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Slow Evolution for Turtle Genome

NEW YORK (GenomeWeb News) – The turtle genome appears to be evolving at an exceptionally slow rate, according to a genome sequencing study appearing online today in Genome Biology.

An international team led by investigators at Washington University and the University of California at Los Angeles sequenced a freshwater turtle species called the western painted turtle, Chrysemys picta bellii, which is widespread in North America.

By analyzing the new genome assembly and comparing it with sequences from other vertebrates, the group got a refined view of turtle relationships with other vertebrates, revealing just how closely turtles cluster with birds and crocodilians — members of the so-called archosaur lineage.

The researchers also unearthed genetic clues that seem to explain some of the specific adaptations found in turtles — from their long life spans to their impressive low temperature and low oxygen tolerance.

Despite the advent of these and other adaptations, though, findings from the study indicate that genome evolution is proceeding at a plodding pace in the turtle lineage, with sequence changes appearing at a fraction of the rate described for humans.

"Turtle genomes evolve at about one-third the rate seen in humans," senior author Richard Wilson, director of the Genome Institute at Washington University, and co-authors noted, "and roughly one-fifth the rate of the fastest-evolving python lineage."

Although the western painted turtle has been well studied in other respects, its genome sequence — along with those of other turtle species — had remained uncharacterized until now, leaving many unanswered questions with regard to the genetics of turtles' many unusual features and adaptations.

"Besides their distinctive shell," authors of the new study explained, "turtles have extremely long lifespans, are often reproductively active at very advanced ages, often determine sex by the temperature at which eggs incubate, are the most anoxia-tolerant tetrapods known, and have the capacity in some species to freeze nearly solid, thaw, and survive with negligible tissue damage."

To explore such adaptations, the team set its sights on the western painted turtle genome. Collaborators at Washington University's Genome Institute did whole-genome shotgun sequencing on genomic DNA from a western painted turtle originating in southern Washington.

Using these shotgun sequences — together with BAC end reads and Illumina reads, which were used for error correction — the researchers produced a 2.59 billion base genome assembly that appears to cover some 93 percent of the western painted turtle genome at a depth of 18-fold, on average.

Within this assembly, the team tracked down 21,796 predicted protein-coding genes as well as transposable elements belonging to almost 80 DNA transposon or RNA-related retrotransposon lineages.

To help annotate the sequence and assess gene expression patterns, investigators also did Roche 454 sequencing on transcripts from several turtle tissues.

Comparisons between the turtle genome and sequences from other sequenced vertebrates suggest that the turtle clusters phylogenetically near the archosaur group.

Such comparisons also made it possible to pick out gene sets that have expanded or contracted in the turtle lineage. For example, the team found evidence suggesting the turtle's lack of teeth is a consequence of pseudogenization affecting some of the same genes that have been lost or degraded in the bird genome.

On the other hand, researchers found that the turtle genome houses expansions to several gene families. Despite the notoriously sluggish adaptive immune function described for turtles in the past, for instance, the turtle genome contains expanded sets of genes involved in innate or adaptive immune system function.

In general, though, the analyses suggest that many turtle traits and adaptations are a consequence of regulatory changes affecting genes shared with other vertebrates, study authors explained. "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."

When they focused on turtle adaptation to low oxygen — using transcriptome data to discern gene expression shifts following anoxia — study authors uncovered 19 genes showing more pronounced expression in brain tissue after exposure to low oxygen. They also identified 23 genes with higher-than-usual expression in the turtle's heart under oxygen-compromised conditions.

Experiments on hatchlings exposed to cold temperatures, meanwhile, hinted that at least one microRNA — miR-29b — might help turtles bounce back after freezing.

With the turtle genome and transcriptome sequences in hand, researchers are optimistic that they will continue to tease apart the genetic patterns contributing to key aspects of turtle biology and adaptation. They also pointed to the possibility of using genetic information on the conservation front to protect endangered turtle and tortoise species.

"The challenge, for comparative biology and conservation alike, is to preserve the remaining diversity of living turtles as we continue to unravel their secrets of success," the study's authors argued.