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Biomedical subjects

Jean Bousquet

Publications and source records attributed to Jean Bousquet.

At least 19 recordsLinked to original sources
PubMed2006

Comparative genome mapping among Picea glauca, P. mariana x P. rubens and P. abies, and correspondence with other Pinaceae.

A composite linkage map was constructed from four individual maps for the conifer Picea glauca (Moench) Voss, from anonymous and gene-specific markfers (714 AFLPs, 38 SSRs, and 53 ESTPs). A total of 12 linkage groups were delineated with an average marker density of 2.7 cM. Macro-synteny and macro-colinearity comparisons with two other composite linkage maps developed for the species complex P. mariana (Mill.) B.S.P. x P. rubens Sarg., and for P. abies (L.) Karst. revealed an identical number of linkage groups and a remarkable conservation of the gene content and gene order of linkage groups over the million years since the split between these taxa. Identical gene order among taxa was observed for 10 of the 12 assembled composite linkage groups. The discovery of one breakdown in synteny between P. glauca and the other two taxa indicated the occurrence of an inter-chromosomal rearrangement involving an insertional translocation. Analysis of marker colinearity also revealed a putative segmental duplication. The combined information from these three Picea genomes validated and improved large-scale genome comparisons at the inter-generic level in the family Pinaceae by allowing for the identification of 11 homoeologous linkage groups between Picea and Pinus, and nine such groups between Picea and Pseudotsuga menziesii. Notably, the analysis of synteny among the three genera revealed a putative case of chromosomal fission and an inter-chromosomal rearrangement in the genome of P. menziesii. Both of these changes are inter-connected, indicating much instability in this part of the P. menziesii genome. Overall, the macro-structure of the Pinaceae genome was well conserved, which is notable given the Cretaceous origin of its main lineages.

Genome, Plant↗
PubMed2006

Allergic rhinitis and its consequences on quality of sleep: An unexplored area.

BACKGROUND: Allergic rhinitis (AR) is common and has been shown to impair social life and sleep. Patients with severe symptoms may have more sleep disturbances than those with a mild form of the disease, but this has never been assessed using a validated tool. The objective of our study was to assess, in patients with AR, whether duration and severity of AR are associated with sleep impairment. METHODS: A nationwide controlled cross-sectional epidemiological study was carried out. A representative sample of 260 French ear, nose, and throat and allergy specialists enrolled 591 patients with AR of at least 1 year's duration. Sleep disorders, sleep quality, and AR were assessed using validated tools (Sleep Disorders Questionnaire, Epworth Sleepiness Scale, and Score for Allergic Rhinitis). The severity of AR was assessed using the Allergic Rhinitis and its Impact on Asthma classification. RESULTS: All dimensions of sleep were impaired by AR, particularly by the severe type. Sleep was significantly more impaired in patients with severe AR than in those with the mild type. The duration of AR (intermittent or persistent) had no effect on sleep. CONCLUSION: These data underline the close relationship between AR and sleep and highlight the need for clinicians, particularly general practitioners, to be attentive in this respect.

Adult↗
PubMed2006

Noninvasive methods for the detection of upper and lower airway inflammation in atopic children.

BACKGROUND: Exhaled nitric oxide (FE(NO)) and exhaled breath condensate (EBC) are noninvasive methods to assess inflammation. OBJECTIVE: To investigate the role of the FE(NO) and of the EBC pH and IL-5 levels in atopic children. METHODS: We evaluated oral and nasal FE(NO) and the pH and IL-5 of oral and nasal EBC in children with atopic dermatitis (AD; n = 18), allergic rhinitis (AR; n = 18), intermittent asthma (n = 21), moderate persistent asthma (n = 18), and healthy controls (HCs; n = 16). RESULTS: Oral FE(NO) was significantly increased in asthma, whereas the nasal values were increased in AR and asthma in comparison with HCs. The pH of oral EBC was lower in AD and asthma than in AR and HCs, whereas the nasal levels were lower in AD, AR, and asthma than in HCs. The oral IL-5 was higher in AD, AR, and asthma in comparison with HCs, whereas the nasal IL-5 concentrations were higher in asthma and AR than in HCs. In AR, the nasal FE(NO) correlated with the IL-5 values and with the disease duration. In intermittent asthma, oral and nasal pH inversely correlated with the exacerbations, whereas in moderate asthma, the nasal IL-5 positively correlated with exacerbations. In AD, the oral and nasal IL-5 positively correlated with the serum IgE. CONCLUSION: These markers of nasal and bronchial inflammation, accessible with noninvasive techniques, might be useful to identify patients with uncontrolled diseases and to verify the usefulness of new therapeutic approaches. CLINICAL IMPLICATIONS: These markers are useful tools to monitor the upper and lower airway inflammation in atopic children.

