Moazzzam Jazi Maryam, Seyedi Seyed Mahdi, Ebrahimie Esmaeil, Ebrahimi Mansour, De Moro Gianluca, Botanga Christopher
Plant Biotechnology Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.
School of Medicine, The University of Adelaide, Adelaide, Australia.
BMC Genomics. 2017 Aug 17;18(1):627. doi: 10.1186/s12864-017-3989-7.
Pistachio (Pistacia vera L.) is one of the most important commercial nut crops worldwide. It is a salt-tolerant and long-lived tree, with the largest cultivation area in Iran. Climate change and subsequent increased soil salt content have adversely affected the pistachio yield in recent years. However, the lack of genomic/global transcriptomic sequences on P. vera impedes comprehensive researches at the molecular level. Hence, whole transcriptome sequencing is required to gain insight into functional genes and pathways in response to salt stress.
RNA sequencing of a pooled sample representing 24 different tissues of two pistachio cultivars with contrasting salinity tolerance under control and salt treatment by Illumina Hiseq 2000 platform resulted in 368,953,262 clean 100 bp paired-ends reads (90 Gb). Following creating several assemblies and assessing their quality from multiple perspectives, we found that using the annotation-based metrics together with the length-based parameters allows an improved assessment of the transcriptome assembly quality, compared to the solely use of the length-based parameters. The generated assembly by Trinity was adopted for functional annotation and subsequent analyses. In total, 29,119 contigs annotated against all of five public databases, including NR, UniProt, TAIR10, KOG and InterProScan. Among 279 KEGG pathways supported by our assembly, we further examined the pathways involved in the plant hormone biosynthesis and signaling as well as those to be contributed to secondary metabolite biosynthesis due to their importance under salinity stress. In total, 11,337 SSRs were also identified, which the most abundant being dinucleotide repeats. Besides, 13,097 transcripts as candidate stress-responsive genes were identified. Expression of some of these genes experimentally validated through quantitative real-time PCR (qRT-PCR) that further confirmed the accuracy of the assembly. From this analysis, the contrasting expression pattern of NCED3 and SOS1 genes were observed between salt-sensitive and salt-tolerant cultivars.
This study, as the first report on the whole transcriptome survey of P. vera, provides important resources and paves the way for functional and comparative genomic studies on this major tree to discover the salinity tolerance-related markers and stress response mechanisms for breeding of new pistachio cultivars with more salinity tolerance.
阿月浑子（Pistacia vera L.）是全球最重要的商业坚果作物之一。它是一种耐盐且长寿的树种，在伊朗的种植面积最大。近年来，气候变化以及随之而来的土壤盐分增加对阿月浑子的产量产生了不利影响。然而，阿月浑子缺乏基因组/全球转录组序列阻碍了在分子水平上的全面研究。因此，需要进行全转录组测序以深入了解响应盐胁迫的功能基因和途径。
通过Illumina Hiseq 2000平台对代表两个耐盐性不同的阿月浑子品种在对照和盐处理下24种不同组织的混合样本进行RNA测序，产生了368,953,262条100 bp的干净双端 reads（90 Gb）。在创建了几个组装体并从多个角度评估其质量后，我们发现与仅使用基于长度的参数相比，将基于注释的指标与基于长度的参数一起使用可以改进对转录组组装质量的评估。采用Trinity生成的组装体进行功能注释和后续分析。总共，29,119个重叠群在包括NR、UniProt、TAIR10、KOG和InterProScan在内的所有五个公共数据库中进行了注释。在我们的组装体支持的279条KEGG途径中，由于它们在盐胁迫下的重要性，我们进一步研究了参与植物激素生物合成和信号传导以及那些有助于次生代谢物生物合成的途径。总共还鉴定出11,337个SSR，其中最丰富的是二核苷酸重复序列。此外，鉴定出13,097个转录本作为候选胁迫响应基因。通过定量实时PCR（qRT-PCR）对其中一些基因的表达进行了实验验证，进一步证实了组装体的准确性。从该分析中，在盐敏感和耐盐品种之间观察到NCED3和SOS1基因的对比表达模式。
本研究作为关于阿月浑子全转录组调查的首次报告，提供了重要资源，并为对这一主要树种进行功能和比较基因组研究铺平了道路，以发现耐盐性相关标记和应激反应机制，用于培育更耐盐的新阿月浑子品种。
