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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.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1253-6) contains supplementary material, which is available to authorized users.

bmc genomics

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