Adolescent↗
PubMed2006

Automated SNP detection from a large collection of white spruce expressed sequences: contributing factors and approaches for the categorization of SNPs.

BACKGROUND: High-throughput genotyping technologies represent a highly efficient way to accelerate genetic mapping and enable association studies. As a first step toward this goal, we aimed to develop a resource of candidate Single Nucleotide Polymorphisms (SNP) in white spruce (Picea glauca [Moench] Voss), a softwood tree of major economic importance. RESULTS: A white spruce SNP resource encompassing 12,264 SNPs was constructed from a set of 6,459 contigs derived from Expressed Sequence Tags (EST) and by using the bayesian-based statistical software PolyBayes. Several parameters influencing the SNP prediction were analysed including the a priori expected polymorphism, the probability score (PSNP), and the contig depth and length. SNP detection in 3' and 5' reads from the same clones revealed a level of inconsistency between overlapping sequences as low as 1%. A subset of 245 predicted SNPs were verified through the independent resequencing of genomic DNA of a genotype also used to prepare cDNA libraries. The validation rate reached a maximum of 85% for SNPs predicted with either PSNP > or = 0.95 or > or = 0.99. A total of 9,310 SNPs were detected by using PSNP > or = 0.95 as a criterion. The SNPs were distributed among 3,590 contigs encompassing an array of broad functional categories, with an overall frequency of 1 SNP per 700 nucleotide sites. Experimental and statistical approaches were used to evaluate the proportion of paralogous SNPs, with estimates in the range of 8 to 12%. The 3,789 coding SNPs identified through coding region annotation and ORF prediction, were distributed into 39% nonsynonymous and 61% synonymous substitutions. Overall, there were 0.9 SNP per 1,000 nonsynonymous sites and 5.2 SNPs per 1,000 synonymous sites, for a genome-wide nonsynonymous to synonymous substitution rate ratio (Ka/Ks) of 0.17. CONCLUSION: We integrated the SNP data in the ForestTreeDB database along with functional annotations to provide a tool facilitating the choice of candidate genes for mapping purposes or association studies.

Algorithms↗
PubMed2006

Natural rubber latex allergy among health care workers: a systematic review of the evidence.

BACKGROUND: Natural rubber latex is a recognized allergen, but a recent meta-analysis failed to find any association between latex exposure and allergy in health care workers (HCWs). OBJECTIVES: A meta-analysis was carried out under the auspices of the French National Regulatory Authority to assess the allergic risk induced by latex gloves in HCWs. METHODS: The risk of work-related exposure to latex for the development of latex allergy was assessed. Prevalence and incidence rates of latex sensitization or allergy were compared in HCWs and in the general population. Exposure-response relationships were assessed in HCWs. RESULTS: Latex allergy was found in 4.32% (range, 4.01% to 4.63%) of HCWs and in 1.37% (range, 0.43% to 2.31%) of the general population. Latex-positive skin prick test responses ranged from 2.1% to 3.7% in the general population and from 6.9% to 7.8% for the HCWs. HCWs exposed to latex showed an increased risk of hand dermatitis (odds ratio [OR], 2.46; 95% CI, 2.11-2.86), asthma or wheezing (OR, 1.55; 95% CI, 1.15-2.08), rhinoconjunctivitis (OR, 2.73; 95% CI, 1.97-3.81), and at least one generic symptom (OR, 1.27; 95% CI, 1.09-1.47). Sensitization to latex was significantly associated with asthma and rhinoconjunctivitis. By contrast, exposure to latex was not associated with a significantly increased risk of positive skin prick test responses to latex (OR, 1.47; 95% CI, 0.94-2.30). CONCLUSION: HCWs have an increased risk of sensitization and allergic symptoms to latex. CLINICAL IMPLICATIONS: Prevention of latex allergy in HCWs is needed.

Cross-Sectional Studies↗
PubMed2006

Levocetirizine improves health-related quality of life and health status in persistent allergic rhinitis.

