Leafy spurge genomics: A model to investigate development, stress responses, and invasiveness of a noxious weed

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

Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: 10/3/2014
Publication Date: 12/11/2015
Citation: Horvath, D., Anderson, J.V., Chao, W.S., Foley, M.E., Dogramaci, M. 2015. Leafy spurge genomics: A model to investigate development, stress responses, and invasiveness of a noxious weed. In: Sablok, G., Ueno, S., Varotto, C., Kumar, S., Kuo, J. editors. Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches. Switzerland: Springer International Publishing. p. 63-78. https://doi.org/10.1007/978-3-319-17157-9.
DOI: https://doi.org/10.1007/978-3-319-17157-9

Interpretive Summary: This is a review paper on the historical development of leafy spurge as a model invasive weed. The paper discusses the development of cDNA and genomic libraries (collections of DNA fragments) from leafy spurge and the development of genomic based tools including a large number of sequences from clones of genes that are actively being transcribed into RNA. Also presented is how these clones were used to develop microarrays (a tool for investigating which genes might be turned on or off following any given treatment or developmental process). This paper goes on to discuss how these microarrays have been used to identify genes and processes that are involved in bud dormancy, invasiveness, and stress responses of leafy spurge. The paper also discusses recent advances in developing a whole genome sequences form leafy spurge using newer sequencing technologies and suggests ways these genomic sequences will assist in further use of leafy spurge to investigate various aspects of leafy spurge biology and ecology.

Technical Abstract: Leafy spurge is wild flower native to Europe that has become an invasive perennial weed in the northern great plains of the US and Canada. Leafy spurge primarily infests range and recreation lands and costs U.S. land managers millions dollars annually. In its invaded range, leafy spurge can form vast monocultures that significantly impact native flora and fauna and has been attributed to reduced populations of endangered species such as the prairie fringed orchid. Leafy spurge has remarkable plasticity and can persist under environmental extremes – primarily due to the formation of hundreds of underground adventitious buds that can form on its extensive and deep root system. We have developed genomics-based tools to assist our investigations related to vegetative production from these underground buds, as well as its responses to stress, and the potential mechanisms leading to the invasiveness of leafy spurge. Towards these ends, we have utilized Sanger-based sequencing to develop EST-databases from leafy spurge and cassava (a related species) transcriptomes, and developed ~23,000 element cDNA microarrays representing all of the unigenes identified in these databases. Additionally, numerous cDNA libraries and genomic libraries have been developed including bacterial artificial chromosome libraries useful for identifying and characterizing promoters of differentially-expressed genes. Finally, to enhance our ability to identify promoter sequences and transcription factors involved in vegetative production, stress responses, and invasiveness, we have incorporated next generation sequencing approaches to fully sequence the leafy spurge genome. Using global transcriptome profiles, next generation sequencing, bioinformatics programs has provided insights into molecular mechanisms and regulatory pathways that make leafy spurge a particularly invasive and difficult weed to control.