting 4–6 months on long-day response of birds. Results indicate that unlike in other photoperiodic birds short-day exposure of winter is not a prerequisite for the termination of photorefractory phase in the reproductive cycle of baya weaver. Artificial long days on the other hand hasten the termination of this phase. Refractory phase in baya weaver, therefore, unlike that in temperate forms, is a temporary state resulting most likely from a sequel of physiological events triggered by long days of spring/summer which temporarily mask the photostimulatory response. Spontaneous termination of photorefractoriness in birds of tropical habitats may have a selective value imparting to the reproductive cycle the necessary elasticity for adaptation to diverse ecological conditions.     

Synthesis of melatonin by the pineal modified photoreceptors of birds immunocytochemical localization of hydroxyindole-O-methyltransferase

Photoperiodic control of several biological rhythms is exerted through the inhibitory effect of light on melatonin synthesis in the pineal organ. Hydroxyindole-O-methyltransferase (HIO-MT), the last acting-enzyme in melatonin biosynthesis, constitutes a specific marker of melatoninergic cells. In the present study, an antibody directed against chicken HIOMT was affinity-purified and used to identify melatoninergic cells in the pineal organ of chicken, quail, sparrow and blackbird. Regardless of the species, intense immunocytochemical reactions were observed in modified photoreceptors, whereas other cellular constituents (mostly glial cells) remained unlabeled. We conclude that modified photoreceptors synthesize melatonin in the avian pineal gland and are thus accountable for the translation of the photoperiodic input into hormonal output.     

Application of chicken microarrays for gene expression analysis in other avian species

Background

With the threat of emerging infectious diseases such as avian influenza, whose natural hosts are thought to be a variety of wild water birds including duck, we are armed with very few genomic resources to investigate large scale immunological gene expression studies in avian species. Multiple options exist for conducting large gene expression studies in chickens and in this study we explore the feasibility of using one of these tools to investigate gene expression in other avian species.

Results

In this study we utilised a whole genome long oligonucleotide chicken microarray to assess the utility of cross species hybridisation (CSH). We successfully hybridised a number of different avian species to this array, obtaining reliable signals. We were able to distinguish ducks that were infected with avian influenza from uninfected ducks using this microarray platform. In addition, we were able to detect known chicken immunological genes in all of the hybridised avian species.

Conclusion

Cross species hybridisation using long oligonucleotide microarrays is a powerful tool to study the immune response in avian species with little available genomic information. The present study validated the use of the whole genome long oligonucleotide chicken microarray to investigate gene expression in a range of avian species.

     

A comparative study on tissue distribution and metabolic adaptation of IMP-GMP 5'-nucleotidase.

1. Activity of a cytoplasmic 5'-nucleotidase which preferentially hydrolyzes IMP and GMP (IMP-GMP 5'-nucleotidase) was determined by a specific immunochemical method in two species of birds and two species of mammals. 2. The activity was markedly high in avian liver, and it increased two-fold in response to a high protein diet in chicken liver. 3. In mammals, the activity was high in testis and spleen. In the rat, the activities in liver, kidney and heart extracts increased by about 30% in response to the high protein diet, while they increased three-fold in regenerating liver. 4. Low activities were detected in skeletal muscles and in erythrocytes of all the species studied.     

Vertebrate ancient opsin photopigment spectra and the avian photoperiodic response

In mammals, photoreception is restricted to cones, rods and a subset of retinal ganglion cells. By contrast, non-mammalian vertebrates possess many extraocular photoreceptors but in many cases the role of these photoreceptors and their underlying photopigments is unknown. In birds, deep brain photoreceptors have been shown to sense photic changes in daylength (photoperiod) and mediate seasonal reproduction. Nonetheless, the specific identity of the opsin photopigment 'sensor' involved has remained elusive. Previously, we showed that vertebrate ancient (VA) opsin is expressed in avian hypothalamic neurons and forms a photosensitive molecule. However, a direct functional link between VA opsin and the regulation of seasonal biology was absent. Here, we report the in vivo and in vitro absorption spectra (λ(max) = ~490 nm) for chicken VA photopigments. Furthermore, the spectral sensitivity of these photopigments match the peak absorbance of the avian photoperiodic response (λ(max) = 492 nm) and permits maximum photon capture within the restricted light environment of the hypothalamus. Such a correspondence argues strongly that VA opsin plays a key role in regulating seasonal reproduction in birds.     

