Endosymbiotic ratchet accelerates divergence after organelle origin: The Paulinella model for plastid evolution: The Paulinella model for plastid evolution.

We hypothesize that as one of the most consequential events in evolution, primary endosymbiosis accelerates lineage divergence, a process we refer to as the endosymbiotic ratchet. Our proposal is supported by recent work on the photosynthetic amoeba, Paulinella, that underwent primary plastid endosymbiosis about 124 Mya. This amoeba model allows us to explore the early impacts of photosynthetic organelle (plastid) origin on the host lineage. The current data point to a central role for effective population size (Ne ) in accelerating divergence post-endosymbiosis due to limits to dispersal and reproductive isolation that reduce Ne , leading to local adaptation. We posit that isolated populations exploit different strategies and behaviors and assort themselves in non-overlapping niches to minimize competition during the early, rapid evolutionary phase of organelle integration. The endosymbiotic ratchet provides a general framework for interpreting post-endosymbiosis lineage evolution that is driven by disruptive selection and demographic and population shifts. Also see the video abstract here: https://youtu.be/gYXrFM6Zz6Q.

Retrotransposition facilitated the establishment of a primary plastid in the thecate amoeba Paulinella.

The evolution of eukaryotic life was predicated on the development of organelles such as mitochondria and plastids. During this complex process of organellogenesis, the host cell and the engulfed prokaryote became genetically codependent, with the integration of genes from the endosymbiont into the host nuclear genome and subsequent gene loss from the endosymbiont. This process required that horizontally transferred genes become active and properly regulated despite inherent differences in genetic features between donor (endosymbiont) and recipient (host). Although this genetic reorganization is considered critical for early stages of organellogenesis, we have little knowledge about the mechanisms governing this process. The photosynthetic amoeba Paulinella micropora offers a unique opportunity to study early evolutionary events associated with organellogenesis and primary endosymbiosis. This amoeba harbors a "chromatophore," a nascent photosynthetic organelle derived from a relatively recent cyanobacterial association (∼120 million years ago) that is independent of the evolution of primary plastids in plants (initiated ∼1.5 billion years ago). Analysis of the genome and transcriptome of Paulinella revealed that retrotransposition of endosymbiont-derived nuclear genes was critical for their domestication in the host. These retrocopied genes involved in photoprotection in cyanobacteria became expanded gene families and were "rewired," acquiring light-responsive regulatory elements that function in the host. The establishment of host control of endosymbiont-derived genes likely enabled the cell to withstand photo-oxidative stress generated by oxygenic photosynthesis in the nascent organelle. These results provide insights into the genetic mechanisms and evolutionary pressures that facilitated the metabolic integration of the host­endosymbiont association and sustained the evolution of a photosynthetic organelle.

Diverse fates of ancient horizontal gene transfers in extremophilic red algae.

Horizontal genetic transfer (HGT) is a common phenomenon in eukaryotic genomes. However, the mechanisms by which HGT-derived genes persist and integrate into other pathways remain unclear. This topic is of significant interest because, over time, the stressors that initially favoured the fixation of HGT may diminish or disappear. Despite this, the foreign genes may continue to exist if they become part of a broader stress response or other pathways. The conventional model suggests that the acquisition of HGT equates to adaptation. However, this model may evolve into more complex interactions between gene products, a concept we refer to as the 'Integrated HGT Model' (IHM). To explore this concept further, we studied specialized HGT-derived genes that encode heavy metal detoxification functions. The recruitment of these genes into other pathways could provide clear examples of IHM. In our study, we exposed two anciently diverged species of polyextremophilic red algae from the Galdieria genus to arsenic and mercury stress in laboratory cultures. We then analysed the transcriptome data using differential and coexpression analysis. Our findings revealed that mercury detoxification follows a 'one gene-one function' model, resulting in an indivisible response. In contrast, the arsH gene in the arsenite response pathway demonstrated a complex pattern of duplication, divergence and potential neofunctionalization, consistent with the IHM. Our research sheds light on the fate and integration of ancient HGTs, providing a novel perspective on the ecology of extremophiles.

A k-mer-Based Approach for Phylogenetic Classification of Taxa in Environmental Genomic Data.

