title: Retained duplicate genes in green alga Chlamydomonas reinhardtii tend to be stress responsive and experience frequent response gains.
abstract: BACKGROUND
  Green algae belong to a group of photosynthetic organisms that occupy diverse habitats, are closely related to land plants, and have been studied as sources of food and biofuel. Although multiple green algal genomes are available, a global comparative study of algal gene families has not been carried out. To investigate how gene families and gene expression have evolved, particularly in the context of stress response that have been shown to correlate with gene family expansion in multiple eukaryotes, we characterized the expansion patterns of gene families in nine green algal species, and examined evolution of stress response among gene duplicates in Chlamydomonas reinhardtii.
  
  
  RESULTS
  Substantial variation in domain family sizes exists among green algal species. Lineage-specific expansion of families occurred throughout the green algal lineage but inferred gene losses occurred more often than gene gains, suggesting a continuous reduction of algal gene repertoire. Retained duplicates tend to be involved in stress response, similar to land plant species. However, stress responsive genes tend to be pseudogenized as well. When comparing ancestral and extant gene stress response state, we found that response gains occur in 13% of duplicate gene branches, much higher than 6% in Arabidopsis thaliana.
  
  
  CONCLUSIONS
  The frequent gains of stress response among green algal duplicates potentially reflect a high rate of innovation, resulting in a species-specific gene repertoire that contributed to adaptive response to stress. This could be further explored towards deciphering the mechanism of stress response, and identifying suitable green algal species for oil production.
authors.affiliation: Cell and Molecular Biology Program, Michigan State University, East Lansing, MI, USA. wuguangx@msu.edu.
authors.forename: Guangxi
authors.initials: G
authors.lastname: Wu
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, MI, USA. davidehuf@gmail.com.
authors.forename: David E
authors.initials: DE
authors.lastname: Hufnagel
authors.affiliation: Biochemie der Pflanzen, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany. alisandra.denton@hhu.de.
authors.forename: Alisandra K
authors.initials: AK
authors.lastname: Denton
authors.affiliation: Cell and Molecular Biology Program, Michigan State University, East Lansing, MI, USA. shius@msu.edu.|Department of Plant Biology, Michigan State University, East Lansing, MI, USA. shius@msu.edu.
authors.forename: Shin-Han
authors.initials: SH
authors.lastname: Shiu
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D005075:Biological Evolution; D016825:Chlamydomonas reinhardtii / Q000235:genetics*; D020131:Genes, Duplicate; D008040:Genetic Linkage; D018745:Genome, Plant; D018384:Oxidative Stress; D011544:Pseudogenes; D012337:RNA, Ribosomal, 18S / Q000235:genetics / Q000378:metabolism
chemical_list: D012337:RNA, Ribosomal, 18S