The effects of macrophage-derived cytokines on lipid metabolism in chicken (Gallus domesticus) hepatocytes and adipocytes

1. The effects of avian and mammalian cytokines on avian lipid metabolism were compared using cultured chicken hepatocytes and adipocytes. 2. Conditioned medium from an endotoxin-stimulated chicken macrophage cell line was used as a source of chicken cytokines. Incubation of chicken adipocytes with conditioned medium greatly decreased their lipoprotein lipase activity. 3. Inhibition of lipoprotein lipase synthesis in similar experiments in mammals has been attributed to the effects of TNF-alpha and/or IL-1, but recombinant human TNF-alpha and IL-1 had no effect on lipoprotein lipase activity in chicken adipocytes. 4. Conditioned medium from chicken macrophages produced a 2-fold increase in lipogenesis in chicken adipocytes but had no effect on lipogenesis in chicken hepatocytes. 5. The results point to major differences between mammals and birds in the way that lipid metabolism responds to cytokines and provide further evidence that mammalian cytokines are ineffective in birds.     

The compositional patterns of the avian genomes and their evolutionary implications

The compositional distributions of large (main-band) DNA fragments from eight birds belonging to eight different orders (including both paleognathous and neognathous species) are very broad and extremely close to each other. These findings, which are paralleled by the compositional similarity of homologous coding sequences and their codon positions, support the idea that birds are a monophyletic group.The compositional distribution of third-codon positions of genes from chicken, the only avian species for which a relatively large number of coding sequences is known, is very broad and bimodal, the minor GC-richer peak reaching 100% GC. The very high compositional heterogeneity of avian genomes is accompanied (as in the case of mammalian genomes) by a very high speciation rate compared to cold-blooded vertebrates which are characterized by genomes that are much less heterogeneous. The higher GC levels attained by avian compared to mammalian genomes might be correlated with the higher body temperature (41–43°C) of birds compared to mammals (37°C).A comparison of GC levels of coding sequences and codon positions from man and chicken revealed very close average GC levels and standard deviations. Homologous coding sequences and codon positions from man and chicken showed a surprisingly high degree of compositional similarity which was, however, higher for GC-poor than for GC-rich sequences. This indicates that GC-poor isochores of warm-blooded vertebrates reflect the composition of the isochores of the genome of the common reptilian ancestor of mammals and birds, which underwent only a small compositional change at the transition from cold- to warm-blooded vertebrates. In contrast, the GC-rich isochores of birds and mammals are the result of large compositional changes at the same evolutionary transition, where were in part different in the two classes of warm-blooded vertebrates.Correspondence to: G. Bernaadi     

Organization of telomere sequences in birds: evidence for arrays of extreme length and for in vivo shortening

Telomeres are the specialized ends of chromosomes consisting of highly conserved repeat (5'-TTAGGG-3')(n) sequences. Lack of information regarding the existence of an in vivo telomere clock function in birds, conflicting data regarding telomere array length in the chicken model, and the paucity of molecular telomere information for other avian species led us to study telomere array organization within and among 18 species and subspecies of birds. Most of the species contained between 2% and 4% telomere sequence per diploid genome. Arrays spanning 0.5-10 kb (Class I) and 10-40 kb (Class II) were observed in all of the species studied. Extremely long arrays, ranging from hundreds of kilobases to 1-2 Mb (Class III) were observed in all except two raptor species, the northern goshawk and American bald eagle. In chicken, there was evidence for shortening of the Class II arrays in vivo, based on intraindividual comparisons of somatic versus germline tissues in birds of different ages; terminally differentiated erythrocyte arrays were, on average, 2.3 kb shorter than sperm (germline) arrays. This study provides the first evidence for the existence of telomere arrays significantly larger than have been described for any vertebrate species to date and for developmentally programmed in vivo telomere shortening in the Aves taxa. The novel finding of megabase-sized telomere arrays may be an important feature of avian karyotypes that contain a large number of very small genetic units, the microchromosomes.     

