The draft genome of the pest tephritid fruit fly Bactrocera tryoni: resources for the genomic analysis of hybridising species

Background

The tephritid fruit flies include a number of economically important pests of horticulture, with a large accumulated body of research on their biology and control. Amongst the Tephritidae, the genus Bactrocera, containing over 400 species, presents various species groups of potential utility for genetic studies of speciation, behaviour or pest control. In Australia, there exists a triad of closely-related, sympatric Bactrocera species which do not mate in the wild but which, despite distinct morphologies and behaviours, can be force-mated in the laboratory to produce fertile hybrid offspring. To exploit the opportunities offered by genomics, such as the efficient identification of genetic loci central to pest behaviour and to the earliest stages of speciation, investigators require genomic resources for future investigations.

Results

We produced a draft de novo genome assembly of Australia’s major tephritid pest species, Bactrocera tryoni. The male genome (650 -700 Mbp) includes approximately 150Mb of interspersed repetitive DNA sequences and 60Mb of satellite DNA. Assessment using conserved core eukaryotic sequences indicated 98% completeness. Over 16,000 MAKER-derived gene models showed a large degree of overlap with other Dipteran reference genomes. The sequence of the ribosomal RNA transcribed unit was also determined. Unscaffolded assemblies of B. neohumeralis and B. jarvisi were then produced; comparison with B. tryoni showed that the species are more closely related than any Drosophila species pair. The similarity of the genomes was exploited to identify 4924 potentially diagnostic indels between the species, all of which occur in non-coding regions.

Conclusions

This first draft B. tryoni genome resembles other dipteran genomes in terms of size and putative coding sequences. For all three species included in this study, we have identified a comprehensive set of non-redundant repetitive sequences, including the ribosomal RNA unit, and have quantified the major satellite DNA families. These genetic resources will facilitate the further investigations of genetic mechanisms responsible for the behavioural and morphological differences between these three species and other tephritids. We have also shown how whole genome sequence data can be used to generate simple diagnostic tests between very closely-related species where only one of the species is scaffolded.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1153) contains supplementary material, which is available to authorized users.     

Bacterial Distribution in the Lungs of Children with Protracted Bacterial Bronchitis

Objectives

Flexible bronchoscopy with bronchoalveolar lavage (FB-BAL) is increasingly used for the microbiological confirmation of protracted bacterial bronchitis (PBB) in children with a chronic wet cough. At our centre, when performing FB-BAL for microbiological diagnosis we sample 6 lobes (including lingula) as this is known to increase the rate of culture positive procedures in children with cystic fibrosis. We investigated if this is also the case in children with PBB.

Methods

We undertook a retrospective case note review of 50 children investigated for suspected PBB between May 2011 and November 2013.

Results

The median (IQR) age at bronchoscopy was 2.9 (1.7–4.4) years and the median (IQR) duration of cough was 11 (8.0–14) months. Positive cultures were obtained from 41/50 (82%) and 16 (39%) of these patients isolated ≥2 organisms. The commonest organisms isolated were Haemophilus influenzae (25 patients), Moraxella catarrhalis (14 patients), Staphylococcus aureus (11 patients) and Streptococcus pneumoniae (8 patients). If only one lobe had been sampled (as per the European Respiratory Society guidance) 17 different organisms would have been missed in 15 patients, 8 of whom would have had no organism cultured at all. The FB-BAL culture results led to an antibiotic other than co-amoxiclav being prescribed in 17/41 (41%) patients.

Conclusions

Bacterial distribution in the lungs of children with PBB is heterogeneous and organisms may therefore be missed if only one lobe is sampled at FB-BAL. Positive FB-BAL results are useful in children with PBB and can influence treatment.     

Avian cholera,post‐hatching survival and selection on hatch characteristics in a long‐lived bird,the common eider Somateria mollisima

Infectious diseases can have dramatic impacts on animal population dynamics, but how they influence vital rates remains understudied. We took advantage of the appearance of an avian cholera epizootic in an arctic colony of common eiders Somateria mollissima to study variation in juvenile survival and selection on hatch characteristics in relation to this highly infectious disease. Avian cholera is one of the most important infectious diseases affecting wild birds and is thought to primarily affect adult survival. Here, we show that avian cholera was associated with a 90% decline in duckling survival, leading to almost zero recruitment. Before the cholera outbreak, there was significant stabilizing selection on hatching date and significant positive directional selection on hatching mass. During cholera outbreaks, selection on hatch characteristics was no longer significant. These results were based on a low sample of surviving ducklings in cholera years, but suggested that date and mass at hatching did no longer affect duckling survival in the presence of cholera. These effects of avian cholera on post‐hatching survival were likely not only the consequence of the disease per se, but also a consequence of an increase in predation rates that followed the emergence of avian cholera. Our results emphasize the dramatic direct and indirect impacts that infectious disease can have on vital rates, and thus population dynamics.     

