A unique isolate of beak and feather disease virus isolated from budgerigars (Melopsittacus undulatus) in South Africa

Beak and feather disease virus (BFDV), the causative agent of psittacine beak and feather disease (PBFD) infects psittaciformes worldwide. We provide an annotated sequence record of three full-length unique genomes of BFDV isolates from budgerigars (Melopsittacus undulatus) from a breeding farm in South Africa. The isolates share >99% nucleotide sequence identity with each other and ~96% nucleotide sequence identity to two recent isolates (Melopsittacus undulatus) from Thailand but only between 91. 6 and 86. 6% identity with all other full-length BFDV sequences. Maximum-likelihood analysis and recombination analysis suggest that the South African budgerigar BFDV isolates are unique to budgerigars, are non-recombinant in origin, and represent a new genotype of BFDV. © 2010 Springer-Verlag.

Ultraviolet vision, fluorescence and mate choice in a parrot, the budgerigar Melopsittacus undulatus

As in many parrots, the plumage of the budgerigar Melopsittacus undulatus reflects near-ultraviolet (UVA) wavelengths (300-400 nm) and exhibits UVA-induced fluorescence. However, there have, to our knowledge, been no tests of whether the yellow fluorescence observed under intense UVA illumination has any role in signalling. Four experiments were carried out on wild-type budgerigars, where the presence and absence of UV reflectance and fluorescence were manipulated using filters. Few studies have attempted to separate the contribution of UV reflectance to plumage hue as opposed to brightness or distinguish between a role in sexual as opposed to social preferences. However, our first experiments show that not only do females consistently prefer UV-reflecting males, but also that the observed preferences are due to removal of UV affecting the perceived hue rather than brightness. Furthermore, we found no effect Of the light environment on male response to females, suggesting that the female preferences relate to plumage colour per se. Whilst UV reflectance appears important in heterosexual choice by, females, it has no detectable influence on same-sex association preferences. The results from the second series of experiments suggest that enhancement of the budgerigar's yellow coloration through fluorescence has no effect on male attractiveness. However, the fluorescent plumage may play a role in signalling by virtue of the fact that it absorbs UVA and so increases contrast with nearby UV-reflecting plumage. Our study provides convincing evidence that UV reflectances can play a role in mate choice in non-passerines, but no evidence that the yellow fluorescence observed under UVA illumination is itself important as a signal.

Relevance of Budgerigars (Melopsittacus undulatus) in Experimental Epidemiology of Newcastle Disease.

This study was carried out to clarify the real role that was played by the budgerigars (Melopsittacus undulatus) in the epidemiological plan, under the perspective of its being an infection source of the Newcastle Disease Virus (NDV). For this, the study used Specific-Pathogen-Free chicks (SPF) that were housed with budgerigars that were inoculated with a pathogenic strain (velogenic viscerotropic) of NDV (EID5o =10815/0.1 mL) pathogenic to chickens, by the ocular-nasal via. Each group was composed by 10 SPF chicks and 5 budgerigars. After 5 days of the inoculation of the budgerigars with NDV, SPF chicks were put together with each group of budgerigars, so that there was a direct contact between both species. Cloaca) swabs and blood samples were collected in both species (budgerigars and SPF chicks) after 13 and 19 days post-challenge, respectively, for genome viral excretion by Reverse Transcription Polymerase Chain Reaction (RTPCR) and antibody's search by the inhibition of hemmaglutination test (HI). Budgerigars did not demonstrate any clinical signs of Newcastle Disease (ND). They were refractory to the clinical disease with the NDV. However, antibody titres from inhibition of Hemagglutination (HI) test were detected 9 and 21 days after challenge. Therefore, it was demonstrated the state of carrier of NDV in this species. In SPF chicks allocated with infected budgerigars, NDV genome was detected 13 and 19 days after challenge. Thus, the transmission of the pathogenic virus from the budgerigars to SPF chicks that were housed together was evident until 19 days of the experimental infection with this pathogen. This reveals the importance of the budgerigars from the epidemiological point of view as a potential source of infection of the NDV to commercial chickens that could be raised near this species.

