Diversity in the Toll-like receptor genes of the Tasmanian devil (Sarcophilus harrisii)

Spatial variation in toll-like receptor diversity in koala populations across their geographic distribution

The koala (Phascolarctos cinereus) is an iconic Australian species that is listed as endangered in the northern parts of its range due to loss of habitat, disease, and road deaths. Diseases contribute significantly to the decline of koala populations, primarily Chlamydia and koala retrovirus. The distribution of these diseases across the species' range, however, is not even. Toll-like receptors (TLRs) play a crucial role in innate immunity by recognising and responding to various pathogens. Variations in TLR genes can influence an individual's susceptibility or resistance to infectious diseases. The aim of this study was to identify koala TLR diversity across the east coast of Australia using 413 re-sequenced genomes at 30 × coverage. We identified 45 single-nucleotide polymorphisms (SNP) leading to 51 alleles within ten TLR genes. Our results show that the diversity of TLR genes in the koala forms four distinct genetic groups, which are consistent with the diversity of the koala major histocompatibility complex (MHC), another key immune gene family. The bioinformatics approach presented here has broad applicability to other threatened species with existing genomic resources.

Restoring faith in conservation action: Maintaining wild genetic diversity through the Tasmanian devil insurance program

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.

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Developed target capture to assess functional diversity at over 500 genes

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Fine-scale structure exists in the genetically depauperate Tasmanian devil

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Insurance metapopulation is representative of wild genetic diversity

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Allele frequencies at disease-associated loci were similar in captivity to the wild

Toll-Like Receptor Expression Profiles in Koala (Phascolarctos cinereus) Peripheral Blood Mononuclear Cells Infected with Multiple KoRV Subtypes

Simple Summary

Koala retrovirus (KoRV) is a major pathogen of koala. Toll-like receptors (TLRs) are important innate immune component that are evolutionary conserved and play a crucial role in the early defense against invading pathogens. The expression profile of TLRs in KoRV infection in koalas is not characterized yet. Therefore, in this study, we characterized TLR expression patterns in koalas infected with KoRV-A only vs. KoRV-A with KoRV-B and/or -C. Using qRT-PCR, we measured TLR2–10 and TLR13 mRNA expression in peripheral blood mononuclear cells (PBMCs) and/or tissues from captive koalas in Japanese zoos. We observed variations in TLR expression in koalas with a range of subtype infection profiles (KoRV-A only vs. KoRV-A with KoRV-B and/or -C). The findings of this study might improve our current understanding of koala’s immune response to KoRV infection.

Abstract

Toll-like receptors (TLRs), evolutionarily conserved pattern recognition receptors, play an important role in innate immunity by recognizing microbial pathogen-associated molecular patterns. Koala retrovirus (KoRV), a major koala pathogen, exists in both endogenous (KoRV-A) and exogenous forms (KoRV-B to J). However, the expression profile of TLRs in koalas infected with KoRV-A and other subtypes is yet to characterize. Here, we investigated TLR expression profiles in koalas with a range of subtype infection profiles (KoRV-A only vs. KoRV-A with KoRV-B and/or -C). To this end, we cloned partial sequences for TLRs (TLR2–10 and TLR13), developed real-time PCR assays, and determined TLRs mRNA expression patterns in koala PBMCs and/or tissues. All the reported TLRs for koala were expressed in PBMCs, and variations in TLR expression were observed in koalas infected with exogenous subtypes (KoRV-B and KoRV-C) compared to the endogenous subtype (KoRV-A) only, which indicates the implications of TLRs in KoRV infection. TLRs were also found to be differentially expressed in koala tissues. This is the first report of TLR expression profiles in koala, which provides insights into koala’s immune response to KoRV infection that could be utilized for the future exploitation of TLR modulators in the maintenance of koala health.

Annotation of immune genes in the extinct thylacine (Thylacinus cynocephalus)

Advances in genome sequencing technology have enabled genomes of extinct species to be sequenced. However, given the fragmented nature of these genome assemblies, it is not clear whether it is possible to comprehensively annotate highly variable and repetitive genes such as those involved in immunity. As such, immune genes have only been investigated in a handful of extinct genomes, mainly in human lineages. In 2018 the genome of the thylacine (Thylacinus cynocephalus), a carnivorous marsupial from Tasmania that went extinct in 1936, was sequenced. Here we attempt to characterise the immune repertoire of the thylacine and determine similarity to its closest relative with a genome available, the Tasmanian devil (Sarcophilus harrisii), as well as other marsupials. Members from all major immune gene families were identified. However, variable regions could not be characterised, and complex families such as the major histocompatibility complex (MHC) were highly fragmented and located across multiple small scaffolds. As such, at a gene level we were unable to reconstruct full-length coding sequences for the majority of thylacine immune genes. Despite this, we identified genes encoding functionally important receptors and immune effector molecules, which suggests the functional capacity of the thylacine immune system was similar to other mammals. However, the high number of partial immune gene sequences identified limits our ability to reconstruct an accurate picture of the thylacine immune repertoire.

