Abstract
BackgroundThe 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.ResultsWe 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.ConclusionsWe 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 materialThe online version of this article (doi:10.1186/s12864-015-1253-6) contains supplementary material, which is available to authorized users.
Highlights
The northern elephant seal, Mirounga angustirostris, is a valuable animal model of fasting adaptation and hypoxic stress tolerance
Sequence-based resources are still lacking for many non-model species such as marine mammals, hampering molecular understanding of unique adaptations and physiology
We present a reference transcriptome for M. angustirostris muscle tissue collected from juvenile animals undergoing a stress challenge experiment
Summary
The northern elephant seal, Mirounga angustirostris, is a valuable animal model of fasting adaptation and hypoxic stress tolerance. No reference sequence is currently available for this and many other marine mammal study systems, hindering molecular understanding of marine adaptations and unique physiology. Advancements in sequencing technologies and computational tools are facilitating sophisticated genomics and transcriptomics studies in non-model organisms [10]. Data reduction tools, and cloud computing are beginning to make sequencing data analysis more approachable for bench and field scientists [12,13,14]. Despite these improvements, sequence-based resources are still lacking for many non-model species such as marine mammals, hampering molecular understanding of unique adaptations and physiology. A handful of marine mammal genomes have been sequenced, annotation remains a challenge, and few transcriptomes are available [15,16,17,18,19,20,21,22]
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