title: The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell.
abstract: The giant, single-celled organism Stentor coeruleus has a long history as a model system for studying pattern formation and regeneration in single cells. Stentor [1, 2] is a heterotrichous ciliate distantly related to familiar ciliate models, such as Tetrahymena or Paramecium. The primary distinguishing feature of Stentor is its incredible size: a single cell is 1 mm long. Early developmental biologists, including T.H. Morgan [3], were attracted to the system because of its regenerative abilities-if large portions of a cell are surgically removed, the remnant reorganizes into a normal-looking but smaller cell with correct proportionality [2, 3]. These biologists were also drawn to Stentor because it exhibits a rich repertoire of behaviors, including light avoidance, mechanosensitive contraction, food selection, and even the ability to habituate to touch, a simple form of learning usually seen in higher organisms [4]. While early microsurgical approaches demonstrated a startling array of regenerative and morphogenetic processes in this single-celled organism, Stentor was never developed as a molecular model system. We report the sequencing of the Stentor coeruleus macronuclear genome and reveal key features of the genome. First, we find that Stentor uses the standard genetic code, suggesting that ciliate-specific genetic codes arose after Stentor branched from other ciliates. We also discover that ploidy correlates with Stentor's cell size. Finally, in the Stentor genome, we discover the smallest spliceosomal introns reported for any species. The sequenced genome opens the door to molecular analysis of single-cell regeneration in Stentor.
authors.affiliation: Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA.
authors.forename: Mark M
authors.initials: MM
authors.lastname: Slabodnick
authors.affiliation: Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA.
authors.forename: J Graham
authors.initials: JG
authors.lastname: Ruby
authors.affiliation: Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA.
authors.forename: Sarah B
authors.initials: SB
authors.lastname: Reiff
authors.affiliation: Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland.
authors.forename: Estienne C
authors.initials: EC
authors.lastname: Swart
authors.affiliation: Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Sager
authors.initials: S
authors.lastname: Gosai
authors.affiliation: Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Sudhakaran
authors.initials: S
authors.lastname: Prabakaran
authors.affiliation: Department of Ob/Gyn, University of California, San Francisco, San Francisco, CA 94143, USA.
authors.forename: Ewa
authors.initials: E
authors.lastname: Witkowska
authors.affiliation: Department of Biology, San Francisco State University, San Francisco, CA 94132, USA.
authors.forename: Graham E
authors.initials: GE
authors.lastname: Larue
authors.affiliation: Department of Ob/Gyn, University of California, San Francisco, San Francisco, CA 94143, USA.
authors.forename: Susan
authors.initials: S
authors.lastname: Fisher
authors.affiliation: Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Robert M
authors.initials: RM
authors.lastname: Freeman
authors.affiliation: Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Gunawardena
authors.affiliation: Department of Biology, Bradley University, Peoria, IL 61625, USA.
authors.forename: William
authors.initials: W
authors.lastname: Chu
authors.affiliation: Department of Biology, Bradley University, Peoria, IL 61625, USA.
authors.forename: Naomi A
authors.initials: NA
authors.lastname: Stover
authors.affiliation: Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Brian D
authors.initials: BD
authors.lastname: Gregory
authors.affiliation: Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland.
authors.forename: Mariusz
authors.initials: M
authors.lastname: Nowacki
authors.affiliation: Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA.
authors.forename: Joseph
authors.initials: J
authors.lastname: Derisi
authors.affiliation: Department of Biology, San Francisco State University, San Francisco, CA 94132, USA. Electronic address: scottwroy@gmail.com.
authors.forename: Scott W
authors.initials: SW
authors.lastname: Roy
authors.affiliation: Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA. Electronic address: wallace.marshall@ucsf.edu.
authors.forename: Wallace F
authors.initials: WF
authors.lastname: Marshall
authors.affiliation: Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA. Electronic address: psood1@gmail.com.
authors.forename: Pranidhi
authors.initials: P
authors.lastname: Sood
mesh_terms: D016798:Ciliophora / Q000235:genetics*; D018503:Genome, Protozoan; D007438:Introns / Q000235:genetics*; D010802:Phylogeny; D017381:Spliceosomes / Q000378:metabolism*; D000073336:Whole Genome Sequencing
keywords: U2 snRNA; cell size; ciliate; genetic code; heterotrichidae; intron evolution; macronucleus; ploidy; regeneration; splicing