Computational Biology
@ Comenius University in Bratislava

H. Bradley Shaffer et al.. The western painted turtle genome, a model for the evolution of extremephysiological adaptations in a slowly evolving lineage. Genome Biology, 14(3):R28. 2013.

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Abstract:

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 inverted question mark 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 
overrepresented. 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 inverted question
marks 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.