Comparative blood transcriptome analysis reveals changes in immunity, and transcripts related to metabolism and development in the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) with age

• The present study utilized RNA-Seq to find differentially expressed genes in the blood tissues of thirteen critically endangered Yangtze finless porpoises with aging. • A total of 478, 442, and 739 differentially expressed genes were identified in calf vs. adult, calf vs. old, and adult vs. old comparisons, respectively. • STEM analysis reveals significant alterations in immune, development, metabolism, and signal transduction pathways in the different age groups. • The current study provides a basis for studying Yangtze finless porpoises development, growth, and aging. The Yangtze finless porpoise (YFP), a critically endangered small odontocete species, is mostly living in the lower and middle sections of the Yangtze River and its two big adjacent lakes. The YFP population experienced a drastic decline due to the threats from various human activities. Comprehending their biology, particularly the immune changes associated with aging, is essential for ensuring their protection. The study aimed to identify genes and pathways in thirteen YFPs blood that are influenced by age, revealing their immune system’s susceptibility to aging and reduced disease response. The current research utilized RNA-Seq to find differentially expressed genes (DEGs) in blood tissues, and we screened 478, 442, and 739 DEGs in comparison groups of calf vs. adult, calf vs. old, and adult vs. old, respectively. STEM, GO and KEGG enrichment analyses revealed significant changes in metabolism, immune-related, development, signal transduction pathways, and aging among the three age-related groups. In the calf vs. adult group, the DEGs were mainly associated with primary immunodeficiency, IgA production, and B cell receptor signaling pathways. In the calf vs. old group, the DEGs were significantly enriched in autoimmune disease, cytokine interactions, and viral/bacterial infections. In the adult vs. old group, the DEGs were primarily linked to cytokine interactions and bile secretion. The current study identifies DEGs affecting immunity, development, and growth in YFPs by comparing blood transcriptomes of calves, adults, and old YFPs. This information provides a basis for studying YFP’s development, growth, and aging and will guide future research on disease prevention, treatment strategies, management, and conservation of YFP.