ArticleGigaScience2022
Best genome sequencing strategies for annotation of complex immune gene families in wildlife.
Article in GigaScience, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 35 citations in OpenAlex.
- Adaptive Immunity in Marsupials.Journal of experimental zoology. Part A, Ecological and integrative physiology · 2026Review
- When cells rebel: a comparative genomics investigation into marsupial cancer susceptibility.Molecular biology and evolution · 2026Article
- Understanding Climate Change Threats to Vertebrate Wildlife by Studying Ecoimmunology Across Biological Scales.Integrative and comparative biology · 2025Review
- Whole-Genome Data to Investigate Recent and Historical Dog Introgression Patterns in Italian Wolves.Ecology and evolution · 2025Article
- Insights into platypus crural gland transcriptomics - venom and beyond.BMC genomics · 2025Article
- Twenty years of tuberculosis-driven selection shaped the evolution of the meerkat major histocompatibility complex.Nature ecology & evolution · 2025Article
- Diverse hosts, diverse immune systems: Evolutionary variation in bat immunology.Annals of the New York Academy of Sciences · 2025Review
- Genomes of two Extinct-in-the-Wild reptiles from Christmas Island reveal distinct evolutionary histories and conservation insights.Molecular ecology resources · 2025Article
- Temporal Loss of Genome-Wide and Immunogenetic Diversity in a Near-Extinct Parrot.Molecular ecology · 2025Article
- MHC Diversity Across Time and Space.Ecology and evolution · 2025Review
- Marsupial cathelicidins: characterization, antimicrobial activity and evolution in this unique mammalian lineage.Frontiers in immunology · 2025Article
- Deep learning-aided inter-species-comparison reveals shared and distinct molecular patterns in cynomolgus monkey and humans following non-specific T cell activation.Frontiers in immunology · 2025Article
- A Genomic-Based Workflow for eDNA Assay Development for a Critically Endangered Turtle,Ecology and evolution · 2025Article
- Using bioinformatics to investigate functional diversity: a case study of MHC diversity in koalas.Immunogenetics · 2024Article
- A genome assembly and transcriptome atlas of the inbred Babraham pig to illuminate porcine immunogenetic variation.Immunogenetics · 2024Article
- Plethora of New Marsupial Genomes Informs Our Knowledge of Marsupial MHC Class II.Genome biology and evolution · 2024Article
- Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial.Nature ecology & evolution · 2024Article
- Translating genomic advances into biodiversity conservation.Nature reviews. Genetics · 2024Review
- ToxCodAn-Genome: an automated pipeline for toxin-gene annotation in genome assembly of venomous lineages.GigaScience · 2024Article
- Comparative genomics of the Natural Killer Complex in carnivores.Frontiers in immunology · 2024Article
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe 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.
resultsGenome 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.
conclusionsOur 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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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.