We like turtles (‘s genomes)

June 2013, Volume 45 No 6 pp 579-714

Jonathan the zombie isn’t the only one who likes turtles. These heroes-in-a-half-shell adorn the cover of the current Nature Genetics, as two species of turtle have just joined the Genome Club (Wang et al. 2013; paper’s free!).

This definitely not one of those genome sequencing studies alluded to recently by John Hawks, that’s “too boring for journals.” Wang and colleagues didn’t just sequence the genomes of soft-shell and green sea turtles ‘just cuz.’ Rather, they use these copious data to address several questions, most interesting of which relate to embryonic development.

First, analysis of gene expression during embryonic development supports what the authors refer to as a “nested hourglass model” of development and gene expression. The hourglass shape serves as analogy for variation across related species over developmental time: there is great variation (in both morphology and gene expression) in the earliest stages of development, then species are more similar at a given developmental stage (the “phylotypic period”), and thereafter variation increases again. This phylotypic period (which I don’t believe is unanimously agreed upon) is arguably the most conserved developmental stage in evolution – all vertebrates, for example, simply must pass through this stage to become good vertebrates. Plus, several studies have found that evolutionarily younger genes tend to be expressed before and after this amorphous phylotypic stage, while more ancient genes are expressed during this time. As the authors state

“According to the recently supported developmental hourglass model … the changes underlying major adult morphological evolution occurred primarily in the developmental stages after the period … that serves as the basic vertebrate body plan.”

So the turtle data generally support this model. However they mention a nested hourglass, because they found evidence of an additional bottleneck, a second hourglass, of conserved gene expression when comparing turtles with their close relative the chicken. In other words, “the most conserved developmental stage changes depending on distantly related species are that are being compared.” So since turtles and chickens are more closely related to one another than to many other vertebrates, they might share another conserved developmental stage. Incidentally, both also make for good soup.

Wang and colleagues also looked for genes relating to some of the unique aspects of turtle anatomy, examining what parts of the genome seem to get kicked up after the phylotypic period. It doesn’t take a trained eye to see that these animals are kinda weird in that their bodies are encased in a flagrant shell, with a carapace on top and plastron on the bottom. Now it turns out this carapace is actually formed from what should, in most other vertebrates, become vertebrae and ribs. So by studying the earliest development of these structures, Wang and colleagues could examine the molecular bases of this carapacial deviation.

Fig. 5 from Wang et al., showing Wnt protein expression in turtle embryos. In a), only Wnt5a is expressed in the ‘carapacial ridge’ during its earliest development. Fig c) is a cross-section indicated in b) showing this expression. NT=neural tube, NC=  notochord. The scale bar is 0.5 mm. Tiny!
The authors were able to identify over 200 miRNAs, and implicate the signalling protein Wnt5a, in the development of the “carapacial ridge” (see the arrows in fig. c above), the embryonic precursors to the carapace. Interestingly, Wnt5a is involved in the development of limb buds (e.g, those big purple circles in the red square in a) above). The precise role of Wnt5a and the miRNAs in turtle shell development has yet to be determined, so this study really sets the stage for future investigations.
ResearchBlogging.orgSo there you have it, a pretty cool paper combining genomics with developmental biology, among other things. And so to close, for your bemusement, here’s a video I shot last week at the awesome Kansas City Zoo, of a turtle attempting to make embryos like in the figure above (sorry for the poor quality). Hang in there, little buddy!
They like tuhtles!
Wang Z, Pascual-Anaya J, Zadissa A, Li W, Niimura Y, Huang Z, Li C, White S, Xiong Z, Fang D, Wang B, Ming Y, Chen Y, Zheng Y, Kuraku S, Pignatelli M, Herrero J, Beal K, Nozawa M, Li Q, Wang J, Zhang H, Yu L, Shigenobu S, Wang J, Liu J, Flicek P, Searle S, Wang J, Kuratani S, Yin Y, Aken B, Zhang G, & Irie N (2013). The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nature genetics, 45 (6), 701-6 PMID: 23624526
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