In the age of genome sequencing, whole-genome data is readily and frequently generated, leading to a wealth of new information that can be used to advance various fields of research. New approaches, such as alignment-free phylogenetic methods that utilize k-mer-based distance scoring, are becoming increasingly popular given their ability to rapidly generate phylogenetic information from whole-genome data. However, these methods have not yet been tested using environmental data, which often tends to be highly fragmented and incomplete. Here, we compare the results of one alignment-free approach (which utilizes the D2 statistic) to traditional multi-gene maximum likelihood trees in 3 algal groups that have high-quality genome data available. In addition, we simulate lower-quality, fragmented genome data using these algae to test method robustness to genome quality and completeness. Finally, we apply the alignment-free approach to environmental metagenome assembled genome data of unclassified Saccharibacteria and Trebouxiophyte algae, and single-cell amplified data from uncultured marine stramenopiles to demonstrate its utility with real datasets. We find that in all instances, the alignment-free method produces phylogenies that are comparable, and often more informative, than those created using the traditional multi-gene approach. The k-mer-based method performs well even when there are significant missing data that include marker genes traditionally used for tree reconstruction. Our results demonstrate the value of alignment-free approaches for classifying novel, often cryptic or rare, species, that may not be culturable or are difficult to access using single-cell methods, but fill important gaps in the tree of life.

Family supplemented patient monitoring after surgery (SMARTER): a pilot stepped-wedge cluster-randomised trial.

BACKGROUND: Mortality after surgery in Africa is twice that in high-income countries. Most deaths occur on wards after patients develop postoperative complications. Family members might contribute meaningfully and safely to early recognition of deteriorating patients. METHODS: This was a stepped-wedge cluster-randomised trial of an intervention training family members to support nursing staff to take and record patient vital signs every 4 h after surgery. Adult inpatients across four surgical wards (clusters) in a Ugandan hospital were included. Clusters crossed once from routine care to the SMARTER intervention at monthly intervals. The primary outcome was frequency of vital sign measurements from arrival on the postoperative ward to the end of the third postoperative day (3 days). RESULTS: We enrolled 1395 patients between April and October 2021. Mean age was 28.2 (range 5-89) yr; 85.7% were female. The most common surgical procedure was Caesarean delivery (74.8%). Median (interquartile range) number of sets of vital signs increased from 0 (0-1) in control wards to 3 (1-8) in intervention wards (incident rate ratio 12.4, 95% confidence interval [CI] 8.8-17.5, P<0.001). Mortality was 6/718 (0.84%) patients in the usual care group vs 12/677 (1.77%) in the intervention group (odds ratio 1.32, 95% CI 0.1-14.7, P=0.821). There was no difference in length of hospital stay between groups (usual care: 2 [2-3] days vs intervention: 2 [2-4] days; hazard ratio 1.11, 95% CI 0.84-1.47, P=0.44). CONCLUSIONS: Family member supplemented vital signs monitoring substantially increased the frequency of vital signs after surgery. Care interventions involving family members have the potential to positively impact patient care. CLINICAL TRIAL REGISTRATION: NCT04341558.

Supporting effective shared decision-making in surgical context: Why framing of choices matters for high-risk patients and clinicians.