Morphology of the vas deferens of the budgerigar (Melopsittacus undulatus)

A morphological study of the budgerigar vas deferens was conducted to demonstrate the electron-microscopic features of its epithelial lining. The analysis showed that the vas deferens of the budgerigar was found to be of a tubular and serpentine structure, continuous with the epididymal region and lined with stereo ciliated pseudostratified epithelium, which contained folds projecting into the tubular lumen and a characteristic brush border. The epithelium consists of ciliated and non-ciliated cells with different electron densities. Ciliated cells were characterized by two morphologically distinct configurations: some cells were columnar and other ciliated cells were longer, thinner and dark. Non-ciliated cells showed apical cytoplasmic expansions, which projected into the tubular lumen as protrusions.

Clinical and immunological aspects of newcastle disease vaccination in budgerigars (Melopsittacus undulatus)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Investigation of the state of virus carrier of newcastle disease in budgerigars (melopsittacus undulatus)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Estudo de parâmetros clínicos e imunitários da vacinação contra a doença de Newcastle e sua importância epidemiológica em periquitosaustralianos (Melopsittacus undulatus)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Hybrid error correction and de novo assembly of single-molecule sequencing reads.

Single-molecule sequencing instruments can generate multikilobase sequences with the potential to greatly improve genome and transcriptome assembly. However, the error rates of single-molecule reads are high, which has limited their use thus far to resequencing bacteria. To address this limitation, we introduce a correction algorithm and assembly strategy that uses short, high-fidelity sequences to correct the error in single-molecule sequences. We demonstrate the utility of this approach on reads generated by a PacBio RS instrument from phage, prokaryotic and eukaryotic whole genomes, including the previously unsequenced genome of the parrot Melopsittacus undulatus, as well as for RNA-Seq reads of the corn (Zea mays) transcriptome. Our long-read correction achieves >99.9% base-call accuracy, leading to substantially better assemblies than current sequencing strategies: in the best example, the median contig size was quintupled relative to high-coverage, second-generation assemblies. Greater gains are predicted if read lengths continue to increase, including the prospect of single-contig bacterial chromosome assembly.

High-coverage sequencing and annotated assemblies of the budgerigar genome.

BACKGROUND: Parrots belong to a group of behaviorally advanced vertebrates and have an advanced ability of vocal learning relative to other vocal-learning birds. They can imitate human speech, synchronize their body movements to a rhythmic beat, and understand complex concepts of referential meaning to sounds. However, little is known about the genetics of these traits. Elucidating the genetic bases would require whole genome sequencing and a robust assembly of a parrot genome. FINDINGS: We present a genomic resource for the budgerigar, an Australian Parakeet (Melopsittacus undulatus) -- the most widely studied parrot species in neuroscience and behavior. We present genomic sequence data that includes over 300× raw read coverage from multiple sequencing technologies and chromosome optical maps from a single male animal. The reads and optical maps were used to create three hybrid assemblies representing some of the largest genomic scaffolds to date for a bird; two of which were annotated based on similarities to reference sets of non-redundant human, zebra finch and chicken proteins, and budgerigar transcriptome sequence assemblies. The sequence reads for this project were in part generated and used for both the Assemblathon 2 competition and the first de novo assembly of a giga-scale vertebrate genome utilizing PacBio single-molecule sequencing. CONCLUSIONS: Across several quality metrics, these budgerigar assemblies are comparable to or better than the chicken and zebra finch genome assemblies built from traditional Sanger sequencing reads, and are sufficient to analyze regions that are difficult to sequence and assemble, including those not yet assembled in prior bird genomes, and promoter regions of genes differentially regulated in vocal learning brain regions. This work provides valuable data and material for genome technology development and for investigating the genomics of complex behavioral traits.

