The mitochondrial and chloroplast genomes of the haptophyte Chrysochromulina tobin contain unique repeat structures and gene profiles

BMC Genomics

Research Article

Rose Ann Cattolico¹  Chloe R Deodato¹  Heather M Hunsperger¹  Blake T Hovde²  Raymond J Monnat³  Laina D Mercer⁴  Shawn R Starkenburg⁵  Ramesh K Jha⁵  Olga Chertkov⁵ 

[1] Department of Biology, University of Washington, Seattle, WA, USA;Department of Genome Sciences, University of Washington, Seattle, WA, USA;Department of Genome Sciences, University of Washington, Seattle, WA, USA;Department of Pathology, University of Washington, Seattle, WA, USA;Department of Statistics, University of Washington, Seattle, WA, USA;Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM, USA;

关键词: Haptophytes;    Chloroplast genome;    Mitochondrial genome;    Repeat structure;    Repeat function;    Chrysochromulina;   

DOI  :  10.1186/1471-2164-15-604

 received in 2014-04-03, accepted in 2014-07-09,  发布年份 2014

来源: Springer

【 摘 要 】

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.

【 授权许可】

Unknown   
© Hovde et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.