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This is due mainly to the lack of genomic information and the complexity of the disease. High throughput sequencing is now an efficient approach for detecting the expression of genes in non-model organisms, thus providing valuable information in spite of the lack of the genome sequence. In an attempt to unravel genes potentially involved in the pine defense against the pathogen, we hereby report the high throughput comparative sequence analysis of infested and non-infested stems of <jats:italic>Pinus pinaster<\/jats:italic> (very susceptible to PWN) and <jats:italic>Pinus pinea<\/jats:italic> (less susceptible to PWN).<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Four cDNA libraries from infested and non-infested stems of <jats:italic>P. pinaster<\/jats:italic> and <jats:italic>P. pinea<\/jats:italic> were sequenced in a full 454 GS FLX run, producing a total of 2,083,698 reads. The putative amino acid sequences encoded by the assembled transcripts were annotated according to Gene Ontology, to assign <jats:italic>Pinus<\/jats:italic> contigs into Biological Processes, Cellular Components and Molecular Functions categories. Most of the annotated transcripts corresponded to <jats:italic>Picea<\/jats:italic> genes-25.4-39.7%, whereas a smaller percentage, matched <jats:italic>Pinus<\/jats:italic> genes, 1.8-12.8%, probably a consequence of more public genomic information available for <jats:italic>Picea<\/jats:italic> than for <jats:italic>Pinus<\/jats:italic>. The comparative transcriptome analysis showed that when <jats:italic>P. pinaster<\/jats:italic> was infested with PWN, the genes malate dehydrogenase, ABA, water deficit stress related genes and PAR1 were highly expressed, while in PWN-infested <jats:italic>P. pinea,<\/jats:italic> the highly expressed genes were ricin B-related lectin, and genes belonging to the SNARE and high mobility group families. Quantitative PCR experiments confirmed the differential gene expression between the two pine species.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Defense-related genes triggered by nematode infestation were detected in both <jats:italic>P. pinaster<\/jats:italic> and <jats:italic>P. pinea<\/jats:italic> transcriptomes utilizing 454 pyrosequencing technology. <jats:italic>P. pinaster<\/jats:italic> showed higher abundance of genes related to transcriptional regulation, terpenoid secondary metabolism (including some with nematicidal activity) and pathogen attack. <jats:italic>P. pinea<\/jats:italic> showed higher abundance of genes related to oxidative stress and higher levels of expression in general of stress responsive genes. This study provides essential information about the molecular defense mechanisms utilized by <jats:italic>P. pinaster<\/jats:italic> and <jats:italic>P. pinea<\/jats:italic> against PWN infestation and contributes to a better understanding of PWD.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2164-13-599","type":"journal-article","created":{"date-parts":[[2012,11,7]],"date-time":"2012-11-07T13:14:10Z","timestamp":1352294050000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":58,"title":["Searching for resistance genes to Bursaphelenchus xylophilus using high throughput screening"],"prefix":"10.1186","volume":"13","author":[{"given":"Carla S","family":"Santos","sequence":"first","affiliation":[]},{"given":"Miguel","family":"Pinheiro","sequence":"additional","affiliation":[]},{"given":"Ana I","family":"Silva","sequence":"additional","affiliation":[]},{"given":"Concei\u00e7\u00e3o","family":"Egas","sequence":"additional","affiliation":[]},{"given":"Marta W","family":"Vasconcelos","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2012,11,7]]},"reference":[{"key":"4567_CR1","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1007\/s10658-009-9574-4","volume":"127","author":"L Huang","year":"2010","unstructured":"Huang L, Ye J, Wu X, Xu X, Sheng J, Zhou Q: Detection of pine wood nematode using a real-time PCR assay to target the DNA topoisomerase I gene. 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