Intron Invasions Trace Algal Speciation and Reveal Nearly Identical Arctic and AntarcticMicromonasPopulations

Abstract

Spliceosomal introns are a hallmark of eukaryotic genes that are hypothesized to play important roles in genome evolution but have poorly understood origins. Although most introns lack sequence homology to each other, new families of spliceosomal introns that are repeated hundreds of times in individual genomes have recently been discovered in a few organisms. The prevalence and conservation of these introner elements (IEs) or introner-like elements in other taxa, as well as their evolutionary relationships to regular spliceosomal introns, are still unknown. Here, we systematically investigate introns in the widespread marine green alga Micromonas and report new families of IEs, numerous intron presence–absence polymorphisms, and potential intron insertion hot-spots. The new families enabled identification of conserved IE secondary structure features and establishment of a novel general model for repetitive intron proliferation across genomes. Despite shared secondary structure, the IE families from each Micromonas lineage bear no obvious sequence similarity to those in the other lineages, suggesting that their appearance is intimately linked with the process of speciation. Two of the new IE families come from an Arctic culture (Micromonas Clade E2) isolated from a polar region where abundance of this alga is increasing due to climate induced changes. The same two families were detected in metagenomic data from Antarctica—a system where Micromonas has never before been reported. Strikingly high identity between the Arctic isolate and Antarctic coding sequences that flank the IEs suggests connectivity between populations in the two polar systems that we postulate occurs through deep-sea currents. Recovery of Clade E2 sequences in North Atlantic Deep Waters beneath the Gulf Stream supports this hypothesis. Our research illuminates the dynamic relationships between an unusual class of repetitive introns, genome evolution, speciation, and global distribution of this sentinel marine alga.

Abundance and Biogeography of Picoprasinophyte Ecotypes and Other Phytoplankton in the Eastern North Pacific Ocean

“…The maximum Micromonas 18S rRNA copies · ml Ϫ1 was observed at the CO (14,613 Ϯ 196), with lower abundances in the Transect survey TZ (949 Ϯ 170) and Drift study (8,080 Ϯ 641). These values likely represent contributions from multiple Micromonas clades, since seven have been characterized to date (12) and several of these cooccur in the southern California bight (17). Micromonas and Ostreococcus clade OI were detected in the same 29 qPCR samples (41 were analyzed), and both were undetectable in the OO.…”

“…The Ostreococcus clade OI qPCR primerprobe set used here was designed to amplify both O. lucimarinus and O. tauri (10) to distinguish them from Ostreococcus clade OII. However, O. lucimarinus and O. tauri share only ϳ90% of their protein-encoding genes (14) and form separate clades using 18S rRNA gene sequences or other markers (12); hence, we have termed O. tauri clade OI/C according to reference 16. A comparative genome analysis has not been published that includes Ostreococcus sp.…”

“…To identify genes for characterizing Bathycoccus and Ostreococcus genetic diversity and for use as ecomarkers in environmental samples, groups of homologous sequences were first identified in the predicted proteomes from B. prasinos (strain Bban7) and three Ostreococcus genomes(taxalistedabove).Bathycoccussequencesfromthreetargetedmetagenomes (19,20) were also used after identifying all possible open reading frames (ORFs; i.e., sequence between stop codons with a minimal length of 60 amino acid residues). The analysis was not performed for Micromonas because, of the seven established clades (12), isolates from only two have complete genome sequences. Clusters of homologs were computed using OrthoMCL (38) based on all versus all BLASTP (39) searches of Bathycoccus and Ostreococcus proteomes, using a cutoff E value of 10 Ϫ100 E. Clusters containing one sequence from each input source were kept to ensure analysis of exclusively single-copy orthologs (i.e., clusters composed of sequences for the four and three Bathycoccus and Ostreococcus predicted proteomes, respectively).…”

“…For example, a circumglobal study on diversity of marine eukaryotes found class II prasinophytes in all 45 samples (9). Molecular phylogenies and field studies have revealed multiple clades or ecotypes within three major class II genera, Bathycoccus, Micromonas, and Ostreococcus (10)(11)(12). Genome analyses demonstrate extensive diversity among Micromonas clades that reflect species level divisions (12,13) and lesser but still notable divergence between Ostreococcus species (14).…”

“…Molecular phylogenies and field studies have revealed multiple clades or ecotypes within three major class II genera, Bathycoccus, Micromonas, and Ostreococcus (10)(11)(12). Genome analyses demonstrate extensive diversity among Micromonas clades that reflect species level divisions (12,13) and lesser but still notable divergence between Ostreococcus species (14). The Bathycoccus genus is thought to consist of a single species (Bathycoccus prasinos), and only one cultured strain (Bban7, also known as RCC1105) has a sequenced genome (15).…”