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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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Hogg CJ. Translating genomic advances into biodiversity conservation. Nat Rev Genet 2024; 25:362-373. [PMID: 38012268 DOI: 10.1038/s41576-023-00671-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2023] [Indexed: 11/29/2023]
Abstract
A key action of the new Global Biodiversity Framework is the maintenance of genetic diversity in all species to safeguard their adaptive potential. To achieve this goal, a translational mindset, which aims to convert results of basic research into direct practical benefits, needs to be applied to biodiversity conservation. Despite much discussion on the value of genomics to conservation, a disconnect between those generating genomic resources and those applying it to biodiversity management remains. As global efforts to generate reference genomes for non-model species increase, investment into practical biodiversity applications is critically important. Applications such as understanding population and multispecies diversity and longitudinal monitoring need support alongside education for policymakers on integrating the data into evidence-based decisions. Without such investment, the opportunity to revolutionize global biodiversity conservation using genomics will not be fully realized.
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Affiliation(s)
- Carolyn J Hogg
- School of Life & Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.
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Dearborn DC, Warren S, Hailer F. Meta-analysis of major histocompatibility complex (MHC) class IIA reveals polymorphism and positive selection in many vertebrate species. Mol Ecol 2022; 31:6390-6406. [PMID: 36208104 PMCID: PMC9729452 DOI: 10.1111/mec.16726] [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: 03/21/2022] [Revised: 09/13/2022] [Accepted: 09/21/2022] [Indexed: 01/13/2023]
Abstract
Pathogen-mediated selection and sexual selection are important drivers of evolution. Both processes are known to target genes of the major histocompatibility complex (MHC), a gene family encoding cell-surface proteins that display pathogen peptides to the immune system. The MHC is also a model for understanding processes such as gene duplication and trans-species allele sharing. The class II MHC protein is a heterodimer whose peptide-binding groove is encoded by an MHC-IIA gene and an MHC-IIB gene. However, our literature review found that class II MHC papers on infectious disease or sexual selection included IIA data only 18% and 9% of the time, respectively. To assess whether greater emphasis on MHC-IIA is warranted, we analysed MHC-IIA sequence data from 50 species of vertebrates (fish, amphibians, birds, mammals) to test for polymorphism and positive selection. We found that the number of MHC-IIA alleles within a species was often high, and covaried with sample size and number of MHC-IIA genes assayed. While MHC-IIA variability tended to be lower than that of MHC-IIB, the difference was only ~25%, with ~3 fewer IIA alleles than IIB. Furthermore, the unexpectedly high MHC-IIA variability showed clear signatures of positive selection in most species, and positive selection on MHC-IIA was stronger in fish than in other surveyed vertebrate groups. Our findings underscore that MHC-IIA can be an important target of selection. Future studies should therefore expand the characterization of MHC-IIA at both allelic and genomic scales, and incorporate MHC-IIA into models of fitness consequences of MHC variation.
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Affiliation(s)
- Donald C Dearborn
- Biology Department, Bates College, 44 Campus Ave, Lewiston, Maine, USA,Roux Institute, Northeastern University, Fore St, Portland, Maine, USA,Co-corresponding authors: and
| | - Sophie Warren
- Biology Department, Bates College, 44 Campus Ave, Lewiston, Maine, USA,Present address: Department of Health Policy, London School of Economics and Political Science, Houghton Street, London WC2A 2AE, UK
| | - Frank Hailer
- Organisms and Environment, School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, Wales, UK,Co-corresponding authors: and
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Peel E, Silver L, Brandies P, Zhu Y, Cheng Y, Hogg CJ, Belov K. Best genome sequencing strategies for annotation of complex immune gene families in wildlife. Gigascience 2022; 11:6780307. [PMID: 36310247 PMCID: PMC9618407 DOI: 10.1093/gigascience/giac100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 08/10/2022] [Accepted: 09/29/2022] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND The biodiversity crisis and increasing impact of wildlife disease on animal and human health provides impetus for studying immune genes in wildlife. Despite the recent boom in genomes for wildlife species, immune genes are poorly annotated in nonmodel species owing to their high level of polymorphism and complex genomic organisation. Our research over the past decade and a half on Tasmanian devils and koalas highlights the importance of genomics and accurate immune annotations to investigate disease in wildlife. Given this, we have increasingly been asked the minimum levels of genome quality required to effectively annotate immune genes in order to study immunogenetic diversity. Here we set out to answer this question by manually annotating immune genes in 5 marsupial genomes and 1 monotreme genome to determine the impact of sequencing data type, assembly quality, and automated annotation on accurate immune annotation. RESULTS Genome quality is directly linked to our ability to annotate complex immune gene families, with long reads and scaffolding technologies required to reassemble immune gene clusters and elucidate evolution, organisation, and true gene content of the immune repertoire. Draft-quality genomes generated from short reads with HiC or 10× Chromium linked reads were unable to achieve this. Despite mammalian BUSCOv5 scores of up to 94.1% amongst the 6 genomes, automated annotation pipelines incorrectly annotated up to 59% of manually annotated immune genes regardless of assembly quality or method of automated annotation. CONCLUSIONS Our results demonstrate that long reads and scaffolding technologies, alongside manual annotation, are required to accurately study the immune gene repertoire of wildlife species.
