Genome of Western Painted Turtle
Another interesting genome paper came out in Genome Biology.
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 overrepresented.
To get an idea about how long it takes between proposal and final publication, this genome sequencing was recommended along with Latimeria chalumnae (‘living fossil’) genome in 2006 under ‘evolution of human proteome’ theme. This 2006 white paper at NCBI presents the big picture on their biological significance.
Based on whatever evidence we found from web, the turtle genome was sequenced around 2009-2010 using Sanger+NGS. We asked the authors on the total cost of sequencing so that our readers get an idea about how dramatic the recent drop in cost of genome sequencing/assembly had been, but did not receive any reply yet. We also noticed that the authors did very comprehensive work on genome analysis, and were surprised that the paper got published in Genome Biology unlike many other comparable genome papers published over the last few months. However, speaking of directly comparable papers, Genome Biology also covered alligator genome paper last year.
