Disparate Population and Holobiont Structure of Pocilloporid Corals Across the Red Sea Gradient Demonstrate Species-Specific Evolutionary Trajectories

Global habitat degradation heightens the need to better understand patterns of genetic connectivity and diversity of marine biota across geographical ranges to guide conservation efforts. Corals across the Red Sea are subject to pronounced environmental differences, but studies so far suggest that animal populations are largely connected, excepting evidence for a genetic break between the northern-central and southern regions. Here, we investigated population structure and holobiont assemblage of two common pocilloporid corals, Pocillopora verrucosa and Stylophora pistillata, across the Red Sea. We found little evidence for population differentiation in P. verrucosa, except for the southernmost site. Conversely, S. pistillata exhibited a complex population structure with evidence for within-reef and regional genetic differentiation, in line with differences in their reproductive mode (P. verrucosa is a broadcast spawner and S. pistillata is a brooder). Analysis for genomic loci under positive selection identified 85 sites (18 of which were in coding sequences) that distinguished the southern P. verrucosa population from the remainder of the Red Sea population. By comparison, we found 128 loci (24 of which were residing in coding sequences) in S. pistillata with evidence for local adaptation at various sites. Functional annotation of the underlying proteins revealed putative roles in the response to stress, lipid metabolism, transport, cytoskeletal rearrangement, and ciliary function (among others). Microbial assemblages of both coral species showed pervasive association with microalgal symbionts from the genus Symbiodinium (former clade A) and bacteria from the genus Endozoicomonas that exhibited significant differences according to host genotype and environment. The disparity of population genetic and holobiont assemblage patterns even between closely related species (family Pocilloporidae) highlights the need for multispecies investigations to better understand the role of the environment in shaping evolutionary trajectories. It further emphasizes the importance of networks of reef reserves to achieve conservation of genetic variants critical to the future survival of coral ecosystems

Environmental latitudinal gradients and host specificity shape Symbiodiniaceae distribution in Red Sea Porites corals

AimTo assess the diversity of algal symbionts of the family Symbiodiniaceae associated with the coral genus Porites in the Red Sea, and to test for host-specificity and environmental variables driving biogeographical patterns of algal symbiont distribution.LocationSaudi Arabian Red SeaTaxonEndosymbiotic dinoflagellates of the family Symbiodiniaceae in association with the reef-building coral genus Porites.MethodsEighty Porites coral specimens were collected along the Saudi Arabian Red Sea coast. Species boundaries were assessed morphologically and genetically (putative Control Region - mtCR; ITS region – ITS). Community composition of symbiotic dinoflagellates of the family Symbiodiniaceae was also assessed. Using the ITS2 marker with the SymPortal framework, Symbiodiniaceae data at the genus, majority ITS2 sequence, and ITS2 type profile were used to assess symbiont diversity and distribution patterns. These were analyzed in relation to coral host diversity, geographic location, and environmental variables.ResultsAmong the 80 Porites samples, 10 morphologies were identified. These corals were clustered into five lineages (clades I to V) by each of the markers independently. Clades I, II, and III each comprised of a single Porites morphology, while clades IV and V contained up to five distinct morphologies. The diversity of Symbiodiniaceae associated with Porites was high and latitudinal differentiation was observed. In particular, a shift from a Cladocopium- to a Durusdinium-dominated community was found along the north-south gradient. Symbiont diversity showed patterns of geographic-specific association at Symbiodiniaceae genus, majority ITS2 sequence, and ITS2 type profile level. Specific associations with host-genotypes (but not morphological species) were also recovered when considering Symbiodiniaceae majority ITS2 sequence and ITS2 type profiles.Main conclusionsThis study provides the first large scale molecular characterization of Symbiodiniaceae communities associated with Porites corals from the Saudi Arabian Red Sea. The use of intragenomic diversity data enabled the resolution of host-symbiont specificity and biogeographical patterns of distribution, previously unachievable with the ITS2 marker alone. Finally, correlation among symbiont diversity and Red Sea environmental gradients was documented

Contrasting Heat Stress Response Patterns of Coral Holobionts Across the Red Sea Suggest Distinct Mechanisms of Thermal Tolerance

