Friday, February 21, 2014

Analyzing the RNA differences between queens and workers

Over the past 30 or so years, biology has entered a second Linnaean revolution, in which our understanding of the relationships among living things has been radically re-organized, in this case driven by DNA and RNA sequencing data. Carl Woese and the identification of Archaea as a third kingdom of life is probably the most dramatic re-interpretation of the tree of life, and I would say that the bounty of viruses and non-culturable prokatyotes in metagenomc samples will eventually contribute a lot of detail.
The new information flow has been enabled by improvements in the sensitivity and throughput of next-generation DNA sequencing. Newer studies can be geared to either detect miniscule amounts of genetic material, or to capture rare variants through deeply analysis. 
This same technology can be used to investigate the relationship between genotype and phenotype. The ability to retrieve sequence from a small, focused sample makes it possible to understand the behavior of genomic material during the adpotion of alternative phenotypes. In  a paper in Molecular Ecology, Feldmeyer et al. have used this same
A queen and workers of Temnothorax ants. 
sequencing technology to analyze RNA expression differences among castes of ants in a colony. A major challenge in evolutionary biology, dating back to Darwin, is to explain the evolution of insect castes, particularly sterile workers, who contribute to the colony without possibility of direct descendants. Since they share so much of their genome, the dramatic phenotypic differences between queens and workers must arise chiefly through different gene expression, which in turn must be influenced by the food the individual receives as a larva, signals within the colony, and the environment. Social insects thus provide a great opportunity to explore the relationship between many copies of a stable genome and the range of phenotypes it can generate.
In the January issue of Molecular Ecology, Feldmeyer et al studied the ants Temnothorax longispinosus, with the overall goal of identifying RNAs which differed among the queens and various worker types. This common woodland species was chosen because some workers maintain the ability to develop ovaries and reproduce if the queen is removed. Thus the genes associated with reproductive ability would be present in a gradient from sterile workers, to fertile workers, to queens.
In the study, RNA was prepared from insects within a single colony—thus, closely related—with RNA prepared separately for each caste. Deep sequencing analysis of the RNA yielded in a very large number of previously undescribed RNA sequences. Furthermore,, the prevalence of completely novel genes was much higher  in workers, suggesting that the RNA repertoire of the worker is more derived, cladistically speaking, than the corresponding repertoire used by  the queen.

My take is that this kind of work is still in its infancy, analogous to the first naturalists to travel into the rain forests, gathering and annotating species. The next Voyage of the Beagle may be happening, with a synthesis to appear decade from now.

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