Molecular evolutionary genomics of birds

Insight into the molecular evolution of birds has been offered by the steady accumulation of avian DNA sequence data, recently culminating in the first draft sequence of an avian genome, that of chicken. By studying avian molecular evolution we can learn about adaptations and phenotypic evolution in birds, and also gain an understanding of the similarities and differences between mammalian and avian genomes. In both these lineages, there is pronounced isochore structure with highly variable GC content. However, while mammalian isochores are decaying, they are maintained in the chicken lineage, which is consistent with a biased gene conversion model where the high and variable recombination rate of birds reinforces heterogeneity in GC. In Galliformes, GC is positively correlated with the rate of nucleotide substitution; the mean neutral mutation rate is 0.12-0.15% at each site per million years but this estimate comes with significant local variation in the rate of mutation. Comparative genomics reveals lower d(N)/d(S) ratios on micro- compared to macrochromosomes, possibly due to population genetic effects or a non-random distribution of genes with respect to chromosome size. A non-random genomic distribution is shown by genes with sex-biased expression, with male-biased genes over-represented and female-biased genes under-represented on the Z chromosome. A strong effect of selection is evident on the non-recombining W chromosome with high d(N)/d(S) ratios and limited polymorphism. Nucleotide diversity in chicken is estimated at 4-5 x 10(-3) which might be seen as surprisingly high given presumed bottlenecks during domestication, but is lower than that recently observed in several natural populations of other species. Several important aspects of the molecular evolutionary process of birds remain to be understood and it can be anticipated that the upcoming genome sequence of a second bird species, the zebra finch, as well as the integration of data on gene expression, shall further advance our knowledge of avian evolution.     

Molecular mechanism of the photoperiodic response of gonads in birds and mammals

Appropriate timing of various seasonal processes is crucial to the survival and reproductive success of animals living in temperate regions. When seasonally breeding animals are subjected to annual changes in day length, dramatic changes in neuroendocrine-gonadal activity take place. However, the molecular mechanism underlying the photoperiodic response of gonads remains unknown for all living organisms. It is well known that a circadian clock is somehow involved in the regulation of photoperiodism. Recently, rhythmic expression of circadian clock genes was observed in the mediobasal hypothalamus (MBH) of Japanese quail. The MBH is believed to be the center for photoperiodism. In addition, long-day-induced hormone conversion of the prohormone thyroxine (T(4)) to the bioactive triiodothyronine (T(3)) by deiodinase in the MBH has been proven to be important to the photoperiodic response of the gonads. Although the regulating mechanism for the photoperiodic response of gonads in birds and mammals has long been considered to be quite different, the long-day-induced expression of the deiodinase gene in the hamster hypothalamus suggests the existence of a conserved regulatory mechanism in avian and mammalian photoperiodism.     

Buoyancy under Control: Underwater Locomotor Performance in a Deep Diving Seabird Suggests Respiratory Strategies for Reducing Foraging Effort

Background

Because they have air stored in many body compartments, diving seabirds are expected to exhibit efficient behavioural strategies for reducing costs related to buoyancy control. We study the underwater locomotor activity of a deep-diving species from the Cormorant family (Kerguelen shag) and report locomotor adjustments to the change of buoyancy with depth.

Methodology/Principal Findings

Using accelerometers, we show that during both the descent and ascent phases of dives, shags modelled their acceleration and stroking activity on the natural variation of buoyancy with depth. For example, during the descent phase, birds increased swim speed with depth. But in parallel, and with a decay constant similar to the one in the equation explaining the decrease of buoyancy with depth, they decreased foot-stroke frequency exponentially, a behaviour that enables birds to reduce oxygen consumption. During ascent, birds also reduced locomotor cost by ascending passively. We considered the depth at which they started gliding as a proxy to their depth of neutral buoyancy. This depth increased with maximum dive depth. As an explanation for this, we propose that shags adjust their buoyancy to depth by varying the amount of respiratory air they dive with.

Conclusions/Significance

Calculations based on known values of stored body oxygen volumes and on deep-diving metabolic rates in avian divers suggest that the variations of volume of respiratory oxygen associated with a respiration mediated buoyancy control only influence aerobic dive duration moderately. Therefore, we propose that an advantage in cormorants - as in other families of diving seabirds - of respiratory air volume adjustment upon diving could be related less to increasing time of submergence, through an increased volume of body oxygen stores, than to reducing the locomotor costs of buoyancy control.     