AIM: In the context of high-risk surgery, shared decision-making (SDM) is important. However, the effectiveness of SDM can be hindered by misalignment between patients and clinicians in their expectations of postoperative outcomes. This study investigated the extent and the effects of this misalignment, as well as its amenability to interventions that encourage perspective-taking. METHOD: Lay participants with a Charlson Comorbidity Index of ≥4 (representing patients) and surgeons and anaesthetists (representing doctors) were recruited. During an online experiment, subjects in both groups forecast their expectations regarding short-term (0, 1 and 3 months after treatment) and long-term (6, 9 and 12 months after treatment) outcomes of different treatment options for one of three hypothetical clinical scenarios - ischaemic heart disease, colorectal cancer or osteoarthritis of the hip - and then chose between surgical or non-surgical treatment. Subjects in both groups were asked to consider the scenarios from their own perspective (Estimation task), and then to adopt the perspective of subjects in the other study group (Perspective task). The decisions of all participants (surgery vs. non-surgical alternative) were analysed using binomial generalized linear mixed models. RESULTS: In total, 55 lay participants and 54 doctors completed the online experiment. Systematic misalignment in expectations between high-risk patients and doctors was observed, with patients expecting better surgical outcomes than clinicians. Patients forecast a significantly higher likelihood of engaging in normal activities in the long term (ß = -1.09, standard error [SE] = 0.20, t = -5.38, p < 0.001), a lower likelihood of experiencing complications in the long term (ß = 0.92, SE = 0.21, t = 4.45, p < 0.001) and a lower likelihood of experiencing depression in both the short term and the long term (ß = 1.01, SE = 0.19, t = 5.38, p < 0.001), than did doctors. Compared with doctors, patients forecast higher estimates of experiencing complications in the short term when a non-surgical alternative was selected (ß = -0.91, SE = 0.26, t = -3.50, p = 0.003). Despite this misalignment, in both groups surgical treatment was strongly preferred (estimation task: 88.7% of doctors and 80% of patients; perspective task: 82.2% of doctors and 90.1% of patients). CONCLUSION: When high-risk surgery is discussed, a non-surgical option may be viewed as 'doing nothing', hence reducing the sense of agency and control. This biases the decision-making process, regardless of the expectations that doctors and patients might have about the outcomes of surgery. Therefore, to improve SDM and to increase the agency and control of patients regarding decisions about their care, we advocate framing the non-surgical treatment options in a way that emphasizes action, agency and change.

Opportunities for shared decision-making about major surgery with high-risk patients: a multi-method qualitative study.

BACKGROUND: Little is known about the opportunities for shared decision-making when older high-risk patients are offered major surgery. This study examines how, when, and why clinicians and patients can share decision-making about major surgery. METHODS: This was a multi-method qualitative study, combining video recordings of preoperative consultations, interviews, and focus groups (33 patients, 19 relatives, 36 clinicians), with observations and documentary analysis in clinics in five hospitals in the UK undertaking major orthopaedic, colorectal, and/or cardiac surgery. RESULTS: Three opportunities for shared decision-making about major surgery were identified. Resolution-focused consultations (cardiac/colorectal) resulted in a single agreed preferred option related to a potentially life-threatening problem, with limited opportunities for shared decision-making. Evaluative and deliberative consultations offered more opportunity. The former focused on assessing the likelihood of benefits of surgery for a presenting problem that was not a threat to life for the patient (e.g., orthopaedic consultations) and the latter (largely colorectal) involved discussion of a range of options while also considering significant comorbidities and patient preferences. The extent to which opportunities for shared decision-making were available, and taken up by surgeons, was influenced by the nature of the presenting problem, clinical pathway, and patient trajectory. CONCLUSIONS: Decisions about major surgery were not always shared between patients and doctors. The nature of the presenting problem, comorbidities, clinical pathways, and patient trajectories all informed the type of consultation and opportunities for sharing decision-making. Our findings have implications for clinicians, with shared decision-making about major surgery most feasible when the focus is on life-enhancing treatment.

Algae obscura: The potential of rare species as model systems.

Model organism research has provided invaluable knowledge about foundational biological principles. However, most of these studies have focused on species that are in high abundance, easy to cultivate in the lab, and represent only a small fraction of extant biodiversity. Here, we present three examples of rare algae with unusual features that we refer to as "algae obscura." The Cyanidiophyceae (Rhodophyta), Glaucophyta, and Paulinella (rhizarian) lineages have all transitioned out of obscurity to become models for fundamental evolutionary research. Insights have been gained into the prevalence and importance of eukaryotic horizontal gene transfer, early Earth microbial community dynamics, primary plastid endosymbiosis, and the origin of Archaeplastida. By reviewing the research that has come from the exploration of these organisms, we demonstrate that underappreciated algae have the potential to help us formulate, refine, and substantiate core hypotheses and that such organisms should be considered when establishing future model systems.

Amoeba Genome Reveals Dominant Host Contribution to Plastid Endosymbiosis.

