Elizabeth C. Ruck

A revision of the genus Cyclophora and description of Astrosyne gen. nov. (Bacillariophyta), two genera with the pyrenoids contained within pseudosepta

Ashworth M.P., Ruck E.C., Lobban C.S., Romanovicz D.K., and Theriot E.C. 2012. A revision of the genus Cyclophora and description of Astrosyne gen. nov. (Bacillariophyta), two genera with the pyrenoids contained within pseudosepta. Phycologia 51: 684–699. DOI: 10.2216/12-004.1 The araphid pennate diatom genus Cyclophora is characterized by an elliptical to circular pseudoseptum at the centre of one valve; C. tenuis is the only commonly reported species. New species have included some with pseudosepta on both valves, and we emended the generic description to accommodate these. Three species of Cyclophora were described from light and scanning electron microscopy: C. castracanei sp. nov., C. tabellariformis sp. nov. and C. minor sp. nov. Of these, C. castracanei was isovalvar with a pseudoseptum on both valves; C. tabellariformis was heterovalvar but differed in shape from the type species; and C. minor was very small and had both iso- and heterovalvar frustules. Other differences included stria density and arrangement of slits in the apical fields. Developmentally, the areolae within the boundary of the pseudoseptum filled in as the pseudoseptum grew. Also described was Astrosyne radiata gen. nov., sp. nov., which possessed a pseudoseptum in both valves but was radially symmetrical in valve outline. Transmission electron microscopy (TEM) observations of cytoplasmic ultrastructural organization and three-gene sequencing (nuclear-encoded small subunit rRNA, rbcL and psbC) of cultured cells was carried out on all except C. minor. TEM showed that pyrenoids were localized within the pseudoseptum in both Cyclophora and Astrosyne. Phylogenetic analysis of the DNA sequences also supported the close relationship between these genera. While A. radiata was not the first radially symmetrical diatom suggested to be derived from an araphid pennate lineage, the localization of pyrenoids within a central pseudoseptum in the valve may be the most distinctive synaopomorphy amongst diatoms with such different valve outlines.

Serial gene losses and foreign DNA underlie size and sequence variation in the plastid genomes of diatoms.

Photosynthesis by diatoms accounts for roughly one-fifth of global primary production, but despite this, relatively little is known about their plastid genomes. We report the completely sequenced plastid genomes for eight phylogenetically diverse diatoms and show them to be variable in size, gene and foreign sequence content, and gene order. The genomes contain a core set of 122 protein-coding genes, with 15 additional genes exhibiting complex patterns of 1) gene losses at varying phylogenetic scales, 2) functional transfers to the nucleus, 3) gene duplication, divergence, and differential retention of paralogs, and 4) acquisitions of putatively functional recombinase genes from resident plasmids. The newly sequenced genomes also contain several previously unreported genes, highlighting how poorly characterized diatom plastid genomes are overall. Genome size variation reflects major expansions of the inverted repeat region in some cases but, more commonly, large-scale expansions of intergenic regions, many of which contain unique open reading frames of likely foreign origin. Although many gene clusters are conserved across species, rearrangements appear to be frequent in most lineages.

Molecular phylogeny of the Cymbellales (Bacillariophyceae, Heterokontophyta) with a comparison of models for accommodating rate variation across sites

Abstract: We reconstructed the phylogeny of representatives from nine genera and three families of the Cymbellales using two nuclear and three chloroplast genes. After rooting with Anomoeoneis, Placoneis was found as sister to a clade composed of Cymbella, Cymbopleura, Encyonema, Gomphonema, and Gomphoneis. The latter group was divided into lineages with mainly heteropolar and dorsiventral valve symmetry. The data and chloroplast morphology also supported a close relationship between Geissleria decussis and Placoneis. Expectedly, the sequenced genes exhibited substantial across-site rate variation (ASRV) that prompted us to assess the stability of the inferred relationships in the face of different approaches for modelling ASRV. While the overall topology remained stable across analyses, relationships between Cymbella and Cymbopleura and within one clade of Gomphonema varied dependent on the employed model. In some cases a strongly supported relationship in one analysis was not recovered by another that differed solely in how the data were partitioned. These topological fluctuations appeared in areas of the tree with the least balanced taxon sampling, and they altered the outcomes of phylogenetic hypotheses tests of monophyly. Assessing how different models for ASRV affect tree topology and clade support values, therefore, seems important in cases of sparse or unbalanced taxon sampling or when assessing the phylogenetic affinity of previously unsampled taxa when lineage-specific biases in base composition or evolutionary rate are more difficult to detect.

