ORCID Profile
0000-0002-8011-1303
Current Organisation
Ghent University
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Genomics | Marine and Estuarine Ecology (incl. Marine Ichthyology) | Genetics | Biological Adaptation | Phycology (incl. Marine Grasses) | Plant Biology | Phylogeny and Comparative Analysis
ANZSRC Socio-Economic Objective (SEO)
Expanding Knowledge in the Biological Sciences | Expanding Knowledge in the Environmental Sciences | Ecosystem Assessment and Management of Coastal and Estuarine Environments |
Related Links
Publications
Genome-wide transcriptome analysis reveals the diversity and function of long non-coding RNAs in dinoflagellates
Publisher: Cold Spring Harbor Laboratory
Date: 29-06-2023
DOI: 10.1101/2023.06.27.546665
Abstract: Dinoflagellates are a erse group of phytoplankton, ranging from harmful bloom-forming microalgae to photosymbionts that are critical for sustaining coral reefs. Genome and transcriptome data from dinoflagellates are revealing extensive genomic ergence and lineage-specific innovation of gene functions. However, most studies thus far have focused on protein-coding genes long non-coding RNAs (lncRNAs), known to regulate gene expression in eukaryotes, are largely unexplored. Here, using both genome and transcriptome data, we identified a combined total of 48,039 polyadenylated lncRNAs in the genomes of three dinoflagellate species: the coral symbionts of Cladocopium proliferum and Durusdinium trenchii , and the bloom-forming Prorocentrum cordatum . These putative lncRNAs are shorter, and have fewer introns and lower G+C-content when compared to protein-coding sequences. Although 37,768 (78.6%) lncRNAs shared no significant similarity with one another, we classified all lncRNAs based on conserved sequence motifs ( k -mers) into distinct clusters following properties of potential protein-binding and/or subcellular localisation. Interestingly, 3708 (7.7%) lncRNAs were differentially expressed in response to heat stress, lifestyle, and/or growth phases, and they shared co-expression patterns with protein-coding genes. Based on inferred triplex interactions between lncRNA and upstream (putative promoter) regions of protein-coding genes, we identified a combined 19,460 putative gene targets for 3,721 lncRNAs 907 genes exhibit differential expression under heat stress. These results reveal for the first time the functional ersity of lncRNAs in dinoflagellates, and demonstrate how lncRNAs, often overlooked in transcriptome data, could regulate gene expression as a molecular response to heat stress in these ecologically important organisms.
Deciphering the nature of the coral–Chromera association
Publisher: Springer Science and Business Media LLC
Date: 10-01-2018
Somatosensory Impairments in the Upper Limb Poststroke
Publisher: SAGE Publications
Date: 10-07-2016
Abstract: Background. A thorough understanding of the presence of different upper-limb somatosensory deficits poststroke and the relation with motor performance remains unclear. Additionally, knowledge about the relation between somatosensory deficits and visuospatial neglect is limited. Objective. To investigate the distribution of upper-limb somatosensory impairments and the association with unimanual and bimanual motor outcomes and visuospatial neglect. Methods. A cross-sectional observational study was conducted, including 122 patients within 6 months after stroke (median = 82 days interquartile range = 57-133 days). Somatosensory measurement included the Erasmus MC modification of the (revised) Nottingham Sensory Assessment (Em-NSA), Perceptual Threshold of Touch (PTT), thumb finding test, 2-point discrimination, and stereognosis subscale of the NSA. Upper-limb motor assessment comprised the Fugl-Meyer assessment, motricity index, Action Research Arm Test, and Adult-Assisting Hand Assessment Stroke. Screening for visuospatial neglect was performed using the Star Cancellation Test. Results. Upper-limb somatosensory impairments were common, with prevalence rates ranging from 21% to 54%. Low to moderate Spearman ρ correlations were found between somatosensory and motor deficits ( r = 0.22-0.61), with the strongest associations for PTT ( r = 0.56-0.61) and stereognosis ( r = 0.51-0.60). Visuospatial neglect was present in 27 patients (22%). Between-group analysis revealed somatosensory deficits that occurred significantly more often and more severely in patients with visuospatial neglect ( P .05). Results showed consistently stronger correlations between motor and somatosensory deficits in patients with visuospatial neglect ( r = 0.44-0.78) compared with patients without neglect ( r = 0.08-0.59). Conclusions. Somatosensory impairments are common in subacute patients poststroke and are related to motor outcome. Visuospatial neglect was associated with more severe upper-limb somatosensory impairments.
