Data from: First insights into the transcriptome and development of new genomic tools of a widespread circum-Mediterranean tree species, Pinus halepensis Mill.

Pinus halepensis is a relevant conifer species for studying adaptive responses to drought and fire regimes in the Mediterranean region. Deciphering the molecular basis of Aleppo pine to the Mediterranean environment is therefore needed. In this study we performed Illumina next-generation sequencing of two phenotypically divergent Pinus halepensis accessions with the aims of i) characterizing the transcriptome through Illumina RNA-Seq of two accessions, phenotypically divergent for adaptive traits link to fire adaptation and drought, ii) performing a functional annotation of the assembled transcriptome, iii) identifying genes with accelerated evolutionary rates, iv) studying the expression levels of the annotated genes, and v) developing gene-based markers for population genomic and association genetic studies. The assembled transcriptome consisted in 48,629 contigs and covered about 54.6 Mbp. The comparison of P. halepensis transcripts to Picea sitchensis protein-coding sequences resulted in the detection of 34,014 SNPs across species, with a Ka/Ks average value of 0.216, suggesting that the majority of the assembled genes are under negative selection. Assembled genes showed an over-representation in expression of genes involved in protein synthesis. Several genes were differentially expressed across the two pine accessions with contrasted phenotypes, including glutathione s-transferase, the cellulose synthase and the cobra-like protein . A large number of new markers (8,248 SSRs and 28,236 SNPs) has been identified which should facilitate future population genomics and association genetics in this species. Our results showed that Illumina next-generation sequencing is a valuable technology to obtain an extensive overview on whole transcriptomes of non-model species with large genomes.阿勒颇松（Pinus halepensis）是研究地中海地区干旱与火格局适应性响应的代表性针叶树种。解析阿勒颇松适应地中海环境的分子基础，因此具备重要研究意义。 本研究对两个在与火适应和干旱适应相关的适应性性状上存在表型分化的阿勒颇松种质开展了Illumina下一代测序，旨在实现以下5项研究目标：① 通过对上述两个种质进行Illumina RNA测序，解析其转录组；② 对组装得到的转录组进行功能注释；③ 鉴定进化速率加快的基因；④ 分析注释基因的表达水平；⑤ 开发基于基因的分子标记，用于种群基因组学与关联遗传学研究。 本次组装获得的转录组包含48629个重叠群（contigs），总覆盖长度约54.6 Mbp。 将阿勒颇松的转录本与西加云杉（Picea sitchensis）的蛋白质编码序列进行比对后，共检测到跨物种的34014个单核苷酸多态性（SNPs），平均Ka/Ks值为0.216，表明大部分组装基因处于负选择压力之下。 组装基因在蛋白质合成相关通路中的表达呈现显著富集。 两个表型存在显著差异的松树种质间存在大量差异表达基因，包括谷胱甘肽S-转移酶、纤维素合酶以及类cobra蛋白。 本研究共鉴定出8248个简单序列重复（SSRs）标记与28236个单核苷酸多态性标记，这类新型分子标记将为该物种后续的种群基因组学与关联遗传学研究提供重要助力。 本研究结果表明，Illumina下一代测序技术是获取大基因组非模式物种全转录组全景信息的有效技术手段。