title: Complete sequence and analysis of the mitochondrial genome of Hemiselmis andersenii CCMP644 (Cryptophyceae).
abstract: BACKGROUND
  Cryptophytes are an enigmatic group of unicellular eukaryotes with plastids derived by secondary (i.e., eukaryote-eukaryote) endosymbiosis. Cryptophytes are unusual in that they possess four genomes-a host cell-derived nuclear and mitochondrial genome and an endosymbiont-derived plastid and 'nucleomorph' genome. The evolutionary origins of the host and endosymbiont components of cryptophyte algae are at present poorly understood. Thus far, a single complete mitochondrial genome sequence has been determined for the cryptophyte Rhodomonas salina. Here, the second complete mitochondrial genome of the cryptophyte alga Hemiselmis andersenii CCMP644 is presented.
  
  
  RESULTS
  The H. andersenii mtDNA is 60,553 bp in size and encodes 30 structural RNAs and 36 protein-coding genes, all located on the same strand. A prominent feature of the genome is the presence of a approximately 20 Kbp long intergenic region comprised of numerous tandem and dispersed repeat units of between 22-336 bp. Adjacent to these repeats are 27 copies of palindromic sequences predicted to form stable DNA stem-loop structures. One such stem-loop is located near a GC-rich and GC-poor region and may have a regulatory function in replication or transcription. The H. andersenii mtDNA shares a number of features in common with the genome of the cryptophyte Rhodomonas salina, including general architecture, gene content, and the presence of a large repeat region. However, the H. andersenii mtDNA is devoid of inverted repeats and introns, which are present in R. salina. Comparative analyses of the suite of tRNAs encoded in the two genomes reveal that the H. andersenii mtDNA has lost or converted its original trnK(uuu) gene and possesses a trnS-derived 'trnK(uuu)', which appears unable to produce a functional tRNA. Mitochondrial protein coding gene phylogenies strongly support a variety of previously established eukaryotic groups, but fail to resolve the relationships among higher-order eukaryotic lineages.
  
  
  CONCLUSIONS
  Comparison of the H. andersenii and R. salina mitochondrial genomes reveals a number of cryptophyte-specific genomic features, most notably the presence of a large repeat-rich intergenic region. However, unlike R. salina, the H. andersenii mtDNA does not possess introns and lacks a Lys-tRNA, which is presumably imported from the cytosol.
authors.affiliation: Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada. eunsookim@dal.ca
authors.forename: Eunsoo
authors.initials: E
authors.lastname: Kim
authors.forename: Christopher E
authors.initials: CE
authors.lastname: Lane
authors.forename: Bruce A
authors.initials: BA
authors.lastname: Curtis
authors.forename: Catherine
authors.initials: C
authors.lastname: Kozera
authors.forename: Sharen
authors.initials: S
authors.lastname: Bowman
authors.forename: John M
authors.initials: JM
authors.lastname: Archibald
mesh_terms: D020418:Algal Proteins / Q000235:genetics; D001482:Base Composition; D001483:Base Sequence; D002874:Chromosome Mapping; D003062:Codon / Q000235:genetics; D044785:Cryptophyta / Q000145:classification / Q000235:genetics*; D017931:DNA Primers / Q000235:genetics; D048028:DNA, Algal / Q000737:chemistry / Q000235:genetics*; D004272:DNA, Mitochondrial / Q000737:chemistry / Q000235:genetics*; D019143:Evolution, Molecular; D054629:Genome, Mitochondrial; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D048030:RNA, Algal / Q000737:chemistry / Q000235:genetics; D012343:RNA, Transfer / Q000737:chemistry / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013045:Species Specificity
chemical_list: D020418:Algal Proteins; D003062:Codon; D017931:DNA Primers; D048028:DNA, Algal; D004272:DNA, Mitochondrial; D048030:RNA, Algal; D012343:RNA, Transfer