Cyber-infrastructure Supporting Fungal and Oomycete Phylogenetics and Genomics

Open Access
Author:
Park, Bongsoo
Graduate Program:
Integrative Biosciences
Degree:
Doctor of Philosophy
Document Type:
Dissertation
Date of Defense:
December 14, 2012
Committee Members:
  • Seogchan Kang, Dissertation Advisor
  • Istvan Albert, Committee Member
  • David Michael Geiser, Committee Member
  • John Edward Carlson, Committee Member
Keywords:
  • Fungi
  • Oomycete
  • Phylogenetics
  • Genomics
  • Database
Abstract:
The rapid increase in genomic and phylogenetic data from fungi and Oomycetes poses a number of challenges to data preservation, dissemination, and utilization. We need comprehensive Cyber-infrastructure supporting genomics and phylogenetics to help fungal biologists and plant pathologists reap the benefits of such data. Advances in sequencing technology also have changed the methods of addressing fundamental research questions about fungal and Oomycete biology. Among pathogenic eukaryotic organisms, Fusarium and Phytophthora are targeted mainly due to their practical importance in agricultural and environmental health and sustainability and/or human health. Phytophthora Database (PD; http://www.phytophthoradb.org/), an online platform, was developed to support accurate and rapid identification of newly isolated Phytophthora and to help characterize and catalog the diversity and evolutionary relationships within the genus. Its sequence database has grown from sequences of 1-9 loci from ~1,500 isolates (representing 82 species) in 2008 to sequences of 1-12 loci from ~2,500 isolates (>130 species). At the same time, the Cyber-infrastructure for Fusarium (CiF; http://www.fusariumdb.org/) was designed to support archiving and utilization of rapidly accumulating data and knowledge for genus Fusarium. The CiF consists of FUSARIUM-ID, Fusarium Comparative Genomics Platform (FCGP), and Fusarium Community Platform (FCP). The FUSARIUM-ID archives phylogenetic marker sequences from most known species along with information associated with characterized isolates and supports strain identification. FCGP provides a comprehensive resource for Fusarium genomics, including multiple functional database and visualization tools including a genome browser and phylogenetic tree viewer. Based on the constructed genomics and phylogenetics platforms, analysis of the species boundaries in the Fusarium oxysporum species complex has been addressed. Species boundaries can be recognized using different species concepts such as the morphological, biological, and phylogenetic species concepts. All these concepts are compatible with the evolutionary species concept. In particular, the phylogenetic species concept has been widely accepted and applied to species recognition in fungi and the genus Fusarium. Previously, phylogenetic hypotheses concerning this species complex were inferred using two loci in various strains of F. oxysporum, but a well-resolved species tree has yet to be defined. In this study, high-resolution phylogenetic analyses were conducted using 40 genomic regions evenly distributed across F. oxysporum chromosomes. Using the sequenced genomes of members of the F. oxysporum species complex, 40 multi-locus markers were selected and used to build phylogenetic trees individually and collectively. Individually constructed phylogenies for 24 loci show the same pattern of topology as the collectively constructed 40 multi-locus phylogeny; however, phylogenies for 12 loci show different topology in phylogenetic trees. Also, four individually-constructed phylogenies show very low bootstrap support on most branches, creating un-resolved trees. Analysis of polymorphic sites at the 40 multi-locus regions shows 89.3% similarity between the Fusarium oxysporum species complex and Fusarium verticillioides, and 96.3% similarity among members of the Fusarium oxysporum species complex. We noticed two distinct groups within the Fusarium oxysporum species complex, however, and Fusarium oxysporum strain II5 (Fusarium oxysporum f.sp cubense) was generally separated from 10 other Fusarium oxysporum species complex strains, suggesting it might be another group of the F. oxysporum species complex. This ongoing study demonstrated the utility of the data and tools in the Fusarium Comparative Genomics Platform (FCGP) in conducting comprehensive phylogenetic analyses.