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

机译：深入了解广谱的地中海-地中海树种Pinus halepensis Mill的转录组和新基因组工具的开发

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Aleppo pine (Pinus halepensis Mill.) is a relevant conifer species for studying adaptive responses to drought and fire regimes in the Mediterranean region. In this study, we performed Illumina next-generation sequencing of two phenotypically divergent Aleppo pine accessions with the aims of (i) characterizing the transcriptome through Illumina RNA-Seq on trees phenotypically divergent for adaptive traits linked 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 of 48 629 contigs and covered about 54.6 Mbp. The comparison of Aleppo pine 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. Several genes were differentially expressed across the two pine accessions with contrasted phenotypes, including a glutathione-s-transferase, a cellulose synthase and a cobra-like protein. A large number of new markers (3334 amplifiable SSRs and 28 236 SNPs) have been identified which should facilitate future population genomics and association genetics in this species. A 384-SNP Oligo Pool Assay for genotyping with the Illumina VeraCode technology has been designed which showed an high overall SNP conversion rate (76.6%). Our results showed that Illumina next-generation sequencing is a valuable technology to obtain an extensive overview on whole transcriptomes of nonmodel species with large genomes. © 2014 John Wiley & Sons Ltd.
机译：阿勒颇松（Pinus halepensis Mill。）是一种相关的针叶树种，用于研究地中海地区对干旱和火灾的适应性反应。在这项研究中，我们对两种表型不同的阿勒颇松种进行了Illumina下一代测序，目的是（i）通过Illumina RNA-Seq在树木上通过与火适应和干旱相关的适应性状在表型上有所差异来表征转录组。（ii）进行组装的转录组的功能注释，（iii）鉴定具有加速进化速率的基因，（iv）研究带注释的基因的表达水平，以及（v）开发用于人群基因组和关联遗传研究的基于基因的标记。组装的转录组由48 629个重叠群组成，覆盖约54.6 Mbp。阿勒颇松树转录本与云杉云杉蛋白编码序列的比较导致在整个物种中检测到34个014个SNP，Ka / Ks平均值为0.216，这表明大多数组装基因处于负选择状态。在两个松树种之间，具有不同表型的几种基因差异表达，包括谷胱甘肽-S-转移酶，纤维素合酶和眼镜蛇样蛋白。已经鉴定出大量新标记（3334个可扩增SSR和28236个SNP），这些标记应有助于该物种的未来种群基因组学和关联遗传学。已设计出一种用于Illumina VeraCode技术进行基因分型的384-SNP Oligo Pool检测法，该方法显示出较高的总SNP转化率（76.6％）。我们的结果表明，Illumina下一代测序是一种有价值的技术，可以广泛地概述具有大基因组的非模型物种的完整转录组。 ©2014 John Wiley＆Sons Ltd.。

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