Understanding gene expression variations between species is pivotal for deciphering the evolutionary diversity in phenotypes. Rhesus macaques ( Macaca mulatta, MMU) and crab-eating macaques ( M. fascicularis, MFA) serve as crucial nonhuman primate biomedical models with different phenotypes. To date, however, large-scale comparative transcriptome research between these two species has not yet been fully explored. Here, we conducted systematic comparisons utilizing newly sequenced RNA-seq data from 84 samples (41 MFA samples and 43 MMU samples) encompassing 14 common tissues. Our findings revealed a small fraction of genes (3.7%) with differential expression between the two species, as well as 36.5% of genes with tissue-specific expression in both macaques. Comparison of gene expression between macaques and humans indicated that 22.6% of orthologous genes displayed differential expression in at least two tissues. Moreover, 19.41% of genes that overlapped with macaque-specific structural variants showed differential expression between humans and macaques. Of these, the FAM220A gene exhibited elevated expression in humans compared to macaques due to lineage-specific duplication. In summary, this study presents a large-scale transcriptomic comparison between MMU and MFA and between macaques and humans. The discovery of gene expression variations not only enhances the biomedical utility of macaque models but also contributes to the wider field of primate genomics.
了解物种间基因表达差异对于揭示物种表型进化及其多样性至关重要。恒河猴( Macaca mulatta)和食蟹猴（ M. fascicularis）作为生物医学研究中关键的非人灵长类动物模型，具有不同的表型特征。然而，两个物种之间的大规模转录组比较研究仍有待开展。本研究利用新测序的RNA-seq数据，对包括14种常见组织在内的84个样本（41个食蟹猴样本和43个恒河猴样本）进行了系统分析。我们的研究发现，只有少数基因（约3.7%）在两个猕猴物种之间显示出差异性表达，而约36.5%的基因在两种猕猴中均呈现出组织特异性表达。我们还对猕猴和人类的基因表达进行了比较，发现约有22.6%的同源基因在至少两种组织中存在表达差异。此外，约19.41%的猕猴谱系特有结构变异位点基因更可能在人类与猕猴之间展现出表达差异。其中， FAM220A基因在人类基因中表达水平较高，这一现象可归因于谱系特异性的重复事件。综上，该研究提供了恒河猴和食蟹猴之间，以及猕猴与人类之间转录组差异的大规模分析，为提升猕猴模型在生物医学领域的应用价值和其在灵长类基因组学中的研究提供了新见解。.
Keywords: Biomedical models; Comparative transcriptomics; Crab-eating macaques; Duplicated genes; Non-human primates; RNA-seq; Rhesus macaques.