The genomic architecture of the passerine MHC region: high repeat content and contrasting evolutionary histories of single copy and tandemly duplicated MHC genes

We used PacBio long-read, 10x genomics linked-read and BioNano optical mapping to create a de novo genome assembly from a female great reed warbler Acrocephalus arundinaceus. Eighteen scaffolds with MHC-genes (MHC-I and / or -IIB genes) and MHC-related genes, i.e. genes expected to be found in the MHC-region such as TAP1 and TAP2, were identified in the genome. The great reed warbler scaffold Aaru_Scaffold 18 shares large-scale homology with chicken chromosome 16, i.e. the chromosome holding the ‘core MHC region’, but the gene content and gene order partly differ. To investigate whether this genomic reorganization is common among passerines, we characterized MHC-genes and MHC-related genes in three additional passerine species with long-read sequenced assemblies hooded crow Corvus cornix, jackdaw Coloeus monedula and zebra finch Taenopygia guttata. Contigs with MHC-genes (MHC-I and / or -IIB genes) and MHC-related genes, i.e. genes expected to be found in the MHC-region such as TAP1 and TAP2, were identified in their genome. The total repeat content in the MHC-scaffolds/contigs, the repeat content within MHC genes and the repeat content between tandemly duplicated MHC genes were analysed.