Plasma cholinesterase characteristics in native Australian birds : significance for monitoring avian species for pesticide exposure

Cholinesterase-inhibiting pesticides are applied throughout Australia to control agricultural pests. Blood plasma cholinesterase (ChE) activity is a sensitive indicator of exposure to organophosphorus insecticides in vertebrates. To aid biomonitoring and provide reference data for wildlife pesticide-risk assessment, plasma acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) activities were characterised in nine species of native bird: King Quails (Excalfactoria chinensis), Budgerigars (Melopsittacus undulatus), White-plumed Honeyeaters (Lichenostomas penicillatus), Yellow-throated Miners (Manorina flavigula), Willie Wagtails (Rhipidura leucophrys), Australian Reed-Warblers (Acrocephalus australis), Brown Songlarks (Cincloramphus cruralis), Double-barred Finches (Taeniopygia bichenovii) and Australasian Pipits (Anthus novaeseelandiae). Plasma ChE activities in all species were within the range of most other avian species and all but one contained AChE and BChE; no AChE was present in King Quail, which has not previously been reported for any species. The lowest detectable plasma AChE activity was 0.10 μmol min^–1 mL^–1 in Budgerigars and the highest was 0.86 μmol min^–1 mL^–1 in Australian Reed-Warblers. BChE in the plasma ranged from 0.37 μmol min^–1 mL^–1 in Double-barred Finches to 0.90 μmol min^–1 mL^–1 in White-plumed Honeyeaters and Australian Reed-Warblers. The lowest proportion of AChE was found in Budgerigars (12.8%) and highest in Willie Wagtails (67.8%). No differences were detected in ChE activity at any time of day in Budgerigars and Zebra Finches (Taeniopygia guttata), although there was a significant difference in all ChE activity between seasons in Zebra Finches.

The role of ultraviolet-A reflectance and ultraviolet-A-induced fluorescence in budgerigar mate choice

Many parrots have plumage that either reflects strongly in the ultraviolet-A (UVA) waveband, between 315-400 nm, or exhibits UVA-induced fluorescence. Previous experimental work on budgerigars (Melopsittacus undulatus) suggests that UVA reflectance plays a role in mate choice, as in other diurnal birds, but evidence for fluorescent cues playing a role is unconvincing. Here we report two experiments on budgerigars, designed to determine whether fluorescent cues play a role in signalling when UVA reflectances are absent, an approach which separates removal of UVA reflectance from removal of fluorescence. First, we determined whether the choices of different females are correlated under these treatment conditions. Secondly, we investigated female preferences for fluorescing and non-fluorescing males when UVA reflections are absent, to determine whether the yellow emissions of fluorescence are playing a role in mate choice. Results from experiment 1 do not suggest that females agree on which males are attractive when UVA reflectances are absent, with only half of the subjects choosing the same male. Neither did different females make the same choices in experiment 2. This lack of agreement provides further evidence that UVA reflectances from males play an important role in female choice in this species. Experiment 2 provides no evidence to suggest that UVA-induced fluorescence plays a role in mate choice. Overall, our study supports previous findings showing that UVA reflectance plays a role in sexual signalling in this species, but provides no evidence to suggest the same for fluorescence when UVA reflectances are absent.

Little Ravens 'Corvus mellori' hunt, kill and eat individuals of two species of shorebird

The Little Raven Corvus mellori is an omnivore that occasionally eats small birds. Most birds taken are thought to be eaten as carrion, though several records exist of ravens hunting and killing Budgerigars Melopsittacus undulates and a Spotted Turtle-Dove Streptopelia chinensis (Higgins et al. 2006). Both cases of bird depredation record Little Ravens attacking from above and stabbing prey to death with their beaks. Here, we report a pair of Little Ravens hunting, killing and eating a lone Sharp-tailed Sandpiper Calidris acuminita at Cheetham Wetlands, near Melbourne, Victoria (37° 53' 56"S, 144° 47' 33"E; 420 ha; see Antos et al. 2007 for a description). We also report an event which strongly implies they hunted and ate an adult Red-capped Plover Charadrius ruficapillus, and observations of hunting and eating eggs and chicks.