Data from: Understanding the genomic basis of adaptive response to variable osmotic niches in freshwater prawns: a comparative intraspecific RNA-Seq analysis of Macrobrachium australiense

Understanding the molecular basis of adaptive response to variable environmental conditions is a central goal of evolutionary biology. Here we sought to identify potential outlier SNPs (single nucleotide polymorphisms) in three wild populations of a freshwater prawn (Macrobrachium australiense) that are exposed to differing osmotic niches by using a comparative transcriptomics approach. De novo assembly of approximately 542 million (75 nt) pair end reads collected from 10 individuals revealed 123,396 longer contigs/transcripts of variable length, that showed 97.38% transcriptome assembly completeness. Differential gene expression (DGE) analysis of major osmoregulatory genes revealed that Calreticulin, Na+/H+ exchanger and V-type (H+) ATPase showed the highest expression levels in the Blunder Creek (low ionic) population, while Crustacean cardiovascular peptide (CCP), Na+/K+-ATPase, Na+/K+/2Cl- Co-transporter (NKCC) and Na+/HCO3 exchanger showed the highest expression levels in the Bulimba Creek (higher ionic) population. In total, 16 gene ontology (GO) term categories were functionally enriched among the three studied populations. We identified 4144 raw and 835 high quality filtered SNPs in the three M. australiense populations, of which 84 SNPs were identified as outliers. Outliers were detected in 4 important osmoregulatory genes that include: Calreticulin, Na+/H+ exchanger, Na+/K+-ATPase and V-type-(H+)-ATPase. All outliers in the osmoregulatory genes were located in non-coding regulatory regions (untranslated regions, UTRs) of the gene. We hypothesize that the outlier SNPs identified here in M. australiense populations exposed naturally to different osmotic conditions influence specific gene expression patterns that allow individuals to respond to local environmental conditions.

解析生物对多变环境条件产生适应性响应的分子基础，是进化生物学的核心研究目标。本研究借助比较转录组学方法，旨在从栖息于不同渗透生态位的3个野生淡水沼虾（Macrobrachium australiense）种群中，筛选潜在的异常单核苷酸多态性（single nucleotide polymorphisms, SNPs）。
研究对10个个体的约5.42亿条75 nt双端测序读段进行从头组装，共获得123396条长度各异的较长重叠群/转录本，转录组组装完整性达97.38%。针对主要渗透调节基因的差异基因表达（Differential gene expression, DGE）分析显示：钙网蛋白（Calreticulin）、钠氢交换体（Na+/H+ exchanger）与V型（H+）ATP酶在布兰德尔溪（低离子强度）种群中表达量最高；而甲壳类心血管肽（Crustacean cardiovascular peptide, CCP）、钠钾ATP酶（Na+/K+-ATPase）、钠钾氯协同转运蛋白（Na+/K+/2Cl- Co-transporter, NKCC）及钠-碳酸氢根交换体（Na+/HCO3 exchanger）在布林巴溪（高离子强度）种群中表达量最高。
本研究的3个受试种群中共富集到16个基因本体（Gene Ontology, GO）功能术语类别。最终在3个M. australiense种群中鉴定出4144个原始SNPs与835个经过高质量过滤的SNPs，其中84个被判定为异常位点。这些异常位点分布于4个关键渗透调节基因中，分别为：钙网蛋白、钠氢交换体、钠钾ATP酶及V型（H+）ATP酶。渗透调节基因内的所有异常位点均位于基因的非编码调控区域，即非翻译区（untranslated regions, UTRs）。
本研究提出假说：在自然暴露于不同渗透条件的M. australiense种群中鉴定出的异常SNPs，可通过调控特定基因表达模式，帮助个体响应局部环境变化。