Global distribution of a wild alga revealed by targeted metagenomics

Eukaryotic phytoplankton play key roles in atmospheric CO2 uptake and sequestration in marine environments 1, 2. Community shifts attributed to climate change have already been reported in the Arctic ocean, where tiny, photosynthetic picoeukaryotes (≤3 μm diameter) have increased, while larger taxa have decreased [3]. Unfortunately, for vast regions of the world's oceans, little is known about distributions of different genera and levels of genetic variation between ocean basins. This lack of baseline information makes it impossible to assess the impacts of environmental change on phytoplankton diversity, and global carbon cycling. A major knowledge impediment is that these organisms are highly diverse, and most remain uncultured [2]. Metagenomics avoids the culturing step and provides insights into genes present in the environment without some of the biases associated with conventional molecular survey methods. However, connecting metagenomic sequences to the organisms containing them is challenging. For many unicellular eukaryotes the reference genomes needed to make this connection are not available. We circumvented this problem using at-sea fluorescence activated cell sorting (FACS) to separate abundant natural populations of photosynthetic eukaryotes and sequence their DNA, generating reference genome information while eliminating the need for culturing [2]. Here, we present the complete chloroplast genome from an Atlantic picoeukaryote population and discoveries it enabled on the evolution, distribution, and potential carbon sequestration role of a tiny, wild alg

Genome Fragmentation Is Not Confined to the Peridinin Plastid in Dinoflagellates

When plastids are transferred between eukaryote lineages through series of endosymbiosis, their environment changes dramatically. Comparison of dinoflagellate plastids that originated from different algal groups has revealed convergent evolution, suggesting that the host environment mainly influences the evolution of the newly acquired organelle. Recently the genome from the anomalously pigmented dinoflagellate Karlodinium veneficum plastid was uncovered as a conventional chromosome. To determine if this haptophyte-derived plastid contains additional chromosomal fragments that resemble the mini-circles of the peridin-containing plastids, we have investigated its genome by in-depth sequencing using 454 pyrosequencing technology, PCR and clone library analysis. Sequence analyses show several genes with significantly higher copy numbers than present in the chromosome. These genes are most likely extrachromosomal fragments, and the ones with highest copy numbers include genes encoding the chaperone DnaK(Hsp70), the rubisco large subunit (rbcL), and two tRNAs (trnE and trnM). In addition, some photosystem genes such as psaB, psaA, psbB and psbD are overrepresented. Most of the dnaK and rbcL sequences are found as shortened or fragmented gene sequences, typically missing the 3′-terminal portion. Both dnaK and rbcL are associated with a common sequence element consisting of about 120 bp of highly conserved AT-rich sequence followed by a trnE gene, possibly serving as a control region. Decatenation assays and Southern blot analysis indicate that the extrachromosomal plastid sequences do not have the same organization or lengths as the minicircles of the peridinin dinoflagellates. The fragmentation of the haptophyte-derived plastid genome K. veneficum suggests that it is likely a sign of a host-driven process shaping the plastid genomes of dinoflagellates

Experimental design and statistical rigor in phylogenomics of horizontal and endosymbiotic gene transfer

A growing number of phylogenomic investigations from diverse eukaryotes are examining conflicts among gene trees as evidence of horizontal gene transfer. If multiple foreign genes from the same eukaryotic lineage are found in a given genome, it is increasingly interpreted as concerted gene transfers during a cryptic endosymbiosis in the organism's evolutionary past, also known as "endosymbiotic gene transfer" or EGT. A number of provocative hypotheses of lost or serially replaced endosymbionts have been advanced; to date, however, these inferences largely have been post-hoc interpretations of genomic-wide conflicts among gene trees. With data sets as large and complex as eukaryotic genome sequences, it is critical to examine alternative explanations for intra-genome phylogenetic conflicts, particularly how much conflicting signal is expected from directional biases and statistical noise. The availability of genome-level data both permits and necessitates phylogenomics that test explicit, a priori predictions of horizontal gene transfer, using rigorous statistical methods and clearly defined experimental controls

