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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Mycology and Nematology Genetic Diversity and Biology Laboratory » Research » Publications at this Location » Publication #334673

Title: Improved 18S small subunit rDNA primers for problematic nematode amplification

item Carta, Lynn
item Li, Shiguang

Submitted to: Journal of Nematology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/2/2018
Publication Date: 12/1/2018
Citation: Carta, L.K., Li, S. 2018. Improved 18S small subunit rDNA primers for problematic nematode amplification. Journal of Nematology. 50(4):533-542.

Interpretive Summary: Nematodes are microscopic worms that attack plants and cause billions of dollars of damage to crops and forest and ornamental trees. One problem with determining the extent of nematode damage is that the nematodes present in many areas are not known, and their species identification often requires extensive microscopic anatomical observation and DNA profiling. Molecular tools called primers used by scientists for identifying nematodes with their DNA sequences used like a fingerprint are sometimes inadequate for certain nematode species. Therefore nearly 300 sequences of agriculturally important nematodes were collected and used to design better primers, and these were tested on nematodes that failed to provide a sequence with the old primers. The new primer tools and methods to use them are detailed so that nematodes important to agricultural trade can be more reliably identified, especially when specimens do not have much DNA. This information will be used by agricultural researchers and diagnosticians in the U.S. and other countries.

Technical Abstract: The 18S small subunit (SSU) ribosomal DNA sequence is one of the most useful molecular loci for identification and phylogeny reconstruction of agriculturally important nematodes. Various pairs of universal primers have been developed to amplify short and long nematode sequences. However, certain nematode taxa are not readily amplified and/or sequenced with the existing primer tools. Frequently, the center region of a roughly 1,000 nucleotide segment has been missing. Therefore, new primers were developed based on a very large 276 taxon alignment of 124 agriculturally important nematode species, and tested on problematic nematode taxa such as Aphelenchoides, Bursaphelenchus, Ditylenchus, and Panagrolaimus. New primers and protocols are provided for successful generation of sequences useful in future investigations of nematode systematics.