Structural rearrangements drive extensive genome divergence between symbiotic and free-living Symbiodinium
Publisher: Cold Spring Harbor Laboratory
Date: 26-09-2019
DOI: 10.1101/783902
Abstract: Symbiodiniaceae are predominantly symbiotic dinoflagellates critical to corals and other reef organisms. Symbiodinium is a basal symbiodiniacean lineage and includes symbiotic and free-living taxa. However, the molecular mechanisms underpinning these distinct lifestyles remain little known. Here, we present high-quality de novo genome assemblies for the symbiotic Symbiodinium tridacnidorum CCMP2592 (genome size 1.3 Gbp) and the free-living Symbiodinium natans CCMP2548 (genome size 0.74 Gbp). These genomes display extensive sequence ergence, sharing only ~1.5% conserved regions (≥90% identity). We predicted 45,474 and 35,270 genes for S. tridacnidorum and S. natans , respectively of the 58,541 homologous gene families, 28.5% are common to both genomes. We recovered a greater extent of gene duplication and higher abundance of repeats, transposable elements and pseudogenes in the genome of S. tridacnidorum than in that of S. natans . These findings demonstrate that genome structural rearrangements are pertinent to distinct lifestyles in Symbiodinium , and may contribute to the vast genetic ersity within the genus, and more broadly in Symbiodiniaceae. Moreover, the results from our whole-genome comparisons against a free-living outgroup support the notion that the symbiotic lifestyle is a derived trait in, and that the free-living lifestyle is ancestral to, Symbiodinium .
Associations Between Sensorimotor Impairments in the Upper Limb at 1 Week and 6 Months After Stroke
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 07-2016
DOI: 10.1097/NPT.0000000000000138
Abstract: Longitudinal information regarding the prevalence of upper limb somatosensory deficits and the association with motor impairment and activity limitations is scarce. The aim of this prospective cohort study was to map the extent and distribution of somatosensory deficits, and to determine associations over time between somatosensory deficits and motor impairment and activity limitations. We recruited 32 participants who were assessed 4 to 7 days after stroke, and reassessed at 6 months. Somatosensory measurements included the Erasmus-modified Nottingham sensory assessment (Em-NSA), perceptual threshold of touch, thumb finding test, 2-point discrimination, and stereognosis subscale of the NSA. Evaluation of motor impairment comprised the Fugl-Meyer assessment, Motricity Index, and Action Research Arm Test. In addition, at 6 months, activity limitation was determined using the adult assisting hand assessment stroke, the ABILHAND, and hand subscale of the Stroke Impact Scale. Somatosensory impairments were common, with 41% to 63% experiencing a deficit in one of the modalities within the first week and 3% to 50% at 6 months. In the acute phase, there were only very low associations between somatosensory and motor impairments ( r = 0.03-0.20), whereas at 6 months, low to moderate associations ( r = 0.32-0.69) were found for perceptual threshold of touch, thumb finding test, and stereognosis with motor impairment and activity limitations. Low associations ( r = 0.01-0.29) were found between somatosensory impairments in the acute phase and motor impairments and activity limitations at 6 months. : This study showed that somatosensory impairments are common and suggests that the association with upper limb motor and functional performance increases with time after stroke. Video Abstract available for more insights from the authors (see Supplemental Digital Content 1, links.lww.com/JNPT/A138).
Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium
Publisher: Elsevier BV
Date: 04-2021
DOI: 10.1016/J.CUB.2021.01.018
Abstract: The green alga Ostreobium is an important coral holobiont member, playing key roles in skeletal decalcification and providing photosynthate to bleached corals that have lost their dinoflagellate endosymbionts. Ostreobium lives in the coral's skeleton, a low-light environment with variable pH and O
Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus Symbiodinium
Publisher: Springer Science and Business Media LLC
Date: 13-04-2021
DOI: 10.1186/S12915-021-00994-6
Abstract: 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. 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 ergence. 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. Our results underscore the potential impact of lifestyle on lineage-specific gene-function innovation, genome ergence, and the ersification of Symbiodinium and Symbiodiniaceae. The ergent features we report, and their putative causes, may also apply to other microbial eukaryotes that have undergone symbiotic phases in their evolutionary history.
