背景:水蚤是研究捕食者诱导的防御的合适模型生物。已经鉴定了在用D.galeata中的鱼激素处理和未处理组之间表现出差异表达的基因和途径。然而,理解可变剪接的意义,在真核生物中调节基因表达的关键过程,这种机制仍然有限。这项研究测量了生活史特征,并对两种韩国D.galeata基因型(KB1和KE2)进行了短读RNA测序和长读同工型测序,以揭示其在捕食胁迫下表型可塑性的遗传机制。
结果:KB1表现出增强生育力和减少体长的策略,而KE2部署了自适应策略来增加身体长度。来自KB1和KE2的全长转录组产生了65,736和57,437个转录本,分别,其中32种差异表达转录本(DES)在两种基因型的捕食应激下共享。两种基因型常见的突出DET与能量代谢和免疫系统有关。此外,在两种基因型中都检测到了对鱼的反应的差异选择性剪接(DAS)事件。两种基因型之间共享的DAS基因可能表明它们在对鱼类捕食的转录后应激反应中的重要作用。钙蛋白酶-3,参与消化和营养吸收,当暴露于鱼类的airomones时,在两种基因型中都被鉴定为DAS基因。此外,编码胸腺肽β的基因,这与增长有关,仅在KB1中发现有统计学意义的DAS,而编码超阿司匹林蛋白,也与增长有关,仅在KE2中识别。此外,转录本编码蛋白质,如含有EGF样结构域的蛋白质,卵黄蛋白原与超氧化物歧化酶融合,和其他人被确定为DAS事件和DES之间的重叠,并可能阐明它们与每个基因型中观察到的表型变异的关联。
结论:我们的发现强调了可变剪接在调节D.galeata捕食胁迫下转录组景观中的关键作用,强调在进化适应研究中整合基因表达和剪接分析的要求。
BACKGROUND: Daphnia galeata is a suitable model organism for investigating predator-induced defense. Genes and pathways exhibiting differential expression between fish kairomone-treated and untreated groups in D. galeata have been identified. However, understanding of the significance of alternative splicing, a crucial process of the regulation of gene expression in eukaryotes, to this mechanism remains limited. This study measured life-history traits and conducted short-read RNA sequencing and long-read isoform sequencing of two Korean D. galeata genotypes (KB1 and KE2) to uncover the genetic mechanism underlying their phenotypic plasticity under predation stress.
RESULTS: KB1 exhibited strategies to enhance fertility and decrease body length when exposed to fish kairomones, while KE2 deployed an adaptive strategy to increase body length. Full-length transcriptomes from KB1 and KE2 yielded 65,736 and 57,437 transcripts, respectively, of which 32 differentially expressed transcripts (DETs) were shared under predation stress across both genotypes. Prominent DETs common to both genotypes were related to energy metabolism and the immune system. Additionally, differential alternative splicing (DAS) events were detected in both genotypes in response to fish kairomones. DAS genes shared between both genotypes may indicate their significant role in the post-transcriptional stress response to fish predation. Calpain-3, involved in digestion and nutrient absorption, was identified as a DAS gene in both genotypes when exposed to fish kairomones. In addition, the gene encoding thymosin beta, which is related to growth, was found to be a statistically significant DAS only in KB1, while that encoding ultraspiracle protein, also associated with growth, was only identified in KE2. Moreover, transcripts encoding proteins such as EGF-like domain-containing protein, vitellogenin fused with superoxide dismutase, and others were identified overlapping between DAS events and DETs and potentially elucidating their association with the observed phenotypic variation in each genotype.
CONCLUSIONS: Our findings highlight the crucial role of alternative splicing in modulating transcriptome landscape under predation stress in D. galeata, emphasizing the requirement for integrating gene expression and splicing analyses in evolutionary adaptation studies.