Abstract
BackgroundHaptophytes are widely and abundantly distributed in both marine and freshwater ecosystems. Few genomic analyses of representatives within this taxon have been reported, despite their early evolutionary origins and their prominent role in global carbon fixation.ResultsThe complete mitochondrial and chloroplast genome sequences of the haptophyte Chrysochromulina tobin (Prymnesiales) provide insight into the architecture and gene content of haptophyte organellar genomes. The mitochondrial genome (~34 kb) encodes 21 protein coding genes and contains a complex, 9 kb tandem repeat region. Similar to other haptophytes and rhodophytes, but not cryptophytes or stramenopiles, the mitochondrial genome has lost the nad7, nad9 and nad11 genes. The ~105 kb chloroplast genome encodes 112 protein coding genes, including ycf39 which has strong structural homology to NADP-binding nitrate transcriptional regulators; a divergent ‘CheY-like’ two-component response regulator (ycf55) and Tic/Toc (ycf60 and ycf80) membrane transporters. Notably, a zinc finger domain has been identified in the rpl36 ribosomal protein gene of all chloroplasts sequenced to date with the exception of haptophytes and cryptophytes - algae that have gained (via lateral gene transfer) an alternative rpl36 lacking the zinc finger motif. The two C. tobin chloroplast ribosomal RNA operon spacer regions differ in tRNA content. Additionally, each ribosomal operon contains multiple single nucleotide polymorphisms (SNPs) - a pattern observed in rhodophytes and cryptophytes, but few stramenopiles. Analysis of small (<200 bp) chloroplast encoded tandem and inverted repeats in C. tobin and 78 other algal chloroplast genomes show that repeat type, size and location are correlated with gene identity and taxonomic clade.ConclusionThe Chrysochromulina tobin organellar genomes provide new insight into organellar function and evolution. These are the first organellar genomes to be determined for the prymnesiales, a taxon that is present in both oceanic and freshwater systems and represents major primary photosynthetic producers and contributors to global ecosystem stability.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-604) contains supplementary material, which is available to authorized users.
Highlights
Haptophytes are widely and abundantly distributed in both marine and freshwater ecosystems
Recent estimates indicate that haptophytes alone may represent “...30-50% of total photosynthetic standing stock in the world’s oceans” [2], where they play a key role in carbon fixation
We have identified ycf80 as a Tic22 translocator protein homolog. ycf80 homologs are found exclusively in the chloroplast genomes of the haptophytes C. tobin, E. huxleyi, P. antarctica and the uncultured prymnesiophyte C19847, as well as rhodophytes
Summary
Haptophytes are widely and abundantly distributed in both marine and freshwater ecosystems. Few genomic analyses of representatives within this taxon have been reported, despite their early evolutionary origins and their prominent role in global carbon fixation. Primary producers fix ~100 gigatons of carbon each year [1]. This production is distributed between terrestrial and aquatic ecosystems [1]. Some haptophyte species are photosynthetic as well as mixotrophic, can live in dysphotic zones where light levels are too low to support photosynthesis [3]. This metabolic versatility may contribute to fitness, and help explain haptophyte prevalence within global algal populations
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