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Silver LW, Hogg CJ, Belov K. Plethora of New Marsupial Genomes Informs Our Knowledge of Marsupial MHC Class II. Genome Biol Evol 2024; 16:evae156. [PMID: 39031605 PMCID: PMC11305139 DOI: 10.1093/gbe/evae156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 05/22/2024] [Accepted: 06/24/2024] [Indexed: 07/22/2024] Open
Abstract
The major histocompatibility complex (MHC) plays a vital role in the vertebrate immune system due to its role in infection, disease and autoimmunity, or recognition of "self". The marsupial MHC class II genes show divergence from eutherian MHC class II genes and are a unique taxon of therian mammals that give birth to altricial and immunologically naive young providing an opportune study system for investigating evolution of the immune system. Additionally, the MHC in marsupials has been implicated in disease associations, including susceptibility to Chlamydia pecorum infection in koalas. Due to the complexity of the gene family, automated annotation is not possible so here we manually annotate 384 class II MHC genes in 29 marsupial species. We find losses of key components of the marsupial MHC repertoire in the Dasyuromorphia order and the Pseudochiridae family. We perform PGLS analysis to show the gene losses we find are true gene losses and not artifacts of unresolved genome assembly. We investigate the associations between the number of loci and life history traits, including lifespan and reproductive output in lineages of marsupials and hypothesize that gene loss may be linked to the energetic cost and tradeoffs associated with pregnancy and reproduction. We found support for litter size being a significant predictor of the number of DBA and DBB loci, indicating a tradeoff between the energetic requirements of immunity and reproduction. Additionally, we highlight the increased susceptibility of Dasyuridae species to neoplasia and a potential link to MHC gene loss. Finally, these annotations provide a valuable resource to the immunogenetics research community to move forward and further investigate diversity in MHC genes in marsupials.
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Affiliation(s)
- Luke W Silver
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, University of Sydney, Sydney, New South Wales 2006, Australia
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Sebastian A, Migalska M, Gaczorek T. AmpliSAS and AmpliHLA: Web Server and Local Tools for MHC Typing of Non-model Species and Human Using NGS Data. Methods Mol Biol 2024; 2809:37-66. [PMID: 38907889 DOI: 10.1007/978-1-0716-3874-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
AmpliSAS and AmpliHLA are tools for automatic genotyping of MHC genes from high-throughput sequencing data. AmpliSAS is designed specifically to analyze amplicon sequencing data from non-model species and it is able to perform de novo genotyping without any previous knowledge of the reference alleles. AmpliHLA is a human specific version; it performs HLA typing by comparing sequenced variants against human reference alleles from the IMGT/HLA database. Both tools are available in AmpliSAT web-server as well as scripts for local/server installation. Here we describe the installation and deployment of AmpliSAS and AmpliHLA Perl scripts and dependencies on a local or a server computer. We will show how to run them in the command line using as examples four genotyping protocols: the first two use amplicon sequencing data to genotype the MHC genes of a passerine bird and human respectively; the third and fourth present the HLA typing of a human cell line starting from RNA and exome sequencing data respectively.
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Affiliation(s)
| | - Magdalena Migalska
- Genomics and Experimental Evolution Group, Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland.
| | - Tomasz Gaczorek
- Genomics and Experimental Evolution Group, Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
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Roth SA, Griffis-Kyle KL, Barnes MA. Batrachochytrium dendrobatidis in the Arid and Thermally Extreme Sonoran Desert. ECOHEALTH 2023; 20:370-380. [PMID: 38243042 DOI: 10.1007/s10393-023-01668-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 12/08/2023] [Indexed: 01/21/2024]
Abstract
Batrachochytrium dendrobatidis (Bd), the causative agent of the devastating global amphibian disease chytridiomycosis, was not projected to threaten amphibians in hot and arid regions due to its sensitivity to heat and desiccation. However, Bd is being detected more frequently than ever in hot and arid regions of Australia and the USA, challenging our current understanding of the environmental tolerances of the pathogen under natural conditions. We surveyed for Bd in an extremely hot and arid portion of the Sonoran Desert, where the pathogen is not projected to occur, and related presence and prevalence of the pathogen to local environmental conditions. We collected eDNA samples from isolated desert water sites including six tinajas and 13 catchments in June and August of 2020 and swabbed a total of 281 anurans of three species (red-spotted toad Anaxyrus punctatus, Couch's spadefoot Scaphiopus couchii, and the Sonoran Desert toad Incillius alvarius) across five catchments and six tinajas from June to September of 2020. Overall, Bd occurred at 68.4% of sites, despite extreme heat and aridity routinely exceeding tolerances established in laboratory studies. Average summer maximum air and water temperatures were 40.7°C and 30.7°C, respectively, and sites received an average of just 16.9 mm of precipitation throughout the summer monsoon season. Prevalence was low (5.7%) across species and life stage. Our results demonstrate that Bd is capable of persisting and infecting amphibians beyond its projected range, indicating a need to account for higher thermal tolerances when quantifying risk of Bd presence and infection.
