PPNEMA: A Resource of Plant-Parasitic Nematodes Multialigned Ribosomal Cistrons

Francesco Rubino,(1) Amalia Voukelatou,(1) Francesca De Luca,(2) Carla De Giorgi,(1) and Marcella Attimonelli(1)

1. Dipartimento di Biochimica e Biologia Molecolare, Bari University, Via E. Orabona 4, 70126 Bari, Italy; 2. Istituto per la Protezione delle Piante, Sezione di Bari, CNR, Via Amendola 165, 70126 Bari, Italy

Abstract

Plant-parasitic nematodes are important pests of crop plants worldwide, and also among the most difficult animals to identify. Their identification based on nuclear ribosomal DNA (rDNA) cistron (18S, 28S, and 5.8S RNA genes, and internal transcribed spacers, ITS1 and ITS2) is becoming a popular tool. Sequences from nuclear ribosomal RNA repeats have been used to demonstrate the identity of isolates from various hosts and to unravel the relationships of cryptic and complex species. In addition, the availability of RNA sequences allows study of phylogenetic relationships between nematodes, also for more complete understanding of their biology as agricultural pests. PPNEMA is a plant-parasitic nematode bioinformatic resource. It consists of a database of ribosomal cistron sequences from various species grouped according to nematode genera, and a search system allowing data to be extracted according to both text and pattern searching. PPNEMA offers to the scientific community a preprocessed archive of plant parasitic nematode sequences useful for nematologists. It is a tool to retrieve plant nematode multialigned sequences for phylogenetic studies or to recognize a nematode by comparing its rDNA sequence with the PPNEMA available genus specific multialignments.

Methods
PPNEMA is a bioinformatic platform allowing the storage, query and analysis of phytoparasites rDNA sequences. It is available on the web at http://www.ppnema.uniba.it. Each sequence in the PPNEMA database related to a fragment of one of the ribosomal RNA genes for a single isolate within a nematode species is identified by a code defining species and function. The sequences derived from the different nematode species are multi-aligned within each nematode genus. However, since not all the sequences span the entire rDNA array, separate multi-alignments of the sequences have been produced for single rRNA genes or for portions of the same gene separately, depending upon the availability of the sequences. Thus, each entry in the database is related to a species-specific functional element. More entries are associated in a group. More groups are available for the same genus and the same functional element. Phylogenetic data and dating are not reported at present in the PPNEMA database since paleontologic information is missing and the only functional element that remains constant indifferent genera is 18S [4], for which the feasibility of construction of phylogenetic trees will be evaluated. The database is physically based on the SQLite DBMS, while the web application is based on an application framework written in Python. At present PPNEMA reports 2405 entries for a total of 26 genera and 405 species grouped in 208 multialignments.

Results
In its current implementation, the database is accessibile through a web application allowing the user to:

References
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