Development and characterization of genomics resources for leafy spurge: A model perennial weed for functional genomics studies

Authors: Anderson, James; Horvath, David; Chao, Wun; Foley, Michael

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 10/31/2006
Publication Date: 12/13/2006
Citation: Anderson, J.V., Horvath, D.P., Chao, W.S., Foley, M.E. 2007. Development and characterization of genomics resources for leafy spurge: A model perennial weed for functional genomics studies. [Abstract]Plant and Animal Genome Conference. W433.

Interpretive Summary: Genomics approaches to study weed biology have so far been limited to a small number of research groups within the weed science community. In most cases, the resources needed for functional genomics studies within desired species do not yet exist. Recently, a commitment was made that allowed the development and characterization of genomic resources for the invasive perennial weed leafy spurge (Euphorbia esula L.). Tissues from leafy spurge, grown under various environmental conditions, were utilized to develop an Expressed Sequence Tag (EST)-database, which is an important resource for studying functional genomics. The EST-database includes 45,314 ESTs with an average read length of 671 nucleotides that represents 19,015 unigenes. Bioinformatics analysis indicated that 74.7% of the unigenes are similar to other known proteins and 15.5 % are novel to leafy spurge. Functional classifications assigned to leafy spurge sequences were proportional to genes identified in the model plant Arabidopsis, with the exception of unclassified or unknowns, and transposable elements which were significantly reduced in leafy spurge. Although the goal of generating these genomics resources is to construct microarrays for functional genomics studies, the use of these resources have already led to proposed new models for signal transduction pathways involved in growth, development, and dormancy in vegetative propagules of perennials.

Technical Abstract: High throughput genomics approaches to study weed biology have so far been limited to a small number of research groups within the weed science community. In most cases, these groups have relied on heterologous approaches, since resources needed for functional genomics studies within desired species do not yet exist. Recently, a commitment was made that allowed the development and characterization of genomic resources for the invasive perennial weed leafy spurge (Euphorbia esula L.). A normalized cDNA library constructed from tissues grown under various environmental conditions was used to develop an Expressed Sequence Tag (EST)-database for leafy spurge. The use of periodic subtractions to reduce redundancy, and a sequencing success rate of 88% yielded 45,314 ESTs with an average read length of 671 nucleotides. These ESTs were assembled into 23,472 unique sequences representing 19,015 unigenes (10,293 clusters and 8,722 singletons). Blast similarity searches identified 18,186 matches, of which 14,205 were non-redundant. Bioinformatics analysis indicated that 74.7% of the unigenes are similar to other known proteins and 15.5 % are novel to leafy spurge. Functional classifications assigned to leafy spurge unique sequences were proportional to functional classifications for genes of Arabidopsis, with the exception of unclassified or unknowns, and transposable elements which were significantly reduced in leafy spurge. Although the goal of generating these genomics resources is to construct high-density microarrays for functional genomics studies, the use of these resources have already led to proposed new models for signal transduction pathways involved in growth, development, and dormancy in vegetative propagules of perennials.