A chromosome-level genome assembly of the bluethroat ( <i>Luscinia s. svecica</i> ; Linnaeus, 1758) uncovers the complex MHC region

Abstract We describe a chromosome-level, pseudo-haplotype-resolved genome assembly from a female bluethroat (Luscinia s. svecica). The assembly comprises two pseudo-haplotypes of 1461 Mb and 1171 Mb, with 77.4% and 88.4% scaffolded into 40 autosomal chromosomes and the W and Z sex chromosomes in pseudo-haplotype one. Assembly completeness is high (BUSCO 99.2% and 94.9%), with 22,462 and 18,769 annotated protein-coding genes for pseudo-haplotypes one and two, respectively. The use of Oxford Nanopore Technologies sequencing enables resolution of genomic regions that are often fragmented in genome assemblies, including the hypervariable Major Histocompatibility Complex (MHC). We find that MHC loci include both the canonical organization of tandemly duplicated MHCIIβ genes with a single MHCIIα, and a distinct arrangement in which MHCI and MHCIIβ loci are interspersed. Substantial structural differences between the two assembled chromosome 35 homologs are resolved across the MHC region.