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Affiliation(s)
- Sadie A Roth
- Department of Natural Resources Management, Texas Tech University, 2500 Broadway, Lubbock, TX, 79409, USA.
| | - Kerry L Griffis-Kyle
- Department of Natural Resources Management, Texas Tech University, 2500 Broadway, Lubbock, TX, 79409, USA
| | - Matthew A Barnes
- Department of Natural Resources Management, Texas Tech University, 2500 Broadway, Lubbock, TX, 79409, USA
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Manes C, Carthy RR, Hull V. A Coupled Human and Natural Systems Framework to Characterize Emerging Infectious Diseases-The Case of Fibropapillomatosis in Marine Turtles. Animals (Basel) 2023; 13:ani13091441. [PMID: 37174478 PMCID: PMC10177368 DOI: 10.3390/ani13091441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/12/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Emerging infectious diseases of wildlife have markedly increased in the last few decades. Unsustainable, continuous, and rapid alterations within and between coupled human and natural systems have significantly disrupted wildlife disease dynamics. Direct and indirect anthropogenic effects, such as climate change, pollution, encroachment, urbanization, travel, and trade, can promote outbreaks of infectious diseases in wildlife. We constructed a coupled human and natural systems framework identifying three main wildlife disease risk factors behind these anthropogenic effects: (i) immune suppression, (ii) viral spillover, and (iii) disease propagation. Through complex and convoluted dynamics, each of the anthropogenic effects and activities listed in our framework can lead, to some extent, to one or more of the identified risk factors accelerating disease outbreaks in wildlife. In this review, we present a novel framework to study anthropogenic effects within coupled human and natural systems that facilitate the emergence of infectious disease involving wildlife. We demonstrate the utility of the framework by applying it to Fibropapillomatosis disease of marine turtles. We aim to articulate the intricate and complex nature of anthropogenically exacerbated wildlife infectious diseases as multifactorial. This paper supports the adoption of a One Health approach and invites the integration of multiple disciplines for the achievement of effective and long-lasting conservation and the mitigation of wildlife emerging diseases.
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Affiliation(s)
- Costanza Manes
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611, USA
- One Health Center of Excellence, University of Florida, Gainesville, FL 32611, USA
| | - Raymond R Carthy
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611, USA
- U.S. Geological Survey, Florida Cooperative Fish and Wildlife Research Unit, University of Florida, Gainesville, FL 32611, USA
| | - Vanessa Hull
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611, USA
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Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories. Proc Natl Acad Sci U S A 2023; 120:e2201076120. [PMID: 36749728 PMCID: PMC9962930 DOI: 10.1073/pnas.2201076120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 Mya. The genomic basis of the unique physiological and ecological traits enabling these species to thrive in diverse marine habitats remains largely unknown. Additionally, many populations have drastically declined due to anthropogenic activities over the past two centuries, and their recovery is a high global conservation priority. We generated and analyzed high-quality reference genomes for the leatherback (Dermochelys coriacea) and green (Chelonia mydas) turtles, representing the two extant sea turtle families. These genomes are highly syntenic and homologous, but localized regions of noncollinearity were associated with higher copy numbers of immune, zinc-finger, and olfactory receptor (OR) genes in green turtles, with ORs related to waterborne odorants greatly expanded in green turtles. Our findings suggest that divergent evolution of these key gene families may underlie immunological and sensory adaptations assisting navigation, occupancy of neritic versus pelagic environments, and diet specialization. Reduced collinearity was especially prevalent in microchromosomes, with greater gene content, heterozygosity, and genetic distances between species, supporting their critical role in vertebrate evolutionary adaptation. Finally, diversity and demographic histories starkly contrasted between species, indicating that leatherback turtles have had a low yet stable effective population size, exhibit extremely low diversity compared with other reptiles, and harbor a higher genetic load compared with green turtles, reinforcing concern over their persistence under future climate scenarios. These genomes provide invaluable resources for advancing our understanding of evolution and conservation best practices in an imperiled vertebrate lineage.
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Forsman AM, Savage AE, Hoenig BD, Gaither MR. DNA metabarcoding across disciplines: sequencing our way to greater understanding across scales of biological organization. Integr Comp Biol 2022; 62:191-198. [PMID: 35687001 DOI: 10.1093/icb/icac090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/03/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
DNA metabarcoding describes the use of targeted DNA (i.e., amplicon) sequencing to identify community constituents from a complex sample containing genetic material from multiple organisms, such as water, soil, gut contents, microbiomes, or biofilms. This molecular approach for characterizing mixed DNA samples relies on the development of "universal primers" that allow for effective amplification of target sequences across a broad range of taxa. Armed with optimized lab protocols and rigorous bioinformatics tools, DNA metabarcoding can produce a wealth of information about the hidden biodiversity of various sample types by probing for organisms' molecular footprints. DNA metabarcoding has received considerable popular press over the last few years because of gut microbiome studies in humans and beyond. However, there are many other applications that are continually integrating molecular biology with other fields of study to address questions that have previously been unanswerable, for both prokaryotic and eukaryotic targets. For example, we can now sample mostly-digested gut contents from virtually any organism to learn about ontogeny and foraging ecology. Water samples collected from different locations can be filtered to extract eDNA (i.e., environmental DNA), revealing the biodiversity of fishes and other taxa targeted by carefully selected primer sets. This universal primer metabarcoding approach has even been extended to looking at diverse gene families within single species, which is particularly useful for complex immune system genetics. The purpose of this SICB symposium was to bring together researchers using DNA metabarcoding approaches to (a) showcase the diversity of applications of this technique for addressing questions spanning ecology, evolution, and physiology, and (b) to spark connections among investigators from different fields that are utilizing similar approaches to facilitate optimization and standardization of metabarcoding methods and analyses. The resulting manuscripts from this symposium represent a great diversity of metabarcoding applications and taxonomic groups of interest.