Transcriptomic Insights into the Life History of Bolidophytes, the Sister Lineage to Diatoms

Diatoms are perhaps the most diverse lineage of eukaryotic algae, with their siliceous cell wall and diplontic life history often considered to have played important roles in their extraordinary diversification. The characteristic diminution of the diatom cell wall over the course of vegetative growth provides a reliable, intrinsic trigger for sexual reproduction, establishing a direct link between the evolution of their cell‐wall and life‐history features. It is unclear, however, whether the diplontic life cycle of diatoms represents an ancestral or derived trait. This uncertainty is based in part on our lack of understanding of the life cycle of the sister lineage to diatoms, which includes a mix of two free‐living and separately classified forms: naked biflagellate unicells in the genus Bolidomonas and silicified forms in the order Parmales. These two forms might represent different life‐history stages, although directly establishing such links can be difficult. We sequenced transcriptomes for Bolidomonas and two diatoms and found that ~0.1% of the coding regions in the two diploid diatoms are heterozygous, whereas Bolidomonas is virtually devoid of heterozygous alleles, consistent with expectations for a haploid genome. These results suggest that Bolidomonas is haploid and predict that parmaleans represent the diploid phase of a haplodiplontic life cycle. These data fill an important gap in our understanding of the origin of the diplontic life history of diatoms, which may represent an evolutionarily derived, adaptive feature.

Licmophora flucticulata sp. nov. (Licmophoraceae, Bacillariophyceae), an unusual flabellate species from Guam and Palau

Lobban C.S., Schefter M. and Ruck E.C. 2011. Licmophora flucticulata sp. nov. (Licmophoraceae, Bacillariophyceae), an unusual new flabellate species from Guam and Palau. Phycologia 50: 11–22. DOI: 10.2216/09-85.1 A new species of Licmophora, L. flucticulata sp. nov., forms distinctive, rippled, fan-shaped colonies on coral reef seaweeds on Western Pacific islands. It is readily observed underwater with the naked eye but is very weakly silicified, and its frustule does not survive normal acid cleaning. Its identity as a Licmophora species was demonstrated with scanning electron microscopy and small-subunit rDNA sequencing. Licmophora flucticulata has exceptionally long, narrow cells cemented into fascicles that attach to the substratum by short, multistranded mucilage stalks. Its valve and colony morphology are compared to that of L. remulus, L. flabellata and L. aurivillii.

Hoarding and horizontal transfer led to an expanded gene and intron repertoire in the plastid genome of the diatom, Toxarium undulatum (Bacillariophyta)

Although the plastid genomes of diatoms maintain a conserved architecture and core gene set, considerable variation about this core theme exists and can be traced to several different processes. Gene duplication, pseudogenization, and loss, as well as intracellular transfer of genes to the nuclear genome, have all contributed to variation in gene content among diatom species. In addition, some noncoding sequences have highly restricted phylogenetic distributions that suggest a recent foreign origin. We sequenced the plastid genome of the marine diatom, Toxarium undulatum, and found that the genome contains three genes (chlB, chlL, and chlN) involved in light-independent chlorophyll a biosynthesis that were not previously known from diatoms. Phylogenetic and syntenic data suggest that these genes were differentially retained in this one lineage as they were repeatedly lost from most other diatoms. Unique among diatoms and other heterokont algae sequenced so far, the genome also contains a large group II intron within an otherwise intact psaA gene. Although the intron is most similar to one in the plastid-encoded psaA gene of some green algae, high sequence divergence between the diatom and green algal introns rules out recent shared ancestry. We conclude that the psaA intron was likely introduced into the plastid genome of T. undulatum, or some earlier ancestor, by horizontal transfer from an unknown donor. This genome further highlights the myriad processes driving variation in gene and intron content in the plastid genomes of diatoms, one of the world’s foremost primary producers.

Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta)

PREMISE OF THE STUDY Diatoms are one of the most species-rich lineages of microbial eukaryotes. Similarities in clade age, species richness, and primary productivity motivate comparisons to angiosperms, whose genomes have been inordinately shaped by whole-genome duplication (WGD). WGDs have been linked to speciation, increased rates of lineage diversification, and identified as a principal driver of angiosperm evolution. We synthesized a large but scattered body of evidence that suggests polyploidy may be common in diatoms as well. METHODS We used gene counts, gene trees, and distributions of synonymous divergence to carry out a phylogenomic analysis of WGD across a diverse set of 37 diatom species. KEY RESULTS Several methods identified WGDs of varying age across diatoms. Determining the occurrence, exact number, and placement of events was greatly impacted by uncertainty in gene trees. WGDs inferred from synonymous divergence of paralogs varied depending on how redundancy in transcriptomes was assessed, gene families were assembled, and synonymous distances (Ks) were calculated. Our results highlighted a need for systematic evaluation of key methodological aspects of Ks-based approaches to WGD inference. Gene tree reconciliations supported allopolyploidy as the predominant mode of polyploid formation, with strong evidence for ancient allopolyploid events in the thalassiosiroid and pennate diatom clades. CONCLUSIONS Our results suggest that WGD has played a major role in the evolution of diatom genomes. We outline challenges in reconstructing paleopolyploid events in diatoms that, together with these results, offer a framework for understanding the impact of genome duplication in a group that likely harbors substantial genomic diversity.

