Biology subjects

Grove, H.

Publications and source records attributed to Grove, H..

3 recordsLinked to original sources

bioRxiv2026

A gapless Landrace pig genome resolves centromeres and telomeres and highlights telomere repeat structures in different pig breeds

The Duroc-derived reference genome Sscrofa11.1 has provided a critical foundation for pig genomics, providing a high-quality reference genome for accurate variant detection and comparative genomics but does not capture breed-specific variation. Here, we present a near-complete, gap-free genome assembly for the Landrace pig (Landrace_v1, GCA_963921485.1), spanning all 20 chromosomes and totaling 2.6 Gb, including 176 Mb of sequence absent from Sscrofa11.1. Comparative analyses with recently published high-quality pig genomes reveal a conserved centromere organization across breeds, accompanied by substantial variation in repeat composition and length, and identify a pig specific pattern of telomere variant repeats across eight pig breeds. The improved resolution of repetitive regions in Landrace_v1 enables more complete reconstruction of complex gene families, including olfactory receptors, and uncovers structural variation at the KIT proto-oncogene receptor tyrosine kinase locus not represented in the Duroc reference. Together, these findings highlight the limitations of single-reference genomes and demonstrate the value of breed-specific assemblies for capturing genomic diversity and improving downstream analyses.

genomics↗

bioRxiv2026

Haplotype assembly without parental sequencing: Genotype-based trio-binning (GT-Trio)

Trio-binning is a robust method for haplotype-resolved assembly, providing the most accurate representation of diploid genomes including complex and haplotype-specific variation. Conventional trio-binning methods depend on parental short-read sequences to differentiate offspring reads originating from the maternal and paternal haplotypes. Here, we present a genotype-based trio-binning pipeline (GT-Trio) which reconstructs parent sequences from phased parental genotypes and uses this as an alternative source of parental information for haplotype assembly. The GT-Trio pipeline was applied to assemble the maternal and paternal haplotypes of three Norwegian Red (NR) cattle individuals, using phased parental genotypes imputed from array to sequence as input. Haplotypes assembled with GT-Trio using all sequence variants as parental input demonstrated assembly quality and phasing accuracy comparable to that achieved with conventional trio-binning. Using lower density subsets of array SNPs led to a slight reduction in accuracy of haplotype separation, accompanied by an increase in size, contiguity and completeness, suggesting a trade-off between assembly quality and phasing accuracy associated with the density of parental genotypes provided as input to the pipeline. Overall, GT-Trio provides a scalable framework for haplotype assembly without parental sequencing and will be applicable in livestock species where genotyping and imputation is performed routinely. The GT-Trio pipeline is available at https://github.com/theahettasch/GT-Trio.

genomics↗

bioRxiv2021

A SARS-CoV-2 spike ferritin nanoparticle vaccine protects against heterologous challenge with B.1.1.7 and B.1.351 virus variants in Syrian golden hamsters

The emergence of SARS-CoV-2 variants of concern (VOC) requires adequate coverage of vaccine protection. We evaluated whether a spike ferritin nanoparticle vaccine (SpFN), adjuvanted with the Army Liposomal Formulation QS21 (ALFQ), conferred protection against the B.1.1.7 and B.1.351 VOCs in Syrian golden hamsters. SpFN-ALFQ was administered as either single or double-vaccination (0 and 4 week) regimens, using a high (10 g) or low (0.2 g) immunogen dose. Animals were intranasally challenged at week 11. Binding antibody responses were comparable between high- and low-dose groups. Neutralizing antibody titers were equivalent against WA1, B.1.1.7, and B.1.351 variants following two high dose two vaccinations. SpFN-ALFQ vaccination protected against SARS-CoV-2-induced disease and viral replication following intranasal B.1.1.7 or B.1.351 challenge, as evidenced by reduced weight loss, lung pathology, and lung and nasal turbinate viral burden. These data support the development of SpFN-ALFQ as a broadly protective, next-generation SARS-CoV-2 vaccine.

immunology↗