A Tasmanian devil breeding program to support wild recovery

Tasmanian devils are threatened in the wild by devil facial tumour disease: a transmissible cancer with a high fatality rate. In response, the Save the Tasmanian Devil Program (STDP) established an 'insurance population' to enable the preservation of genetic diversity and natural behaviours of devils. This breeding program includes a range of institutions and facilities, from zoo-based intensive enclosures to larger, more natural environments, and a strategic approach has been required to capture and maintain genetic diversity, natural behaviours and to ensure reproductive success. Laboratory-based research, particularly genetics, in tandem with adaptive management has helped the STDP reach its goals, and has directly contributed to the conservation of the species in the wild. Here we review this work and show that the Tasmanian devil breeding program is a powerful example of how genetic research can be used to understand and improve reproductive success in a threatened species.

Pathogen-associated selection on innate immunity genes (TLR4, TLR7) in a neotropical rodent in landscapes differing in anthropogenic disturbance

Toll-like receptors (TLRs) form part of the innate immune system and can recognize structurally conserved pathogen-associated molecular pattern (PAMP) molecules. Their functional importance in the resistance to pathogens has been documented in laboratory experimental settings and in humans. TLR diversity, however, has been rarely investigated in wildlife species. How the genetic diversity of TLRs is associated with various pathogens and how it is shaped by habitat disturbance are understudied. Therefore, we investigated the role of genetic diversity in the functionally important parts of TLR4 and TLR7 genes in resistance towards gastrointestinal nematodes and Hepacivirus infection. We chose a generalist study species, the rodent Proechimys semispinosus, because it is highly abundant in three Panamanian landscapes that differ in their degree of anthropogenic modification. We detected only two TLR7 haplotypes that differed by one synonymous single-nucleotide polymorphism (SNP) position. The TLR4 variability was higher, and we detected four TLR4 haplotypes that differed at one synonymous SNP and at three amino acid positions within the leucine-rich repeat region. Only TLR4 haplotypes had different frequencies in each landscape. Using generalized linear models, we found evidence that nematode loads and virus prevalence were influenced by both specific TLR4 haplotypes and landscape. Here, the variable “landscape” served as a surrogate for the important influential ecological factors distinguishing landscapes in our study, i.e. species diversity and host population density. Individuals carrying the common TLR4_Ht1 haplotype were less intensely infected by the most abundant strongyle nematode. Individuals carrying the rare TLR4_Ht3 haplotype were all Hepacivirus-positive, where those carrying the rare haplotype TLR4_Ht4 were less often infected by Hepacivirus than individuals with other haplotypes. Our study highlights the role of TLR diversity in pathogen resistance and the importance of considering immune genetic as well as ecological factors in order to understand the effects of anthropogenic changes on wildlife health.

Genetic diversity of toll-like receptor genes in the vulnerable Chinese egret (Egretta eulophotes)

Toll-like receptor (TLR) genes have recently been employed to assess genetic diversity, as they can be used to infer both demographic history and adaptation to environments with different pathogen pressure. Here, we sampled 120 individuals of the Chinese egret (Egretta eulophotes), a globally vulnerable species, from four breeding populations across China. We assessed the levels of genetic diversity, selection pressure, and population differentiation at seven TLR loci (TLR1LB, TLR2A, TLR3, TLR4, TLR5, TLR7, and TLR15). Using a variety of metrics (SNPs, heterozygosity, nucleotides, haplotypes), our analyses showed that genetic diversity was lower at 4 of the 7 TLR loci in the vulnerable Chinese egret compared to the more common little egret (Egretta garzetta). The selection test indicated TLRs, except for TLR5, were under purifying selection in TLR evolution, suggesting that low TLR genetic diversity in the Chinese egret may be caused by purifying selection. Moreover, analysis of molecular variance indicated low but significant population differentiation among four populations at all of the TLR loci in this egret. However, some comparisons based on fixation index analyses did not show significant population differentiation, and Bayesian clustering showed admixture. Our finding suggested that these four populations of the Chinese egret in China may be considered a single unit for conservation planning. These results, the new report of TLR genetic diversity in a long-distance migratory vulnerable Ardeid species, will provide fundamental TLR information for further studies on the conservation genetics of the Chinese egret and other Ardeids.

