Transcriptomic profiles of spring and summer populations of the Southern Ocean salp, Salpa thompsoni, in the Western Antarctic Peninsula region

Polar Biology volume 40, pages1261–1276(2017)Cite this article

Abstract

The Southern Ocean salp, Salpa thompsoni (Tunicata, Thaliacea), is a pivotal species in the pelagic ecosystem of the Western Antarctic Peninsula (WAP), one of the fastest warming regions of the world oceans. This study produced a complete reference transcriptome for S. thompsoni containing 216,931 sequences; 41,210 (18%) were associated with predicted, hypothetical, or known proteins; 13,058 (6%) were mapped and annotated. Whole-transcriptome (RNA-seq) analysis of 39 samples collected during austral spring and summer 2011 in the WAP and in summer 2009 in the Indian Sector revealed clustering of samples by regions, seasons, and areas (Bray–Curtis similarity). The highest numbers of differentially expressed genes at the 4×, 20×, and 100× fold-change levels were found between salps collected during spring versus summer 2011 in the WAP (analysis of variance, ANOVA). Spring versus summer samples showed significant differential expression of 77 genes associated with environmental stress response and 51 genes associated with sexual reproduction (paired t tests, p < 0.05), with significant association between expression of these genes and temperature at the collection site shown by multidimensional scaling analysis. Gene Ontology (GO) term enrichment analysis identified 41 GO terms responsible for spring versus summer differences, including 156 genes associated with translation (i.e., protein synthesis). The reference transcriptome and characterization of time/space patterns of whole-transcriptome and target gene differential expression provide a foundation for functional analysis and identification of molecular markers of physiological condition, life history events, and responses to climate change in this key species in Antarctic pelagic ecosystems.

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Acknowledgements

The authors thank the Captain and crew of the Polarstern (cruise ANT-XXVII-2), the LM Gould (cruise LMG11-10), and the Umitaka Maru (cruise UM08-09), and the participating scientists for their valuable assistance and support. Access to UM08-09 environmental data was provided by Fuminori Hashihama (Tokyo University of Marine Science and Technology). We are grateful to Claudia Koerting (University of Connecticut) for her expertise and access to multiuser laboratory instrumentation. Thanks are due to Craig Obergfell and Nathaniel Jue (University of Connecticut) for providing support with next-generation sequencing technologies and data analysis and to the University of Connecticut Center for Genome Innovation for access to instrumentation, training, and support for this research. Funding was provided by NSF Antarctic Research (Award No. PLR-1044982 to AB and RJO) and the University of Connecticut Department of Marine Sciences.

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Author notes

  1. Batta-Lona PG

    Present address: Department of Marine Biotechnology, CICESE, Ensenada, BC, Mexico

  2. Maas AE

    Present address: Bermuda Institute of Ocean Sciences, St. George’s, GE01, Bermuda

Affiliations

  1. Department of Marine Sciences, University of Connecticut, Groton, CT, 06340, USA

    Batta-Lona PG & Bucklin A

  2. Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA

    Maas AE & Wiebe PH

  3. Department of Molecular and Cell Biology, Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA

    O’Neill RJ

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Correspondence to Bucklin A.

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PG, BL., AE, M., RJ, O. et al. Transcriptomic profiles of spring and summer populations of the Southern Ocean salp, Salpa thompsoni, in the Western Antarctic Peninsula region. Polar Biol 40, 1261–1276 (2017). https://doi.org/10.1007/s00300-016-2051-6

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Keywords

  • Salpa thompsoni
  • Environmental transcriptomics
  • RNA-seq
  • Gene expression
  • Southern Ocean