BACKGROUND: Allergic rhinitis is a chronic respiratory disorder with a detrimental impact on health-related quality of life (HRQOL) and health status. Enhancement and maintenance of patient function and well-being are therefore considered as essential. OBJECTIVE: To determine whether long-term treatment with levocetirizine 5mg improves HRQOL and health status in persistent allergic rhinitis (PER) patients assessed with RQLQ and SF-36 scales over a 6-month period. METHODS: The Xyzal in PER Trial (XPERT) was a multi-center, double-blind, parallel-group study. A total of 551 patients were randomized to receive levocetirizine 5mg or placebo once daily for 6 months and assessed for symptoms, HRQOL (Rhinoconjunctivitis Quality of Life Questionnaire: RQLQ) and health status (SF-36). Sensitivity of the RQLQ and SF-36 to disease severity was tested to ensure their suitability for use in PER patients. Treatment effect was assessed by means of repeated measures analyses. RESULTS: Over the 6-month treatment period, levocetirizine showed statistically significant improvements over placebo in HRQOL (P < 0.001 for all RQLQ domains and overall scores) and health status (P < or = 0.004 for SF-36 physical and mental summary scores; P < 0.05 for all SF-36 scales). The relative improvement of levocetirizine over placebo exceeded the predefined clinically meaningful threshold of 30% for all RQLQ scores and the improvement from baseline was 3 times the established MID for RQLQ. CONCLUSION: The RQLQ and SF-36 could be used to measure HRQOL and health status in PER patients. Long-term treatment with levocetirizine provides sustained improvement of HRQOL and reduces disease burden in PER patients.

Cetirizine↗
PubMed2006

Influence of patients' characteristics and disease management on asthma control.

BACKGROUND: Although asthma control is a major outcome in disease management, little is known about its determinants. OBJECTIVES: We sought to study the relationships between asthma control and patient characteristics or asthma management. METHODS: Asthmatic patients (age 18-50 years) who were regular customers of pharmacies and had a prescription for an antiasthma medication were recruited consecutively. Patients completed a questionnaire, which was complemented by computerized pharmacy records of previously dispensed medications. Asthma control (adequate/inadequate) was assessed with the Asthma Control Test. Determinants of asthma control were identified by means of multivariate logistic regression analysis. RESULTS: The mean age of the 1351 patients included was 36.8 years (SD, 9.8), and 55.8% were women. A minority of patients were considered to have had their symptoms adequately controlled. Smoking, female sex, and a body mass index of greater than 30 kg/m2 were all independent determinants of inadequate control. Compared with patients receiving inhaled corticosteroid monotherapy, those who were dispensed fixed combinations of inhaled corticosteroids and long-acting beta-agonists presented with a significantly lower risk of inadequate asthma control (odds ratio, 0.58; 95% CI, 0.35-0.96). CONCLUSION: Asthma control varied according to both the patients' characteristics and therapy. CLINICAL IMPLICATIONS: Our results strongly support the need to improve asthma control, especially in primary care and in women. A regular use of fixed controller combinations, helping patients to quit smoking, or addressing weight issues might contribute to improvement in asthma control.

Adolescent↗
PubMed2006

ARIA update: I--Systematic review of complementary and alternative medicine for rhinitis and asthma.

Complementary-alternative medicines are extensively used in the treatment of allergic rhinitis and asthma, but evidence-based recommendations are lacking. To provide evidence-based recommendations, the literature was searched by using MedLine and the Cochrane Library to March 2005 (Key words: Asthma [OR] Rhinitis, [AND] Complementary [OR] Alternative Medicine, [OR] Herbal, [OR] Acupuncture, [OR] Homeopathy, [OR] Alternative Treatment). Randomized trials, preferably double-blind and published in English, were selected. The articles were evaluated by a panel of experts. Quality of reporting was assessed by using the scale validated by Jadad. The methodology of clinical trials with complementary-alternative medicine was frequently inadequate. Meta-analyses provided no clear evidence for the efficacy of acupuncture in rhinitis and asthma. Some positive results were described with homeopathy in good-quality trials in rhinitis, but a number of negative studies were also found. Therefore it is not possible to provide evidence-based recommendations for homeopathy in the treatment of allergic rhinitis, and further trials are needed. A limited number of studies of herbal remedies showed some efficacy in rhinitis and asthma, but the studies were too few to make recommendations. There are also unresolved safety concerns. Therapeutic efficacy of complementary-alternative treatments for rhinitis and asthma is not supported by currently available evidence.

Acupuncture↗
PubMed2006

Decoupled mitochondrial and chloroplast DNA population structure reveals Holocene collapse and population isolation in a threatened Mexican-endemic conifer.

