Genome-sequencing studies indicate that all humans carry many genetic variants predicted to cause loss of function (LoF) of protein-coding genes, suggesting unexpected redundancy in the human genome. ...Here we apply stringent filters to 2951 putative LoF variants obtained from 185 human genomes to determine their true prevalence and properties. We estimate that human genomes typically contain ~100 genuine LoF variants with ~20 genes completely inactivated. We identify rare and likely deleterious LoF alleles, including 26 known and 21 predicted severe disease—causing variants, as well as common LoF variants in nonessential genes. We describe functional and evolutionary differences between LoF-tolerant and recessive disease genes and a method for using these differences to prioritize candidate genes found in clinical sequencing studies.
Rhinovirus infection is a major cause of asthma exacerbations.
We studied nasal and bronchial mucosal inflammatory responses during experimental rhinovirus-induced asthma exacerbations.
We used ...nasosorption on days 0, 2–5 and 7 and bronchosorption at baseline and day 4 to sample mucosal lining fluid to investigate airway mucosal responses to rhinovirus infection in patients with allergic asthma (n=28) and healthy non-atopic controls (n=11), by using a synthetic absorptive matrix and measuring levels of 34 cytokines and chemokines using a sensitive multiplex assay.
Following rhinovirus infection asthmatics developed more upper and lower respiratory symptoms and lower peak expiratory flows compared to controls (all P<0.05). Asthmatics also developed higher nasal lining fluid levels of an anti-viral pathway (including IFN-γ, IFN-λ/IL-29, CXCL11/ITAC, CXCL10/IP10 and IL-15) and a type 2 inflammatory pathway (IL-4, IL-5, IL-13, CCL17/TARC, CCL11/eotaxin, CCL26/eotaxin-3) (area under curve day 0–7, all P<0.05). Nasal IL-5 and IL-13 were higher in asthmatics at day 0 (P<0.01) and levels increased by days 3 and 4 (P<0.01). A hierarchical correlation matrix of 24 nasal lining fluid cytokine and chemokine levels over 7days demonstrated expression of distinct interferon-related and type 2 pathways in asthmatics. In asthmatics IFN-γ, CXCL10/IP10, CXCL11/ITAC, IL-15 and IL-5 increased in bronchial lining fluid following viral infection (all P<0.05).
Precision sampling of mucosal lining fluid identifies robust interferon and type 2 responses in the upper and lower airways of asthmatics during an asthma exacerbation. Nasosorption and bronchosorption have potential to define asthma endotypes in stable disease and at exacerbation.
•Following rhinovirus infection asthmatics have increased interferons and type 2 inflammation in airway mucosal lining fluid.•Nasosorption cytokines and chemokines showed distinct pathways of interferon and type 2 inflammation in asthma.•Precision mucosal sampling has potential for stratifying molecular endotypes of asthma.•Validation of nasosorption and bronchosorption will be required for selection of asthmatics for therapy with biologics.
Experimental human rhinovirus (HRV) infection causes more severe upper and lower respiratory tract symptoms in allergic asthmatics than in healthy controls. There is greater induction of cytokines and chemokines in nasal and bronchial mucosal lining fluid (MLF) of asthmatics: with distinct pathways of type 2 and anti-viral/regulatory inflammation.
Subject to further validation, analysis of MLF may prove useful in stratification of patients with asthma, and the definition of molecular endotypes.
Interpretation
Nasosorption and bronchosorption are precision sampling methods with potential for widespread application in respiratory and other mucosal diseases (e.g. gastrointestinal diseases).
Biomarkers identified in nasosorption and bronchosorption samples will need to be validated compared to established airway sampling methods, in a range of asthma phenotypes, and with current and novel therapies.
The Atlantic herring is a model species for exploring the genetic basis for ecological adaptation, due to its huge population size and extremely low genetic differentiation at selectively neutral ...loci. However, such studies have so far been hampered because of a highly fragmented genome assembly. Here, we deliver a chromosome-level genome assembly based on a hybrid approach combining a de novo Pacific Biosciences (PacBio) assembly with Hi-C-supported scaffolding. The assembly comprises 26 autosomes with sizes ranging from 12.4 to 33.1 Mb and a total size, in chromosomes, of 726 Mb, which has been corroborated by a high-resolution linkage map. A comparison between the herring genome assembly with other high-quality assemblies from bony fishes revealed few inter-chromosomal but frequent intra-chromosomal rearrangements. The improved assembly facilitates analysis of previously intractable large-scale structural variation, allowing, for example, the detection of a 7.8-Mb inversion on Chromosome 12 underlying ecological adaptation. This supergene shows strong genetic differentiation between populations. The chromosome-based assembly also markedly improves the interpretation of previously detected signals of selection, allowing us to reveal hundreds of independent loci associated with ecological adaptation.