Adaptive genetic diversity and evidence of population genetic structure in the endangered Sierra Madre Sparrow (Xenospiza baileyi)

The magnitude and distribution of genetic diversity through space and time can provide useful information relating to evolutionary potential and conservation status in threatened species. In assessing genetic diversity in species that are of conservation concern, several studies have focused on the use of Toll-like receptors (TLRs). TLRs are innate immune genes related to pathogen resistance, and polymorphisms may reflect not only levels of functional diversity, but may also be used to assess genetic diversity within and among populations. Here, we combined four potentially adaptive markers (TLRs) with one mitochondrial (COI) marker to evaluate genetic variation in the endangered Sierra Madre Sparrow (Xenospiza baileyi). This species offers an ideal model to investigate population and evolutionary genetic processes that may be occurring in a habitat restricted endangered species with disjunct populations (Mexico City and Durango), the census sizes of which differ by an order of magnitude. TLRs diversity in the Sierra Madre Sparrow was relatively high, which was not expected given its two small, geographically isolated populations. Genetic diversity was different (but not significantly so) between the two populations, with less diversity seen in the smaller Durango population. Population genetic structure between populations was due to isolation and different selective forces acting on different TLRs; population structure was also evident in COI. Reduction of genetic diversity in COI was observed over 20 years in the Durango population, a result likely caused by habitat loss, a factor which may be the main cause of diversity decline generally. Our results provide information related to the ways in which adaptive variation can be altered by demographic changes due to human-mediated habitat alterations. Furthermore, our findings may help to guide conservation schemes for both populations and their restricted habitat.

The Value of Reference Genomes in the Conservation of Threatened Species

Conservation initiatives are now more crucial than ever-over a million plant and animal species are at risk of extinction over the coming decades. The genetic management of threatened species held in insurance programs is recommended; however, few are taking advantage of the full range of genomic technologies available today. Less than 1% of the 13505 species currently listed as threated by the International Union for Conservation of Nature (IUCN) have a published genome. While there has been much discussion in the literature about the importance of genomics for conservation, there are limited examples of how having a reference genome has changed conservation management practice. The Tasmanian devil (Sarcophilus harrisii), is an endangered Australian marsupial, threatened by an infectious clonal cancer devil facial tumor disease (DFTD). Populations have declined by 80% since the disease was first recorded in 1996. A reference genome for this species was published in 2012 and has been crucial for understanding DFTD and the management of the species in the wild. Here we use the Tasmanian devil as an example of how a reference genome has influenced management actions in the conservation of a species.

Lessons learnt from the Tasmanian devil facial tumour regarding immune function in cancer

Genetic and genomic technologies have facilitated a greater understanding of the Tasmanian devil immune system and the origins, evolution and spread of devil facial tumour disease (DFTD). DFTD is a contagious cancer that has caused significant declines in devil populations across Tasmania. Immune responses to DFTD are rarely detected, allowing the cancer to pass between individuals and proliferate unimpeded. Early immunosenscence in devils appears to decrease anti-tumour immunity in older animals compared to younger animals, which may increase susceptibility to DFTD and explain high DFTD prevalence in this age group. Devils also have extremely low major histocompatibility complex (MHC) diversity, and multiple alleles are shared with the tumour, lowering histocompatibility barriers which may have contributed to DFTD evolution. DFTD actively evades immune attack by down-regulating cell-surface MHC I molecules, making it effectively invisible to the immune system. Altered MHC I profiles should activate natural killer (NK) cell anti-tumour responses, but these are absent in DFTD infection. Recent immunisation and immunotherapy using modified DFTD cells has induced an anti-DFTD immune response and regression of DFTD in some devils. Knowledge gained from immune responses to a transmissible cancer in devils will ultimately reveal useful insights into immunity to cancer in humans and other species.

