Reliability and Utility of Standard Gene Sequence Barcodes for the Identification and Differentiation of Cyst Nematodes of the Genus Heterodera.

Difficulties inherent in the morphological identification of cyst nematodes of the genus Heterodera Schmidt, 1871, an important lineage of plant parasites, has led to broad adoption of molecular methods for diagnosing and differentiating species. The pool of publicly available sequence data has grown significantly over the past few decades, and over half of all known species of Heterodera have been characterized using one or more molecular markers commonly employed in DNA barcoding (18S, internal transcribed spacer [ITS], 28S, coxI). But how reliable are these data and how useful are these four markers for differentiating species? We downloaded all 18S, ITS, 28S, and coxI gene sequences available on the National Center for Biotechnology Information (NCBI) database, GenBank, for all species of Heterodera for which data were available. Using a combination of sequence comparison and tree-based phylogenetic methods, we evaluated this dataset for erroneous or otherwise problematic sequences and examined the utility of each molecular marker for the delineation of species. Although we find the rate of obviously erroneous sequences to be low, all four molecular markers failed to differentiate between at least one species pair. Our results suggest that while a combination of multiple markers is best for species identification, the coxI marker shows the most utility for species differentiation and should be favored over 18S, ITS, and 28S, where resources are limited. Presently, less than half the valid species of Heterodera have a sequence of coxI available, and only a third have more than one sequence of this marker.

A catalogue of the nematode slide collection from the late W.L. Nicholas held at National Research Collections Australia, CSIRO.

A catalogue is presented of the nematode slide collection of W.L. Nicholas, which is deposited in the National Research Collections Australia at CSIRO. This is the most extensive slide collection of free-living marine and estuarine nematodes from Australia to date, and consists of 553 putative species, collected across a wide range of Australias eastern and northern regions over the course of nearly 40 years. The collection contains mostly marine and estuarine free-living nematodes collected on coarse substrate in littoral habitats. The most abundant genera were Desmodora, Theristus, and Onyx. Most taxa were found rarely, being recorded only once, and repeated sampling at several sandy beach sites revealed only a small proportion of the fauna on more than one occasion. A significant proportion of the taxa were also found to be widespread, occurring on more than one occasion at more than one location, with Theristus sp., Onyx sp., and Viscosia sp. occurring in the greatest number of localities. The catalogue adds an additional 90 species and 160 genera to the documented fauna of Australian free-living nematodes verifiable by specimens in permanent collections. It thus provides a better framework for studying nematode biodiversity and biogeography in the region.