Chihuahua spruce (Picea chihuahuana Martínez) is a montane subtropical conifer endemic to the Sierra Madre Occidental in northwestern México. Range-wide variation was investigated using maternally inherited mitochondrial (mtDNA) and paternally inherited chloroplast (cpDNA) DNA markers. Among the 16 mtDNA regions analysed, only two mitotypes were detected, while the study of six cpDNA microsatellite markers revealed eight different chlorotypes. The average cpDNA diversity (H = 0.415) was low but much higher than that for mtDNA (H = 0). The distribution of mitotypes revealed two clear nonoverlapping areas (G(ST) = N(ST) = 1), one including northern populations and the second one including the southern and central stands, suggesting that these two regions may represent different ancestral populations. The cpDNA markers showed lower population differentiation (G(ST) = 0.362; R(ST) = 0.230), implying that the two ancestral populations continued to exchange pollen after their initial geographic separation. A lack of a phylogeographic structure was revealed by different spatial analyses of cpDNA (G(ST) > R(ST); and samova), and reduced cpDNA gene flow was noted among populations (Nm = 0.873). Some stands deviated significantly from the mutation-drift equilibrium, suggesting recent bottlenecks. Altogether, these various trends are consistent with the hypothesis of a population collapse during the Holocene warming and suggest that most of the modern P. chihuahuana populations are now effectively isolated with their genetic diversity essentially modelled by genetic drift. The conservation efforts should focus on most southern populations and on the northern and central stands exhibiting high levels of genetic diversity. Additional mtDNA sequence analysis confirmed that P. martinezii (Patterson) is not conspecific with P. chihuahuana, and thus deserves separate conservation efforts.

Base Sequence↗
PubMed2006

Contrasting microsatellite variation between subalpine and western larch, two closely related species with different distribution patterns.

Subalpine larch (Larix lyallii Parl.) and western larch (Larix occidentalis Nutt.) represent two closely related species with contrasting abundance and distribution patterns in Western North America. Genetic diversity at seven informative microsatellite loci was determined for 19 populations of subalpine larch and nine populations of western larch. Contrasting genetic diversity and patterns of population differentiation were observed between the two species. The overall within-population genetic diversity parameters were lower in subalpine larch (A = 3.2; A(P) = 3.6; H(E) = 0.418) than in western larch (A(P) = 5.51; H(E) = 0.580), a pattern that is likely related to historical or demographic factors. No evidence of interspecific hybridization was observed. Significantly more population differentiation (theta = 0.15; R(ST) = 0.07), consistent with more restricted gene flow, was observed for subalpine larch as compared to western larch (theta = 0.05; R(ST) = 0.04). Under the assumption of an infinite allele mutation model, 12 of the 19 subalpine larch populations showed signs of deviation from the mutation-drift equilibrium, which suggests Holocene population bottlenecks and fluctuations in effective population size for this species. None of the western larch populations deviated significantly from the mutation-drift equilibrium. For both species, Mantel's test revealed a significant positive relationship between geographical and genetic distances indicative of isolation by distance. A similar geographical structure was detected in both species, suggesting at least two genetically distinct glacial populations in each species. The various implications for gene conservation are discussed.

Biological Evolution↗
PubMed2006

Prevention of recurrent respiratory tract infections in children using a ribosomal immunotherapeutic agent: a clinical review.

Recurrent respiratory tract infections (RRTIs) in children constitute a serious problem worldwide. Some children experience considerable morbidity as a result of RRTIs and receive repeated courses of antibacterials that are not effective against viral infectious agents and can increase bacterial resistance. Furthermore, the direct and indirect costs of RRTIs to the community are substantial. In this article, we review the available clinical evidence relating to use of the bacterial immunostimulant Ribomunyl for the prevention of RRTIs in children. The product is composed of ribosomal fractions from four bacteria involved in RRTIs as well as a membrane fraction from one of these bacteria (Klebsiella pneumoniae). Ribomunyl stimulates production of specific humoral and secretory antibodies against the four bacterial strains included in the compound. The product also stimulates non-specific immunity. Thus, Ribomunyl stimulates both the innate and acquired immune systems and offers preventive efficacy against both bacterial and viral infections. To perform this review, we searched the MEDLINE database for articles on Ribomunyl and then included only those publications that described placebo-controlled studies, complied with Good Clinical Practice standards, used the product in official registered indications, and administered it at the recommended dosages. In this way, we were able to generate a comprehensive profile of use of the product and draw valid conclusions about its clinical role. In clinical trials of children, Ribomunyl reduced the number of upper or lower RRTIs, the primary outcome measures. Other favorable results relating to efficacy parameters that served as secondary outcome measures in these studies included a reduction in antibacterial treatments, shorter duration of recurrent episodes, reduced need for other medications such as expectorants, smaller number of lost school days or parent absenteeism from work, less fever, and reduced hearing loss. Studies focusing on particular conditions, such as otitis media, or those that included specific patient groups, such as very young children, reported similar findings. Adverse events occurred very rarely and were mild. Their frequency was similar to that reported in placebo groups, and consisted mostly of fever, otorhinolaryngologic symptoms, and cutaneous events. In conclusion, this review clearly demonstrated that Ribomunyl is effective in preventing upper and lower RRTIs in children. Ribomunyl provided a reduction in the number, duration, and severity of infectious episodes and, thereby, reduced antibacterial use and the likelihood of consequent development of bacterial resistance. Ribomunyl also decreased absence from work or school, which has important economic consequences.

