Elsevier

Gene

Volume 476, Issues 1–2, 1 May 2011, Pages 20-26
Gene

Complex repeat structures and novel features in the mitochondrial genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana

https://doi.org/10.1016/j.gene.2011.02.001Get rights and content

Abstract

The mitochondrial genome of the raphid pennate diatom Phaeodactylum tricornutum has several novel features compared with the mitochondrial genomes of the centric diatom Thalassiosira pseudonana and the araphid pennate diatom Synedra acus. It is almost double the size (77,356 bp) due to a 35,454 bp sequence block consisting of an elaborate combination of direct repeats, making it the largest stramenopile (heterokont) mitochondrial genome known. In addition, the cox1 gene has a + 1 translational frameshift involving Pro codons CCC and CCT, the first translational frameshift to be detected in an algal mitochondrial genome. The nad9 and rps14 genes are fused by the insertion of an in-frame sequence and cotranscribed. The nad11 gene is split into two parts corresponding to the FeS and molybdate-binding domains, but both parts are still on the mitochondrial genome, in contrast to the brown algae where the second domain appears to have been transferred to the nucleus. In contrast to P. tricornutum, the repeat region of T. pseudonana consists of a much smaller 4790 bp string of almost identical double-hairpin elements, evidence of slipped-strand mispairing and active gene conversion. The diatom mitochondrial genomes have undergone considerable gene rearrangement since the three lineages of diatoms diverged, but all three have kept their repeat regions segregated from their relatively compact coding regions.

Introduction

The stramenopiles (heterokonts) are one of the major groups of eukaryotes, including both photosynthetic and non-photosynthetic taxa. The photosynthetic stramenopile algae include major contributors to the ocean biota such as the diatoms, macroscopic brown seaweeds, chrysophytes, raphidophytes and xanthophytes. The non-photosynthetic stramenopiles include the oomycetes, labyrinthulids and bicosoecids. This diverse assemblage is unified by ultrastructural features, particularly the unique tripartite tubular hairs called mastigonemes (Patterson, 1989, Patterson, 1999, Adl et al., 2005), and by sequence relatedness and molecular phylogenetic analyses (Andersen, 2004). Molecular data also support the monophyly of the photosynthetic heterokonts, but their exact relationship to the non-photosynthetic heterokonts is not so well resolved. A study using mitochondrial genome sequences supported the idea that the oomycetes are sister group to the photosynthetic stramenopiles, with the non-photosynthetic bicosoecid Cafeteria basal to them (Oudot-Le Secq et al., 2006). Multigene phylogenies of nuclear genes also put the labyrinthulid Thraustochytrium in the basal group (Riisberg et al., 2000).

Mitochondrial genomes come in all shapes and sizes (Bullerwell and Gray, 2004, Burger et al., 2003). In general, animal genomes are small and circular, encoding 36–37 genes, whereas fungal genomes are more diverse, encoding from 20 to more than 50 genes. Plant mitochondrial genomes appear to be very large in size and probably consist of linear and branched concatenates, although they map as a circle and carry only 60–70 genes (Oldenburg and Bendich, 2001, Kubo and Newton, 2008). In the last few years, a number of mitochondrial genomes from other major eukaryotic divisions have been sequenced, and it is clear that there is a great variety in size, conformation and unique structural features in the mitochondrial genome universe. The organism carrying the largest number of mitochondrial genes is a Jakobid, Reclinomonas americana, with 97 genes including the eubacterial RNA polymerase subunits which are missing in all other mitochondrial genomes (Lang et al., 1997). In other eukaryotes so far examined, the bacterial polymerase has been replaced by a nucleus-encoded phage-type single unit RNA polymerase. However, the mitochondrial genome of the brown alga Pylaiella littoralis does encode a phage-type RNA polymerase gene that is transcribed and therefore has the potential to be functional (Rousvoal et al., 1998).

A number of stramenopile mitochondrial genomes have been sequenced, in particular those of brown algae (reviewed by Oudot-Le Secq et al., 2006) and the plant-pathogenic oomycetes (reviewed by Martin et al., 2007). The mitochondrial sequence of the centric diatom Thalassiosira pseudonana has been deposited in Genbank and used for molecular phylogeny (Oudot-Le Secq et al., 2006), but no analysis of its structure has been published. The sequence of the araphid pennate diatom Synedra acus was published while this manuscript was in preparation (Ravin et al., 2010). In this work, we report the complete mitochondrial genome sequence of a third type of diatom, the raphid pennate Phaeodactylum tricornutum. These represent the three major categories of diatom: the centrics distinguished by radial symmetry and the pennates with bilateral symmetry; the latter being divided into raphid pennates that have a slit in the silica frustule associated with gliding motility (raphe) whereas the araphid pennates do not (Graham and Wilcox, 2000).

The Phaeodactylum tricornutum mitochondrial genome has several novel features, including a large block of repeats (about 35 kbp) uninterrupted by genes, which make it almost double the size of the other two diatom mitochondrial genomes. The nature of the repeats is completely different from those in the smaller (< 5 kbp) repeat regions of T. pseudonana and S. acus. We compare these diatom mitochondrial genomes with those of other photosynthetic heterokonts, and with representatives of two major sister groups: the cryptophytes Rhodomonas salina and Hemiselmis andersonii and the haptophyte Emiliania huxleyii (Hauth et al., 2007; Kim et al., 2008, Sanchez-Puerta et al., 2004).

Section snippets

Sequencing and assembly

The mitochondrial genome sequences were obtained as part of the whole genome sequencing of Thalassiosira pseudonana (Armbrust et al., 2004) and Phaeodactylum tricornutum (Bowler et al., 2008) at the U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, USA. The monoclonal culture of Phaeodactylum tricornutum chosen for sequencing was CCAP1055/1, derived from a single cell of strain CCMP632. The sequences of all three genomes (nuclear, chloroplast, mitochondrion) of this diatom

Structural features of the mitochondrial genomes

Both P. tricornutum and T. pseudonana mitochondrial genomes map as circles, but they are markedly different in size (Table 1). Each has a block of repeat sequences, segregated in one region of the genome, but the repeat block in P. tricornutum is so large (35 454 bp) that it accounts for almost half the total genome size of 77,356 bp. Aside from the repeat region, both genomes are relatively compact: the average intergenic spacer is only 157 bp for T. pseudonana compared to 841 bp for P.

Stramenopile (heterokont) mitochondrial genomes follow a common pattern

We now have enough mitochondrial genome sequences from stramenopiles to make some generalizations about gene content and organization. In addition to sequences from the three major types of diatom (P. tricornutum, T. pseudonana and S. acus), there are now sequences for at least six brown algae (Oudot-Le Secq et al., 2006, Yotsukura et al., 2010), the chrysophytes Chrysodidimus synuroideus (Chesnick et al., 2000) and Ochromonas danica (NC_002571) and the raphidophytes Heterosigma akashiwo (Karol

Acknowledgments

Sequencing and assembly were carried out at the US DOE Joint Genome Institute, and finishing was done at Stanford University. We thank our colleagues at JGI for their assistance, particularly Jane Grimwood, as well as Igor Grigoriev, Alan Kuo, Robert Otillar and Chris Bowler. Financial support was provided by a grant from the Natural Sciences and Engineering Council of Canada to B.R.G.

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