Unitary pseudogenes are a class of unprocessed pseudogenes without functioning counterparts in the genome. They constitute only a small fraction of annotated pseudogenes in the human genome. However, ...as they represent distinct functional losses over time, they shed light on the unique features of humans in primate evolution.
We have developed a pipeline to detect human unitary pseudogenes through analyzing the global inventory of orthologs between the human genome and its mammalian relatives. We focus on gene losses along the human lineage after the divergence from rodents about 75 million years ago. In total, we identify 76 unitary pseudogenes, including previously annotated ones, and many novel ones. By comparing each of these to its functioning ortholog in other mammals, we can approximately date the creation of each unitary pseudogene (that is, the gene 'death date') and show that for our group of 76, the functional genes appear to be disabled at a fairly uniform rate throughout primate evolution - not all at once, correlated, for instance, with the 'Alu burst'. Furthermore, we identify 11 unitary pseudogenes that are polymorphic - that is, they have both nonfunctional and functional alleles currently segregating in the human population. Comparing them with their orthologs in other primates, we find that two of them are in fact pseudogenes in non-human primates, suggesting that they represent cases of a gene being resurrected in the human lineage.
This analysis of unitary pseudogenes provides insights into the evolutionary constraints faced by different organisms and the timescales of functional gene loss in humans.
Beetles represent almost one-fourth of all described species, and knowledge about their relationships and evolution adds to our understanding of biodiversity. We performed a comprehensive ...phylogenetic analysis of Coleoptera inferred from three genes and nearly 1900 species, representing more than 80% of the world's recognized beetle families. We defined basal relationships in the Polyphaga supergroup, which contains over 300,000 species, and established five families as the earliest branching lineages. By dating the phylogeny, we found that the success of beetles is explained neither by exceptional net diversification rates nor by a predominant role of herbivory and the Cretaceous rise of angiosperms. Instead, the pre-Cretaceous origin of more than 100 present-day lineages suggests that beetle species richness is due to high survival of lineages and sustained diversification in a variety of niches.
The domestic pig is known as an excellent model for human immunology and the two species share many pathogens. Susceptibility to infectious disease is one of the major constraints on swine ...performance, yet the structure and function of genes comprising the pig immunome are not well-characterized. The completion of the pig genome provides the opportunity to annotate the pig immunome, and compare and contrast pig and human immune systems.
The Immune Response Annotation Group (IRAG) used computational curation and manual annotation of the swine genome assembly 10.2 (Sscrofa10.2) to refine the currently available automated annotation of 1,369 immunity-related genes through sequence-based comparison to genes in other species. Within these genes, we annotated 3,472 transcripts. Annotation provided evidence for gene expansions in several immune response families, and identified artiodactyl-specific expansions in the cathelicidin and type 1 Interferon families. We found gene duplications for 18 genes, including 13 immune response genes and five non-immune response genes discovered in the annotation process. Manual annotation provided evidence for many new alternative splice variants and 8 gene duplications. Over 1,100 transcripts without porcine sequence evidence were detected using cross-species annotation. We used a functional approach to discover and accurately annotate porcine immune response genes. A co-expression clustering analysis of transcriptomic data from selected experimental infections or immune stimulations of blood, macrophages or lymph nodes identified a large cluster of genes that exhibited a correlated positive response upon infection across multiple pathogens or immune stimuli. Interestingly, this gene cluster (cluster 4) is enriched for known general human immune response genes, yet contains many un-annotated porcine genes. A phylogenetic analysis of the encoded proteins of cluster 4 genes showed that 15% exhibited an accelerated evolution as compared to 4.1% across the entire genome.
This extensive annotation dramatically extends the genome-based knowledge of the molecular genetics and structure of a major portion of the porcine immunome. Our complementary functional approach using co-expression during immune response has provided new putative immune response annotation for over 500 porcine genes. Our phylogenetic analysis of this core immunome cluster confirms rapid evolutionary change in this set of genes, and that, as in other species, such genes are important components of the pig's adaptation to pathogen challenge over evolutionary time. These comprehensive and integrated analyses increase the value of the porcine genome sequence and provide important tools for global analyses and data-mining of the porcine immune response.
