Atlas of tissue-specific and tissue-preferential gene expression in ecologically and economically significant conifer Pinus sylvestris.

Despite their ecological and economical importance, conifers genomic resources are limited, mainly due to the large size and complexity of their genomes. Additionally, the available genomic resources lack complete structural and functional annotation. Transcriptomic resources have been commonly used to compensate for these deficiencies, though for most conifer species they are limited to a small number of tissues, or capture only a fraction of the genes present in the genome. Here we provide an atlas of gene expression patterns for conifer Pinus sylvestris across five tissues: embryo, megagametophyte, needle, phloem and vegetative bud. We used a wide range of tissues and focused our analyses on the expression profiles of genes at tissue level. We provide comprehensive information of the per-tissue normalized expression level, indication of tissue preferential upregulation and tissue-specificity of expression. We identified a total of 48,001 tissue preferentially upregulated and tissue specifically expressed genes, of which 28% have annotation in the Swiss-Prot database. Even though most of the putative genes identified do not have functional information in current biological databases, the tissue-specific patterns discovered provide valuable information about their potential functions for further studies, as for example in the areas of plant physiology, population genetics and genomics in general. As we provide information on tissue specificity at both diploid and haploid life stages, our data will also contribute to the understanding of evolutionary rates of different tissue types and ploidy levels.

尽管针叶树在生态和经济方面具有重要意义，但其基因组资源有限，这主要是由于它们的基因组庞大且复杂。此外，现有的基因组资源缺乏完整的结构和功能注释。转录组资源通常被用于弥补这些不足，然而对于大多数针叶树物种来说，这些资源仅限于少数组织，或者仅涵盖基因组中存在的一部分基因。在此，我们提供了欧洲赤松（Pinus sylvestris）在五种组织（胚胎、雌配子体、针叶、韧皮部和营养芽）中的基因表达模式图谱。我们使用了多种组织，并将分析重点放在组织层面的基因表达谱上。我们提供了每个组织标准化表达水平的综合信息、组织优先上调的指示以及表达的组织特异性。我们总共鉴定出48001个组织优先上调和组织特异性表达的基因，其中28%在瑞士蛋白质数据库（Swiss - Prot database）中有注释。尽管鉴定出的大多数假定基因在当前的生物数据库中没有功能信息，但所发现的组织特异性模式为进一步研究其潜在功能提供了有价值的信息，例如在植物生理学、群体遗传学以及一般的基因组学等领域。由于我们提供了二倍体和单倍体生命阶段的组织特异性信息，我们的数据也将有助于理解不同组织类型和倍性水平的进化速率。