Akira S (2001) Toll-like receptors and innate immunity. Adv Immunol 78:1–56

Article  PubMed  Google Scholar 

Akira S, Takeda K, Kaisho T (2001) Toll-like receptors: Critical proteins linking innate and acquired immunity. Nat Immunol 2(8):675–680

Article  PubMed  Google Scholar 

Aljanabi SM, Martinez I (1997) Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic Acids Res 25(22):4692–4693. https://doi.org/10.1093/nar/25.22.4692

Article  PubMed  Google Scholar 

Allendorf FW, Hohenlohe PA, Luikart G (2010) Genomics and the future of conservation genetics. Nat Rev Genet 11(10):697–709. https://doi.org/10.1038/nrg2844

Article  PubMed  Google Scholar 

Ammar R, Paton TA, Torti D, Shlien A, Bader GD (2015) Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes. F1000Res 4:17. https://doi.org/10.12688/f1000research.6037.2

Article  PubMed  Google Scholar 

Babik W (2010) Methods for MHC genotyping in non-model vertebrates. Mol Ecol Resour 10(2):237–251. https://doi.org/10.1111/j.1755-0998.2009.02788.x

Article  PubMed  Google Scholar 

Beyer HL, de Villiers D, Loader J, Robbins A, Stigner M, Forbes N, Hanger J (2018) Management of multiple threats achieves meaningful koala conservation outcomes. J Appl Ecol 55(4):1966–1975. https://doi.org/10.1111/1365-2664.13127

Article  Google Scholar 

Bidon T, Schreck N, Hailer F, Nilsson MA, Janke A (2015) Genome-wide search identifies 1.9Mb from the polar bear Y chromosome for evolutionary analyses. Genome Biol Evol 7(7):2010–2022. https://doi.org/10.1093/gbe/evv103

Article  PubMed  Google Scholar 

Bjorkman PJ, Parham P (1990) Structure, function, and diversity of class I major histocompatibility complex molecules. Annu Rev Biochem 59:253–288. https://doi.org/10.1146/annurev.bi.59.070190.001345

Article  PubMed  Google Scholar 

Cheng Y, Stuart A, Morris K, Taylor R, Siddle H, Deakin J, Jones M, Amemiya CT, Belov K (2012) Antigen-presenting genes and genomic copy number variations in the Tasmanian devil MHC. BMC Genom 13:87. https://doi.org/10.1186/1471-2164-13-87

Article  Google Scholar 

Cheng Y, Polkinghorne A, Gillett A, Jones EA, O’Meally D, Timms P, Belov K (2018) Characterisation of MHC class I genes in the koala. Immunogenetics 70(2):125–133. https://doi.org/10.1007/s00251-017-1018-2

Article  PubMed  Google Scholar 

Cheng Y, Grueber C, Hogg CJ, Belov K (2022) Improved high-throughput MHC typing for non-model species using long-read sequencing. Mol Ecol Resour 22(3):862–876. https://doi.org/10.1111/1755-0998.13511

Article  PubMed  Google Scholar 

Cockram FA, Jackson AR (1974) Letter: Isolation of a Chlamydia from cases of keratoconjunctivitis in koalas. Aust Vet J 50(2):82–83. https://doi.org/10.1111/j.1751-0813.1974.tb05265.x

Article  PubMed  Google Scholar 

Cresswell P, Ackerman AL, Giodini A, Peaper DR, Wearsch PA (2005) Mechanisms of MHC class I-restricted antigen processing and cross-presentation [Review]. Immunol Rev 207:145–157. https://doi.org/10.1111/j.0105-2896.2005.00316.x

Article  PubMed  Google Scholar 

Cristescu R, Sherwin WB, Handasyde K, Cahill V, Cooper DW (2009) Detecting bottlenecks using BOTTLENECK 1.2.02 in wild populations: the importance of the microsatellite structure. Conserv Genet 11(3):1043–1049. https://doi.org/10.1007/s10592-009-9949-2

Article  Google Scholar 

Cui J, Frankham GJ, Johnson RN, Polkinghorne A, Timms P, O’Meally D, Cheng Y, Belov K (2015) SNP marker discovery in koala TLR genes. PLoS One 10(3):e0121068. https://doi.org/10.1371/journal.pone.0121068

Article  PubMed  Google Scholar 

Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, Genomes Project Analysis, G (2011) The variant call format and VCFtools. Bioinformatics 27(15):2156–2158. https://doi.org/10.1093/bioinformatics/btr330

Article  PubMed  Google Scholar 

Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H (2021) Twelve years of SAMtools and BCFtools. GigaScience 10(2):. https://doi.org/10.1093/gigascience/giab008

Delage WJ, Thevenon J, Lemaitre C (2020) Towards a better understanding of the low recall of insertion variants with short-read based variant callers. BMC Genom 21(1):762. https://doi.org/10.1186/s12864-020-07125-5