Corals from the northern Red Sea, in particular the Gulf of Aqaba (GoA), have exceptionally high bleaching thresholds approaching \u3e5℃ above their maximum monthly mean (MMM) temperatures. These elevated thresholds are thought to be due to historical selection, as corals passed through the warmer Southern Red Sea during recolonization from the Arabian Sea. To test this hypothesis, we determined thermal tolerance thresholds of GoA versus central Red Sea (CRS) Stylophora pistillata corals using multi-temperature acute thermal stress assays to determine thermal thresholds. Relative thermal thresholds of GoA and CRS corals were indeed similar and exceptionally high (~7℃ above MMM). However, absolute thermal thresholds of CRS corals were on average 3℃ above those of GoA corals. To explore the molecular underpinnings, we determined gene expression and microbiome response of the coral holobiont. Transcriptomic responses differed markedly, with a strong response to the thermal stress in GoA corals and their symbiotic algae versus a remarkably muted response in CRS colonies. Concomitant to this, coral and algal genes showed temperature-induced expression in GoA corals, while exhibiting fixed high expression (front-loading) in CRS corals. Bacterial community composition of GoA corals changed dramatically under heat stress, whereas CRS corals displayed stable assemblages. We interpret the response of GoA corals as that of a resilient population approaching a tipping point in contrast to a pattern of consistently elevated thermal resistance in CRS corals that cannot further attune. Such response differences suggest distinct thermal tolerance mechanisms that may affect the response of coral populations to ocean warming

Molecular and Historical Aspects of Corn Belt Dent Diversity

Tens-of-thousands of open-pollinated cultivars of corn (Zea mays L.) are being maintained in germplasm banks. Knowledge of the amount and distribution of genetic variation within and among accessions can aid end users in choosing among them. We estimated molecular genetic variation and looked for influences of pedigree, adaptation, and migration in the genetic makeup of conserved Corn-Belt Dent-related germplasm. Plants sampled from 57 accessions representing Corn-Belt Dents, Northern Flints, Southern Dents, plus 12 public inbreds, were genotyped at 20 simple sequence repeat (SSR) loci. For 47 of the accessions, between 5 and 23 plants per accession were genotyped (mean = 9.3). Mean number of alleles per locus was 6.5 overall, 3.17 within accessions, and 3.20 within pooled inbreds. Mean gene diversity was 0.53 within accessions and 0.61 within pooled inbreds. Open-pollinated accessions showed a tendency toward inbreeding (FIS = 0.09), and 85% of genetic variation was shared among them. A Fitch-Margoliash tree strongly supported the distinctiveness of flint from dent germplasm but did not otherwise reveal evidence of genetic structure. Mantel tests revealed significant correlations between genetic distance and geographical (r = 0.54, P= 0.04) or maturity zone (r = 0.33, P = 0.03) distance only if flint germplasm was included in the analyses. A significant correlation (r = 0.76, P \u3c 0.01) was found between days to pollen shed and maturity zone of accession origin. Pedigree, rather than migration or selection, has most influenced the genetic structure of the extant representatives of the open-pollinated cultivars at these SSR loci

An annotated list of ornamentals naturally found infected by Brevipalpus mite-transmitted viruses

The first cases of ornamental plants found infected by Brevipalpus transmitted viruses (BTV) were described in the 1990's from the region of Piracicaba, State of São Paulo, Brazil; subsequent cases were from other regions in the country and other American countries. Currently, 37 ornamental plant species (for the sake of simplicity, orchids being considered as a single species), belonging to 18 families of dicotyledons, have been reported hosting BTV. Because of the non systemic type of infection of these viruses, the localized diseases they cause are unimportant usually, but they have the potential to cause economic losses if severe outbreaks of Brevipalpus mite populations occur. Some ornamentals may serve as reservoirs to BTV known to cause serious damage to food crops as Citrus leprosis virus- cytoplasmic type (CiLV-C), passion fruit green spot virus (PFGSV) and Coffee ringspot virus (CoRSV).Os primeiros casos de plantas ornamentais encontradas naturalmente infetadas por vírus transmitidos por Brevipalpus (Acari: Tenuipalpidae) (VTB) foram registrados nos anos 1990 na região de Piracicaba, Estado de São Paulo, e ocorrências subseqüentes foram observadas em várias outras regiões do país e de outros países das Américas. Atualmente acham-se relatadas 37 espécies de ornamentais (para efeito de simplificação, orquídeas foram consideradas como única espécie) pertencentes a 18 famílias botânicas. Pelo fato de causarem apenas infecções localizadas, geralmente nas folhas, VTB em ornamentais não causam preocupações aos produtores, mas potencialmente podem causar perdas econômicas se ocorrerem explosões populacionais do ácaro vetor. Plantas ornamentais podem servir de reservatório de VTB de importância econômica como os vírus da leprose dos citros-tipo citoplasmático (CiLV-C), da mancha verde do maracujá (PFGSV) e da mancha anular do cafeeiro (CoRSV)

Health Impairments in Children and Adolescents After Hospitalization for Acute COVID-19 or MIS-C

