Chicken RJF Reference Genome Sequence containing MHCY and NOR Ribosomal Genes

The MHCY region is a polymorphic gene region that influences immune responses in chickens. Understanding the genomics of the region will help in genetic selection of chickens raised for meat and eggs. The nucleotide sequence for the MHCY region has been especially hard to assemble due to the presence of many retroelements (principally CR1 and retroviral LTRS) and the presence of gene blocks of highly similar. Four contigs were identified. These did not assemble into a single sequence. One contig contains a portion of the NOR (Nucleolar Organizer Region) sequence. This provides sequence data for ribosomal RNA genes (and intervening sequence) closely adjacent to MHCY. The SMRT data was the first sequence data that allowed large regions of MHCY to be sequenced. Here we deposit additional PacBio data and Illumina data for some clones.