title: Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano.
abstract: The free-living flatworm, Macrostomum lignano has an impressive regenerative capacity. Following injury, it can regenerate almost an entirely new organism because of the presence of an abundant somatic stem cell population, the neoblasts. This set of unique properties makes many flatworms attractive organisms for studying the evolution of pathways involved in tissue self-renewal, cell-fate specification, and regeneration. The use of these organisms as models, however, is hampered by the lack of a well-assembled and annotated genome sequences, fundamental to modern genetic and molecular studies. Here we report the genomic sequence of M. lignano and an accompanying characterization of its transcriptome. The genome structure of M. lignano is remarkably complex, with ∼75% of its sequence being comprised of simple repeats and transposon sequences. This has made high-quality assembly from Illumina reads alone impossible (N50=222 bp). We therefore generated 130× coverage by long sequencing reads from the Pacific Biosciences platform to create a substantially improved assembly with an N50 of 64 Kbp. We complemented the reference genome with an assembled and annotated transcriptome, and used both of these datasets in combination to probe gene-expression patterns during regeneration, examining pathways important to stem cell function.
authors.affiliation: Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724;
authors.forename: Kaja
authors.initials: K
authors.lastname: Wasik
authors.affiliation: Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724;
authors.forename: James
authors.initials: J
authors.lastname: Gurtowski
authors.affiliation: Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Molecular and Cellular Biology Graduate Program, Stony Brook University, NY 11794;
authors.forename: Xin
authors.initials: X
authors.lastname: Zhou
authors.affiliation: Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724;
authors.forename: Olivia Mendivil
authors.initials: OM
authors.lastname: Ramos
authors.affiliation: Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom;
authors.forename: M Joaquina
authors.initials: MJ
authors.lastname: Delás
authors.affiliation: Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom;
authors.forename: Giorgia
authors.initials: G
authors.lastname: Battistoni
authors.affiliation: Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724;
authors.forename: Osama
authors.initials: O
authors.lastname: El Demerdash
authors.affiliation: Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom;
authors.forename: Ilaria
authors.initials: I
authors.lastname: Falciatori
authors.affiliation: Department of Evolutionary Biology, Zoological Institute, University of Basel, 4051 Basel, Switzerland;
authors.forename: Dita B
authors.initials: DB
authors.lastname: Vizoso
authors.affiliation: Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089;
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Smith
authors.affiliation: Department of Evolutionary Biology, Institute of Zoology and Center for Molecular Biosciences Innsbruck, University of Innsbruck, A-6020 Innsbruck, Austria.
authors.forename: Peter
authors.initials: P
authors.lastname: Ladurner
authors.affiliation: Department of Evolutionary Biology, Zoological Institute, University of Basel, 4051 Basel, Switzerland;
authors.forename: Lukas
authors.initials: L
authors.lastname: Schärer
authors.affiliation: Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724;
authors.forename: W Richard
authors.initials: WR
authors.lastname: McCombie
authors.affiliation: Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom; greg.hannon@cruk.cam.ac.uk mschatz@cshl.edu.
authors.forename: Gregory J
authors.initials: GJ
authors.lastname: Hannon
authors.affiliation: Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; greg.hannon@cruk.cam.ac.uk mschatz@cshl.edu.
authors.forename: Michael
authors.initials: M
authors.lastname: Schatz
mesh_terms: D000818:Animals; D001483:Base Sequence; D016000:Cluster Analysis; D020869:Gene Expression Profiling / Q000379:methods; D063990:Gene Ontology; D017238:Genes, Helminth / Q000235:genetics; D049751:Genome, Helminth / Q000235:genetics*; D015801:Helminth Proteins / Q000145:classification / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D010986:Platyhelminths / Q000166:cytology / Q000235:genetics / Q000502:physiology; D012038:Regeneration / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid; D013234:Stem Cells / Q000378:metabolism; D059467:Transcriptome / Q000235:genetics*
chemical_list: D015801:Helminth Proteins
keywords: Macrostomum; flatworm; genome; neoblast; regeneration