DOI: 10.5061/dryad.fqz612jv6
title: The genomic architecture of the passerine MHC region: high repeat content and contrasting evolutionary histories of single copy and tandemly duplicated MHC genes

description: The Major Histocompatibility Complex (MHC) is of central importance to the
 immune system, and an optimal MHC diversity is believed to maximize
 pathogen elimination. Birds show substantial variation in MHC diversity,
 ranging from few genes in most bird orders to very many genes in
 passerines. Our understanding of the evolutionary trajectories of the MHC
 in passerines is hampered by lack of data on genomic organization.
 Therefore, we assemble and annotate the MHC genomic region of the great
 reed warbler (Acrocephalus arundinaceus), using long-read sequencing and
 optical mapping. The MHC region is large (&gt;5.5Mb), characterized by
 structural changes compared to hitherto investigated bird orders and shows
 higher repeat content than the genome average. These features were
 supported by analyses in three additional passerines. MHC genes in
 passerines are found in two different chromosomal arrangements, either as
 single copy MHC genes located among non-MHC genes, or as tandemly
 duplicated tightly linked MHC genes. Some single copy MHC genes are old
 and putative orthologs among species. In contrast tandemly duplicated MHC
 genes are monophyletic within species and have evolved by simultaneous
 gene duplication of several MHC genes. Structural differences in the MHC
 genomic region among bird orders seem substantial compared to mammals and
 have possibly been fuelled by clade-specific immune system adaptations.
 Our study provides methodological guidance in characterizing complex
 genomic regions, constitutes a resource for MHC research in birds, and
 calls for a revision of the general belief that avian MHC has a conserved
 gene order and small size compared to mammals.
description: We used PacBio long-read, 10x
 genomics linked-read and BioNano optical mapping to create a <em>de
 novo</em> genome assembly from a female great reed
 warbler <em>Acrocephalus
 arundinaceus</em>. Eighteen scaffolds with MHC-genes
 (MHC-I and / or -IIB genes) and MHC-related
 genes, <em>i.e.</em> 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, <em>i.e.</em> 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 <em>Corvus
 cornix</em>, jackdaw <em>Coloeus
 monedula</em>  and
 zebra finch <em>Taenopygia
 guttata</em>. Contigs with MHC-genes (MHC-I and
 / or -IIB genes) and MHC-related genes, <em>i.e.</em> 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.
description: MHC-I and MHC-IIB genes in open reading frame after manual
 curation as fasta files, repeat content within MHC genes (intragenic) and
 between tandemly duplicated MHC-IIB genes (intergenic) as xls-files, and
 gene order in MHC and MHC-related scaffolds/contigs as gff-files in great
 reed warbler, hooded
 crow, jackdaw and zebra
 finch genomes.