title: Comparative genomic analysis of retrogene repertoire in two green algae Volvox carteri and Chlamydomonas reinhardtii.
abstract: Retroposition, one of the processes of copying the genetic material, is an important RNA-mediated mechanism leading to the emergence of new genes. Because the transcription controlling segments are usually not copied to the new location in this mechanism, the duplicated gene copies (retrocopies) become pseudogenized. However, few can still survive, e.g. by recruiting novel regulatory elements from the region of insertion. Subsequently, these duplicated genes can contribute to the formation of lineage-specific traits and phenotypic diversity. Despite the numerous studies of the functional retrocopies (retrogenes) in animals and plants, very little is known about their presence in green algae, including morphologically diverse species. The current availability of the genomes of both uni- and multicellular algae provides a good opportunity to conduct a genome-wide investigation in order to fill the knowledge gap in retroposition phenomenon in this lineage.
  
  
  
  Here we present a comparative genomic analysis of uni- and multicellular algae, Chlamydomonas reinhardtii and Volvox carteri, respectively, to explore their retrogene complements. By adopting a computational approach, we identified 141 retrogene candidates in total in both genomes, with their fraction being significantly higher in the multicellular Volvox. Majority of the retrogene candidates showed signatures of functional constraints, thus indicating their functionality. Detailed analyses of the identified retrogene candidates, their parental genes, and homologs of both, revealed that most of the retrogene candidates were derived from ancient retroposition events in the common ancestor of the two algae and that the parental genes were subsequently lost from the respective lineages, making many retrogenes 'orphan'.
  
  
  
  We revealed that the genomes of the green algae have maintained many possibly functional retrogenes in spite of experiencing various molecular evolutionary events during a long evolutionary time after the retroposition events. Our first report about the retrogene set in the green algae provides a good foundation for any future investigation of the repertoire of retrogenes and facilitates the assessment of the evolutionary impact of retroposition on diverse morphological traits in this lineage.
  
  
  
  This article was reviewed by William Martin and Piotr Zielenkiewicz.
authors.affiliation: Institute of Bioinformatics, Faculty of Medicine, University of Muenster, 48149, Muenster, Germany.
authors.forename: Marcin
authors.initials: M
authors.lastname: Jąkalski
authors.affiliation: Graduate School of Information Science and Technology, Hokkaido University, Sapporo, 060-0814, Japan.|Present address: Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, Sapporo, 062-8517, Japan.
authors.forename: Kazutaka
authors.initials: K
authors.lastname: Takeshita
authors.affiliation: Institute of Bioinformatics, Faculty of Medicine, University of Muenster, 48149, Muenster, Germany.|Present address: Julius Kühn-Institute, Institute for Resistance Research and Stress Tolerance, 06484, Quedlinburg, Germany.
authors.forename: Mathieu
authors.initials: M
authors.lastname: Deblieck
authors.affiliation: Graduate School of Information Science and Technology, Hokkaido University, Sapporo, 060-0814, Japan.
authors.forename: Kanako O
authors.initials: KO
authors.lastname: Koyanagi
authors.affiliation: Department of Bioinformatics, Faculty of Biology, Adam Mickiewicz University, 61-614, Poznań, Poland.
authors.forename: Izabela
authors.initials: I
authors.lastname: Makałowska
authors.affiliation: Graduate School of Information Science and Technology, Hokkaido University, Sapporo, 060-0814, Japan.
authors.forename: Hidemi
authors.initials: H
authors.lastname: Watanabe
authors.affiliation: Institute of Bioinformatics, Faculty of Medicine, University of Muenster, 48149, Muenster, Germany. wojmak@uni-muenster.de.
authors.forename: Wojciech
authors.initials: W
authors.lastname: Makałowski
mesh_terms: D020418:Algal Proteins / Q000235:genetics* / Q000378:metabolism; D016825:Chlamydomonas reinhardtii / Q000235:genetics*; D018745:Genome, Plant; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D018626:Retroelements; D044446:Volvox / Q000235:genetics*
chemical_list: D020418:Algal Proteins; D010940:Plant Proteins; D018626:Retroelements
keywords: Chlamydomonas; Comparative genomics; Green algae; Multicellularity; Retrogenes; Retroposition; Volvox