Transcriptome profiling in conifers and the PiceaGenExpress database show patterns of diversification within gene families and interspecific conservation in vascular gene expression

Abstract

BackgroundConifers have very large genomes (13 to 30 Gigabases) that are mostly uncharacterized although extensive cDNA resources have recently become available. This report presents a global overview of transcriptome variation in a conifer tree and documents conservation and diversity of gene expression patterns among major vegetative tissues.ResultsAn oligonucleotide microarray was developed from Picea glauca and P. sitchensis cDNA datasets. It represents 23,853 unique genes and was shown to be suitable for transcriptome profiling in several species. A comparison of secondary xylem and phelloderm tissues showed that preferential expression in these vascular tissues was highly conserved among Picea spp. RNA-Sequencing strongly confirmed tissue preferential expression and provided a robust validation of the microarray design. A small database of transcription profiles called PiceaGenExpress was developed from over 150 hybridizations spanning eight major tissue types. In total, transcripts were detected for 92% of the genes on the microarray, in at least one tissue. Non-annotated genes were predominantly expressed at low levels in fewer tissues than genes of known or predicted function. Diversity of expression within gene families may be rapidly assessed from PiceaGenExpress. In conifer trees, dehydrins and late embryogenesis abundant (LEA) osmotic regulation proteins occur in large gene families compared to angiosperms. Strong contrasts and low diversity was observed in the dehydrin family, while diverse patterns suggested a greater degree of diversification among LEAs.ConclusionTogether, the oligonucleotide microarray and the PiceaGenExpress database represent the first resource of this kind for gymnosperm plants. The spruce transcriptome analysis reported here is expected to accelerate genetic studies in the large and important group comprised of conifer trees.

CNVs into the wild: screening the genomes of conifer trees (Picea spp.) reveals fewer gene copy number variations in hybrids and links to adaptation

“…Expression levels for 81.5% of the gene CNVs were previously assessed in various organs at different stages of development in white spruce for a total of eight tissues [38]. Gene CNVs appeared expressed in wide range of tissues and organs, including vegetative buds, foliage, primary and secondary xylem, phelloderm, roots, megagametophyte and embryogenic cells with no significant enrichment for any of them.…”

“…Genome draft assemblies have been obtained for the diploid genomes of white spruce [33, 34] and Norway spruce [35] but are highly fragmented. However, considerable genome resources are available for white spruce including a gene catalog [36], sequence capture datasets [37], and a gene expression database [38]. …”

De novo assembly and characterization of stress transcriptome and regulatory networks under temperature, salt and hormone stresses in Lilium lancifolium

“…This technology could also efficiently generate the functional genomic data and protein annotation for non-model organisms [16,17]. Successfully, many studies have assessed global gene expression of several plants in response to various environmental stimuli, including Populus euphratica [18,19], Cybidium sinense [20,21], Zea mays [22], Sea-buckthorn [23] Soybean [24].…”

Forest tree genomics: 10 achievements from the past 10 years and future prospects

“…Microarray and RNA sequencing methods have recently provided critical advances for the genome-wide profiling of gene expression. Transcriptomics is developing rapidly in conifers, with the recent advent of large genomic resources (Lorenz et al 2012;Raherison et al 2012;Canales et al 2014), including draft genomes for Picea (Birol et al 2013;Nystedt et al 2013) and Pinus .…”