A single loss of photosynthesis in diatoms

Loss of photosynthesis is a common and often repeated trajectory in nearly all major groups of photosynthetic eukaryotes. One small subset of ‘apochloritic’ diatoms in the genus Nitzschia have lost their ability to photosynthesize and require extracellular carbon for growth. Similar to other secondarily nonphotosynthetic taxa, apochloritic diatoms maintain colorless plastids with highly reduced plastid genomes. Although the narrow taxonomic breadth of apochloritic diatoms suggests a single loss of photosynthesis in the common ancestor of these species, previous phylogenetic analyses suggested that photosynthesis was lost multiple times. We sequenced additional phylogenetic markers from the nuclear and mitochondrial genomes for a larger set of taxa and found that the best trees for datasets representing all three genetic compartments provided low to moderate support for monophyly of apochloritic Nitzschia, consistent with a single loss of photosynthesis in diatoms. We sequenced the plastid genome of one apochloritic species and found that it was highly similar in all respects to the plastid genome of another apochloritic Nitzschia species, indicating that streamlining of the plastid genome had completed prior to the split of these two species. Finally, it is increasingly clear that some locales host relatively large numbers apochloritic Nitzschia species that span the phylogenetic diversity of the group, indicating that these species co-exist because of resource abundance or resource partitioning in ecologically favorable habitats. A better understanding of the phylogeny and ecology of this group, together with emerging genomic resources, will help identify the factors that have driven and maintained the loss of photosynthesis in this group, a rare event in diatoms.

Morphological diversity and phylogeny of the diatom genus Entomoneis (Bacillariophyta) in marine plankton: six new species from the Adriatic Sea

The diatom genus Entomoneis is known from the benthos and plankton of marine, brackish, and freshwaters. Entomoneis includes diatoms with a bilobate keel elevated above the valve surface, a sigmoid canal raphe, and numerous girdle bands. Owing mostly to the scarcity of molecular data for a diverse set of species, the phylogeny of Entomoneis has not been investigated in depth. The few previous studies that included Entomoneis were focused on broader questions and the available data were from a small number of either unidentified Entomoneis or well‐known species (e.g., E. paludosa). Since the first description of new species combining both molecular and morphological characters (E. tenera), we have continued to cultivate and investigate Entomoneis in the plankton of the Adriatic Sea. Combined multigene phylogeny (SSU rDNA sequences, rbcL, and psbC genes) and morphological observations (LM, SEM and TEM) revealed six new Entomoneis species supported by phylogenetic and morphological data: E. pusilla, E. gracilis, E. vilicicii, E. infula, E. adriatica, and E. umbratica. The most important morphological features for species delineation were cell shape, the degree and mode of torsion, valve apices, the appearance and structure of the transition between keel and valve body, the ultrastructure and the shape of the girdle bands, and the arrangement and density of perforations along the valve and valvocopulae. Our results highlight the underappreciated diversity of Entomoneis and call for a more in‐depth morphological and molecular investigation of this genus especially in planktonic habitats.

Recurrent Loss, Horizontal Transfer, and the Obscure Origins of Mitochondrial Introns in Diatoms (Bacillariophyta)

Abstract We sequenced mitochondrial genomes from five diverse diatoms (Toxarium undulatum, Psammoneis japonica, Eunotia naegelii, Cylindrotheca closterium, and Nitzschia sp.), chosen to fill important phylogenetic gaps and help us characterize broadscale patterns of mitochondrial genome evolution in diatoms. Although gene content was strongly conserved, intron content varied widely across species. The vast majority of introns were of group II type and were located in the cox1 or rnl genes. Although recurrent intron loss appears to be the principal underlying cause of the sporadic distributions of mitochondrial introns across diatoms, phylogenetic analyses showed that intron distributions superficially consistent with a recurrent-loss model were sometimes more complicated, implicating horizontal transfer as a likely mechanism of intron acquisition as well. It was not clear, however, whether diatoms were the donors or recipients of horizontally transferred introns, highlighting a general challenge in resolving the evolutionary histories of many diatom mitochondrial introns. Although some of these histories may become clearer as more genomes are sampled, high rates of intron loss suggest that the origins of many diatom mitochondrial introns are likely to remain unclear.