Transcriptome analysis of northern elephant seal (Mirounga angustirostris) muscle tissue provides a novel molecular resource and physiological insights

Abstract

Background: The northern elephant seal, Mirounga angustirostris, is a valuable animal model of fasting adaptation and hypoxic stress tolerance. However, no reference sequence is currently available for this and many other marine mammal study systems, hindering molecular understanding of marine adaptations and unique physiology.

Results: We sequenced a transcriptome of M. angustirostris derived from muscle sampled during an acute stress challenge experiment to identify species-specific markers of stress axis activation and recovery. De novo assembly generated 164,966 contigs and a total of 522,699 transcripts, of which 68.70% were annotated using mouse, human, and domestic dog reference protein sequences. To reduce transcript redundancy, we removed highly similar isoforms in large gene families and produced a filtered assembly containing 336,657 transcripts. We found that a large number of annotated genes are associated with metabolic signaling, immune and stress responses, and muscle function. Preliminary differential expression analysis suggests a limited transcriptional response to acute stress involving alterations in metabolic and immune pathways and muscle tissue maintenance, potentially driven by early response transcription factors such as Cebpd.

Conclusions: We present the first reference sequence for Mirounga angustirostris produced by RNA sequencing of muscle tissue and cloud-based de novo transcriptome assembly. We annotated 395,102 transcripts, some of which may be novel isoforms, and have identified thousands of genes involved in key physiological processes. This resource provides elephant seal-specific gene sequences, complementing existing metabolite and protein expression studies and enabling future work on molecular pathways regulating adaptations such as fasting, hypoxia, and environmental stress responses in marine mammals.

Figure 1

M. angustirostris (A) orthologs and (B) homologs of mouse ( M. musculus , red), human ( H. sapiens , blue), and domestic dog ( C. familiaris , green) genes.

Figure 2

Top gene ontology (GO) categories represented in the entire transcriptome. Numbers of genes in the entire M. angustirostris transcriptome that mapped to top GO biological process, cellular component, and molecular function terms are shown.

Figure 3

Top 20 KEGG pathways represented by annotated M. angustirostris homologs and orthologs of mouse genes.

Figure 4

M. angustirostris genes differentially expressed during an acute stress challenge. Genes differentially expressed during (A) acute stress (baseline (0 hr) versus 2 hr after ACTH administration) and (B) stress recovery (2 hr versus 24 hr after ACTH administration) conditions. Log2 fold change for each gene is shown on the x-axis, with -log10 adjusted p-value (false discovery rate < 0.05) on the y-axis. Genes that are differentially expressed at p < 0.05 are shown in red, with all other genes in grey.

Figure 5

Gene ontology categories overrepresented in differentially expressed gene datasets. Top GO biological process terms enriched in gene sets differentially expressed during acute stress (A) and recovery (B) conditions.