Coevolution of the Toll-Like Receptor 4 Complex with Calgranulins and Lipopolysaccharide

Toll-like receptor 4 (TLR4) induces inflammation in response to both pathogen- and host-derived molecules. Lipopolysaccharide (LPS) recognition by TLR4 has been shown to occur across the amniotes, but endogenous signaling through TLR4 has not been validated outside of placental mammals. To determine whether endogenous danger signaling is also shared across amniotes, we studied the evolution of TLR4-activation by the calgranulin proteins (S100A8, S100A9, and S100A12), a clade of host molecules that potently activate TLR4 in placental mammals. We performed phylogenetic and syntenic analysis and found MRP-126—a gene in birds and reptiles—is likely orthologous to the mammalian calgranulins. We then used an ex vivo TLR4 activation assay to establish that calgranulin pro-inflammatory activity is not specific to placental mammals, but is also exhibited by representative marsupial and sauropsid species. This activity is strongly dependent on the cofactors CD14 and MD-2 for all species studied, suggesting a conserved mode of activation across the amniotes. Ortholog complementation experiments between the calgranulins, TLR4, CD14, and MD-2 revealed extensive lineage specific-coevolution and multi-way interactions between components that are necessary for the activation of NF-κB signaling by calgranulins and LPS. Our work demonstrates that calgranulin activation of TLR4 evolved at least ~320 million years ago and has been conserved in the amniote innate immune system.

Transcriptome sequencing of the long-nosed bandicoot (Perameles nasuta) reveals conservation and innovation of immune genes in the marsupial order Peramelemorphia

Bandicoots are omnivorous marsupials of the order Peramelemorphia. Conservation concerns and their unique biological characteristics suggest peramelomorphs are worthy research subjects, but knowledge of their genetics and immunology has lagged behind that of other high-profile marsupials. Here, we characterise the transcriptome of the long-nose bandicoot (Perameles nasuta), the first high-throughput data set from any peramelomorph. We investigate the immune gene repertoire of the bandicoot, with a focus on key immune gene families, and compare to previously characterised marsupial and mammalian species. We find that the immune gene complement in bandicoot is often conserved with respect to other marsupials; however, the diversity of expressed transcripts in several key families, such as major histocompatibility complex, T cell receptor μ and natural killer cell receptors, appears greater in the bandicoot than other Australian marsupials, including devil and koala. This transcriptome is an important first step for future studies of bandicoots and the bilby, allowing for population level analysis and construction of bandicoot-specific immunological reagents and assays. Such studies will be critical to understanding the immunology and physiology of Peramelemorphia and to inform the conservation of these unique marsupials.

The toll-like receptor ligands Hiltonol® (polyICLC) and imiquimod effectively activate antigen-specific immune responses in Tasmanian devils (Sarcophilus harrisii)

Devil facial tumour disease (DFTD) describes two genetically distinct transmissible tumours that pose a significant threat to the survival of the Tasmanian devil. A prophylactic vaccine could protect devils from DFTD transmission. For this vaccine to be effective, potent immune adjuvants will be required. Toll-like receptors (TLRs) promote robust immune responses in human cancer studies and are highly conserved across mammalian species. In this study, we investigated the proficiency of TLR ligands for immune activation in the Tasmanian devil using in vitro mononuclear cell stimulations and in vivo immunisation trials with a model antigen. We identified two such TLR ligands, polyICLC (Hiltonol^®) (TLR3) and imiquimod (TLR7), that in combination induced significant IFNγ production from Tasmanian devil lymphocytes in vitro. Immunisation with these ligands and the model antigen keyhole limpet haemocyanin activated robust antigen-specific primary, secondary and long-term memory IgG responses. Our results support the conserved nature of TLR signaling across mammalian species. PolyICLC and imiquimod will be trialed as immune adjuvants in future DFTD vaccine formulations.

The identification of immune genes in the milk transcriptome of the Tasmanian devil (Sarcophilus harrisii)

Tasmanian devil (Sarcophilus harrisii) pouch young, like other marsupials, are born underdeveloped and immunologically naïve, and are unable to mount an adaptive immune response. The mother’s milk provides nutrients for growth and development as well as providing passive immunity. To better understand immune response in this endangered species, we set out to characterise the genes involved in passive immunity by sequencing and annotating the transcriptome of a devil milk sample collected during mid-lactation. At mid-lactation we expect the young to have heightened immune responses, as they have emerged from the pouch, encountering new pathogens. A total of 233,660 transcripts were identified, including approximately 17,827 unique protein-coding genes and 846 immune genes. The most highly expressed transcripts were dominated by milk protein genes such as those encoding early lactation protein, late lactation proteins, α-lactalbumin, α-casein and β-casein. There were numerous highly expressed immune genes including lysozyme, whey acidic protein, ferritin and major histocompatibility complex I and II. Genes encoding immunoglobulins, antimicrobial peptides, chemokines and immune cell receptors were also identified. The array of immune genes identified in this study reflects the importance of the milk in providing immune protection to Tasmanian devil young and provides the first insight into Tasmanian devil milk.

