skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

Explore Research Products in the PAR
It may take a few hours for recently added research products to appear in PAR search results.


Title: The swan genome and transcriptome, it is not all black and white
Abstract Background The Australian black swan ( Cygnus atratus ) is an iconic species with contrasting plumage to that of the closely related northern hemisphere white swans. The relative geographic isolation of the black swan may have resulted in a limited immune repertoire and increased susceptibility to infectious diseases, notably infectious diseases from which Australia has been largely shielded. Unlike mallard ducks and the mute swan ( Cygnus olor ), the black swan is extremely sensitive to highly pathogenic avian influenza. Understanding this susceptibility has been impaired by the absence of any available swan genome and transcriptome information. Results Here, we generate the first chromosome-length black and mute swan genomes annotated with transcriptome data, all using long-read based pipelines generated for vertebrate species. We use these genomes and transcriptomes to show that unlike other wild waterfowl, black swans lack an expanded immune gene repertoire, lack a key viral pattern-recognition receptor in endothelial cells and mount a poorly controlled inflammatory response to highly pathogenic avian influenza. We also implicate genetic differences in SLC45A2 gene in the iconic plumage of the black swan. Conclusion Together, these data suggest that the immune system of the black swan is such that should any avian viral infection become established in its native habitat, the black swan would be in a significant peril.  more » « less
Award ID(s):
2021795
PAR ID:
10415471
Author(s) / Creator(s):
; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; more » ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; « less
Date Published:
Journal Name:
Genome Biology
Volume:
24
Issue:
1
ISSN:
1474-760X
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ; ; ; ; ; ; ; ; ; ; et al (, Nature)
    Zoonoses are infectious diseases transmitted from animals to humans. Bats have been suggested to harbour more zoonotic viruses than any other mammalian order1. Infections in bats are largely asymptomatic2,3, indicating limited tissue-damaging inflammation and immunopathology. To investigate the genomic basis of disease resistance, the Bat1K project generated reference-quality genomes of ten bat species, including potential viral reservoirs. Here we describe a systematic analysis covering 115 mammalian genomes that revealed that signatures of selection in immune genes are more prevalent in bats than in other mammalian orders. We found an excess of immune gene adaptations in the ancestral chiropteran branch and in many descending bat lineages, highlighting viral entry and detection factors, and regulators of antiviral and inflammatory responses. ISG15, which is an antiviral gene contributing to hyperinflammation during COVID-19 (refs. 4,5), exhibits key residue changes in rhinolophid and hipposiderid bats. Cellular infection experiments show species- specific antiviral differences and an essential role of protein conjugation in antiviral function of bat ISG15, separate from its role in secretion and inflammation in humans. Furthermore, in contrast to humans, ISG15 in most rhinolophid and hipposiderid bats has strong anti-SARS-CoV-2 activity. Our work reveals molecular mechanisms that contribute to viral tolerance and disease resistance in bats. 
    more » « less
  2. ; ; (, Viruses)
    The timing and magnitude of the immune response (i.e., the immunodynamics) associated with the early innate immune response to viral infection display distinct trends across influenza A virus subtypes in vivo. Evidence shows that the timing of the type-I interferon response and the overall magnitude of immune cell infiltration are both correlated with more severe outcomes. However, the mechanisms driving the distinct immunodynamics between infections of different virus strains (strain-specific immunodynamics) remain unclear. Here, computational modeling and strain-specific immunologic data are used to identify the immune interactions that differ in mice infected with low-pathogenic H1N1 or high-pathogenic H5N1 influenza viruses. Computational exploration of free parameters between strains suggests that the production rate of interferon is the major driver of strain-specific immune responses observed in vivo, and points towards the relationship between the viral load and lung epithelial interferon production as the main source of variance between infection outcomes. A greater understanding of the contributors to strain-specific immunodynamics can be utilized in future efforts aimed at treatment development to improve clinical outcomes of high-pathogenic viral strains. 
    more » « less
  3. ; ; ; ; ; ; ; (, Molecular Ecology)
    ABSTRACT RNA viruses are infamous for their ability to cross species barriers, posing threats to global health and security. Influenza A virus (IAV) is naturally found in avian hosts but periodically spills over into marine wildlife. IAV outbreaks occur in the Northwest Atlantic, but grey seals (Halichoerus grypus) appear to be less susceptible to IAV compared to other species. The subclinical nature of IAV infection in addition to life history factors suggest grey seals are a potential wild reservoir host for IAV. We investigated differential gene expression among grey seals naturally exposed to IAV to elucidate genetic mechanisms involved in grey seal disease resistance. RNA sequencing was conducted on blood samples (N = 31) collected from grey seal pups in Massachusetts, US between 2014 and 2019. Samples were grouped for analysis based on presence/absence of viral RNA and antibodies. In the presence of IAV RNA, we observed widespread down‐regulation of genes, including immune genes, potentially as a result of IAV‐induced host shutoff. Immune down‐regulation occurred in acute stage of IAV infection (+ viral RNA, − antibodies), followed by up‐regulation of protein production in peak stage (+ viral RNA, + antibodies), possibly as a result of increased viral replication. Evidence of an activated immune response was observed in late stage of infection (− viral RNA, + antibodies) with up‐regulated adaptive immunity genes. We hypothesize that the combination of down‐ and up‐regulated immune gene expression may prevent overstimulation of the immune response, acting as an adaptation in grey seals to resist IAV‐associated mortality. 
    more » « less
  4. ; ; ; ; ; ; ; ; ; ; et al (, Virology)
    Tomar, Jasmine (Ed.)
    While mammals can be infected by influenza A virus either sporadically or with well adapted lineages, aquatic birds are the natural reservoir of the pathogen. So far most of the knowledge on influenza virus dynamics was however gained on mammalian models. In this study, we infected turkeys using a low pathogenic avian influenza virus and determined the infection dynamics with a target-cell limited model. Results showed that turkeys had a different set of infection characteristics, compared with humans and ponies. The viral clearance rates were similar between turkeys and ponies but higher than that in humans. The cell death rates and cell to cell transmission rates were similar between turkeys and humans but higher than those in ponies. Overall, this study indicated the variations of within-host dynamics of influenza infection in avian, humans, and other mammalian systems. 
    more » « less
  5. ; ; ; (, Proceedings of the National Academy of Sciences)
    Some bacteria and archaea possess an immune system, based on the CRISPR-Cas mechanism, that confers adaptive immunity against viruses. In such species, individual prokaryotes maintain cassettes of viral DNA elements called spacers as a memory of past infections. Typically, the cassettes contain several dozen expressed spacers. Given that bacteria can have very large genomes and since having more spacers should confer a better memory, it is puzzling that so little genetic space would be devoted by prokaryotes to their adaptive immune systems. Here, assuming that CRISPR functions as a long-term memory-based defense against a diverse landscape of viral species, we identify a fundamental tradeoff between the amount of immune memory and effectiveness of response to a given threat. This tradeoff implies an optimal size for the prokaryotic immune repertoire in the observational range. 
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Save / Share this Record
  • Send to Email