Eukaryotic photosynthetic organelles, plastids, are the powerhouses of many aquatic and terrestrial ecosystems. The canonical plastid in algae and plants originated >1 Ga and therefore offers limited insights into the initial stages of organelle evolution. To address this issue, we focus here on the photosynthetic amoeba Paulinella micropora strain KR01 (hereafter, KR01) that underwent a more recent (∼124 Ma) primary endosymbiosis, resulting in a photosynthetic organelle termed the chromatophore. Analysis of genomic and transcriptomic data resulted in a high-quality draft assembly of size 707 Mb and 32,361 predicted gene models. A total of 291 chromatophore-targeted proteins were predicted in silico, 208 of which comprise the ancestral organelle proteome in photosynthetic Paulinella species with functions, among others, in nucleotide metabolism and oxidative stress response. Gene coexpression analysis identified networks containing known high light stress response genes as well as a variety of genes of unknown function ("dark" genes). We characterized diurnally rhythmic genes in this species and found that over 49% are dark. It was recently hypothesized that large double-stranded DNA viruses may have driven gene transfer to the nucleus in Paulinella and facilitated endosymbiosis. Our analyses do not support this idea, but rather suggest that these viruses in the KR01 and closely related P. micropora MYN1 genomes resulted from a more recent invasion.

Evidence for a robust photosystem II in the photosynthetic amoeba Paulinella.

Paulinella represents the only known case of an independent primary plastid endosymbiosis, outside Archaeplastida, that occurred c. 120 (million years ago) Ma. These photoautotrophs grow very slowly in replete culture medium with a doubling time of 6-7 d at optimal low light, and are highly sensitive to photodamage under moderate light levels. We used genomic and biophysical methods to investigate the extreme slow growth rate and light sensitivity of Paulinella, which are key to photosymbiont integration. All photosystem II (PSII) genes except psb28-2 and all cytochrome b6 f complex genes except petM and petL are present in Paulinella micropora KR01 (hereafter, KR01). Biophysical measurements of the water oxidation complex, variable chlorophyll fluorescence, and photosynthesis-irradiance curves show no obvious evidence of PSII impairment. Analysis of photoacclimation under high-light suggests that although KR01 can perform charge separation, it lacks photoprotection mechanisms present in cyanobacteria. We hypothesize that Paulinella species are restricted to low light environments because they are deficient in mitigating the formation of reactive oxygen species formed within the photosystems under peak solar intensities. The finding that many photoprotection genes have been lost or transferred to the host-genome during endosymbiont genome reduction, and may lack light-regulation, is consistent with this hypothesis.

Surgery in older patients: learning from shared decision-making in intensive care.

An increasing number of older patients are having surgical treatments. Similar to older patients admitted to intensive care, they present with additional problems including multimorbidity, frailty, and cognitive impairment. In both intensive care and surgical settings, comprehensive assessment can inform targeted interventions and shared decision-making. We explore the challenges faced by older patients, and by the clinicians treating them.

Hypothesis: Trans-splicing Generates Evolutionary Novelty in the Photosynthetic Amoeba Paulinella.

Plastid primary endosymbiosis has occurred twice, once in the Archaeplastida ancestor and once in the Paulinella (Rhizaria) lineage. Both events precipitated massive evolutionary changes, including the recruitment and activation of genes that are horizontally acquired (HGT) and the redeployment of existing genes and pathways in novel contexts. Here we address the latter aspect in Paulinella micropora KR01 (hereafter, KR01) that has independently evolved spliced leader (SL) trans-splicing (SLTS) of nuclear-derived transcripts. We investigated the role of this process in gene regulation, novel gene origination, and endosymbiont integration. Our analysis shows that 20% of KR01 genes give rise to transcripts with at least one (but in some cases, multiple) sites of SL addition. This process, which often occurs at canonical cis-splicing acceptor sites (internal introns), results in shorter transcripts that may produce 5'-truncated proteins with novel functions. SL-truncated transcripts fall into four categories that may show: (i) altered protein localization, (ii) altered protein function, structure, or regulation, (iii) loss of valid alternative start codons, preventing translation, or (iv) multiple SL addition sites at the 5'-terminus. The SL RNA genes required for SLTS are putatively absent in the heterotrophic sister lineage of photosynthetic Paulinella species. Moreover, a high proportion of transcripts derived from genes of endosymbiotic gene transfer (EGT) and HGT origin contain SL sequences. We hypothesize that truncation of transcripts by SL addition may facilitate the generation and expression of novel gene variants and that SLTS may have enhanced the activation and fixation of foreign genes in the host genome of the photosynthetic lineages, playing a key role in primary endosymbiont integration.