Adjuvants, Immunologic↗
PubMed2006

Role of ribomunyl((r)) in the prevention of recurrent respiratory tract infections in adults : overview of clinical results.

Recurrent respiratory tract infections (RRTIs) in adults are the result of an imbalance between lung defense mechanisms, and bacterial burden. Antibacterial treatments can temporarily restore the equilibrium between host and bacterial load, but do not prevent recurrence of infection. An alternative approach to prevent recurrence of infection is treatment with an immunostimulant, which provides immune protection against repeated bacterial and viral infection. All immunostimulant products are bacterial in origin: lysates (first generation immunostimulants), or bacterial extracts, like bacterial ribosomes, or membrane proteoglycans. This review highlights the current state of knowledge regarding the use of immunostimulants in adults with RRTIs, taking the ribosomal immunostimulant Ribomunyl((R)) as an example. Many studies are available on the mechanism of action and clinical efficacy in prevention of RRTIs in adults treated with Ribomunyl((R)). The effect of this immunostimulant on anti-infectious responses is explained by a stimulation of both nonspecific (innate) and specific (adaptive) immunity. In order to obtain a global overview of the therapeutic efficacy of Ribomunyl((R)) the most pertinent trials were selected from the literature based on adequate patient numbers and good methodology. Results of double-blind placebo-controlled trials using Ribomunyl((R)) for the treatment of different upper or lower RRTIs have demonstrated a statistically significant reduction in the number of infectious episodes and as a consequence, a decrease in antibacterial consumption, after 3 and 6 months of treatment. The tolerance profile of Ribomunyl((R)) was good in all studies. Economic evaluations suggest that savings can be made in healthcare expenditure, in patients with recurrent episodes of infection. It is concluded that Ribomunyl((R)) is effective in preventing and reducing upper and lower respiratory tract infections in adults. The product may also have an impact on reducing the development of bacterial resistance, as a result of fewer courses of antibacterials required to treat patients with RRTIs.

Adjuvants, Immunologic↗
PubMed2005

Simple sequence repeat (SSR) markers in the ectomycorrhizal fungus Laccaria bicolor for environmental monitoring of introduced strains and molecular ecology applications.

Simple sequence repeat (SSR) markers were developed from SSR-enriched genome libraries for the ectomycorrhizal basidiomycete Laccaria bicolor. Seven markers were single-locus and amplified unambiguously in L. bicolor. The seven SSR markers were further characterized using an array of 15 L. bicolor strains representative of diverse origins worldwide. The observed number of alleles per locus varied from 5-9 and the values of observed heterozygosity from 0.167 to 0.667. The seven SSR loci could be amplified from DNA extracted from root tips of L. bicolor inoculated pine seedlings. All the L. bicolor ectomycorrhizas analysed exhibited the same SSR multi-locus profile as that detected for the UAMH8232 inoculant strain. The set of markers described represents a potent tool for the monitoring of introduced strains of L. bicolor and for molecular ecology applications.

Biomarkers↗
PubMed2005

Severity and impairment of allergic rhinitis in patients consulting in primary care.

