Table 3_Maternal provisioning and zygotic activation: transcriptomic dynamics of early atlantic halibut (Hippoglossus hippoglossus) embryogenesis.xlsx

IntroductionIn Atlantic halibut (Hippoglossus hippoglossus) aquaculture, egg and larval quality remain major bottlenecks. Most transcriptomic and proteomic studies compare freshly fertilized eggs of good versus poor quality, assuming early molecular differences explain hatching success. However, many lethal phenotypes arise only after the mid-blastula transition (MBT), suggesting that early comparisons may overlook key developmental processes.
MethodsWe performed stage-resolved RNA sequencing of Atlantic halibut embryos spanning unfertilized egg (UF), cleavage (8C, 16C), blastula (BL), 25% epiboly (25 EB), and blastopore closure (50 degree-days, 50 dd). Differential expression analysis (DESeq2 with LFC shrinkage), Gene Ontology (GO) overrepresentation (PANTHER, REVIGO), and curated axis-patterning gene sets from zebrafish orthologs were used to map transcriptional dynamics.
ResultsMinimal transcriptional change occurred during cleavage (UF–16C), dominated by maternal transcripts. A pronounced transcriptional shift emerged at MBT (16C→BL), marked by upregulation of canonical developmental pathways (Wnt, BMP, Notch) and axis-specification genes (e.g., bmp2b, chrd, wnt8b, fgf8a). These pathways remained active through gastrulation (BL→25 EB), alongside enrichment of morphogenetic processes such as mesoderm formation and left–right symmetry. By 50 dd, expression shifted toward lineage differentiation programs involving neurons, muscle, and cranial skeleton. Axis-regulator dynamics showed that dorso–ventral (D–V) patterning is initiated by maternal factors but reinforced by zygotic cascades, whereas anterior–posterior (A–P) patterning is primarily zygotic.
DiscussionOur results demonstrate that the decisive transcriptional programs underlying axis formation and organogenesis are activated from MBT onward. These findings imply that comparisons limited to unfertilized or early cleavage stages cannot capture the biology determining embryo viability. Stage-resolved analyses encompassing MBT and gastrulation are therefore essential for identifying transcriptomic markers of egg and larval quality in halibut.

引言：在大西洋庸鲽（Hippoglossus hippoglossus）的水产养殖中，鱼卵与幼体质量始终是制约产业发展的核心瓶颈。现有多数转录组学与蛋白质组学研究均以优质与劣质新鲜受精卵为对照，假设早期分子差异可解释孵化成功率的差异。然而，诸多致死表型仅在中囊胚转换（mid-blastula transition, MBT）后才会显现，这表明早期的对照研究可能忽略了关键的发育进程。
方法：本研究对大西洋庸鲽胚胎开展了阶段分辨率RNA测序，样本覆盖未受精卵（unfertilized egg, UF）、卵裂期（8C、16C）、囊胚期（blastula, BL）、25%外包期（25% epiboly, 25 EB）以及胚孔闭合期（50度日，50 dd）。研究采用带有对数折叠变化（LFC）收缩校正的DESeq2工具进行差异表达分析、基于PANTHER与REVIGO的基因本体（Gene Ontology, GO）功能富集分析，以及基于斑马鱼同源基因的经人工整理的轴模式基因集，对转录组动态变化进行系统解析。
结果：卵裂期（UF至16C）的转录组变化极微，主要由母源转录本主导。在中囊胚转换（MBT）阶段（16C至BL）出现了显著的转录组重编程，表现为经典发育通路（Wnt、BMP、Notch）与轴特化基因（如bmp2b、chrd、wnt8b、fgf8a）的显著上调。上述通路在原肠胚形成阶段（BL至25 EB）持续活跃，同时伴随中胚层形成、左右对称性建立等形态发生过程的功能富集。至50 dd阶段，基因表达谱转向神经元、肌肉与颅面部骨骼相关的谱系分化程序。轴调控因子的动态变化显示：背腹轴（dorso-ventral, D-V）模式构建由母源因子启动，但通过合子级联反应得以强化；而前后轴（anterior-posterior, A-P）模式构建则主要依赖合子源性调控。
讨论：本研究结果表明，轴形成与器官发生背后的关键转录程序自中囊胚转换（MBT）阶段起才被激活。上述研究结果提示，仅以未受精卵或早期卵裂期为对照的研究，无法揭示决定胚胎存活能力的核心生物学机制。因此，涵盖中囊胚转换与原肠胚形成阶段的阶段分辨率转录组分析，是鉴定大西洋庸鲽鱼卵与幼体质量相关转录组标志物的必要手段。