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Affiliation(s)
- Anna M Forsman
- Department of Biology, University of Central Florida, Orlando, FL, USA.,Genomics & Bioinformatics Cluster, University of Central Florida, Orlando, FL, USA
| | - Anna E Savage
- Department of Biology, University of Central Florida, Orlando, FL, USA
| | - Brandon D Hoenig
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michelle R Gaither
- Department of Biology, University of Central Florida, Orlando, FL, USA.,Genomics & Bioinformatics Cluster, University of Central Florida, Orlando, FL, USA
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Longo AV. Metabarcoding approaches in amphibian disease ecology: Disentangling the functional contributions of skin bacteria on disease outcome. Integr Comp Biol 2022; 62:252-261. [PMID: 35640913 DOI: 10.1093/icb/icac062] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/10/2022] [Accepted: 05/25/2022] [Indexed: 01/09/2023] Open
Abstract
Molecular technologies have revolutionized the field of wildlife disease ecology, allowing the detection of outbreaks, novel pathogens, and invasive strains. In particular, metabarcoding approaches, defined here as tools used to amplify and sequence universal barcodes from a single sample (e.g., 16S rRNA for bacteria, ITS for fungi, 18S rRNA for eukaryotes), are expanding our traditional view of host-pathogen dynamics by integrating microbial interactions that modulate disease outcome. Here, I provide an analysis from the perspective of the field of amphibian disease ecology, where the emergence of multi-host pathogens has caused global declines and species extinctions. I re-analyzed an experimental mesocosm dataset to infer the functional profiles of the skin microbiomes of coqui frogs (Eleutherodactylus coqui), an amphibian species that is consistently found infected with the fungal pathogen Batrachochytrium dendrobatidis and has high turnover of skin bacteria driven by seasonal shifts. I found that the metabolic activities of microbiomes operate at different capacities depending on the season. Global enrichment of predicted functions was more prominent during the warm-wet season, indicating that microbiomes during the cool-dry season were either depauperate, resistant to new bacterial colonization, or that their functional space was more saturated. These findings suggest important avenues to investigate how microbes regulate population growth and contribute to host physiological processes. Overall, this study highlights the current challenges and future opportunities in the application of metabarcoding to investigate the causes and consequences of disease in wild systems.
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Affiliation(s)
- Ana V Longo
- University of Florida, Department of Biology, PO Box 118525, Gainesville, FL
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Martin KR, Mansfield KL, Savage AE. Adaptive evolution of major histocompatibility complex class I immune genes and disease associations in coastal juvenile sea turtles. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211190. [PMID: 35154791 PMCID: PMC8825991 DOI: 10.1098/rsos.211190] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 01/06/2022] [Indexed: 05/12/2023]
Abstract
Characterizing polymorphism at the major histocompatibility complex (MHC) genes is key to understanding the vertebrate immune response to disease. Despite being globally afflicted by the infectious tumour disease fibropapillomatosis (FP), immunogenetic variation in sea turtles is minimally explored. We sequenced the α 1 peptide-binding region of MHC class I genes (162 bp) from 268 juvenile green (Chelonia mydas) and 88 loggerhead (Caretta caretta) sea turtles in Florida, USA. We recovered extensive variation (116 alleles) and trans-species polymorphism. Supertyping analysis uncovered three functional MHC supertypes corresponding to the three well-supported clades in the phylogeny. We found significant evidence of positive selection at seven amino acid sites in the class I exon. Random forest modelling and risk ratio analysis of Ch. mydas alleles uncovered one allele weakly associated with smooth FP tumour texture, which may be associated with disease outcome. Our study represents the first characterization of MHC class I diversity in Ch. mydas and the largest sample of sea turtles used to date in any study of adaptive genetic variation, revealing tremendous genetic variation and high adaptive potential to viral pathogen threats. The novel associations we identified between MHC diversity and FP outcomes in sea turtles further highlight the importance of evaluating genetic predictors of disease, including MHC and other functional markers.
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Affiliation(s)
- Katherine R. Martin
- Department of Biology, University of Central Florida, 4110 Libra Drive, Orlando, FL 32816, USA
| | - Katherine L. Mansfield
- Department of Biology, University of Central Florida, 4110 Libra Drive, Orlando, FL 32816, USA
| | - Anna E. Savage
- Department of Biology, University of Central Florida, 4110 Libra Drive, Orlando, FL 32816, USA
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