Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano.
- Wasik K Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724;
- Gurtowski J Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724;
- Zhou X 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;
- Ramos OM Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724;
- Delás MJ 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;
- Battistoni G 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;
- El Demerdash O Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724;
- Falciatori I 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;
- Vizoso DB Department of Evolutionary Biology, Zoological Institute, University of Basel, 4051 Basel, Switzerland;
- Smith AD Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089;
- Ladurner P Department of Evolutionary Biology, Institute of Zoology and Center for Molecular Biosciences Innsbruck, University of Innsbruck, A-6020 Innsbruck, Austria.
- Schärer L Department of Evolutionary Biology, Zoological Institute, University of Basel, 4051 Basel, Switzerland;
- McCombie WR Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724;
- Hannon GJ 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.
- Schatz M Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; greg.hannon@cruk.cam.ac.uk mschatz@cshl.edu.
- 2015-09-23
Published in:
- Proceedings of the National Academy of Sciences of the United States of America. - 2015
Macrostomum
flatworm
genome
neoblast
regeneration
Animals
Base Sequence
Cluster Analysis
Gene Expression Profiling
Gene Ontology
Genes, Helminth
Genome, Helminth
Helminth Proteins
Molecular Sequence Data
Phylogeny
Platyhelminths
Regeneration
Sequence Homology, Nucleic Acid
Stem Cells
Transcriptome
English
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.
- Language
-
- English
- Open access status
- bronze
- Identifiers
-
- DOI 10.1073/pnas.1516718112
- PMID 26392545
- Persistent URL
- https://sonar.ch/global/documents/53605
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