Polarella glacialis genomes encode tandem repeats of single-exon genes with functions critical to adaptation of dinoflagellates
Publisher: Cold Spring Harbor Laboratory
Date: 16-07-2019
DOI: 10.1101/704437
Abstract: Dinoflagellates are taxonomically erse, ecologically important phytoplankton in marine and freshwater environments. Here, we present two draft diploid genome assemblies of the free-living dinoflagellate Polarella glacialis , isolated from the Arctic and Antarctica. For each genome, guided using full-length transcriptome data, we predicted ,000 high-quality genes. About 68% of the genome is repetitive sequence long terminal repeats likely contribute to intra-species structural ergence and distinct genome sizes (3.0 and 2.7 Gbp). Of all genes, ∼40% are encoded unidirectionally, ∼25% comprised of 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. Our results elucidate how selection acts within the context of a complex genome structure to facilitate local adaptation. Since 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 environments.
Functional network connectivity is altered in patients with upper limb somatosensory impairments in the acute phase post stroke: A cross-sectional study
Publisher: Public Library of Science (PLoS)
Date: 12-10-2018
Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions
Publisher: Springer Science and Business Media LLC
Date: 24-05-2020
DOI: 10.1186/S12915-020-00782-8
Abstract: Dinoflagellates are taxonomically erse 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 erse 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 erse free-living species is still lacking. 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 ergence 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. 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.
Analysis of Porphyra Membrane Transporters Demonstrates Gene Transfer among Photosynthetic Eukaryotes and Numerous Sodium-Coupled Transport Systems
Publisher: Oxford University Press (OUP)
Date: 14-02-2012
Abstract: Membrane transporters play a central role in many cellular processes that rely on the movement of ions and organic molecules between the environment and the cell, and between cellular compartments. Transporters have been well characterized in plants and green algae, but little is known about transporters or their evolutionary histories in the red algae. Here we examined 482 expressed sequence tag contigs that encode putative membrane transporters in the economically important red seaweed Porphyra (Bangiophyceae, Rhodophyta). These contigs are part of a comprehensive transcriptome dataset from Porphyra umbilicalis and Porphyra purpurea. Using phylogenomics, we identified 30 trees that support the expected monophyly of red and green algae lants (i.e. the Plantae hypothesis) and 19 expressed sequence tag contigs that show evidence of endosymbiotic/horizontal gene transfer involving stramenopiles. The majority (77%) of analyzed contigs encode transporters with unresolved phylogenies, demonstrating the difficulty in resolving the evolutionary history of genes. We observed molecular features of many sodium-coupled transport systems in marine algae, and the potential for coregulation of Porphyra transporter genes that are associated with fatty acid biosynthesis and intracellular lipid trafficking. Although both the tissue-specific and subcellular locations of the encoded proteins require further investigation, our study provides red algal gene candidates associated with transport functions and novel insights into the biology and evolution of these transporters.
Mismatch between observed and perceived upper limb function: an eye-catching phenomenon after stroke
Publisher: Informa UK Limited
Date: 22-03-2018
DOI: 10.1080/09638288.2018.1442504
Abstract: To investigate the relation between observed and perceived upper limb motor function in patients with chronic stroke. We investigated 32 patients at six months after stroke with the Fugl-Meyer Assessment (observed function) and hand subscale of the Stroke Impact Scale (perceived function). Spearman correlation was calculated to relate observed and perceived function. Through cut-off scores, we ided our s le in low (Fugl-Meyer Assessment <31/66) and good observed function, and low (hand subscale of Stroke Impact Scale <61/100) and good perceived function. Scatterplot and hierarchical clustering analysis was conducted to detect distinct groups. A strong positive relation was found between observed and perceived function (r = 0.84). Three groups could be identified a "low match group" of patients with low observed and low perceived function (n = 11, 34%), a "good match group" containing patients with good observed and good perceived function (n = 15, 47%), and a "mismatch group" comprising patients with good observed but low perceived function (n = 6, 19%). In our chronic s le, one in five patients showed good upper limb observed but low perceived function. Measuring both observed and perceived arm and hand function seems warranted together with considering a differential therapy approach for the distinct groups. Implications for rehabilitation A considerable group of patients in the chronic phase post-stroke have good motor function in their affected upper limb, but nevertheless perceive a restricted ability. In order to identify a mismatch in people with chronic stroke, both observed and perceived upper limb motor function should be assessed. Besides common measurement tools for observed function like the Fugl-Meyer Assessment, perceived function can be evaluated by means of the hand function section of the Stroke Impact Scale. For patients with good observed but low perceived function, an additional rehabilitation strategy should be considered, potentially including awareness of ability and a self-efficacy approach.
