title: Ocean acidification research in the 'post-genomic' era: Roadmaps from the purple sea urchin Strongylocentrotus purpuratus.
abstract: Advances in nucleic acid sequencing technology are removing obstacles that historically prevented use of genomics within ocean change biology. As one of the first marine calcifiers to have its genome sequenced, purple sea urchins (Strongylocentrotus purpuratus) have been the subject of early research exploring genomic responses to ocean acidification, work that points to future experiments and illustrates the value of expanding genomic resources to other marine organisms in this new 'post-genomic' era. This review presents case studies of S. purpuratus demonstrating the ability of genomic experiments to address major knowledge gaps within ocean acidification. Ocean acidification research has focused largely on species vulnerability, and studies exploring mechanistic bases of tolerance toward low pH seawater are comparatively few. Transcriptomic responses to high pCO₂ seawater in a population of urchins already encountering low pH conditions have cast light on traits required for success in future oceans. Secondly, there is relatively little information on whether marine organisms possess the capacity to adapt to oceans progressively decreasing in pH. Genomics offers powerful methods to investigate evolutionary responses to ocean acidification and recent work in S. purpuratus has identified genes under selection in acidified seawater. Finally, relatively few ocean acidification experiments investigate how shifts in seawater pH combine with other environmental factors to influence organism performance. In S. purpuratus, transcriptomics has provided insight into physiological responses of urchins exposed simultaneously to warmer and more acidic seawater. Collectively, these data support that similar breakthroughs will occur as genomic resources are developed for other marine species.
authors.affiliation: Department of Biological Sciences, California State University East Bay, Hayward, CA 94542, USA. Electronic address: tyler.evans@csueastbay.edu.
authors.forename: Tyler G
authors.initials: TG
authors.lastname: Evans
authors.affiliation: Department of Biology, California State University Dominguez Hills, Carson, CA 90747, USA.
authors.forename: Jacqueline L
authors.initials: JL
authors.lastname: Padilla-Gamiño
authors.affiliation: Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
authors.forename: Morgan W
authors.initials: MW
authors.lastname: Kelly
authors.affiliation: Department of Biology, University of Vermont, Burlington, VT 05405, USA.
authors.forename: Melissa H
authors.initials: MH
authors.lastname: Pespeni
authors.affiliation: Department of Integrative Biology, Oregon State University, Corvallis, OR 97331-2914, USA.
authors.forename: Francis
authors.initials: F
authors.lastname: Chan
authors.affiliation: Department of Integrative Biology, Oregon State University, Corvallis, OR 97331-2914, USA.
authors.forename: Bruce A
authors.initials: BA
authors.lastname: Menge
authors.affiliation: Department of Evolution and Ecology and Bodega Marine Laboratory, University of California Davis, Bodega Bay, CA 94923, USA.
authors.forename: Brian
authors.initials: B
authors.lastname: Gaylord
authors.affiliation: Department of Geology and Bodega Marine Laboratory, University of California Davis, Bodega Bay, CA 94923, USA.
authors.forename: Tessa M
authors.initials: TM
authors.lastname: Hill
authors.affiliation: Department of Geology, University of California Davis, Davis, CA 95616, USA.
authors.forename: Ann D
authors.initials: AD
authors.lastname: Russell
authors.affiliation: Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA 93950, USA.
authors.forename: Stephen R
authors.initials: SR
authors.lastname: Palumbi
authors.affiliation: Department of Evolution and Ecology and Bodega Marine Laboratory, University of California Davis, Bodega Bay, CA 94923, USA.
authors.forename: Eric
authors.initials: E
authors.lastname: Sanford
authors.affiliation: Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106-9620, USA.
authors.forename: Gretchen E
authors.initials: GE
authors.lastname: Hofmann
mesh_terms: D000223:Adaptation, Psychological; D000818:Animals; D002245:Carbon Dioxide / Q000737:chemistry; D057231:Climate Change; D023281:Genomics; D006801:Humans; D006863:Hydrogen-Ion Concentration; D012623:Seawater / Q000737:chemistry; D047270:Strongylocentrotus purpuratus / Q000235:genetics* / Q000502:physiology
chemical_list: D002245:Carbon Dioxide
keywords: Adaptation; Climate change; Gene expression; Genomics; Ocean acidification; RNA-seq; Strongylocentrotus purpuratus; Transcriptomics; Urchin