Identification and analysis of divergent immune gene families within the Tasmanian devil genome

Background

The Tasmanian devil (Sarcophilus harrisii) is being threatened with extinction in the wild by a disease known as devil facial tumour disease (DFTD). In order to prevent the spread of this disease a thorough understanding of the Tasmanian devil immune system and its response to the disease is required. In 2011 and 2012 two genome sequencing projects of the Tasmania devil were released. This has provided us with the raw data required to begin to investigate the Tasmanian devil immunome in depth. In this study we characterise immune gene families of the Tasmanian devil. We focus on immunoglobulins, T cell receptors and cytokine families.

Results

We identify and describe 119 cytokines including 40 interleukins, 39 chemokines, 8 interferons, 18 tumour necrosis family cytokines and 14 additional cytokines. Constant regions for immunoglobulins and T cell receptors were also identified. The repertoire of genes in these families was similar to the opossum, however devil specific duplications were seen and orthologs to eutherian genes not previously identified in any marsupial were also identified.

Conclusions

By using multiple data sources as well as targeted search methods, highly divergent genes across the Tasmanian devil immune system were identified and characterised. This understanding will allow for the development of devil specific assays and reagents and allow for future studies into the immune response of the Tasmanian devil immune system to DFTD.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2206-9) contains supplementary material, which is available to authorized users.

Toll-like receptor signaling is functional in immune cells of the endangered Tasmanian devil

Devil facial tumour disease (DFTD) is a fatally transmissible cancer that threatens the Tasmanian devil population. As Tasmanian devils do not produce an immune response against DFTD cells, an effective vaccine will require a strong adjuvant. Activation of innate immune system cells through toll-like receptors (TLRs) could provide this stimulation. It is unknown whether marsupials, including Tasmanian devils, express functional TLRs. We isolated RNA from peripheral blood mononuclear cells and, with PCR, detected transcripts for TLRs 2, 3, 4, 5, 6, 7, 8, 9, 10 and 13. Stimulation of the mononuclear cells with agonists to these TLRs increased the expression of downstream TLR signaling products (IL1α, IL6, IL12A and IFNβ). Our data provide the first evidence that TLR signaling is functional in the mononuclear cells of the Tasmanian devil. Future DFTD vaccination trials will incorporate TLR agonists to enhance the immune response against DFTD.

Lack of genetic diversity across diverse immune genes in an endangered mammal, the Tasmanian devil (Sarcophilus harrisii)

The Tasmanian devil (Sarcophilus harrisii) is threatened with extinction due to the spread of devil facial tumour disease. Polymorphisms in immune genes can provide adaptive potential to resist diseases. Previous studies in diversity at immune loci in wild species have almost exclusively focused on genes of the major histocompatibility complex (MHC); however, these genes only account for a fraction of immune gene diversity. Devils lack diversity at functionally important immunity loci, including MHC and Toll-like receptor genes. Whether there are polymorphisms at devil immune genes outside these two families is unknown. Here, we identify polymorphisms in a wide range of key immune genes, and develop assays to type single nucleotide polymorphisms (SNPs) within a subset of these genes. A total of 167 immune genes were examined, including cytokines, chemokines and natural killer cell receptors. Using genome-level data from ten devils, SNPs within coding regions, introns and 10 kb flanking genes of interest were identified. We found low polymorphism across 167 immune genes examined bioinformatically using whole-genome data. From this data, we developed long amplicon assays to target nine genes. These amplicons were sequenced in 29-220 devils and found to contain 78 SNPs, including eight SNPS within exons. Despite the extreme paucity of genetic diversity within these genes, signatures of balancing selection were exhibited by one chemokine gene, suggesting that remaining diversity may hold adaptive potential. The low functional diversity may leave devils highly vulnerable to infectious disease, and therefore, monitoring and preserving remaining diversity will be critical for the long-term management of this species. Examining genetic variation in diverse immune genes should be a priority for threatened wildlife species. This study can act as a model for broad-scale immunogenetic diversity analysis in threatened species.

SNP marker discovery in koala TLR genes

Toll-like receptors (TLRs) play a crucial role in the early defence against invading pathogens, yet our understanding of TLRs in marsupial immunity is limited. Here, we describe the characterisation of nine TLRs from a koala immune tissue transcriptome and one TLR from a draft sequence of the koala genome and the subsequent development of an assay to study genetic diversity in these genes. We surveyed genetic diversity in 20 koalas from New South Wales, Australia and showed that one gene, TLR10 is monomorphic, while the other nine TLR genes have between two and 12 alleles. 40 SNPs (16 non-synonymous) were identified across the ten TLR genes. These markers provide a springboard to future studies on innate immunity in the koala, a species under threat from two major infectious diseases.