Is There Full or Proportional Somatosensory Recovery in the Upper Limb After Stroke? Investigating Behavioral Outcome and Neural Correlates
Publisher: SAGE Publications
Date: 10-07-2018
Abstract: Background. Proportional motor recovery in the upper limb has been investigated, indicating about 70% of the potential for recovery of motor impairment within the first months poststroke. Objective. To investigate whether the proportional recovery rule is applicable for upper-limb somatosensory impairment and to study underlying neural correlates of impairment and outcome at 6 months. Methods. A total of 32 patients were evaluated at 4 to 7 days and 6 months using the Erasmus MC modification of the revised Nottingham Sensory Assessment (NSA) for impairment of (1) somatosensory perception (exteroception) and (2) passive somatosensory processing (sharp/blunt discrimination and proprioception) (3) active somatosensory processing was evaluated using the stereognosis component of the NSA. Magnetic resonance imaging scans were obtained within 1 week poststroke, from which lesion load (LL) was calculated for key somatosensory tracts. Results. Somatosensory perception fully recovered within 6 months. Passive and active somatosensory processing showed proportional recovery of 86% (95% CI = 79%-93%) and 69% (95% CI = 49%-89%), respectively. Patients with somatosensory impairment at 4 to 7 days showed significantly greater thalamocortical and insulo-opercular tracts (TCT and IOT) LL ( P .05) in comparison to patients without impairment. Sensorimotor tract disruption at 4 to 7 days did not provide significant contribution above somatosensory processing score at 4 to 7 days when predicting somatosensory processing outcome at 6 months. Conclusions. Our s le of stroke patients assessed early showed full somatosensory perception but proportional passive and active somatosensory processing recovery. Disruption of both the TCT and IOT early after stroke appears to be a factor associated with somatosensory impairment but not outcome.
The transcriptomic response of the coral Acropora digitifera to a competent Symbiodinium strain: the symbiosome as an arrested early phagosome
Publisher: Wiley
Date: 18-05-2016
DOI: 10.1111/MEC.13659
Abstract: Despite the ecological significance of the relationship between reef-building corals and intracellular photosynthetic dinoflagellates of the genus Symbiodinium, very little is known about the molecular mechanisms involved in its establishment. Indeed, microarray-based analyses point to the conclusion that host gene expression is largely or completely unresponsive during the establishment of symbiosis with a competent strain of Symbiodinium. In this study, the use of Illumina RNA-Seq technology allowed detection of a transient period of differential expression involving a small number of genes (1073 transcripts <3% of the transcriptome) 4 h after the exposure of Acropora digitifera planulae to a competent strain of Symbiodinium (a clade B strain). This phenomenon has not previously been detected as a consequence of both the lower sensitivity of the microarray approaches used and the s ling times used. The results indicate that complex changes occur, including transient suppression of mitochondrial metabolism and protein synthesis, but are also consistent with the hypothesis that the symbiosome is a phagosome that has undergone early arrest, raising the possibility of common mechanisms in the symbiotic interactions of corals and symbiotic sea anemones with their endosymbionts.
Voxel-based lesion-symptom mapping of stroke lesions underlying somatosensory deficits
Publisher: Elsevier BV
Date: 2016
Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium
Publisher: Cold Spring Harbor Laboratory
Date: 22-07-2020
DOI: 10.1101/2020.07.21.211367
Abstract: The green alga Ostreobium is an important coral holobiont member, playing key roles in skeletal decalcification and providing photosynthate to bleached corals that have lost their dinoflagellate endosymbionts. Ostreobium lives in the coral’s skeleton, a low-light environment with variable pH and O□ availability. We present the Ostreobium nuclear genome and a metatranscriptomic analysis of healthy and bleached corals to improve our understanding of Ostreobium ’s adaptations to its extreme environment and its roles as a coral holobiont member. The Ostreobium genome has 10,663 predicted protein-coding genes and shows adaptations for life in low and variable light conditions and other stressors in the endolithic environment. This alga presents a rich repertoire of light-harvesting complex proteins but lacks many genes for photoprotection and photoreceptors. It also has a large arsenal of genes for oxidative stress response. An expansion of extracellular peptidases suggests that Ostreobium may supplement its energy needs by feeding on the organic skeletal matrix, and a erse set of fermentation pathways allow it to live in the anoxic skeleton at night. Ostreobium depends on other holobiont members for vitamin B12, and our metatranscriptomes identify potential bacterial sources. Metatranscriptomes showed Ostreobium becoming a dominant agent of photosynthesis in bleached corals and provided evidence for variable responses among coral s les and different Ostreobium genotypes. Our work provides a comprehensive understanding of the adaptations of Ostreobium to its extreme environment and an important genomic resource to improve our comprehension of coral holobiont resilience, bleaching and recovery.
