A Phylogenetic Framework for the Tylenchida
Taxa Needed For This Project
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This database (as proposed) is part of a USDA NRI CSREES funded project to create a phylogenetic framework for tylenchid nematodes, and serves as a clearinghouse for morphological and molecular evolutionary information concerning the Tylenchid branch of the Nematode Tree of Life.
The database will be a front-end implementation of the NemaToL database (nematol.unh.edu) specifically geared to agriculture-oriented users interested in plant parasitic and insect parasitic tylenchid nematodes. Directly linked to the dedicated NemaToL database, the BYU database will offer user-friendly search functions that allow rapid access to nematode voucher video images, DNA sequences, phylogenetic analyses and trees, and data associated with the voucher specimens, such as ecological and taxonomic information.
Here is a sample archival voucher video. The voucher is linked to its DNA and permanent slide museum specimen accession numbers/collection information, and is accessible through searchable databases via this web site. Permanent slide collections are curated at the Nebraska State Museum (H. W. Manter Laboratory of Parasitology) and the UC Riverside Nematode Collection. Frozen tissues will be stored at the UC Davis Nematode Collection and the HWML. Additional permanent slide material will be deposited in the USDA Nematode Collection.
U. S. agriculture is economically threatened by nematode plant pathogens including many of the more than 2000 species of Infraorder Tylenchida. This immediate, growing threat is exacerbated by loss of nematicides and increasing global trade/travel, that broadens distribution of exotic nematodes. The result includes regulatory concerns and urgency for novel approaches to nematode management. Most promising of these approaches is exploitation of genomics to target molecular aspects of nematode pathogen biology, leading to more sophisticated engineering of plant resistance via GMO hosts, and to the ability to confound expression of specific nematode parasitism genes. However, these revolutionary approaches require a solid basis for establishing the origin and maintenance of parasitism genes, and definition of their distribution across the enormous genetic diversity of Tylenchida. Apart from an evolutionary framework (phylogeny) the relevant diverse molecular genetic patterns cannot be meaningfully and efficiently explored, compared and extended. Thus, the proposed objective is to develop a robust tylenchid phylogeny and thereby support novel approaches to nematode management. Rapid progress and cost-savings by sharing value-added resources/support (including databases, voucher curation and analytical tools) is ensured through unique linkage to NSF-funded initiatives to develop a deep level phylogeny of Nematoda. Herein, a preliminary analysis of SSU rRNA genes from >130 taxa will guide strategies of taxon and character sampling. Having demonstrated the value for improved phylogenetic resolution of Tylenchida, we will pursue use of the LSU rRNA and several protein coding genes. The study engages broad systematic/molecular expertise with ongoing worldwide contacts and exchange of materials.
The most promising novel approaches to managing nematode pests are through understanding and exploiting genomic and molecular aspects of pathogenesis, survival strategies and reproduction. Efficient progress, however, requires comprehensive and resolved phylogenies, and particularly so in the order Tylenchida , that includes most agricultural pests. The practical need for a phylogenetic framework is rooted in the heterogeneity of Tylenchida’s more than 2000 described species and the nearly 400 species of Aphelenchida. Tylenchida hosts include invertebrates, fungi and plants; plant parasitic strategies include migratory ectoparasitism, burrowing endoparasitism, and sedentary ecto- and endoparasitism; some strategies are associated with little apparent impact on host cells and others induce profound host transformations. Based on a few species, early evidence is that whereas some genes involved in parasitism are conserved, others are specialized between putative “close relatives” and even between species of a particular genus. Preliminary phylogenies suggest that feeding strategies within Tylenchida are highly convergent; for example sedentary endoparasitism with host cell transformations apparently has arisen at least six times, and we cannot assume that the mechanisms and genes behind these separate systems are congruent ---or that knowledge of one system provides a basis to predict or understand another. Although presently it is not realistic to unravel the genomics of every plant parasite, it is feasible to decipher underlying mechanisms of patterns of pathogenesis, survival strategies and reproduction through tylenchid-model systems. However, rational and efficient selection of, and prediction from, such models requires the framework of a comprehensive, reliable and highly resolved phylogeny of Tylenchida. For example, preliminary trees based on SSU rRNA support both root knot (Meloidogyne) and cyst (Heteroderidae) nematodes as monophyletic but reject the widely held view that these two groups of sedentary endoparasites collectively are closely related and that mechanisms and genes of parasitism are necessarily shared. An alternate hypothesis that Heteroderidae share a clade with Hoplolaimidae (largely but not exclusively migratory ectoparasites) suggests new models that recognize diversity and a basis for potentially informative genetic (with respect to parasitism genomics) comparison. Beyond cyst nematodes, phylogenetic resolution is basic to efficiently extending the growing understanding of parasitism mechanisms and genomics to the diverse range of sedentary and migratory tylenchid parasites of major agricultural importance. Recent initiatives toward a “deep level” phylogenetic overview of Nematoda provide a unique “window of opportunity” that can be leveraged to efficiently, rapidly, and cost-effectively develop a much-needed highly-resolved tylenchid phylogeny within this broader scheme.
Some of the most promising approaches to controlling plant parasitic nematodes involve the identification and manipulation of parasitism genes in nematodes, and resistance genes in plants. However, in the absence of a resolved tylenchid phylogeny, most researchers must infer phylogenetic relationships from classifications. Preliminary analyses show that most of the families within the group are paraphyletic, and that no sister taxon relationships can be inferred with confidence for any of the families.
The lack of a resolved tylenchid phylogeny has major consequences on the extrapolation and extension of understanding the genomes of plant parasitic nematodes, and the role of the “parasitome” in plant pathology. Indeed, without a resolved phylogeny, it is impossible to infer with reason even the most basic and biologically fundamental questions concerning plant pathogenic nematodes; the origin and maintenance of the genetic, morphological, and even ecological associations between nematodes and their plant hosts. Thus, the primary goal of the proposed research is the empowerment of all other research programs in plant nematology.