title: Collembolan Transcriptomes Highlight Molecular Evolution of Hexapods and Provide Clues on the Adaptation to Terrestrial Life.
abstract: BACKGROUND
  Collembola (springtails) represent a soil-living lineage of hexapods in between insects and crustaceans. Consequently, their genomes may hold key information on the early processes leading to evolution of Hexapoda from a crustacean ancestor.
  
  
  METHODS
  We assembled and annotated transcriptomes of the Collembola Folsomia candida and Orchesella cincta, and performed comparative analysis with protein-coding gene sequences of three crustaceans and three insects to identify adaptive signatures associated with the evolution of hexapods within the pancrustacean clade.
  
  
  RESULTS
  Assembly of the springtail transcriptomes resulted in 37,730 transcripts with predicted open reading frames for F. candida and 32,154 for O. cincta, of which 34.2% were functionally annotated for F. candida and 38.4% for O. cincta. Subsequently, we predicted orthologous clusters among eight species and applied the branch-site test to detect episodic positive selection in the Hexapoda and Collembola lineages. A subset of 250 genes showed significant positive selection along the Hexapoda branch and 57 in the Collembola lineage. Gene Ontology categories enriched in these genes include metabolism, stress response (i.e. DNA repair, immune response), ion transport, ATP metabolism, regulation and development-related processes (i.e. eye development, neurological development).
  
  
  CONCLUSIONS
  We suggest that the identified gene families represent processes that have played a key role in the divergence of hexapods within the pancrustacean clade that eventually evolved into the most species-rich group of all animals, the hexapods. Furthermore, some adaptive signatures in collembolans may provide valuable clues to understand evolution of hexapods on land.
authors.affiliation: Department of Ecological Science, VU University Amsterdam, Amsterdam, The Netherlands.
authors.forename: A
authors.initials: A
authors.lastname: Faddeeva
authors.affiliation: EMBL-European Bioinformatics Institute, Cambridge, United Kingdom.
authors.forename: R A
authors.initials: RA
authors.lastname: Studer
authors.affiliation: Department of Ecological Science, VU University Amsterdam, Amsterdam, The Netherlands.
authors.forename: K
authors.initials: K
authors.lastname: Kraaijeveld
authors.affiliation: Microarray Facility, VU Medical Center, Amsterdam, The Netherlands.
authors.forename: D
authors.initials: D
authors.lastname: Sie
authors.affiliation: Microarray Facility, VU Medical Center, Amsterdam, The Netherlands.
authors.forename: B
authors.initials: B
authors.lastname: Ylstra
authors.affiliation: Department of Ecological Science, VU University Amsterdam, Amsterdam, The Netherlands.
authors.forename: J
authors.initials: J
authors.lastname: Mariën
authors.affiliation: Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands.
authors.forename: H J M
authors.initials: HJ
authors.lastname: op den Camp
authors.affiliation: Keygene NV, Wageningen, The Netherlands.
authors.forename: E
authors.initials: E
authors.lastname: Datema
authors.affiliation: Leiden Genome Technology Center, Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.
authors.forename: J T
authors.initials: JT
authors.lastname: den Dunnen
authors.affiliation: Department of Ecological Science, VU University Amsterdam, Amsterdam, The Netherlands.
authors.forename: N M
authors.initials: NM
authors.lastname: van Straalen
authors.affiliation: Department of Ecological Science, VU University Amsterdam, Amsterdam, The Netherlands.
authors.forename: D
authors.initials: D
authors.lastname: Roelofs
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D000818:Animals; D001181:Arthropods / Q000145:classification* / Q000235:genetics*; D001483:Base Sequence; D005075:Biological Evolution; D019143:Evolution, Molecular; D059014:High-Throughput Nucleotide Sequencing; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D059467:Transcriptome / Q000235:genetics