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.

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.

Ocorrência de Megabacteriose em Periquitos Autralianos, Canários e Agapornis na Região de Ribeirão Preto- Estado de São Paulo - Brasil

Este trabalho tem como objetivo relatar a ocorrência de um agente etiológico, denominado na Europa, Australia e EUA como megabactéria, observado em estômago de pequenas aves (canários belgas, agapornis e periquitos australianos), provenientes da região de Ribeirão Preto, Estado de São Paulo/SP. As necropsias de 64 aves silvestres (4 periquitos australianos, 12 agapornis e 48 canários), realizadas no perído de 1994 a 1997, foram analisadas, constatando-se em 56% dos casos a presença de estruturas filiformes, acidofílicas sob coloração Giemsa, gram positivas, existentes no muco do proventrículo, descritas na literatura como megabactérias. Foram testados diversos tipos de meios de cultura para reprodução in vitro deste microrganismo. Foram ainda comparadas as dimensões (comprimento e largura) dessa bactéria obtida apartir do esfregaço fresco de muco proventricular e da megabactéria proveniente de cultivo in vitro. Também foram listados os principais achados macroscópicos do animais portadores desta bactéria.

Characterization of an unidentified Sarcocystis falcatula-like parasite from the South American opossum, Didelphis albiventris from Brazil

An unidentified isolate of a Sarcocystis falcatula-like parasite was obtained from the lungs of budgerigars (Melopsittacus undulatus) fed sporocysts from a naturally-infected South American opossum, Didelphis albiventris from Brazil. Four captive budgerigars fed sporocysts from the opossum intestine died of acute sarcocystosis 8, 10, and 12 days after oral inoculation (DAI); one budgerigar was killed 12 DAI when it was lethargic. Schizonts and merozoites found in the lungs of the budgerigars reacted mildly with polyclonal S. falcatula antibody. The parasite was isolated in equine kidney cell cultures inoculated with lung tissue from a budgerigar that was killed 12 DAI. Two budgerigars inoculated subcutaneously with 100,000 culture-derived S. falcatula merozoites developed acute sarcocystosis and S. falcatula-like schizonts were found in their lungs 15 and 16 DAI. Four budgerigars kept as unfed controls in the same environment remained free of Sarcocystis infection. The parasite underwent schizogony in African green monkey kidney cells and bovine turbinate cells. Merozoites divided by endopolygeny, often leaving a residual body. Polymerase chain reaction studies using primers JNB33/JNB54 and Hinf I and Dra I digestion indicated that the isolate was not S. falcatula. Results of this study indicated that the South American opossum, D. albiventris, is a definitive host for yet another S. falcatula-like parasite.

Leveduras patogênicas em fezes de aves de cativeiro: relação fenotípica e genotípica entre os isolados

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

A genomic perspective on a new bacterial genus and species from the Alcaligenaceae family, Basilea psittacipulmonis

BACKGROUND A novel Gram-negative, non-haemolytic, non-motile, rod-shaped bacterium was discovered in the lungs of a dead parakeet (Melopsittacus undulatus) that was kept in captivity in a petshop in Basel, Switzerland. The organism is described with a chemotaxonomic profile and the nearly complete genome sequence obtained through the assembly of short sequence reads. RESULTS Genome sequence analysis and characterization of respiratory quinones, fatty acids, polar lipids, and biochemical phenotype is presented here. Comparison of gene sequences revealed that the most similar species is Pelistega europaea, with BLAST identities of only 93% to the 16S rDNA gene, 76% identity to the rpoB gene, and a similar GC content (~43%) as the organism isolated from the parakeet, DSM 24701 (40%). The closest full genome sequences are those of Bordetella spp. and Taylorella spp. High-throughput sequencing reads from the Illumina-Solexa platform were assembled with the Edena de novo assembler to form 195 contigs comprising the ~2 Mb genome. Genome annotation with RAST, construction of phylogenetic trees with the 16S rDNA (rrs) gene sequence and the rpoB gene, and phylogenetic placement using other highly conserved marker genes with ML Tree all suggest that the bacterial species belongs to the Alcaligenaceae family. Analysis of samples from cages with healthy parakeets suggested that the newly discovered bacterial species is not widespread in parakeet living quarters. CONCLUSIONS Classification of this organism in the current taxonomy system requires the formation of a new genus and species. We designate the new genus Basilea and the new species psittacipulmonis. The type strain of Basilea psittacipulmonis is DSM 24701 (= CIP 110308 T, 16S rDNA gene sequence Genbank accession number JX412111 and GI 406042063).

Modelling oil droplet absorption spectra and spectral sensitivities of bird cone photoreceptors

Birds have four spectrally distinct types of single cones that they use for colour vision. It is often desirable to be able to model the spectral sensitivities of the different cone types, which vary considerably between species. However, although there are several mathematical models available for describing the spectral absorption of visual pigments, there is no model describing the spectral absorption of the coloured oil droplets found in three of the four single cone types. In this paper, we describe such a model and illustrate its use in estimating the spectral sensitivities of single cones. Furthermore, we show that the spectral locations of the wavelengths of maximum absorbance (lambda(max)) of the short- (SWS), medium- (MWS) and long- (LWS) wavelength-sensitive visual pigments and the cut-off wavelengths (lambda(cut)) of their respective C-, Y- and R-type oil droplets can be predicted from the lambda(max) of the ultraviolet- (UVS)/violet- ( VS) sensitive visual pigment.