Perioperative Care Pathways in Low- and Lower-Middle-Income Countries: Systematic Review and Narrative Synthesis.

BACKGROUND: Safe and effective care for surgical patients requires high-quality perioperative care. In high-income countries (HICs), care pathways have been shown to be effective in standardizing clinical practice to optimize patient outcomes. Little is known about their use in low- and middle-income countries (LMICs) where perioperative mortality is substantially higher. METHODS: Systematic review and narrative synthesis to identify and describe studies in peer-reviewed journals on the implementation or evaluation of perioperative care pathways in LMICs. Searches were conducted in MEDLINE, EMBASE, CINAHL Plus, WHO Global Index, Web of Science, Scopus, Global Health and SciELO alongside citation searching. Descriptive statistics, taxonomy classifications and framework analyses were used to summarize the setting, outcome measures, implementation strategies, and facilitators and barriers to implementation. RESULTS: Twenty-seven studies were included. The majority of pathways were set in tertiary hospitals in lower-middle-income countries and were focused on elective surgery. Only six studies were assessed as high quality. Most pathways were adapted from international guidance and had been implemented in a single hospital. The most commonly reported barriers to implementation were cost of interventions and lack of available resources. CONCLUSIONS: Studies from a geographically diverse set of low and lower-middle-income countries demonstrate increasing use of perioperative pathways adapted to resource-poor settings, though there is sparsity of literature from low-income countries, first-level hospitals and emergency surgery. As in HICs, addressing patient and clinician beliefs is a major challenge in improving care. Context-relevant and patient-centered research, including qualitative and implementation studies, would make a valuable contribution to existing knowledge.

Barriers to Quality Perioperative Care Delivery in Low- and Middle-Income Countries: A Qualitative Rapid Appraisal Study.

BACKGROUND: Provision of timely, safe, and affordable surgical care is an essential component of any high-quality health system. Increasingly, it is recognized that poor quality of care in the perioperative period (before, during, and after surgery) may contribute to significant excess mortality and morbidity. Therefore, improving access to surgical procedures alone will not address the disparities in surgical outcomes globally until the quality of perioperative care is addressed. We aimed to identify key barriers to quality perioperative care delivery for 3 "Bellwether" procedures (cesarean delivery, emergency laparotomy, and long-bone fracture fixation) in 5 low- and middle-income countries (LMICs). METHODS: Ten hospitals representing secondary and tertiary facilities from 5 LMICs were purposefully selected: 2 upper-middle income (Colombia and South Africa); 2 lower-middle income (Sri Lanka and Tanzania); and 1 lower income (Uganda). We used a rapid appraisal design (pathway mapping, ethnography, and interviews) to map out and explore the complexities of the perioperative pathway and care delivery for the Bellwether procedures. The framework approach was used for data analysis, with triangulation across different data sources to identify barriers in the country and pattern matching to identify common barriers across the 5 LMICs. RESULTS: We developed 25 pathway maps, undertook >30 periods of observation, and held >40 interviews with patients and clinical staff. Although the extent and impact of the barriers varied across the LMIC settings, 4 key common barriers to safe and effective perioperative care were identified: (1) the fragmented nature of the care pathways, (2) the limited human and structural resources available for the provision of care, (3) the direct and indirect costs of care for patients (even in health systems for which care is ostensibly free of charge), and (4) patients' low expectations of care. CONCLUSIONS: We identified key barriers to effective perioperative care in LMICs. Addressing these barriers is important if LMIC health systems are to provide safe, timely, and affordable provision of the Bellwether procedures.

Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus Symbiodinium.

