Background: Despite their ecological and economical importance, conifers still have limited genomic resources, mainly due to the large size and complexity of their genomes. In addition, several of 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 the currently available transcriptomes are limited to a small number of tissues, or capture only a fraction of the genes present in the genome. Results: Here we provide an atlas of gene expression patterns for conifer Pinus sylvestris grown under natural conditions across five tissues: embryo, megagametophyte, needle, phloem, and vegetative bud. Compared to previous studies, we used a wider 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, and indication of tissue preferential upregulation or tissue preferential 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. The annotated genes were associated with a total of 84,498 GO terms, of which 1,834 had significant enrichment in different processes and functions, for example glyoxylate cycle in megagametophyte and defense response in needle. Even though most of the genes originating from the transcriptome do not have functional information in current biological databases, the tissue-specific patterns identified here provide valuable information about their potential functions for further studies. Conclusions: The genes identified in this study will contribute to improve the annotation of the already available and forthcoming conifer genomes. This atlas of gene expression also provides ground to further the research 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.

中文翻译：

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具有生态和经济意义的针叶树樟子松组织特异性和组织优先基因表达图谱

背景：尽管针叶树具有生态和经济意义，但其基因组资源仍然有限，这主要是由于其基因组的大小和复杂性。另外，一些可用的基因组资源缺乏完整的结构和功能注释。转录组学资源通常用于弥补这些不足，尽管对于大多数针叶树种而言，当前可用的转录组仅限于少数组织，或仅捕获基因组中存在的一部分基因。结果：在这里，我们提供了在自然条件下在五个组织（胚胎，大配子体，针，韧皮部和植物芽）上生长的针叶树樟子松的基因表达模式图集。与以前的研究相比，我们使用了更广泛的组织，并将我们的分析集中于组织水平上基因的表达概况。我们提供有关每个组织标准化表达水平的全面信息，并指示组织优先上调或组织优先表达。我们鉴定出总共48,001个组织优先上调和组织特异性表达的基因，其中28％在Swiss-Prot数据库中具有注释。带注释的基因与总共84,498个GO术语相关，其中1,834个在不同过程和功能（例如，大型配子体中的乙醛酸循环和针叶的防御反应）中具有显着的富集。即使大多数来自转录组的基因在当前的生物学数据库中都没有功能信息，这里确定的组织特异性模式提供了有关其潜在功能的有价值的信息，供进一步研究。结论：本研究中鉴定的基因将有助于改善已经可用和即将到来的针叶树基因组的注释。该基因表达图谱也为一般植物生理学，群体遗传学和基因组学领域的进一步研究提供了基础。当我们提供有关二倍体和单倍体生命阶段的组织特异性的信息时，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。该基因表达图谱也为一般植物生理学，群体遗传学和基因组学领域的进一步研究提供了基础。当我们提供有关二倍体和单倍体生命阶段的组织特异性的信息时，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。该基因表达图谱也为一般植物生理学，群体遗传学和基因组学领域的进一步研究提供了基础。当我们提供有关二倍体和单倍体生命阶段的组织特异性的信息时，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。