Effects of sexual maturation and Salmonella infection on the expression of Toll-like receptors in the chicken vagina

Toll-like receptors (TLRs) are a critical component of the innate immune response in many vertebrates, including avian species. The recent findings of chicken TLRs (cTLRs) expression in ovarian follicles and in the chicken ovary in vivo, as well as the changes in their expression in response to lipopolysaccharide or Salmonella enteritidis (SE) infection, have broad implications for reproductive physiology and for the prevention of transmission of zoonotic diseases to humans through the consumption of contaminated poultry eggs. Because the main route of egg contamination is from infection of the oviduct and mainly from the vagina, the aim of this study was to investigate the expression of the ten cTLRs identified to date in the chicken oviduct in vivo, to determine whether sexual maturation affects their mRNA abundance and to investigate whether SE infection alters the expression of TLRs in the chicken vagina. RNA was extracted from the vagina of healthy prepubertal, sexually mature and aged birds, and from sexually mature and aged SE infected birds. RT-PCR analysis revealed that all types of cTLRs apart from TLR1-1 were expressed in the vagina of sexually mature birds. Quantitative real-time PCR analysis revealed that the mRNA abundance of TLR2-1, 2-2 and 4 differ with respect to sexual maturation in the chicken vagina. SE infection resulted in a significant induction of TLR5 and 15 in the vagina of sexually mature birds, and in a significant induction of TLR2-1, 4 and 15 in the vagina of aged birds, while a significant down-regulation was observed for TLR7 in the vagina of sexually mature birds. These findings suggest that a TLR mediated immune response mechanism exists in the chicken vagina, playing a crucial role in preventing microbial pathogens from being incorporated into newly forming eggs.     

The role of humoral factors in the regression of leukemia in chickens as measured by in vitro colony formation

Leukemic myeloblasts induced by avian myeloblastosis virus in the chicken formed small compact (type II) colonies in semi-solid agar medium. Normal yolk sac cells from 12-day old embryos formed large diffuse (type I) colonies under the same conditions. Type I colony formation (but not type II) was strictly dependent upon the presence in the medium of a colony stimulating factor (CSF) present in fresh chicken serum or conditioned medium. Serum CSF levels were determined for normal, leukemic, and birds which had spontaneously regressed from myeloblastic leukemia. When type I colony formation was used as the assay, serum CSF levels of leukemic birds were found to be significantly lower than levels in either normal or regressed birds. When the same sera were tested for their ability to induce type II colonies, leukemic birds demonstrated a significantly higher CSF level than either normal or regressed sera. Regressed chickens had serum CSF levels similar to normal birds.     

Characterization of the first growth hormone gene sequence for a passerine bird--the pied flycatcher (Ficedula hypoleuca).

While the growth hormone (GH) gene has been characterized in a broad range of vertebrates, surprisingly little is known about this gene in birds. In order to extend knowledge of the GH gene in avian species and non-domestic species, the pied flycatcher (Ficedula hypoleuca) GH gene has been sequenced in this study. The overall average pairwise sequence divergence level was 0.08 among all available avian sequences and 0.27 among other taxa. However, the overall genetic organization of the gene is quite conserved. The similarity of the GH gene sequence of pied flycatchers with those of chicken and duck suggests that the rapid bursts of molecular evolution observed in mammalian and fish GH have not occurred during the divergence of passerine and non-passerine birds.     

The effects of locomotion on the structural characteristics of avian limb bones

Despite the wide range of locomotor adaptations in birds, little detailed attention has been given to the relationships between the quantitative structural characteristics of avian limb bones and bird behaviour. Possible differences in forelimb relative to hindlimb strength across species have been especially neglected. We generated cross‐sectional, geometric data from peripheral quantitative computed tomography scans of the humerus and femur of 127 avian skeletons, representing 15 species of extant birds in 13 families. The sample includes terrestrial runners, arboreal perchers, hindlimb‐propelled divers, forelimb‐propelled divers and dynamic soarers. The hindlimb‐propelled diving class includes a recently flightless island form. Our results demonstrate that locomotor dynamics can be differentiated in most cases based on cross‐sectional properties, and that structural proportions are often more informative than bone length proportions for determining behaviour and locomotion. Recently flightless forms, for example, are more easily distinguished using structural ratios than using length ratios. A proper phylogenetic context is important for correctly interpreting structural characteristics, especially for recently flightless forms. Some of the most extreme adaptations to mechanical loading are seen in aquatic forms. Penguins have forelimbs adapted to very high loads. Aquatic species differ from non‐aquatic species on the basis of relative cortical thickness. The combination of bone structural strength and relative cortical area of the humerus successfully differentiates all of our locomotor groups. The methods used in this study are highly applicable to fossil taxa, for which morphology is known but behaviour is not. The use of bone structural characteristics is particularly useful in palaeontology not only because it generates strong signals for many locomotor guilds, but also because analysing such traits does not require knowledge of body mass, which can be difficult to estimate reliably for fossil taxa. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 153 , 601–624.