BACKGROUND: Dinoflagellates in the family Symbiodiniaceae are important photosynthetic symbionts in cnidarians (such as corals) and other coral reef organisms. Breakdown of the coral-dinoflagellate symbiosis due to environmental stress (i.e. coral bleaching) can lead to coral death and the potential collapse of reef ecosystems. However, evolution of Symbiodiniaceae genomes, and its implications for the coral, is little understood. Genome sequences of Symbiodiniaceae remain scarce due in part to their large genome sizes (1-5 Gbp) and idiosyncratic genome features. RESULTS: Here, we present de novo genome assemblies of seven members of the genus Symbiodinium, of which two are free-living, one is an opportunistic symbiont, and the remainder are mutualistic symbionts. Integrating other available data, we compare 15 dinoflagellate genomes revealing high sequence and structural divergence. Divergence among some Symbiodinium isolates is comparable to that among distinct genera of Symbiodiniaceae. We also recovered hundreds of gene families specific to each lineage, many of which encode unknown functions. An in-depth comparison between the genomes of the symbiotic Symbiodinium tridacnidorum (isolated from a coral) and the free-living Symbiodinium natans reveals a greater prevalence of transposable elements, genetic duplication, structural rearrangements, and pseudogenisation in the symbiotic species. CONCLUSIONS: Our results underscore the potential impact of lifestyle on lineage-specific gene-function innovation, genome divergence, and the diversification of Symbiodinium and Symbiodiniaceae. The divergent features we report, and their putative causes, may also apply to other microbial eukaryotes that have undergone symbiotic phases in their evolutionary history.

Why is primary endosymbiosis so rare?

Endosymbiosis is a relationship between two organisms wherein one cell resides inside the other. This affiliation, when stable and beneficial for the 'host' cell, can result in massive genetic innovation with the foremost examples being the evolution of eukaryotic organelles, the mitochondria and plastids. Despite its critical evolutionary role, there is limited knowledge about how endosymbiosis is initially established and how host-endosymbiont biology is integrated. Here, we explore this issue, using as our model the rhizarian amoeba Paulinella, which represents an independent case of primary plastid origin that occurred c. 120 million yr ago. We propose the 'chassis and engine' model that provides a theoretical framework for understanding primary plastid endosymbiosis, potentially explaining why it is so rare.

Understanding the performance of a pan-African intervention to reduce postoperative mortality: a mixed-methods process evaluation of the ASOS-2 trial.

BACKGROUND: The African Surgical OutcomeS-2 (ASOS-2) trial tested an enhanced postoperative surveillance intervention to reduce postoperative mortality in Africa. We undertook a concurrent evaluation to understand the process of intervention delivery. METHODS: Mixed-methods process evaluation, including field notes, interviews, and post-trial questionnaire responses. Qualitative analysis used the framework method with subsequent creation of comparative case studies, grouping hospitals by intervention fidelity. A post-trial questionnaire was developed using initial qualitative analyses. Categorical variables were summarised as count (%) and continuous variables as median (inter-quartile range [IQR]). Odds ratios (OR) were used to rank influences by impact on fidelity. RESULTS: The dataset included eight in-depth case studies, and 96 questionnaire responses (response rate 67%) plus intervention fidelity data for each trial site. Overall, 57% (n=55/96) of hospitals achieved intervention delivery using an inclusive definition of fidelity. Delivery of the ASOS-2 interventions and data collection presented a significant burden to the investigators, outstripping limited resources. The influences most associated with fidelity were: surgical staff enthusiasm for the trial (OR=3.0; 95% confidence interval [CI], 1.3-7.0); nursing management support of the trial (OR=2.6; 95% CI, 1.1-6.5); performance of a dummy run (OR=2.6; 95% CI, 1.1-6.1); nursing colleagues seeing the value of the intervention(s) (OR=2.1; 95% CI, 0.9-5.7); and site investigators' belief in the effectiveness of the intervention (OR=3.2; 95% CI, 1.2-9.4). CONCLUSIONS: ASOS-2 has proved that coordinated interventional research across Africa is possible, but delivering the ASOS-2 interventions was a major challenge for many investigators. Future improvement science efforts must include better planning for intervention delivery, additional support to investigators, and promotion of strong inter-professional teamwork. CLINICAL TRIAL REGISTRATION: ClinicalTrials gov NCT03853824.

Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions.

