NAR Molecular Biology Database Collection entry number 726

http://www.ppnema.uniba.it

De Giorgi C.¹, Rubino F.¹, Voukelatou A.¹, De Luca F.² and Attimonelli M.¹

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

Contact m.attimonelli@biologia.uniba.it

Plant-parasitic nematodes are important pests of crop plants worldwide, and also among the most difficult animals to identify. Their identification based on sequences of nuclear ribosomal DNA (rDNA) cistron (18S, 28S and 5.8S RNA genes, and Internal Transcribed Spacers, ITS1 and ITS2) is currently becoming a popular tool. Each rDNA repeating cistron is arranged as follows: an external region (IGS), a small ribosomal subunit (18S) gene, an internal transcribed spacer 1 (ITS1), the 5.8S gene, another internal transcribed spacer 2 (ITS2), large ribosomal subunit (28S) gene, and lastly an intergenic spacer region (IGS). 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 which suffer from confusion in published taxonomy. 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 well-integrated, web-based, Plant-Parasitic Nematode bioinformatic resource. It consists of a database of Ribosomal Cistron sequences from various species of plant-parasitic nematodes grouped according to nematode genera, and a Search system allowing data to be extracted according to both text and pattern searching. The database contains 2405 sequences from 26 different genera, organised in 208 multi-aligned groups. The sequences extracted from primary DBs were analysed in order to detect non-redundant sequences by CleanUP software. Within each genera group, multi-alignments of sequences were produced for ribosomal genes and fragments of the genes themselves. Alignments were guided with the Caenorhabditis elegans genome as reference sequence. The database was implemented in MySQL DBMS. Sequences were multi-aligned using both ClustalW and DIALIGN programs. PPNEMA also contains a newly developed tool for characterising an anonymous sequence by comparing it with groups of multi-aligned sequences by means of pattern searching approaches. A system allowing the submission of new sequences is under development. PPNEMA is freely available at http://www.ppnema.uniba.it.

The availability of the PPNEMA database, related sequences are organised in clusters (groups), can highlight small shared sub-sequences among genera, species and populations thus offering the scientific community a pre-processed archive of plant parasitic nematode sequences useful for nematologists interested in both characterisation of new species and phylogenetic relationships.

We would like to thank Dr. Annalisa Marsico for her contribution to the database design during her stay in our Department within the Master program in BIOINFORMATICA “Alberto del Lungo” organised at the Siena University (Italy). This work was supported by the University of Bari and by “PROGETTO DI RICERCA MIUR-PNR FIRB "Laboratorio Internazionale di Bioinformatica"”.

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