OBJECTIVES: To evaluate risk factors for postdischarge sequelae in children and adolescents hospitalized for acute coronavirus disease 2019 (COVID-19) or multisystem inflammatory syndrome in children (MIS-C). METHODS: Multicenter prospective cohort study conducted in 25 United States pediatric hospitals. Patients <21-years-old, hospitalized May 2020 to May 2021 for acute COVID-19 or MIS-C with follow-up 2 to 4 months after admission. We assessed readmissions, persistent symptoms or activity impairment, and new morbidities. Multivariable regression was used to calculate adjusted risk ratios (aRR) and 95% confidence intervals (CI). RESULTS: Of 358 eligible patients, 2 to 4 month survey data were available for 119 of 155 (76.8%) with acute COVID-19 and 160 of 203 (78.8%) with MIS-C. Thirteen (11%) patients with acute COVID-19 and 12 (8%) with MIS-C had a readmission. Thirty-two (26.9%) patients with acute COVID-19 had persistent symptoms (22.7%) or activity impairment (14.3%) and 48 (30.0%) with MIS-C had persistent symptoms (20.0%) or activity impairment (21.3%). For patients with acute COVID-19, persistent symptoms (aRR, 1.29 [95% CI, 1.04-1.59]) and activity impairment (aRR, 1.37 [95% CI, 1.06-1.78]) were associated with more organ systems involved. Patients with MIS-C and pre-existing respiratory conditions more frequently had persistent symptoms (aRR, 3.09 [95% CI, 1.55-6.14]) and those with obesity more frequently had activity impairment (aRR, 2.52 [95% CI, 1.35-4.69]). New morbidities were infrequent (9% COVID-19, 1% MIS-C). CONCLUSIONS: Over 1 in 4 children hospitalized with acute COVID-19 or MIS-C experienced persistent symptoms or activity impairment for at least 2 months. Patients with MIS-C and respiratory conditions or obesity are at higher risk of prolonged recovery

Velocity-space sensitivity of the time-of-flight neutron spectrometer at JET

The velocity-space sensitivities of fast-ion diagnostics are often described by so-called weight functions. Recently, we formulated weight functions showing the velocity-space sensitivity of the often dominant beam-target part of neutron energy spectra. These weight functions for neutron emission spectrometry (NES) are independent of the particular NES diagnostic. Here we apply these NES weight functions to the time-of-flight spectrometer TOFOR at JET. By taking the instrumental response function of TOFOR into account, we calculate time-of-flight NES weight functions that enable us to directly determine the velocity-space sensitivity of a given part of a measured time-of-flight spectrum from TOFOR

Relationship of edge localized mode burst times with divertor flux loop signal phase in JET

A phase relationship is identified between sequential edge localized modes (ELMs) occurrence times in a set of H-mode tokamak plasmas to the voltage measured in full flux azimuthal loops in the divertor region. We focus on plasmas in the Joint European Torus where a steady H-mode is sustained over several seconds, during which ELMs are observed in the Be II emission at the divertor. The ELMs analysed arise from intrinsic ELMing, in that there is no deliberate intent to control the ELMing process by external means. We use ELM timings derived from the Be II signal to perform direct time domain analysis of the full flux loop VLD2 and VLD3 signals, which provide a high cadence global measurement proportional to the voltage induced by changes in poloidal magnetic flux. Specifically, we examine how the time interval between pairs of successive ELMs is linked to the time-evolving phase of the full flux loop signals. Each ELM produces a clear early pulse in the full flux loop signals, whose peak time is used to condition our analysis. The arrival time of the following ELM, relative to this pulse, is found to fall into one of two categories: (i) prompt ELMs, which are directly paced by the initial response seen in the flux loop signals; and (ii) all other ELMs, which occur after the initial response of the full flux loop signals has decayed in amplitude. The times at which ELMs in category (ii) occur, relative to the first ELM of the pair, are clustered at times when the instantaneous phase of the full flux loop signal is close to its value at the time of the first ELM

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism

Local adaptation constrains the distribution potential of heat-tolerant Symbiodinium from the Persian/Arabian Gulf

The symbiotic association of corals and unicellular algae of the genus Symbiodinium in the southern Persian/Arabian Gulf (PAG) display an exceptional heat tolerance, enduring summer peak temperatures of up to 36?°C. As yet, it is not clear whether this resilience is related to the presence of specific symbiont types that are exclusively found in this region. Therefore, we used molecular markers to identify the symbiotic algae of three Porites species along &gt;1000?km of coastline in the PAG and the Gulf of Oman and found that a recently described species, Symbiodinium thermophilum, is integral to coral survival in the southern PAG, the world’s hottest sea. Despite the geographic isolation of the PAG, we discovered that representatives of the S. thermophilum group can also be found in the adjacent Gulf of Oman providing a potential source of thermotolerant symbionts that might facilitate the adaptation of Indian Ocean populations to the higher water temperatures expected for the future. However, corals from the PAG associated with S. thermophilum show strong local adaptation not only to high temperatures but also to the exceptionally high salinity of their habitat. We show that their superior heat tolerance can be lost when these corals are exposed to reduced salinity levels common for oceanic environments elsewhere. Consequently, the salinity prevailing in most reefs outside the PAG might represent a distribution barrier for extreme temperature-tolerant coral/Symbiodinium associations from the PAG