Comparative Genomics:

I am interested in establishing high resolution comparative maps between rice, maize and other cereals; investigating gene organization in completed plant genomes (rice, Arabidopsis, poplar and ultimately maize); investigating gene annotation and alternative splicing; and, identifying and characterizing rapidly evolving genes in maize. High resolution comparative maps between cereal genomes allow the information gained in one species to be leveraged in another. For example, the relationships between cereal genomes allows phenotypic information (QTL) mapped in rice to be tentatively localized in maize, and this can influence candidate gene approaches and map based cloning of loci affecting agronomic traits, general plant biology, speciation, and the evolution of cereal genomes. As maize genomic sequence becomes available more comprehensive and higher resolution comparative genomic analysis can be undertaken. Examining maize and rice synteny in the context of the available phenotypic data will identify genes in co-linear segments that are associated with agronomically important traits, and these can be used to identify similar sequences (ESTs, GSSs) from less understood crop genomes for marker development.

Comparative genomics at a much finer level (small genomic segments or single genes) will identify differences in gene structure such as added/deleted exons, large insertions/deletions within introns, or new genomic locations from rearrangement. I am interested in investigating how such changes come about, and what are their developmental and evolutionary consequences? Comparative genomics provides many examples of structural differences and experimental biology (transgenics, RNAi, tDNA insertion, tilling and phenotype analysis) can be used to investigate functional consequences.

Gene Annotation and gene structure:

Maize genome sequence is the knowledge infrastructure for the next generation of plant molecular genetics and crop improvement, and will provide the foundation for improving maize and other cereal crops. A broad understanding of the genes present in maize would provide the identities, and eventually the map positions, of many of the genes responsible for controlling agronomically important traits. However, the products of ongoing and future maize sequencing projects are collections of large contiguous nucleotide segments for which there is no a priori knowledge of content or function.  Therefore, high throughput computational tools that can accurately identify genes within maize genomic sequence are absolutely necessary for annotating and understanding the maize genome.  In collaboration with Dr. Michael Brent at Washington University (http://www.cs.wustl.edu/~brent/), I am attempting to improve gene prediction in maize by identifying a comprehensive "training set" of complete and annotated maize gene models; and, using these to optimize TWINSCAN to accurately identify maize genes in un-annotated maize genome sequence.  TWINSCAN is a next-generation gene discovery tool developed by Michael Brent.  Originally designed for human gene prediction, it improves gene detection by integrating traditional probability models like those underlying GENSCAN and FGENESH with information from the alignments between two genomes.  The essential idea is that functional sequences, such as protein coding regions and splice sites, show different patterns of evolutionary conservation than sequences under little selective pressure, such as the central regions of introns.  We are attempting to improve gene prediction in maize by identifying a comprehensive "training set" of complete and annotated maize gene models that will be used to optimize TWINSCAN to accurately identify maize genes in un-annotated maize genome sequence. The training set will consist of EST validated maize gene models collected from both public and proprietary (Monsanto) sources. Ultimately, maize trained TWINSCAN will be thoroughly benchmarked, a selection of maize predictions will be wet-bench verified, and available pubic maize genomic sequence will be re-annotated with TWINSCAN. 

Alternative Splicing:

While alternative splicing is extensive in humans and other higher animal genomes, it is less common in plants. I am interested in examining the frequency of splicing in maize as well as the frequency of different types of splicing (skipped exon, alternative 5', alternative 3' etc.). This may address the evolution of splicing mechanisms in plants; and, identify sequence signals associated with alternatively spliced exons that could be used to improve alternatively spliced gene prediction. It has been suggested that alternative splicing creates transcriptome diversification, which may account for diversity among organisms with relatively similar gene sets (i.e. Mammals). Identifying alternatively spliced genes in maize will allow us to address whether or not spliced genes (and the variants) are conserved among plant species, and if not, this may identify genes involved in speciation.

Rapidly evolving genes:

Genes within a genome evolve at different rates. Highly conserved genes evolve very slowly while some others evolve rapidly. For example, genes that play roles in disease and viral resistance tend to evolve at much faster rates than do genes involved in information storage or transfer (RNA or DNA processing). In addition, genes that are rapidly evolving are likely to be associated with adaptive divergence between species. I am attempting to identify rapidly evolving genes in maize using comparative genomics, and these will be used to investigate functional aspects such as tissue localization, expression profiles, and their diversity across maize accessions, which may indicate whether any of these have been selected for during maize domestication. It is possible that germplasm accessions have different and potentially superior alleles at such positively selected loci, and these may provide alleles for crop improvement.

Cereal crop improvement for developing countries:

I am a member of a scientific team consisting of representatives of the Syngenta Foundation, ILRI, ICRASAT and Cornell University assembled to advise on sorghum and millet improvement projects in participation with the activities of the 'Biosciences East and Central Africa' (BECA) research institution.  My main interests lie in developing gene associated markers for sorhgum and millet to aid in marker assisted breeding programs.

Bacterial Genomics:

I collaborate on a  project to generate, annotate and analyze the genome sequence of two entomopathogenic Xenorhabdus bacteria. These are gram-negative bacterium belonging to the Enterobacteriaceae family, and represent one of the few emerging models for understanding both beneficial (mutualistic) and detrimental (pathogenic) relationships. Xenorhabdus are mutualists and colonize the intestine of a non-feeding stage of Steinernema nematodes, and the nematode is the vector that shelters the bacteria from the competitive soil environment and shuttles Xenorhabdus into insect hosts.  The bacteria functions as a potent pathogen that participates in the killing of diverse insects, which serve as the nutrient source for the development and reproduction of the nematode. Approximately 100 laboratories in 60 countries study entomopathogenic nematodes (EPNs) and their bacterial symbionts with interests ranging from molecular genetics to biological control. The EPN-bacteria complex (EPNB) is used as a biological control agent against dozens of insect pests in agriculture, horticulture and backyard gardens.

In adapting to this specialized life style, X. nematophila has evolved functions necessary to be both a symbiont, providing beneficial functions for one animal (the nematode) and a pathogen, causing death of another (the insect).  This combination makes it an excellent model to understand both types of relationships.  Furthermore, the symbiotic interaction between S. carpocapsae and X. nematophila is species-specific; other species of Xenorhabdus cannot colonize S. carpocapsae, although they can colonize their own Steinernematid hosts. Therefore, the S. carpocapsae-X. nematophila model system can be further exploited as a model to understand host-range specificity.  This phenomenon is not well understood and has implications in important agricultural and medical issues, such as the effective use of probiotic treatments and prevention of pathogen transmission from animals to humans.

The life cycle of Xenorhabdus and its nematode host depends on the protection of the insect cadaver against invasion by soil microorganisms, and Xenorhabdus spp. produce numerous antibiotic and antimycotic compounds that suppress contamination and putrefaction of the insect.  Xenorhabdus produces many other useful products including insecticidal, nematicidal, antiulcer, antineoplastic, antiviral, and insect repellent.  Xenorhabdus produces numerous exoenzymes including lipases, lecithinases, proteases, hemolysins and DNases that degrade macromolecules to provide a nutrient source for bacterial and nematode growth or function as virulence factors.  The major secreted protease of X. nematophila is a 60-kDa serine protease, while X. nematophila secretes two distinct hemolytic activities which are active against insect hemocytes.