BACKGROUND: Allergic rhinitis is a disease impairing quality of life, sleep, and work. A new classification for allergic rhinitis, Allergic Rhinitis and its Impact on Asthma (ARIA), has recently been proposed. OBJECTIVE: To study the effect of allergic rhinitis using ARIA definitions to determine severity and duration. METHODS: A total of 3052 patients consulting general practitioners for allergic rhinitis were studied. Patients were classified according to the 4 classes of ARIA. In all patients, quality of life (Rhinoconjunctivitis Quality-of-Life Questionnaire), sleep (Jenkins questionnaire), and work performance (Allergy-Specific Work Productivity and Activity Impairment questionnaire) were assessed. RESULTS: Mild intermittent rhinitis was diagnosed in 11% of the patients, mild persistent rhinitis in 8%, moderate/severe intermittent rhinitis in 35%, and moderate/severe persistent rhinitis in 46%. The severity of rhinitis has more of an effect on quality of life, sleep, daily activities, and work performance than the duration of rhinitis. In moderate/severe rhinitis, more than 80% of patients report impaired activities, as opposed to only 40% with mild rhinitis. CONCLUSION: It seems that the term moderate/severe should be replaced by severe. A study in the general population is necessary, however, to assess the prevalence of the 4 ARIA classes of allergic rhinitis, especially in patients who are not consulting physicians for their symptoms.

Adult↗
PubMed2005

A composite linkage map from two crosses for the species complex Picea mariana x Picea rubens and analysis of synteny with other Pinaceae.

Four individual linkage maps were constructed from two crosses for the species complex Picea mariana (Mill.) B.S.P. x Picea rubens Sarg in order to integrate their information into a composite map and to compare with other Pinaceae. For all individual linkage maps, 12 major linkage groups were recovered with 306 markers per map on average. Before building the composite linkage map, the common male parent between the two crosses made it possible to construct a reference linkage map to validate the relative position of homologous markers. The final composite map had a length of 2,319 cM (Haldane) and contained a total of 1,124 positioned markers, including 1,014 AFLPs, 3 RAPDs, 53 SSRs, and 54 ESTPs, assembled into 12 major linkage groups. Marker density of the composite map was statistically homogenous and was much higher (one marker every 2.1 cM) than that of the individual linkage maps (one marker every 5.7 to 7.1 cM). Synteny was well conserved between individual, reference, and composite linkage maps and 94% of homologous markers were colinear between the reference and composite maps. The combined information from the two crosses increased by about 24% the number of anchor markers compared to the information from any single cross. With a total number of 107 anchor markers (SSRs and ESTPs), the composite linkage map is a useful starting point for large-scale genome comparisons at the intergeneric level in the Pinaceae. Comparisons of this map with those in Pinus and Pseudotsuga allowed the identification of one breakdown in synteny where one linkage group homologous to both Picea and Pinus corresponded to two linkage groups in Pseudotsuga. Implications for the evolution of the Pinaceae genome are discussed.

Chromosome Mapping↗
PubMed2005

Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters.

BACKGROUND: The sequencing and analysis of ESTs is for now the only practical approach for large-scale gene discovery and annotation in conifers because their very large genomes are unlikely to be sequenced in the near future. Our objective was to produce extensive collections of ESTs and cDNA clones to support manufacture of cDNA microarrays and gene discovery in white spruce (Picea glauca [Moench] Voss). RESULTS: We produced 16 cDNA libraries from different tissues and a variety of treatments, and partially sequenced 50,000 cDNA clones. High quality 3' and 5' reads were assembled into 16,578 consensus sequences, 45% of which represented full length inserts. Consensus sequences derived from 5' and 3' reads of the same cDNA clone were linked to define 14,471 transcripts. A large proportion (84%) of the spruce sequences matched a pine sequence, but only 68% of the spruce transcripts had homologs in Arabidopsis or rice. Nearly all the sequences that matched the Populus trichocarpa genome (the only sequenced tree genome) also matched rice or Arabidopsis genomes. We used several sequence similarity search approaches for assignment of putative functions, including blast searches against general and specialized databases (transcription factors, cell wall related proteins), Gene Ontology term assignation and Hidden Markov Model searches against PFAM protein families and domains. In total, 70% of the spruce transcripts displayed matches to proteins of known or unknown function in the Uniref100 database (blastx e-value < 1e-10). We identified multigenic families that appeared larger in spruce than in the Arabidopsis or rice genomes. Detailed analysis of translationally controlled tumour proteins and S-adenosylmethionine synthetase families confirmed a twofold size difference. Sequences and annotations were organized in a dedicated database, SpruceDB. Several search tools were developed to mine the data either based on their occurrence in the cDNA libraries or on functional annotations. CONCLUSION: This report illustrates specific approaches for large-scale gene discovery and annotation in an organism that is very distantly related to any of the fully sequenced genomes. The ArboreaSet sequences and cDNA clones represent a valuable resource for investigations ranging from plant comparative genomics to applied conifer genetics.

Arabidopsis↗