Factors affecting the dispersal of large‐scale releases of the Queensland fruit fly,Bactrocera tryoni

This study investigated two factors potentially affecting the spatial distribution of Queensland fruit fly Bactrocera tryoni (Froggatt) after release from a single point. First, the effect of age at release was investigated using a single cohort of 205 000 males from a mass‐rearing strain used for sterile insect releases. Approximately half were released as immature males and the remainder as sexually mature males (1 week later). Males were collected over 3 weeks from a grid of 135 traps, each containing a pheromone/insecticide bait, positioned between 4 and 500 m from the release point. Variation in the distribution of fly density around the release point was assessed by regressing trapped fly counts against distance. Unexpectedly, no significant differences were found in the spatial distribution of the flies. Second, the effect of inbreeding on spatial distribution was investigated using replicated simultaneous releases of two strains of B. tryoni. One strain was the existing (inbred) mass‐rearing strain that has been selected for high productivity in a mass‐rearing facility. The second strain was deliberately outbred but also selected for high productivity. Almost 100 000 males of each strain were released over the two experiments. Regression of trappings against distance differed significantly between strains in only one of five releases, but in all cases the outbred strain had a greater dispersal distance. As our trapping grid was not regular but contained gaps of up to 100 m, a small preliminary experiment investigated whether flies move faster along tree rows or across open fields. At distances up to 100 m, we found no detectable difference in fly distributions. These results are primarily relevant to the large‐scale point releases carried out as part of an existing B. tryoni sterile insect programme and are discussed in that context.     

Biochemical basis of muscular fatigue associated with repetitious contractions of skeletal muscle

The decline in force generating capabilities of skeletal muscle associated with prolonged, repetitive low force producing contractions does have a biochemical basis. It is our view that an alteration in neuromuscular transmission results in an uncoupling of excitation-contraction via disturbances in Ca2+ imbalance, an uncoupling of energy utilization and production may result, which affect a favourable cellular environment for the initiation of myofilament degradation. The myofilament dissolution may be the last stage in this fatigue process and associated with only extreme conditions of muscle use.     

Mutations in the Sup-38 Gene of Caenorhabditis Elegans Suppress Muscle-Attachment Defects in Unc-52 Mutants

Mutations in the unc-52 locus of Caenorhabditis elegans have been classified into three different groups based on their complex pattern of complementation. These mutations result in progressive paralysis (class 1 mutations) or in lethality (class 2 and 3 mutations). The paralysis exhibited by animals carrying class 1 mutations is caused by disruption of the myofilaments at their points of attachment to the cell membrane in the body wall muscle cells. We have determined that mutations of this class also have an effect on the somatic gonad, and this may be due to a similar disruption in the myoepithelial sheath cells of the uterus, or in the uterine muscle cells. Mutations that suppress the body wall muscle defects of the class 1 unc-52 mutations have been isolated, and they define a new locus, sup-38. Only the muscle disorganization of the Unc-52 mutants is suppressed; the gonad abnormalities are not, and the suppressors do not rescue the lethal phenotype of the class 2 and class 3 mutations. The suppressor mutations on their own exhibit a variable degree of gonad and muscle disorganization. Putative null sup-38 mutations cause maternal-effect lethality which is rescued by a wild-type copy of the locus in the zygote. These loss-of-function mutations have no effect on the body wall muscle structure.     

New Routes for Aerobic Biodegradation of Dimethylsulfoniopropionate

Dimethylsulfoniopropionate (DMSP), an osmolyte in marine plants, is biodegraded by cleavage of dimethyl sulfide (DMS) or by demethylation to 3-methiolpropionate (MMPA) and 3-mercaptopropionate (MPA). Sequential demethylation has been observed only with anoxic slurries of coastal sediments. Bacteria that grew aerobically on MMPA and DMSP were isolated from marine environments and phytoplankton cultures. Enrichments with DMSP selected for bacteria that generated DMS, whereas MMPA enrichments selected organisms that produced methanethiol (CH₃SH) from either DMSP or MMPA. A bacterium isolated on MMPA grew on MMPA and DMSP, but rapid production of CH₃SH from DMSP occurred only with DMSP-grown cells. Low levels of MPA accumulated during growth on MMPA, indicating demethylation as well as demethiolation of MMPA. The alternative routes for DMSP biodegradation via MMPA probably impact on net DMS fluxes to the marine atmosphere.     

Apoptosis: A Functional Paradigm for Programmed Plant Cell Death Induced by a Host-Selective Phytotoxin and Invoked during Development

The host-selective AAL toxins secreted by Alternaria alternata f sp lycopersici are primary chemical determinants in the Alternaria stem canker disease of tomato. The AAL toxins are members of a new class of sphinganine analog mycotoxins that cause cell death in both animals and plants. Here, we report detection of stereotypic hallmarks of apoptosis during cell death induced by these toxins in tomato. DNA ladders were observed during cell death in toxin-treated tomato protoplasts and leaflets. The intensity of the DNA ladders was enhanced by Ca2+ and inhibited by Zn2+. The progressive delineation of fragmented DNA into distinct bodies, coincident with the appearance of DNA ladders, also was observed during death of toxin-treated tomato protoplasts. In situ analysis of cells dying during development in both onion root caps and tomato leaf tracheary elements revealed DNA fragmentation localized to the dying cells as well as the additional formation of apoptotic-like bodies in sloughing root cap cells. We conclude that the fundamental elements of apoptosis, as characterized in animals, are conserved in plants. The apoptotic process may be expressed during some developmental transitions and is the functional process by which symptomatic lesions are formed in the Alternaria stem canker disease of tomato. Sphinganine analog mycotoxins may be used to characterize further signaling pathways leading to apoptosis in plants.