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Affiliation(s)
- Emma Peel
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, University of Sydney, Sydney NSW 2006, Australia
| | - Luke Silver
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Parice Brandies
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Ying Zhu
- Sichuan Provincial Academy of Natural Resource Sciences, Chengdu, Sichuan 610000, China
| | - Yuanyuan Cheng
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, University of Sydney, Sydney NSW 2006, Australia
| | - Katherine Belov
- Correspondence address. Katherine Belov, School of Life and Environmental Sciences, Rm 206, RMC Gunn Building (B19), The University of Sydney, Sydney, NSW 2006, Australia. E-mail:
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Farquharson KA, McLennan EA, Cheng Y, Alexander L, Fox S, Lee AV, Belov K, Hogg CJ. Restoring faith in conservation action: Maintaining wild genetic diversity through the Tasmanian devil insurance program. iScience 2022; 25:104474. [PMID: 35754729 PMCID: PMC9218385 DOI: 10.1016/j.isci.2022.104474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 04/06/2022] [Accepted: 05/20/2022] [Indexed: 11/28/2022] Open
Abstract
Conservation breeding programs aim to maintain 90% wild genetic diversity, but rarely assess functional diversity. Here, we compare both genome-wide and functional diversity (in over 500 genes) of Tasmanian devils (Sarcophilus harrisii) within the insurance metapopulation and across the species’ range (64,519 km2). Populations have declined by 80% since 1996 due to a contagious cancer, devil facial tumor disease (DFTD). However, predicted local extinctions have not occurred. Recent suggestions of selection for “resistance” alleles in the wild precipitated concerns that insurance population devils may be unsuitable for translocations. Using 830 wild samples collected at 31 locations between 2012 and 2021, and 553 insurance metapopulation devils, we show that the insurance metapopulation is representative of current wild genetic diversity. Allele frequencies at DFTD-associated loci were not substantially different between captive and wild devils. Methods presented here are valuable for others investigating evolutionary potential in threatened species, particularly ones under significant selective pressures. Developed target capture to assess functional diversity at over 500 genes Fine-scale structure exists in the genetically depauperate Tasmanian devil Insurance metapopulation is representative of wild genetic diversity Allele frequencies at disease-associated loci were similar in captivity to the wild
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Affiliation(s)
| | - Elspeth A McLennan
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Yuanyuan Cheng
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Lauren Alexander
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Samantha Fox
- Save the Tasmanian Devil Program, NRE Tasmania, Hobart, Tas 7001, Australia.,Toledo Zoo, 2605 Broadway, Toledo, OH 43609, USA
| | - Andrew V Lee
- Save the Tasmanian Devil Program, NRE Tasmania, Hobart, Tas 7001, Australia.,Toledo Zoo, 2605 Broadway, Toledo, OH 43609, USA
| | - Katherine Belov
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia.,San Diego Zoo Wildlife Alliance, PO BOX 120551, San Diego, CA 92112, USA
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Gigliotti AK, Bowen WD, Hammill MO, Puryear WB, Runstadler J, Wenzel FW, Cammen KM. Sequence diversity and differences at the highly duplicated MHC-I gene reflect viral susceptibility in sympatric pinniped species. J Hered 2022; 113:525-537. [PMID: 35690352 PMCID: PMC9584807 DOI: 10.1093/jhered/esac030] [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: 02/18/2022] [Accepted: 06/08/2022] [Indexed: 11/12/2022] Open
Abstract
Differences in disease susceptibility among species can result from rapid host-pathogen coevolution and differences in host species ecology that affect the strength and direction of natural selection. Among two sympatric pinniped species that differ in sociality and putative disease exposure, we investigate observed differences in susceptibility through an analysis of a highly variable, duplicated gene family involved in the vertebrate immune response. Using high-throughput amplicon sequencing, we characterize diversity at the two exons that encode the peptide binding region of the major histocompatibility complex class I (MHC-I) gene in harbor (N = 60) and gray (N = 90) seal populations from the Northwest Atlantic. Across species, we identified 106 full-length exon 2 and 103 exon 3 sequence variants and a minimum of 11 duplicated MHC-I loci. The sequence variants clustered in 15 supertypes defined by the physiochemical properties of the peptide binding region, including a putatively novel Northwest Atlantic MHC-I diversity sublineage. Trans-species polymorphisms, dN/dS ratios, and evidence of gene conversion among supertypes are consistent with balancing selection acting on this gene. High functional redundancy suggests particularly strong selection among gray seals at the novel Northwest Atlantic MHC-I diversity sublineage. At exon 2, harbor seals had a significantly greater number of variants per individual than gray seals, but fewer supertypes. Supertype richness and private supertypes are hypothesized to contribute to observed differences in disease resistance between species, as consistently, across the North Atlantic and many disease outbreaks, gray seals appear to be more resistant to respiratory viruses than harbor seals.
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Affiliation(s)
| | - W Don Bowen
- Bedford Institute of Oceanography, Dartmouth, NS, Canada
| | - Michael O Hammill
- Fisheries and Oceans Canada, Maurice Lamontagne Institute, Mont-Joli, QC, Canada
| | - Wendy B Puryear
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, USA
| | - Jonathan Runstadler
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, USA
| | - Frederick W Wenzel
- Protected Species Branch, NOAA, NMFS, Northeast Fisheries Science Center, Woods Hole, MA, USA
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