Biocomplexity and the Genome Perspective

High-throughput DNA sequencing and parallel gene expression assay technologies shift the rate-limiting step of obtaining molecular biological insight from experimental data generation to data analysis [1,6,67,68]. As entire genomes are sequenced, an interesting phenomenon recurs: about half of newly-sequenced genes are of unknown function [2,58,66,82,102,113]. Organisms have evolved a diversity of responses to fluctuating environments, including mechanisms to alleviate abiotic stress and to regulate biotic interactions. Some of the mysterious genes are probably involved in buffering organisms to their changing environment via dynamic responses. Functional genomics studies exploit high-throughput techniques to understand how organisms respond to and interact with their surroundings, but are limited in that they generally employ those genes whose function has previously been characterized.

The ability to study genomes from a global perspective provides unprecedented challenges and opportunities. The challenges include identifying a minimal viable genome [61,85] and developing a ``periodic table of genes'' [67,68]. An equally provocative goal is to catalog all genes in a model plant genome and their functions by 2010 AD [7,31]. To synthesize a coherent understanding of this information, biologists can apply a ``systems view of biology'' [7,131] or biological complexity as the evolution of a complex adaptive system that emerged from interactions among many different individuals [35], and resulted in irreversible evolutionary transitions [78]. At another level (mundane but pragmatic), biologists can deploy computational methods to analyze the volumes of data that result from high-throughput technologies, and facilitate the design of laboratory experiments [6,131].

Making sense of biocomplexity suggests distinct challenges. To understand how organisms interact with and discriminate between beneficial and antagonistic symbionts, the challenge is to understand the biochemical function of newly-sequenced genes. To consider how coevolution results in interdependent species interactions requires understanding the molecular evolutionary processes that produced them. The ultimate goal is synthetic: to understand better the mechanisms of interactions between symbionts as a result of coevolutionary adaptation [91,116].

This contribution develops and tests several techniques to interpret data obtained from expressed sequence tag (EST) sequencing experiments, and thus relieve the analytic bottleneck associated with high-throughput sequencing and expression array technologies. The focus is on the mutualistic association between Medicago truncatula, a model legume [33], and an endosymbiont, the arbuscular mycorrhizal (AM) Zygomycete fungi from the order Glomales [3,63,97].