title: A pangenomic analysis of the Nannochloropsis organellar genomes reveals novel genetic variations in key metabolic genes.
abstract: BACKGROUND
  Microalgae in the genus Nannochloropsis are photosynthetic marine Eustigmatophytes of significant interest to the bioenergy and aquaculture sectors due to their ability to efficiently accumulate biomass and lipids for utilization in renewable transportation fuels, aquaculture feed, and other useful bioproducts. To better understand the genetic complement that drives the metabolic processes of these organisms, we present the assembly and comparative pangenomic analysis of the chloroplast and mitochondrial genomes from Nannochloropsis salina CCMP1776.
  
  
  RESULTS
  The chloroplast and mitochondrial genomes of N. salina are 98.4% and 97% identical to their counterparts in Nannochloropsis gaditana. Comparison of the Nannochloropsis pangenome to other algae within and outside of the same phyla revealed regions of significant genetic divergence in key genes that encode proteins needed for regulation of branched chain amino synthesis (acetohydroxyacid synthase), carbon fixation (RuBisCO activase), energy conservation (ATP synthase), protein synthesis and homeostasis (Clp protease, ribosome).
  
  
  CONCLUSIONS
  Many organellar gene modifications in Nannochloropsis are unique and deviate from conserved orthologs found across the tree of life. Implementation of secondary and tertiary structure prediction was crucial to functionally characterize many proteins and therefore should be implemented in automated annotation pipelines. The exceptional similarity of the N. salina and N. gaditana organellar genomes suggests that N. gaditana be reclassified as a strain of N. salina.
authors.affiliation: Bioscience Division, Los Alamos National Laboratory, Los Alamos 87545, NM, USA. shawns@lanl.gov.
authors.forename: Shawn R
authors.initials: SR
authors.lastname: Starkenburg
authors.forename: Kyungyoon J
authors.initials: KJ
authors.lastname: Kwon
authors.forename: Ramesh K
authors.initials: RK
authors.lastname: Jha
authors.forename: Cedar
authors.initials: C
authors.lastname: McKay
authors.forename: Michael
authors.initials: M
authors.lastname: Jacobs
authors.forename: Olga
authors.initials: O
authors.lastname: Chertkov
authors.forename: Scott
authors.initials: S
authors.lastname: Twary
authors.forename: Gabrielle
authors.initials: G
authors.lastname: Rocap
authors.forename: Rose Ann
authors.initials: RA
authors.lastname: Cattolico
mesh_terms: D025181:ATP Synthetase Complexes / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D000595:Amino Acid Sequence; D002736:Chloroplasts / Q000235:genetics; D016678:Genome; D054629:Genome, Mitochondrial; D008928:Mitochondria / Q000235:genetics; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D005810:Multigene Family; D017433:Protein Structure, Secondary; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D058009:Stramenopiles / Q000235:genetics*; D059467:Transcriptome
chemical_list: D025181:ATP Synthetase Complexes