Unknown,Transcriptomics,Genomics,Proteomics

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A transcriptomic resource for Douglas-fir seed development and analysis of transcription during late megagametophyte development

ABSTRACT: We developed a transcriptome resource for Douglas-fir covering key developmental stages of megagametophytes over time: prefertilization, fertilization, embryogenesis, and early, unfertilized abortion. Extracted RNA was sequenced using large-scale sequencing and reads were assembled to generate a de novo reference transcriptome of 105,505 predicted high-confidence transcripts. Expression levels were estimated based on alignment of the original reads to the reference. 200â400 megagametophytes were dissected and pooled per sample on four dates from either pollinated or unpollinated cones: June 10, June 22, June 30, and July 6 2011. These dates coincided with key events in seed development: corrosion cavity formation, fertilization, embryogenesis, or the early stages of abortion in the unpollinated treatment. Sporophytic tissue (i.e. cone bracts and cone scales) were added for comparison. PolyA RNA was used for Illumina sequencing.

ORGANISM(S): Pseudotsuga menziesii

SUBMITTER: Juergen Ehlting

PROVIDER: E-GEOD-83425 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Analysis of gene-expression profiles by microarrays can be very useful to characterize new potential candidate genes, key regulatory networks, and to define phenotypes or molecular signatures to improve the diagnosis or classification of the disease. We have used this approach in the study of one of the major causes of allergic diseases in Mediterranean countries, the olive pollen response, in order to find differential molecular markers among five clinical groups, Non-allergic, Asymptomatic, Allergic but not to olive pollen, Non-treated, olive pollen allergic patients and Olive pollen allergic patients (under specific-immunotherapy). The results of gene-expression by principal components analysis (PCA) clearly showed five clusters of samples that correlated with the five clinical groups. Analysis of differential gene-expression by multiple testing, and functional analysis by KEGG and Gene-Ontology revealed differential genes and pathways among the 5 clinical groups. The study population comprised 28 subjects, selected from a previous immunological study (Aguerri et al. Eur. J. Inflammation 2012, in press), from Andalusia, who were recruited in 2 olive pollen exposure situations: during (April-June) and outside the pollen season (October-December). We established 5 groups, and 6 subjects from each group were selected for gene-expression analysis: Group 1, non-allergic subjects; Group 2, asymptomatic subjects (diagnosed with olive pollen allergy by skin testing, with no seasonal respiratory symptoms [rhinitis and/or asthma], and who consulted for adverse reaction to drugs); Group 3, patients who were allergic, but not to olive pollen; Group 4, non-treated olive pollenM-bM-^@M-^Sallergic; and Group 5, olive pollenM-bM-^@M-^Sallergic patients (receiving olive pollenM-bM-^@M-^Sspecific immunotherapy).The subjects were unrelated and recruited at the Allergy Service of 4 hospitals in Andalusia (Granada, JaM-CM-)n, Sevilla, and MM-CM-!laga). Olive pollenM-bM-^@M-^Sallergic patients fulfilled the following criteria: seasonal rhinitis and/or asthma from April to June, a positive skin prick test result for O. europaea pollen extract (ALK AbellM-CM-3, Madrid, Spain), and no previous immunotherapy. Informed consent was obtained from each subject. Ethical approval for the study was obtained from the Ethical and Research Committee of the participating hospitals. PBMCs were isolated from heparin-containing peripheral blood samples taken during and outside pollen season, by gradient centrifugation on Lymphoprep (Comercial Rafer, Zaragoza, Spain) following the manufacturerM-bM-^@M-^Ys instructions.

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A transcriptomic resource for Douglas-fir seed development and analysis of transcription during late megagametophyte development

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