BACKGROUND: Dinoflagellates are taxonomically diverse and ecologically important phytoplankton that are ubiquitously present in marine and freshwater environments. Mostly photosynthetic, dinoflagellates provide the basis of aquatic primary production; most taxa are free-living, while some can form symbiotic and parasitic associations with other organisms. However, knowledge of the molecular mechanisms that underpin the adaptation of these organisms to diverse ecological niches is limited by the scarce availability of genomic data, partly due to their large genome sizes estimated up to 250 Gbp. Currently available dinoflagellate genome data are restricted to Symbiodiniaceae (particularly symbionts of reef-building corals) and parasitic lineages, from taxa that have smaller genome size ranges, while genomic information from more diverse free-living species is still lacking. RESULTS: Here, we present two draft diploid genome assemblies of the free-living dinoflagellate Polarella glacialis, isolated from the Arctic and Antarctica. We found that about 68% of the genomes are composed of repetitive sequence, with long terminal repeats likely contributing to intra-species structural divergence and distinct genome sizes (3.0 and 2.7 Gbp). For each genome, guided using full-length transcriptome data, we predicted > 50,000 high-quality protein-coding genes, of which ~40% are in unidirectional gene clusters and ~25% comprise single exons. Multi-genome comparison unveiled genes specific to P. glacialis and a common, putatively bacterial origin of ice-binding domains in cold-adapted dinoflagellates. CONCLUSIONS: Our results elucidate how selection acts within the context of a complex genome structure to facilitate local adaptation. Because most dinoflagellate genes are constitutively expressed, Polarella glacialis has enhanced transcriptional responses via unidirectional, tandem duplication of single-exon genes that encode functions critical to survival in cold, low-light polar environments. These genomes provide a foundational reference for future research on dinoflagellate evolution.

Evidence That Inconsistent Gene Prediction Can Mislead Analysis of Dinoflagellate Genomes.

Comparative algal genomics often relies on predicted genes from de novo assembled genomes. However, the artifacts introduced by different gene-prediction approaches, and their impact on comparative genomic analysis remain poorly understood. Here, using available genome data from six dinoflagellate species in the Symbiodiniaceae, we identified methodological biases in the published genes that were predicted using different approaches and putative contaminant sequences in the published genome assemblies. We developed and applied a comprehensive customized workflow to predict genes from these genomes. The observed variation among predicted genes resulting from our workflow agreed with current understanding of phylogenetic relationships among these taxa, whereas the variation among the previously published genes was largely biased by the distinct approaches used in each instance. Importantly, these biases affect the inference of homologous gene families and synteny among genomes, thus impacting biological interpretation of these data. Our results demonstrate that a consistent gene-prediction approach is critical for comparative analysis of dinoflagellate genomes.

Analysis of the Draft Genome of the Red Seaweed Gracilariopsis chorda Provides Insights into Genome Size Evolution in Rhodophyta.

Red algae (Rhodophyta) underwent two phases of large-scale genome reduction during their early evolution. The red seaweeds did not attain genome sizes or gene inventories typical of other multicellular eukaryotes. We generated a high-quality 92.1 Mb draft genome assembly from the red seaweed Gracilariopsis chorda, including methylation and small (s)RNA data. We analyzed these and other Archaeplastida genomes to address three questions: 1) What is the role of repeats and transposable elements (TEs) in explaining Rhodophyta genome size variation, 2) what is the history of genome duplication and gene family expansion/reduction in these taxa, and 3) is there evidence for TE suppression in red algae? We find that the number of predicted genes in red algae is relatively small (4,803-13,125 genes), particularly when compared with land plants, with no evidence of polyploidization. Genome size variation is primarily explained by TE expansion with the red seaweeds having the largest genomes. Long terminal repeat elements and DNA repeats are the major contributors to genome size growth. About 8.3% of the G. chorda genome undergoes cytosine methylation among gene bodies, promoters, and TEs, and 71.5% of TEs contain methylated-DNA with 57% of these regions associated with sRNAs. These latter results suggest a role for TE-associated sRNAs in RNA-dependent DNA methylation to facilitate silencing. We postulate that the evolution of genome size in red algae is the result of the combined action of TE spread and the concomitant emergence of its epigenetic suppression, together with other important factors such as changes in population size.