The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage

BACKGROUND

We describe the genome of the western painted turtle, Chrysemys picta bellii, one of the most widespread, abundant, and well-studied turtles. We place the genome into a comparative evolutionary context, and focus on genomic features associated with tooth loss, immune function, longevity, sex differentiation and determination, and the species' physiological capacities to withstand extreme anoxia and tissue freezing.

RESULTS

Our phylogenetic analyses confirm that turtles are the sister group to living archosaurs, and demonstrate an extraordinarily slow rate of sequence evolution in the painted turtle. The ability of the painted turtle to withstand complete anoxia and partial freezing appears to be associated with common vertebrate gene networks, and we identify candidate genes for future functional analyses. Tooth loss shares a common pattern of pseudogenization and degradation of tooth-specific genes with birds, although the rate of accumulation of mutations is much slower in the painted turtle. Genes associated with sex differentiation generally reflect phylogeny rather than convergence in sex determination functionality. Among gene families that demonstrate exceptional expansions or show signatures of strong natural selection, immune function and musculoskeletal patterning genes are consistently over-represented.

CONCLUSIONS

Our comparative genomic analyses indicate that common vertebrate regulatory networks, some of which have analogs in human diseases, are often involved in the western painted turtle's extraordinary physiological capacities. As these regulatory pathways are analyzed at the functional level, the painted turtle may offer important insights into the management of a number of human health disorders.

A vertebrate case study of the quality of assemblies derived from next-generation sequences

The unparalleled efficiency of next-generation sequencing (NGS) has prompted widespread adoption, but significant problems remain in the use of NGS data for whole genome assembly. We explore the advantages and disadvantages of chicken genome assemblies generated using a variety of sequencing and assembly methodologies. NGS assemblies are equivalent in some ways to a Sanger-based assembly yet deficient in others. Nonetheless, these assemblies are sufficient for the identification of the majority of genes and can reveal novel sequences when compared to existing assembly references.

Mammographic screening: measurement of the cost in a population based programme in Victoria, Australia

STUDY OBJECTIVES

To estimate the cost per woman participating in a mammographic screening programme, and to describe methods for measuring costs.

DESIGN

Expenditure, resource usage, and throughput were monitored over a 12 month period. Unit costs for each phase of the screening process were estimated and linked with the probabilities of each screening outcome to obtain the cost per woman screened and the cost per breast cancer detected.

SETTING

A pilot, population based Australian programme offering free two-view mammographic screening.

PARTICIPANTS

A total of 5986 women aged 50-69 years who lived in the target area, were listed on the electoral roll, had no previous breast cancer, and attended the programme.

RESULTS

Unit costs for recruitment, screening, and recall mammography were $17.54, $60.04, and $175.54, respectively. The costs of clinical assessment for women with subsequent clear, benign, malignant (palpable), and malignant (impalpable) diagnoses were $173.71, $527.29, $436.62, and $567.22, respectively. The cost per woman screened was $117.70, and the cost per breast cancer detected was $11,550.

CONCLUSIONS

The cost per woman screened is a key variable in assessment of the cost effectiveness of mammographic screening, and is likely to vary between health care settings. Its measurement is justified if decisions about health care services are to be based on cost effectiveness criteria.