Abstract
Cetaceans are a group of secondary aquatic mammals whose ancestors returned to the ocean from land, and during evolution, their immune systems adapted to the aquatic environment. Their skin, as the primary barrier to environmental pathogens, supposedly evolved to adapt to a new living environment. However, the immune system in the skin of cetaceans and the associated molecular mechanisms are still largely unknown. To better understand the immune system, we extracted RNA from the sperm whale’s (Physeter macrocephalus) skin and performed PacBio full-length sequencing and RNA-seq sequencing. We obtained a total of 96,350 full-length transcripts with an average length of 1705 bp and detected 5150 genes that were associated with 21 immune-related pathways by gene annotation enrichment analysis. Moreover, we found 89 encoding genes corresponding to 33 proteins were annotated in the NOD-like receptor (NLR)-signaling pathway, including NOD1, NOD2, RIP2, and NF-κB genes, which were discussed in detail and predicted to play essential roles in the immune system of the sperm whale. Furthermore, NOD1 was highly conservative during evolution by the sequence comparison and phylogenetic tree. These results provide new information about the immune system in the skin of cetaceans, as well as the evolution of immune-related genes.
Highlights
Cetaceans are a group of secondary aquatic mammals whose ancestors returned to the ocean from land and gradually evolved into the dominant group of marine mammals approximately 53 million years ago [1], which is one of the most dramatic events in the history of biological evolution
All consensus sequences (CCS) reads were further classified into four categories, full-length non-chimeric (FLnc), chimeric, non-full-length, and short reads
89 encoding genes corresponding to 33 proteins related to the nucleotide-binding oligomerization domain (NOD)-like receptor-signaling pathway of innate immunity were discovered in the skin of the sperm whale
Summary
Cetaceans (whales, dolphins, and porpoise) are a group of secondary aquatic mammals whose ancestors returned to the ocean from land and gradually evolved into the dominant group of marine mammals approximately 53 million years ago [1], which is one of the most dramatic events in the history of biological evolution. They are the largest living toothed whale and are found in all oceans of the world [3,4]. Sperm whales are the deepest diving whales, who can dive to a depth of 3000 m and stay underwater for at least 138 min [5]. These characteristics imply they may have unique adaptations and an important phylogenetic position [6,7]. Since 2012, it has been included in the Red List of Threatened Species by the International Union for the Conservation of Nature and Natural Resources (IUCN) [8]
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