2021
DOI: 10.1111/1755-0998.13511
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Improved high‐throughput MHC typing for non‐model species using long‐read sequencing

Abstract: The major histocompatibility complex (MHC) plays a critical role in the vertebrate immune system. Accurate MHC typing is critical to understanding not only host fitness and disease susceptibility, but also the mechanisms underlying host‐pathogen co‐evolution. However, due to the high degree of gene duplication and diversification of MHC genes, it is often technically challenging to accurately characterise MHC genetic diversity in non‐model species. Here we conducted a systematic review to identify common issue… Show more

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Cited by 13 publications
(6 citation statements)
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“…Devils from south-western Tasmania represent different genetic diversity (neutral and functional) than the rest of Tasmania ( Figures 2 , 4 , and S3–S9 ). This differentiation is similar to the recently reported differences in the major histocompatibility complex (MHC) Class I genes for this species ( Cheng et al., 2021 ) and is likely driven by geographic isolation during the Pleistocene glaciation in Tasmania ( Lewis, 1944 ). Three individuals that were sourced from Macquarie Heads (depicted as black dots in Figures 1 C and 1D) during the original founder intakes for the IP in 2008 were included in the analysis here.…”
Section: Discussionsupporting
confidence: 87%
See 1 more Smart Citation
“…Devils from south-western Tasmania represent different genetic diversity (neutral and functional) than the rest of Tasmania ( Figures 2 , 4 , and S3–S9 ). This differentiation is similar to the recently reported differences in the major histocompatibility complex (MHC) Class I genes for this species ( Cheng et al., 2021 ) and is likely driven by geographic isolation during the Pleistocene glaciation in Tasmania ( Lewis, 1944 ). Three individuals that were sourced from Macquarie Heads (depicted as black dots in Figures 1 C and 1D) during the original founder intakes for the IP in 2008 were included in the analysis here.…”
Section: Discussionsupporting
confidence: 87%
“…Seven additional locations (Forestier Peninsula/Murdunna, Tasman Peninsula, Fingal Valley, Robbins Island, Sandy Cape, Stony Head and Takone) were sampled by the STDP as part of other projects. A further four locations (south-west Tasmania, Silver Plains, Strathgordon and Lyell Highway) were specifically selected for sampling for this project and others based on their geographic distance from other sampling locations, including the remote and largely inaccessible south-west Tasmania that was sampled as part of a public crowdfunding effort to discover whether devils inhabited there ( Cheng et al., 2021 ). Samples from the insurance population (IP) founder intake from Macquarie Heads (2008) were also included to assess how devils may be moving from north-western to south-western Tasmania.…”
Section: Methodsmentioning
confidence: 99%
“…To tackle these genomic questions, MHC research should take advantage of improvements in long‐read sequencing technologies, as several recent studies have done (Cheng et al, 2021 ; Fuselli et al, 2018 ; He et al, 2021 ). PacBio and NanoPore sequencing now can generate reads from 10s to 100s of kb (Amarasinghe et al, 2020 ; Hon et al, 2020 ), circumventing the problems inherent in making MHC assemblies from short sequencing reads (He et al, 2021 ).…”
Section: Discussionmentioning
confidence: 99%
“…However, this obstacle may be overcome by using long-read (LR) sequencing approaches. 25 Although it is possible to assess the overall variability and diversity in this region by genotyping microsatellite (MSAT) loci within the MHC, 26 expressed MHC loci will always be the prime candidates for such studies. So far, mostly MHC class II genes have been analyzed in this context.…”
Section: Introductionmentioning
confidence: 99%