Genome Evolution of a Tertiary Dinoflagellate Plastid

The dinoflagellates have repeatedly replaced their ancestral peridinin-plastid by plastids derived from a variety of algal lineages ranging from green algae to diatoms. Here, we have characterized the genome of a dinoflagellate plastid of tertiary origin in order to understand the evolutionary processes that have shaped the organelle since it was acquired as a symbiont cell. To address this, the genome of the haptophyte-derived plastid in Karlodinium veneficum was analyzed by Sanger sequencing of library clones and 454 pyrosequencing of plastid enriched DNA fractions. The sequences were assembled into a single contig of 143 kb, encoding 70 proteins, 3 rRNAs and a nearly full set of tRNAs. Comparative genomics revealed massive rearrangements and gene losses compared to the haptophyte plastid; only a small fraction of the gene clusters usually found in haptophytes as well as other types of plastids are present in K. veneficum. Despite the reduced number of genes, the K. veneficum plastid genome has retained a large size due to expanded intergenic regions. Some of the plastid genes are highly diverged and may be pseudogenes or subject to RNA editing. Gene losses and rearrangements are also features of the genomes of the peridinin-containing plastids, apicomplexa and Chromera, suggesting that the evolutionary processes that once shaped these plastids have occurred at multiple independent occasions over the history of the Alveolata

Evolution of the apicoplast and its hosts: from heterotrophy to autotrophy and back again

The photosynthetic origin of apicomplexan parasites was proposed upon the discovery of a reduced non-photosynthetic plastid termed the apicoplast in their cells. Although it is clear that the apicoplast has evolved through a secondary endosymbiosis, its particular origin within the red or green plastid lineage remains controversial. The recent discovery of Chromera velia, the closest known photosynthetic relative to apicomplexan parasites, sheds new light on the evolutionary history of alveolate plastids. Here we review our knowledge on the evolutionary history of Apicomplexa and particularly their plastids, with a focus on the pathway by which they evolved from free-living heterotrophs through photoautotrophs to omnipresent obligatory intracellular parasites. New sequences from C. velia (histones H2A, H2B; GAPDH, TufA) and phylogenetic analyses are also presented and discussed here

Tetrapyrrole synthesis of photosynthetic chromerids is likely homologous to the unusual pathway of apicomplexan parasites

Most photosynthetic eukaryotes synthesize both heme and chlorophyll via a common tetrapyrrole biosynthetic pathway starting from glutamate. This pathway was derived mainly from cyanobacterial predecessor of the plastid and differs from the heme synthesis of the plastid-lacking eukaryotes. Here, we show that the coral-associated alveolate Chromera velia, the closest known photosynthetic relative to Apicomplexa, possesses a tetrapyrrole pathway that is homologous to the unusual pathway of apicomplexan parasites. We also demonstrate that, unlike other eukaryotic phototrophs, Chromera synthesizes chlorophyll from glycine and succinyl-CoA rather than glutamate. Our data shed light on the evolution of the heme biosynthesis in parasitic Apicomplexa and photosynthesis-related biochemical processes in their ancestors

Genome sequence of the marine photoheterotrophic bacterium erythrobacter sp. strain NAP1.

Here we report the full genome sequence of marine phototrophic bacterium Erythrobacter sp. strain NAP1. The 3.3-Mb genome contains a full set of photosynthetic genes organized in one 38.9-kb cluster; however, it does not contain genes for CO2 or N2 fixation, thereby confirming that the organism is a photoheterotroph

Global distribution of a wild alga revealed by targeted metagenomics

Eukaryotic phytoplankton play key roles in atmospheric CO2 uptake and sequestration in marine environments 1, 2. Community shifts attributed to climate change have already been reported in the Arctic ocean, where tiny, photosynthetic picoeukaryotes (≤3 μm diameter) have increased, while larger taxa have decreased [3]. Unfortunately, for vast regions of the world's oceans, little is known about distributions of different genera and levels of genetic variation between ocean basins. This lack of baseline information makes it impossible to assess the impacts of environmental change on phytoplankton diversity, and global carbon cycling. A major knowledge impediment is that these organisms are highly diverse, and most remain uncultured [2]. Metagenomics avoids the culturing step and provides insights into genes present in the environment without some of the biases associated with conventional molecular survey methods. However, connecting metagenomic sequences to the organisms containing them is challenging. For many unicellular eukaryotes the reference genomes needed to make this connection are not available. We circumvented this problem using at-sea fluorescence activated cell sorting (FACS) to separate abundant natural populations of photosynthetic eukaryotes and sequence their DNA, generating reference genome information while eliminating the need for culturing [2]. Here, we present the complete chloroplast genome from an Atlantic picoeukaryote population and discoveries it enabled on the evolution, distribution, and potential carbon sequestration role of a tiny, wild alga