Article  Google Scholar 

Ebler J, Ebert P, Clarke WE, Rausch T, Audano PA, Houwaart T, Mao Y, Korbel JO, Eichler EE, Zody MC, Dilthey AT, Marschall T (2022) Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes. Nat Genet 54(4):518–525. https://doi.org/10.1038/s41588-022-01043-w

Article  PubMed  Google Scholar 

Eizaguirre C, Baltazar-Soares M (2014) Evolutionary conservation—evaluating the adaptive potential of species. Evol Appl 7(9):963–967. https://doi.org/10.1111/eva.12227

Article  Google Scholar 

Fabijan J, Caraguel C, Jelocnik M, Polkinghorne A, Boardman WSJ, Nishimoto E, Johnsson G, Molsher R, Woolford L, Timms P, Simmons G, Hemmatzadeh F, Trott DJ, Speight N (2019) Chlamydia pecorum prevalence in South Australian koala (Phascolarctos cinereus) populations: identification and modelling of a population free from infection. Sci Rep 9(1):6261. https://doi.org/10.1038/s41598-019-42702-z

Article  PubMed  Google Scholar 

Flot JF (2010) seqphase: A web tool for interconverting phase input/output files and fasta sequence alignments. Mol Ecol Resour 10(1):162–166. https://doi.org/10.1111/j.1755-0998.2009.02732.x

Article  PubMed  Google Scholar 

Fuentes-Pardo AP, Ruzzante DE (2017) Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations. Mol Ecol 26(20):5369–5406. https://doi.org/10.1111/mec.14264

Article  PubMed  Google Scholar 

Fuselli S, Baptista RP, Panziera A, Magi A, Guglielmi S, Tonin R, Benazzo A, Bauzer LG, Mazzoni CJ, Bertorelle G (2018) A new hybrid approach for MHC genotyping: high-throughput NGS and long read MinION nanopore sequencing, with application to the non-model vertebrate Alpine chamois (Rupicapra rupicapra). Heredity 121(4):293–303. https://doi.org/10.1038/s41437-018-0070-5

Article  PubMed  Google Scholar 

Gaughran SJ, Quinzin MC, Miller JM, Garrick RC, Edwards DL, Russello MA, Poulakakis N, Ciofi C, Beheregaray LB, Caccone A (2018) Theory, practice, and conservation in the age of genomics: The Galápagos giant tortoise as a case study. Evol Appl 11(7):1084–1093. https://doi.org/10.1111/eva.12551

Article  PubMed  Google Scholar 

Gruber B, Unmack PJ, Berry OF, Georges A (2018) dartr: An r package to facilitate analysis of SNP data generated from reduced representation genome sequencing. Mol Ecol Resour 18(3):691–699. https://doi.org/10.1111/1755-0998.12745

Article  PubMed  Google Scholar 

Grueber CE, Sutton JT, Heber S, Briskie JV, Jamieson IG, Robertson BC (2017) Reciprocal translocation of small numbers of inbred individuals rescues immunogenetic diversity [Article]. Mol Ecol 26(10):2660–2673. https://doi.org/10.1111/mec.14063

Article  PubMed  Google Scholar 

Hanger JJ, Bromham LD, McKee JJ, O’Brien TM, Robinson WF (2000) The nucleotide sequence of koala (Phascolarctos cinereus) retrovirus: a novel type C endogenous virus related to Gibbon ape leukemia virus [Article]. J Virol 74(9):4264–4272. https://doi.org/10.1128/jvi.74.9.4264-4272.2000

Article  PubMed  Google Scholar 

Heimeier D, Garland EC, Eichenberger F, Garrigue C, Vella A, Baker CS, Carroll EL (2024) A pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies. Mol Ecol Resour 24(5):e13955. https://doi.org/10.1111/1755-0998.13955

Article  PubMed  Google Scholar 

Hermsen EM, Young LJ, Old JM (2017) Major histocompatibility complex class II in the red-tailed phascogale (Phascogale calura). Aust Mammal 39(1):28–32. https://doi.org/10.1071/Am16002

Article  Google Scholar 

Hogg CJ, Ottewell K, Latch P, Rossetto M, Biggs J, Gilbert A, Richmond S, Belov K (2022) Threatened Species Initiative: Empowering conservation action using genomic resources. Proc Natl Acad Sci USA 119(4):e2115643118. https://doi.org/10.1073/pnas.2115643118

Article  PubMed  Google Scholar 

Hogg CJ, Silver L, McLennan EA, Belov K (2023) Koala Genome Survey: An open data resource to improve conservation planning. Genes (Basel) 14(3):546. https://doi.org/10.3390/genes14030546

Article  PubMed  Google Scholar 

Hu Q, Huang X, Jin Y, Zhang R, Zhao A, Wang Y, Zhou C, Liu W, Liu X, Li C, Fan G, Zhuo M, Wang X, Ling F, Luo W (2022) Long-read assembly of major histocompatibility complex and killer cell immunoglobulin-like receptor genome regions in cynomolgus macaque. Biol Dir 17(1):36.