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United States Department of Agriculture

Agricultural Research Service

Title: Minimum Phylogenetic Coverage: An Additional Criterion to Guide the Selection of Microbial Pathogens for Initial Genomic Sequencing Efforts

Author
item Goodwin, Stephen

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 2, 2004
Publication Date: July 25, 2004
Citation: Goodwin, S.B. 2004. Minimum phylogenetic coverage: an additional criterion to guide the selection of microbial pathogens for initial genomic sequencing efforts. Phytopathology. 94(8):800-804.

Interpretive Summary: The scientific community has made a persuasive case to increase funding for genomic sequencing of microbial plant pathogens, and a number of objective criteria were developed to guide the selection of sequencing targets. However, this task still is complicated for the fungi and Oomycetes, which are extremely diverse evolutionarily. Lack of a target number of species to be sequenced makes the effort seem somewhat unfocused, which may hinder efforts to increase funding. These deficiencies could be overcome by consideration of evolutionary relationships, yet most molecular biologists and many plant pathologists are not well versed in fungal evolution. To solve this problem, a cluster analysis of conserved DNA sequences was performed for all fungi and Oomycetes that have been proposed for genomic sequencing. The analysis revealed that many of the species proposed previously are very closely related, while other important groups are not represented at all. A minimum phylogenetic coverage (MPC) of the fungi and Oomycetes that have been proposed for genomic sequencing can be achieved by choosing one representative from each of the 12 major clusters of the evolutionary tree. A second round of 14 species could be sequenced to cover the major sub-branches within each of the 12 major clusters. Molecular biologists and plant pathologists could use this approach to prioritize the list of species for sequencing. MPC also would assure participation by the largest number of scientists as most would have access to a sequenced genome from a close relative of their organism of interest. MPC provides a logical criterion for prioritizing fungi and Oomycetes for genomic sequencing and could serve as a rallying point to unify molecular biologists, mycologists and plant pathologists towards a common goal.

Technical Abstract: The scientific community has made a persuasive case to increase funding for genomic sequencing of microbial plant pathogens, and a number of objective criteria were developed to guide the selection of sequencing targets. However, this task still is complicated for the fungi and Oomycetes, which are extremely diverse evolutionarily. Lack of a definite target number of organisms to be sequenced makes the effort seem somewhat unfocused, and this perception may hinder efforts to increase the level of funding. These problems can be overcome by consideration of phylogenetic relationships. A phylogenetic analysis of 18S ribosomal RNA sequences revealed that many of the species proposed for genomic sequencing are very closely related. By choosing one representative from each of the major clusters on the 18S tree, a minimum phylogenetic coverage (MPC) of the fungi and oomycetes that have been proposed for genomic sequencing can be achieved by including seven Ascomycetes, four Basidiomycetes, and one Oomycete. A second round of 14 species could be sequenced to cover the major sub-branches within each of the 12 major clusters. This approach defines a tangible goal for genomic sequencing that could be used to lobby for additional funding. MPC also would assure support and participation by the largest number of plant pathologists as most would have access to a sequenced genome from a close relative of their organism of interest. Allocating funds for this effort might be achieved best through a competitive bidding process among sequencing centers rather than the traditional grants programs. MPC provides a logical criterion for prioritizing fungi and Oomycetes for genomic sequencing that could serve as a rallying point to unify plant pathologists towards achieving a common goal.

Last Modified: 12/19/2014
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