Genome data for avian MHC

Long-read sequencing technology has the potential to greatly improve our
understanding of the Major Histocompatibility Complex (MHC), which is a
major component of the adaptive immune system, but it has been difficult
to study because of highly repetitive regions. In this study we used
genomes based on long-read sequencing to predict the number and location
of MHC loci in a broad range of bird taxa. We also examined species that
had not previously been studied at the MHC but had a published genome.
Overall, in the long-read based genomes of 28 species, we found that there
was extremely large variation in the number of MHC loci in passerines,
particularly in manakins (up to 193 class II loci), which had previously
not been studied at the MHC. Overall, there were greater numbers of both
class I and II loci in passerines than non-passerines. Our results provide
the first direct evidence from passerine genomes of this high level of
duplication. We also found different duplication patterns; i.e., in some
species both MHC class I and II genes were duplicated together, while in
most species they were duplicated separately. Our study shows that
long-read sequencing can provide dramatic increases in our knowledge of
MHC structure, although further improvements in chromosome level assembly
are needed to study the mechanisms producing these high levels of
duplication.