Comparative transcriptomic analyses of Chromera and Symbiodiniaceae
Publisher: Wiley
Date: 24-06-2020
Tightly constrained genome reduction and relaxation of purifying selection during secondary plastid endosymbiosis
Publisher: Cold Spring Harbor Laboratory
Date: 29-05-2021
DOI: 10.1101/2021.05.27.446077
Abstract: Endosymbiosis, the establishment of a former free-living prokaryotic or eukaryotic cell as an organelle inside a host cell, can dramatically alter the genomic architecture of the endosymbiont. Plastids, the light harvesting organelles of photosynthetic eukaryotes, are excellent models to study this phenomenon because plastid origin has occurred multiple times in evolution. Here, we investigate the genomic signature of molecular processes acting through secondary plastid endosymbiosis – the origination of a new plastid from a free-living eukaryotic alga. We used phylogenetic comparative methods to study gene loss and changes in selective regimes on plastid genomes, focusing on the green lineage that has given rise to three independent lineages with secondary plastids (euglenophytes, chlorarachniophytes, Lepidodinium ). Our results show an overall increase in gene loss associated with secondary endosymbiosis, but this loss is tightly constrained by retention of genes essential for plastid function. The data show that secondary plastids have experienced temporary relaxation of purifying selection during secondary endosymbiosis. However, this process is tightly constrained as well, with selection relaxed only relative to the background in primary plastids, but purifying selection remaining strong in absolute terms even during the endosymbiosis events. Selection intensity rebounds to pre-endosymbiosis levels following endosymbiosis events, demonstrating the changes in selection efficiency during different phases of secondary plastid origin. Independent endosymbiosis events in the euglenophytes, chlorarachniophytes, and Lepidodinium differ in their degree of relaxation of selection, highlighting the different evolutionary contexts of these events. This study reveals the selection-drift interplay during secondary endosymbiosis, and evolutionary parallels during the process of organelle origination.
Dual RNA‐sequencing analyses of a coral and its native symbiont during the establishment of symbiosis
Publisher: Wiley
Date: 21-09-2020
DOI: 10.1111/MEC.15612
Genomes of Symbiodiniaceae reveal extensive sequence divergence but conserved functions at family and genus levels
Publisher: Cold Spring Harbor Laboratory
Date: 10-10-2019
DOI: 10.1101/800482
Abstract: Dinoflagellates of the family Symbiodiniaceae (Order Suessiales) are predominantly symbiotic, and many are known for their association with corals. The genetic and functional ersity among Symbiodiniaceae is well acknowledged, but the genome-wide sequence ergence among these lineages remains little known. Here, we present de novo genome assemblies of five isolates from the basal genus Symbiodinium , encompassing distinct ecological niches. Incorporating existing data from Symbiodiniaceae and other Suessiales (15 genome datasets in total), we investigated genome features that are common or unique to these Symbiodiniaceae, to genus Symbiodinium , and to the in idual species S. microadriaticum and S. tridacnidorum . Our whole-genome comparisons reveal extensive sequence ergence, with no sequence regions common to all 15. Based on similarity of k -mers from whole-genome sequences, the distances among Symbiodinium isolates are similar to those between isolates of distinct genera. We observed extensive structural rearrangements among symbiodiniacean genomes those from two distinct Symbiodinium species share the most (853) syntenic gene blocks. Functions enriched in genes core to Symbiodiniaceae are also enriched in those core to Symbiodinium. Gene functions related to symbiosis and stress response exhibit similar relative abundance in all analysed genomes. Our results suggest that structural rearrangements contribute to genome sequence ergence in Symbiodiniaceae even within a same species, but the gene functions have remained largely conserved in Suessiales. This is the first comprehensive comparison of Symbiodiniaceae based on whole-genome sequence data, including comparisons at the intra-genus and intra-species levels.
Nuclear genome of a pedinophyte pinpoints genomic innovation and streamlining in the green algae.