The Consensus Coding Sequence (CCDS) project (http://www.ncbi.nlm.nih.gov/CCDS/) is a collaborative effort to maintain a dataset of protein-coding regions that are identically annotated on the human ...and mouse reference genome assemblies by the National Center for Biotechnology Information (NCBI) and Ensembl genome annotation pipelines. Identical annotations that pass quality assurance tests are tracked with a stable identifier (CCDS ID). Members of the collaboration, who are from NCBI, the Wellcome Trust Sanger Institute and the University of California Santa Cruz, provide coordinated and continuous review of the dataset to ensure high-quality CCDS representations. We describe here the current status and recent growth in the CCDS dataset, as well as recent changes to the CCDS web and FTP sites. These changes include more explicit reporting about the NCBI and Ensembl annotation releases being compared, new search and display options, the addition of biologically descriptive information and our approach to representing genes for which support evidence is incomplete. We also present a summary of recent and future curation targets.
Successful embryonic development and offspring sex ratios of marine turtles are determined by thermal conditions experienced during incubation, rendering them potentially vulnerable to anthropogenic ...climate change. With the rate of projected temperature rises likely to outpace the adaptive capacity of long‐lived species such as marine turtles, there is growing interest in management interventions aimed at mitigating the effects of climate change at nesting grounds. In this study, we experimentally tested the impacts of artificial nest shading on the incubation temperature, hatching success, and predicted offspring sex ratio of green turtle (Chelonia mydas) clutches at Ascension Island. Clutches (n = 97) were sampled from 2 nesting beaches with naturally contrasting thermal environments (one hot; one cool) and either left as in situ controls or relocated to shaded or unshaded hatcheries on their beach of origin. Compared to unshaded experimental clutches, shading reduced mean incubation temperatures and sex‐determining temperatures (i.e., middle third of embryonic development) by 0.5–0.9°C and 0.5–1.2°C respectively, with the reduction being greater on the hotter beach. Shading also differentially affected hatchling output across the 2 sites: on the hot beach, shading significantly improved hatching success by ~23% but had minimal effects on offspring sex ratio; whereas on the cooler beach, shading did not impact hatching success but resulted in ~12% more male offspring. Interestingly, mean incubation temperatures of in situ controls did not differ significantly from shaded clutches, and were significantly cooler than unshaded experimental clutches, suggesting relocation may have negated some of the benefits of shading. Our results demonstrated that artificial shading may be a viable approach for partially offsetting climate change impacts on nesting marine turtles; however, scalability will be a major challenge in achieving conservation objectives at high‐density nesting sites like Ascension Island.
Successful embryonic development and offspring sex ratios of marine turtles are determined by thermal conditions experienced during incubation, rendering them potentially vulnerable to anthropogenic climate change. Therefore, there is growing interest in management interventions aimed at mitigating the effects of climate change at nesting grounds. In this study, we experimentally tested the impacts of artificial nest shading on the incubation temperature, hatching success and predicted offspring sex ratio of green turtle clutches at Ascension Island. Our results demonstrate that artificial nest shading may be a viable approach for conservation practitioners to partially alleviate the impacts of climate change on nesting marine turtles; however, scalability of such measures will likely be a major challenge at high‐density nesting sites like Ascension Island.
The great diversity of the "Phytophaga" (weevils, longhorn beetles and leaf beetles) has been attributed to their co-radiation with the angiosperms based on matching age estimates for both groups, ...but phylogenetic information and molecular clock calibrations remain insufficient for this conclusion.
A phylogenetic analysis of the leaf beetles (Chrysomelidae) was conducted based on three partial ribosomal gene markers (mitochondrial rrnL, nuclear small and large subunit rRNA) including over 3000 bp for 167 taxa representing most major chrysomelid lineages and outgroups. Molecular clock calibrations and confidence intervals were based on paleontological data from the oldest (K-T boundary) leaf beetle fossil, ancient feeding traces ascribed to hispoid Cassidinae, and the vicariant split of Nearctic and Palearctic members of the Timarchini.
The origin of the Chrysomelidae was dated to 73-79 Mya (confidence interval 63-86 Mya), and most subfamilies were post-Cretaceous, consistent with the ages of all confirmed body fossils. Two major monocot feeding chrysomelid lineages formed widely separated clades, demonstrating independent colonization of this ancient (early Cretaceous) angiosperm lineage.
Previous calibrations proposing a much older origin of Chrysomelidae were not supported. Therefore, chrysomelid beetles likely radiated long after the origin of their host lineages and their diversification was driven by repeated radiaton on a pre-existing diverse resource, rather than ancient host associations.
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