Publisher: Wiley
Date: 06-01-2022
DOI: 10.1111/NPH.17926
Abstract: The genomic ersity underpinning high ecological and species ersity in the green algae (Chlorophyta) remains little known. Here, we aimed to track genome evolution in the Chlorophyta, focusing on loss and gain of homologous genes, and lineage-specific innovations of the core Chlorophyta. We generated a high-quality nuclear genome for pedinophyte YPF701, a sister lineage to others in the core Chlorophyta and incorporated this genome in a comparative analysis with 25 other genomes from erse Viridiplantae taxa. The nuclear genome of pedinophyte YPF701 has an intermediate size and gene number between those of most prasinophytes and the remainder of the core Chlorophyta. Our results suggest positive selection for genome streamlining in the Pedinophyceae, independent from genome minimisation observed among prasinophyte lineages. Genome expansion was predicted along the branch leading to the UTC clade (classes Ulvophyceae, Trebouxiophyceae and Chlorophyceae) after ergence from their last common ancestor with pedinophytes, with genomic novelty implicated in a range of basic biological functions. Results emphasise multiple independent signals of genome minimisation within the Chlorophyta, as well as the genomic novelty arising before ersification in the UTC clade, which may underpin the success of this species-rich clade in a ersity of habitats.
Nuclear genome of a pedinophyte pinpoints genomic innovation and streamlining in the green algae
Publisher: Cold Spring Harbor Laboratory
Date: 05-10-2021
DOI: 10.1101/2021.10.04.463119
Abstract: The genomic ersity underpinning high ecological and species ersity in the green algae (Chlorophyta) remains little known. Here, we aimed to track genome evolution in the Chlorophyta, focusing on loss and gain of homologous genes, and lineage-specific innovations of the Core Chlorophyta. We generated a high-quality nuclear genome for pedinophyte YPF701, a sister lineage to others in the Core Chlorophyta, and incorporated this genome in a comparative analysis with 25 other genomes from erse Viridiplantae taxa. The nuclear genome of pedinophyte YPF701 has an intermediate size and gene number between those of most early- erging prasinophytes and the remainder of the Core Chlorophyta. Our results suggest positive selection for genome streamlining in Pedinophyceae, independent from genome minimisation observed among prasinophyte lineages. Genome expansion was predicted along the branch leading to the UTC clade (classes Ulvophyceae, Trebouxiophyceae and Chlorophyceae) after ergence from their common ancestor with pedinophytes, with genomic novelty implicated in a range of basic biological functions. These results emphasise multiple independent signals of genome minimisation within the Chlorophyta, as well as the genomic novelty arising prior to ersification in the UTC clade, which may underpin the success of this species-rich clade in a ersity of habitats.
Close relationship between coral-associated Chromera strains despite major differences within the Symbiodiniaceae
Publisher: Cold Spring Harbor Laboratory
Date: 04-11-2019
DOI: 10.1101/825992
Abstract: Reef-building corals live in a mutualistic relationship with photosynthetic algae (family Symbiodiniaceae) that usually provide most of the energy required by the coral host. This relationship is sensitive to temperature stress as little as a 1°C increase often leading to collapse of the association. This sensitivity has led to interest in the potential of more stress tolerant algae to supplement or substitute for the normal Symbiodiniaceae mutualists. In this respect, the apicomplexan-like microalga Chromera is of particular interest due to its greater temperature tolerance. We generated a de novo transcriptome for a Chromera strain isolated from a GBR coral ( “GBR Chromera” ) and compared to those of the reference strain of Chromera (“Sydney Chromera ”), and to those of Symbiodiniaceae ( Fugacium, Cladocopium and Breviolum ), as well as the apicomplexan parasite, Plasmodium falciparum . By contrast with the Symbiodiniaceae, the two Chromera strains had a high level of sequence similarity evident by very low levels of ergence in orthologous genes. Although KEGG categories provide few criteria by which true coral mutualists might be identified, they do supply a molecular rationalization for the ubiquitous association of Cladocopium strains with Indo-Pacific reef corals. The presence of HSP20 genes may underlie the higher thermal tolerance of Chromera .
A genomic view of the reef-building coral Porites lutea and its microbial symbionts
Publisher: Springer Science and Business Media LLC
Date: 23-09-2019
DOI: 10.1038/S41564-019-0532-4
Abstract: Corals and the reef ecosystems that they support are in global decline due to increasing anthropogenic pressures such as climate change
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